Starting phenix.real_space_refine on Tue Jun 25 05:22:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r11_14227/06_2024/7r11_14227.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r11_14227/06_2024/7r11_14227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r11_14227/06_2024/7r11_14227.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r11_14227/06_2024/7r11_14227.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r11_14227/06_2024/7r11_14227.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r11_14227/06_2024/7r11_14227.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.057 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 39 5.16 5 C 4392 2.51 5 N 1131 2.21 5 O 1307 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 180": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 183": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 510": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/modules/chem_data/mon_lib" Total number of atoms: 6870 Number of models: 1 Model: "" Number of chains: 4 Chain: "D" Number of atoms: 4802 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 587, 4795 Classifications: {'peptide': 587} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 561} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 587, 4795 Classifications: {'peptide': 587} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 561} Chain breaks: 1 bond proxies already assigned to first conformer: 4920 Chain: "A" Number of atoms: 1969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1969 Classifications: {'peptide': 250} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 235} Chain breaks: 1 Chain: "D" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 71 Unusual residues: {' ZN': 1, 'NAG': 5} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 7.61, per 1000 atoms: 1.11 Number of scatterers: 6870 At special positions: 0 Unit cell: (75.46, 95.942, 141.218, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 39 16.00 O 1307 8.00 N 1131 7.00 C 4392 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS D 133 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 344 " - pdb=" SG CYS D 361 " distance=2.03 Simple disulfide: pdb=" SG CYS D 530 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " " NAG A1302 " - " ASN A 331 " " NAG D 701 " - " ASN D 432 " " NAG D 703 " - " ASN D 53 " " NAG D 704 " - " ASN D 103 " " NAG D 705 " - " ASN D 546 " " NAG D 706 " - " ASN D 90 " Time building additional restraints: 2.85 Conformation dependent library (CDL) restraints added in 2.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 702 " pdb="ZN ZN D 702 " - pdb=" NE2 HIS D 374 " 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 7 sheets defined 51.4% alpha, 8.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'D' and resid 20 through 53 removed outlier: 3.841A pdb=" N HIS D 34 " --> pdb=" O ASP D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 58 through 81 removed outlier: 3.535A pdb=" N MET D 62 " --> pdb=" O ASN D 58 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 101 Processing helix chain 'D' and resid 103 through 107 removed outlier: 4.169A pdb=" N VAL D 107 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 129 Processing helix chain 'D' and resid 146 through 155 removed outlier: 3.562A pdb=" N ASN D 154 " --> pdb=" O GLU D 150 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 176 removed outlier: 4.175A pdb=" N LYS D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 194 removed outlier: 3.528A pdb=" N ASN D 194 " --> pdb=" O MET D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 205 Processing helix chain 'D' and resid 219 through 223 Processing helix chain 'D' and resid 226 through 233 removed outlier: 3.676A pdb=" N GLU D 232 " --> pdb=" O HIS D 228 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ILE D 233 " --> pdb=" O THR D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 252 Processing helix chain 'D' and resid 253 through 256 removed outlier: 4.476A pdb=" N ILE D 256 " --> pdb=" O PRO D 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 253 through 256' Processing helix chain 'D' and resid 265 through 267 No H-bonds generated for 'chain 'D' and resid 265 through 267' Processing helix chain 'D' and resid 275 through 280 removed outlier: 4.162A pdb=" N SER D 280 " --> pdb=" O ASN D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 301 Processing helix chain 'D' and resid 305 through 319 Processing helix chain 'D' and resid 326 through 331 Processing helix chain 'D' and resid 365 through 385 removed outlier: 3.589A pdb=" N ALA D 384 " --> pdb=" O GLN D 380 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N TYR D 385 " --> pdb=" O TYR D 381 " (cutoff:3.500A) Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.520A pdb=" N ARG D 393 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 399 through 413 removed outlier: 3.553A pdb=" N