Starting phenix.real_space_refine on Sun Aug 4 13:51:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xln_38454/08_2024/8xln_38454.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xln_38454/08_2024/8xln_38454.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.78 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xln_38454/08_2024/8xln_38454.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xln_38454/08_2024/8xln_38454.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xln_38454/08_2024/8xln_38454.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xln_38454/08_2024/8xln_38454.cif" } resolution = 3.78 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4904 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 37 5.16 5 C 4211 2.51 5 N 1073 2.21 5 O 1272 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D GLU 171": "OE1" <-> "OE2" Residue "D TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 6593 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 4862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4862 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 27, 'TRANS': 568} Chain: "A" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 193, 1533 Classifications: {'peptide': 193} Link IDs: {'PTRANS': 13, 'TRANS': 179} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "H" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.52, per 1000 atoms: 0.69 Number of scatterers: 6593 At special positions: 0 Unit cell: (75.375, 102.51, 110.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 37 16.00 O 1272 8.00 N 1073 7.00 C 4211 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.04 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA H 3 " - " MAN H 4 " ALPHA1-6 " BMA H 3 " - " MAN H 5 " BETA1-4 " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG H 2 " - " BMA H 3 " NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG D 701 " - " ASN D 322 " " NAG D 702 " - " ASN D 432 " " NAG E 1 " - " ASN D 53 " " NAG F 1 " - " ASN D 546 " " NAG G 1 " - " ASN D 90 " " NAG H 1 " - " ASN D 103 " Time building additional restraints: 2.96 Conformation dependent library (CDL) restraints added in 1.1 seconds 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1490 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 4 sheets defined 54.6% alpha, 5.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.827A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N ASP D 38 " --> pdb=" O HIS D 34 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU D 39 " --> pdb=" O GLU D 35 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 80 Processing helix chain 'D' and resid 90 through 105 removed outlier: 3.581A pdb=" N LYS D 94 " --> pdb=" O ASN D 90 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN D 96 " --> pdb=" O THR D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 129 Processing helix chain 'D' and resid 146 through 155 removed outlier: 4.285A pdb=" N GLU D 150 " --> pdb=" O PRO D 146 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N MET D 152 " --> pdb=" O LEU D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 172 removed outlier: 3.852A pdb=" N ARG D 169 " --> pdb=" O TRP D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 194 removed outlier: 4.119A pdb=" N LEU D 179 " --> pdb=" O GLN D 175 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 219 through 252 removed outlier: 4.449A pdb=" N ILE D 223 " --> pdb=" O ARG D 219 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLU D 224 " --> pdb=" O GLY D 220 " (cutoff:3.500A) Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 275 through 279 Processing helix chain 'D' and resid 293 through 301 removed outlier: 3.807A pdb=" N MET D 297 " --> pdb=" O VAL D 293 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL D 298 " --> pdb=" O THR D 294 " (cutoff:3.500A) Processing helix chain 'D' and resid 303 through 318 Processing helix chain 'D' and resid 324 through 331 Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.692A pdb=" N GLY D 377 " --> pdb=" O HIS D 373 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N HIS D 378 " --> pdb=" O HIS D 374 " (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 Processing helix chain 'D' and resid 399 through 412 removed outlier: 4.019A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 422 Processing helix chain 'D' and resid 431 through 447 removed outlier: 4.007A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 448 through 466 removed outlier: 4.326A pdb=" N PHE D 452 " --> pdb=" O GLY D 448 " (cutoff:3.500A) Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 485 removed outlier: 3.756A pdb=" N VAL D 485 " --> pdb=" O LYS D 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.852A pdb=" N THR D 519 " --> pdb=" O TYR D 515 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 561 removed outlier: 3.974A pdb=" N GLN D 552 " --> pdb=" O THR D 548 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LEU D 560 " --> pdb=" O ASN D 556 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLY D 561 " --> pdb=" O MET D 557 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 575 Processing helix chain 'D' and resid 581 through 599 Proline residue: D 590 - end of helix Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.074A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 371 removed outlier: 3.776A pdb=" N PHE A 371 " --> pdb=" O ILE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 386 through 390 removed outlier: 3.688A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 416 through 421 Processing sheet with id=AA1, first strand: chain 'D' and resid 347 through 350 removed outlier: 3.774A pdb=" N ARG D 357 " --> pdb=" O TRP D 349 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.605A pdb=" N ILE A 358 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LYS A 378 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 453 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 300 hydrogen bonds defined for protein. 846 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: 1.75 Time building geometry restraints manager: 3.08 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: 2079 1.35 - 1.47: 1780 1.47 - 1.59: 2860 1.59 - 1.71: 0 1.71 - 1.83: 58 Bond restraints: 6777 Sorted by residual: bond pdb=" C HIS D 265 " pdb=" N LEU D 266 " ideal model delta sigma weight residual 1.334 1.311 0.024 1.52e-02 4.33e+03 2.43e+00 bond pdb=" C1 NAG H 2 " pdb=" O5 NAG H 2 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.33e+00 bond pdb=" C1 NAG E 1 " pdb=" O5 NAG E 1 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.24e+00 bond pdb=" C1 BMA H 3 " pdb=" C2 BMA H 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.18e+00 bond pdb=" C1 NAG E 2 " pdb=" O5 NAG E 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 ... (remaining 6772 not shown) Histogram of bond angle deviations from ideal: 98.32 - 105.46: 148 105.46 - 112.61: 3497 112.61 - 119.75: 2236 119.75 - 126.90: 3216 126.90 - 134.05: 118 Bond angle restraints: 9215 Sorted by residual: angle pdb=" C CYS D 133 " pdb=" CA CYS D 133 " pdb=" CB CYS D 133 " ideal model delta sigma weight residual 110.42 116.59 -6.17 1.99e+00 2.53e-01 9.62e+00 angle pdb=" C ALA D 264 " pdb=" N HIS D 265 " pdb=" CA HIS D 265 " ideal model delta sigma weight residual 121.54 127.44 -5.90 1.91e+00 2.74e-01 9.54e+00 angle pdb=" CA LEU D 162 " pdb=" CB LEU D 162 " pdb=" CG LEU D 162 " ideal model delta sigma weight residual 116.30 124.64 -8.34 3.50e+00 8.16e-02 5.68e+00 angle pdb=" C ALA D 384 " pdb=" N TYR D 385 " pdb=" CA TYR D 385 " ideal model delta sigma weight residual 122.65 118.78 3.87 1.66e+00 3.63e-01 5.42e+00 angle pdb=" C GLN D 102 " pdb=" N ASN D 103 " pdb=" CA ASN D 103 " ideal model delta sigma weight residual 122.31 117.77 4.54 2.00e+00 2.50e-01 5.15e+00 ... (remaining 9210 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.62: 3821 21.62 - 43.23: 293 43.23 - 64.85: 42 64.85 - 86.46: 29 86.46 - 108.08: 11 Dihedral angle restraints: 4196 sinusoidal: 1876 harmonic: 2320 Sorted by residual: 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 -175.25 89.25 1 1.00e+01 1.00e-02 9.47e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual -86.00 -171.32 85.32 1 1.00e+01 1.00e-02 8.82e+01 dihedral pdb=" CA ARG A 403 " pdb=" C ARG A 403 " pdb=" N GLY A 404 " pdb=" CA GLY A 404 " ideal model delta harmonic sigma weight residual 180.00 159.56 20.44 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 4193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 827 0.054 - 0.107: 170 0.107 - 0.161: 12 0.161 - 0.215: 0 0.215 - 0.268: 2 Chirality restraints: 1011 Sorted by residual: chirality pdb=" C5 BMA G 3 " pdb=" C4 BMA G 3 " pdb=" C6 BMA G 3 " pdb=" O5 BMA G 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.80e+00 chirality pdb=" C5 BMA H 3 " pdb=" C4 BMA H 3 " pdb=" C6 BMA H 3 " pdb=" O5 BMA H 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.75e+00 chirality pdb=" CA ASN D 103 " pdb=" N ASN D 103 " pdb=" C ASN D 103 " pdb=" CB ASN D 103 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.25e-01 ... (remaining 1008 not shown) Planarity restraints: 1178 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 234 " 0.040 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO D 235 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO D 235 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 235 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU D 145 " -0.038 5.00e-02 4.00e+02 5.75e-02 5.29e+00 pdb=" N PRO D 146 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 146 " -0.030 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 " 0.020 2.00e-02 2.50e+03 1.94e-02 4.69e+00 pdb=" CG ASN D 103 " -0.030 2.00e-02 2.50e+03 pdb=" OD1 ASN D 103 " 0.007 2.00e-02 2.50e+03 pdb=" ND2 ASN D 103 " -0.014 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " 0.017 2.00e-02 2.50e+03 ... (remaining 1175 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 201 2.71 - 3.26: 6861 3.26 - 3.80: 10402 3.80 - 4.35: 12276 4.35 - 4.90: 21018 Nonbonded interactions: 50758 Sorted by model distance: nonbonded pdb=" O ILE D 151 " pdb=" OG SER D 155 " model vdw 2.162 3.040 nonbonded pdb=" OG SER D 317 " pdb=" O SER D 545 " model vdw 2.258 3.040 nonbonded pdb=" O ASN A 334 " pdb=" N VAL A 362 " model vdw 2.276 3.120 nonbonded pdb=" O PHE D 327 " pdb=" OG SER D 331 " model vdw 2.329 3.040 nonbonded pdb=" O MET D 152 " pdb=" NH2 ARG D 161 " model vdw 2.355 3.120 ... (remaining 50753 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' } 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: 2.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.110 Find NCS groups from input model: 0.080 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8062 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 : 0.004 0.039 6777 Z= 0.237 Angle : 0.647 8.339 9215 Z= 0.317 Chirality : 0.043 0.268 1011 Planarity : 0.005 0.061 1171 Dihedral : 17.143 108.077 2685 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % 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: 0.46 (0.31), residues: 785 helix: 1.78 (0.27), residues: 377 sheet: 0.15 (0.80), residues: 50 loop : -1.34 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 477 HIS 0.005 0.001 HIS D 265 PHE 0.013 0.001 PHE D 369 TYR 0.027 0.001 TYR D 385 ARG 0.003 0.000 ARG D 460 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 194 ASN cc_start: 0.7537 (m-40) cc_final: 0.7149 (m110) REVERT: D 270 MET cc_start: 0.8346 (tpp) cc_final: 0.7723 (tpp) REVERT: A 467 ASP cc_start: 0.6564 (m-30) cc_final: 0.6347 (m-30) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.2021 time to fit residues: 23.2768 Evaluate side-chains 51 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.6980 chunk 59 optimal weight: 0.4980 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 45 optimal weight: 0.0010 chunk 70 optimal weight: 0.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 51 ASN D 96 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 6777 Z= 0.176 Angle : 0.595 10.114 9215 Z= 0.297 Chirality : 0.041 0.156 1011 Planarity : 0.005 0.051 1171 Dihedral : 9.425 71.517 1163 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 0.72 % Allowed : 7.94 % Favored : 91.34 % 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: 0.46 (0.30), residues: 785 helix: 1.80 (0.26), residues: 375 sheet: -0.40 (0.72), residues: 54 loop : -1.26 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 436 HIS 0.003 0.001 HIS D 265 PHE 0.012 0.001 PHE A 400 TYR 0.029 0.001 TYR D 385 ARG 0.005 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 249 MET cc_start: 0.8417 (tpp) cc_final: 0.7952 (ttt) REVERT: D 270 MET cc_start: 0.8120 (tpp) cc_final: 0.7646 (tpp) REVERT: A 467 ASP cc_start: 0.6607 (m-30) cc_final: 0.6364 (m-30) outliers start: 5 outliers final: 2 residues processed: 68 average time/residue: 0.1710 time to fit residues: 16.3222 Evaluate side-chains 56 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 54 time to evaluate : 0.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain A residue 405 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 0.3980 chunk 21 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 56 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8069 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6777 Z= 0.165 Angle : 0.558 6.476 9215 Z= 0.281 Chirality : 0.041 0.172 1011 Planarity : 0.005 0.052 1171 Dihedral : 7.843 62.407 1163 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.30 % Allowed : 10.53 % Favored : 88.17 % 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: 0.47 (0.31), residues: 785 helix: 1.90 (0.27), residues: 375 sheet: -0.21 (0.73), residues: 54 loop : -1.42 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 477 HIS 0.002 0.001 HIS D 374 PHE 0.011 0.001 PHE D 464 TYR 0.022 0.001 TYR D 385 ARG 0.004 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 270 MET cc_start: 0.8120 (tpp) cc_final: 0.7589 (tpp) REVERT: A 391 CYS cc_start: 0.4427 (p) cc_final: 0.3567 (p) REVERT: A 467 ASP cc_start: 0.6637 (m-30) cc_final: 0.6367 (m-30) outliers start: 9 outliers final: 6 residues processed: 70 average time/residue: 0.1380 time to fit residues: 14.3961 Evaluate side-chains 62 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 56 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 470 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 0.0980 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 75 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 ASN ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 6777 Z= 0.200 Angle : 0.582 14.421 9215 Z= 0.294 Chirality : 0.041 0.292 1011 Planarity : 0.004 0.050 1171 Dihedral : 7.255 58.811 1163 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 1.44 % Allowed : 13.42 % Favored : 85.14 % 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: 0.50 (0.31), residues: 785 helix: 1.90 (0.27), residues: 375 sheet: 0.90 (0.86), residues: 42 loop : -1.50 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 477 HIS 0.003 0.001 HIS D 378 PHE 0.011 0.001 PHE D 369 TYR 0.017 0.001 TYR D 385 ARG 0.003 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 7 residues processed: 65 average time/residue: 0.1484 time to fit residues: 14.3850 Evaluate side-chains 62 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 55 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 470 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.3980 chunk 64 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 6777 Z= 0.196 Angle : 0.568 14.048 9215 Z= 0.286 Chirality : 0.040 0.222 1011 Planarity : 0.004 0.052 1171 Dihedral : 6.027 43.663 1163 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 1.30 % Allowed : 15.44 % Favored : 83.26 % 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: 0.49 (0.31), residues: 785 helix: 1.93 (0.27), residues: 373 sheet: 0.86 (0.88), residues: 42 loop : -1.53 (0.32), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 477 HIS 0.003 0.001 HIS D 265 PHE 0.011 0.001 PHE D 369 TYR 0.016 0.001 TYR D 385 ARG 0.003 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.715 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 249 MET cc_start: 0.8444 (tpp) cc_final: 0.8098 (mtm) REVERT: D 270 MET cc_start: 0.7776 (tpt) cc_final: 0.7187 (tpp) outliers start: 9 outliers final: 8 residues processed: 67 average time/residue: 0.1469 time to fit residues: 14.3042 Evaluate side-chains 64 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 470 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 75 optimal weight: 0.0980 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 340 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 6777 Z= 0.202 Angle : 0.571 13.758 9215 Z= 0.288 Chirality : 0.040 0.196 1011 Planarity : 0.004 0.051 1171 Dihedral : 5.749 38.748 1163 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 1.30 % Allowed : 16.45 % Favored : 82.25 % 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: 0.44 (0.31), residues: 785 helix: 1.91 (0.27), residues: 373 sheet: -0.10 (0.80), residues: 50 loop : -1.46 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 477 HIS 0.003 0.001 HIS D 265 PHE 0.011 0.001 PHE D 369 TYR 0.015 0.001 TYR D 385 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 182 GLU cc_start: 0.8182 (tt0) cc_final: 0.7970 (tt0) REVERT: D 239 HIS cc_start: 0.8090 (t70) cc_final: 0.7740 (t70) REVERT: D 249 MET cc_start: 0.8453 (tpp) cc_final: 0.8095 (mtm) outliers start: 9 outliers final: 8 residues processed: 68 average time/residue: 0.1476 time to fit residues: 14.6662 Evaluate side-chains 65 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 470 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 75 optimal weight: 0.0470 chunk 47 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 overall best weight: 0.7480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 6777 Z= 0.186 Angle : 0.579 13.192 9215 Z= 0.289 Chirality : 0.040 0.193 1011 Planarity : 0.004 0.049 1171 Dihedral : 5.549 36.186 1163 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 1.73 % Allowed : 17.03 % Favored : 81.24 % 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: 0.47 (0.31), residues: 785 helix: 1.94 (0.27), residues: 372 sheet: -0.18 (0.81), residues: 50 loop : -1.44 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 477 HIS 0.003 0.001 HIS D 265 PHE 0.010 0.001 PHE D 464 TYR 0.021 0.001 TYR D 385 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 60 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 182 GLU cc_start: 0.8053 (tt0) cc_final: 0.7820 (tt0) REVERT: D 239 HIS cc_start: 0.8083 (OUTLIER) cc_final: 0.7720 (t70) REVERT: D 249 MET cc_start: 0.8448 (tpp) cc_final: 0.8172 (mtp) REVERT: D 270 MET cc_start: 0.7640 (tpt) cc_final: 0.7367 (tpp) REVERT: D 332 MET cc_start: 0.8924 (tpt) cc_final: 0.8578 (tpt) outliers start: 12 outliers final: 10 residues processed: 70 average time/residue: 0.1430 time to fit residues: 14.8181 Evaluate side-chains 69 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 58 time to evaluate : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 470 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.4980 chunk 7 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 6777 Z= 0.205 Angle : 0.588 12.859 9215 Z= 0.295 Chirality : 0.040 0.189 1011 Planarity : 0.004 0.046 1171 Dihedral : 5.472 36.234 1163 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 2.02 % Allowed : 17.03 % Favored : 80.95 % 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: 0.40 (0.31), residues: 785 helix: 1.91 (0.27), residues: 372 sheet: -0.71 (0.70), residues: 60 loop : -1.43 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 477 HIS 0.003 0.001 HIS D 265 PHE 0.011 0.001 PHE D 369 TYR 0.019 0.001 TYR D 385 ARG 0.003 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 60 time to evaluate : 0.720 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 182 GLU cc_start: 0.8110 (tt0) cc_final: 0.7854 (tt0) REVERT: D 239 HIS cc_start: 0.8063 (OUTLIER) cc_final: 0.7685 (t70) REVERT: D 249 MET cc_start: 0.8445 (tpp) cc_final: 0.8150 (mtp) REVERT: D 332 MET cc_start: 0.8990 (tpt) cc_final: 0.8661 (tpt) outliers start: 14 outliers final: 10 residues processed: 71 average time/residue: 0.1480 time to fit residues: 15.3228 Evaluate side-chains 70 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 59 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 470 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6777 Z= 0.185 Angle : 0.585 12.693 9215 Z= 0.290 Chirality : 0.040 0.188 1011 Planarity : 0.004 0.049 1171 Dihedral : 5.246 34.767 1163 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 2.02 % Allowed : 16.88 % Favored : 81.10 % 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: 0.44 (0.31), residues: 785 helix: 2.00 (0.27), residues: 367 sheet: -0.36 (0.80), residues: 50 loop : -1.47 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 477 HIS 0.003 0.001 HIS D 265 PHE 0.011 0.001 PHE A 400 TYR 0.020 0.001 TYR D 385 ARG 0.002 0.000 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 61 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 182 GLU cc_start: 0.8097 (tt0) cc_final: 0.7842 (tt0) REVERT: D 239 HIS cc_start: 0.8020 (OUTLIER) cc_final: 0.7659 (t70) REVERT: D 249 MET cc_start: 0.8403 (tpp) cc_final: 0.8174 (mtp) REVERT: D 270 MET cc_start: 0.7586 (tpt) cc_final: 0.7287 (tpp) REVERT: D 332 MET cc_start: 0.8977 (tpt) cc_final: 0.8631 (tpt) outliers start: 14 outliers final: 12 residues processed: 71 average time/residue: 0.1432 time to fit residues: 14.9326 Evaluate side-chains 72 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 408 SER Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 470 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.5980 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 6 optimal weight: 0.4980 chunk 47 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 49 optimal weight: 0.0170 chunk 65 optimal weight: 0.7980 chunk 18 optimal weight: 0.0980 chunk 57 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 overall best weight: 0.4018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 6777 Z= 0.162 Angle : 0.581 12.466 9215 Z= 0.286 Chirality : 0.040 0.198 1011 Planarity : 0.004 0.050 1171 Dihedral : 4.909 33.073 1163 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 1.88 % Allowed : 17.17 % Favored : 80.95 % 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: 0.43 (0.31), residues: 785 helix: 1.89 (0.27), residues: 375 sheet: -0.00 (0.83), residues: 47 loop : -1.48 (0.32), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS D 265 PHE 0.014 0.001 PHE A 400 TYR 0.021 0.001 TYR D 385 ARG 0.002 0.000 ARG A 466 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1570 Ramachandran restraints generated. 785 Oldfield, 0 Emsley, 785 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 59 time to evaluate : 0.741 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 171 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8443 (mm-30) REVERT: D 182 GLU cc_start: 0.8105 (tt0) cc_final: 0.7847 (tt0) REVERT: D 239 HIS cc_start: 0.7972 (OUTLIER) cc_final: 0.7618 (t70) REVERT: D 249 MET cc_start: 0.8425 (tpp) cc_final: 0.8108 (mtm) REVERT: D 270 MET cc_start: 0.7541 (tpt) cc_final: 0.7243 (tpp) outliers start: 13 outliers final: 11 residues processed: 70 average time/residue: 0.1508 time to fit residues: 15.5435 Evaluate side-chains 71 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 54 ILE Chi-restraints excluded: chain D residue 239 HIS Chi-restraints excluded: chain D residue 267 LEU Chi-restraints excluded: chain D residue 455 MET Chi-restraints excluded: chain D residue 468 ILE Chi-restraints excluded: chain D residue 503 LEU Chi-restraints excluded: chain D residue 506 VAL Chi-restraints excluded: chain D residue 539 LEU Chi-restraints excluded: chain A residue 368 ILE Chi-restraints excluded: chain A residue 405 ASN Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 470 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 1.9990 chunk 61 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 chunk 63 optimal weight: 0.5980 chunk 7 optimal weight: 0.0980 chunk 11 optimal weight: 0.0980 chunk 54 optimal weight: 0.4980 chunk 3 optimal weight: 0.0980 chunk 44 optimal weight: 0.8980 chunk 70 optimal weight: 0.0870 chunk 41 optimal weight: 1.9990 overall best weight: 0.1558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.110103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.088652 restraints weight = 17497.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.091111 restraints weight = 9863.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.092791 restraints weight = 6894.738| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 6777 Z= 0.157 Angle : 0.567 12.301 9215 Z= 0.277 Chirality : 0.039 0.179 1011 Planarity : 0.004 0.053 1171 Dihedral : 4.361 29.764 1163 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.15 % Allowed : 17.89 % Favored : 80.95 % 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: 0.55 (0.31), residues: 785 helix: 1.96 (0.27), residues: 375 sheet: 0.58 (0.84), residues: 44 loop : -1.46 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS D 265 PHE 0.011 0.001 PHE A 400 TYR 0.022 0.001 TYR D 385 ARG 0.002 0.000 ARG D 393 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1492.48 seconds wall clock time: 27 minutes 19.37 seconds (1639.37 seconds total)