ALA D 403 " --> pdb=" O GLY D 399 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VAL D 404 " --> pdb=" O PHE D 400 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLY D 405 " --> pdb=" O HIS D 401 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N MET D 408 " --> pdb=" O VAL D 404 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N SER D 409 " --> pdb=" O GLY D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 414 through 421 Processing helix chain 'D' and resid 431 through 447 removed outlier: 3.692A pdb=" N GLU D 435 " --> pdb=" O ASP D 431 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR D 445 " --> pdb=" O LYS D 441 " (cutoff:3.500A) Processing helix chain 'D' and resid 449 through 466 Processing helix chain 'D' and resid 469 through 471 No H-bonds generated for 'chain 'D' and resid 469 through 471' Processing helix chain 'D' and resid 472 through 484 removed outlier: 3.688A pdb=" N LYS D 476 " --> pdb=" O GLN D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 499 through 502 Processing helix chain 'D' and resid 503 through 508 Processing helix chain 'D' and resid 513 through 533 removed outlier: 3.631A pdb=" N LEU D 520 " --> pdb=" O TYR D 516 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N PHE D 523 " --> pdb=" O THR D 519 " (cutoff:3.500A) Processing helix chain 'D' and resid 538 through 542 removed outlier: 3.609A pdb=" N LYS D 541 " --> pdb=" O PRO D 538 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N CYS D 542 " --> pdb=" O LEU D 539 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 538 through 542' Processing helix chain 'D' and resid 547 through 559 removed outlier: 3.716A pdb=" N MET D 557 " --> pdb=" O LYS D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 565 through 572 Processing helix chain 'D' and resid 581 through 588 removed outlier: 3.621A pdb=" N PHE D 588 " --> pdb=" O LEU D 584 " (cutoff:3.500A) Processing helix chain 'D' and resid 588 through 600 Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.102A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 370 removed outlier: 4.460A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 385 through 390 removed outlier: 3.989A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing sheet with id=AA1, first strand: chain 'D' and resid 262 through 263 removed outlier: 6.277A pdb=" N LEU D 262 " --> pdb=" O VAL D 488 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 347 through 352 removed outlier: 6.032A pdb=" N ASP D 355 " --> pdb=" O LEU D 351 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 328 removed outlier: 6.889A pdb=" N ILE A 326 " --> pdb=" O ASN A 542 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 550 " --> pdb=" O VAL A 539 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N ILE A 584 " --> pdb=" O SER A 555 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N VAL A 576 " --> pdb=" O LEU A 585 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.294A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.460A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'A' and resid 473 through 474 302 hydrogen bonds defined for protein. 855 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: 1.80 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 - 1.34: 2188 1.34 - 1.46: 1733 1.46 - 1.58: 3074 1.58 - 1.70: 0 1.70 - 1.81: 60 Bond restraints: 7055 Sorted by residual: bond pdb=" N ARG D 582 " pdb=" CA ARG D 582 " ideal model delta sigma weight residual 1.461 1.493 -0.032 9.20e-03 1.18e+04 1.21e+01 bond pdb=" N ASN D 580 " pdb=" CA ASN D 580 " ideal model delta sigma weight residual 1.455 1.493 -0.038 1.26e-02 6.30e+03 9.32e+00 bond pdb=" N VAL A 539 " pdb=" CA VAL A 539 " ideal model delta sigma weight residual 1.457 1.492 -0.034 1.14e-02 7.69e+03 9.14e+00 bond pdb=" N ILE D 54 " pdb=" CA ILE D 54 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.13e+00 bond pdb=" N VAL D 581 " pdb=" CA VAL D 581 " ideal model delta sigma weight residual 1.458 1.499 -0.041 1.37e-02 5.33e+03 8.74e+00 ... (remaining 7050 not shown) Histogram of bond angle deviations from ideal: 99.83 - 106.67: 217 106.67 - 113.51: 3767 113.51 - 120.34: 2672 120.34 - 127.18: 2838 127.18 - 134.02: 94 Bond angle restraints: 9588 Sorted by residual: angle pdb=" CA THR D 55 " pdb=" C THR D 55 " pdb=" O THR D 55 " ideal model delta sigma weight residual 121.60 117.83 3.77 1.21e+00 6.83e-01 9.70e+00 angle pdb=" N GLN D 524 " pdb=" CA GLN D 524 " pdb=" C GLN D 524 " ideal model delta sigma weight residual 111.07 107.92 3.15 1.07e+00 8.73e-01 8.69e+00 angle pdb=" CA ASN D 53 " pdb=" CB ASN D 53 " pdb=" CG ASN D 53 " ideal model delta sigma weight residual 112.60 115.44 -2.84 1.00e+00 1.00e+00 8.08e+00 angle pdb=" N ARG D 245 " pdb=" CA ARG D 245 " pdb=" C ARG D 245 " ideal model delta sigma weight residual 111.07 108.07 3.00 1.07e+00 8.73e-01 7.85e+00 angle pdb=" CA ASN D 580 " pdb=" C ASN D 580 " pdb=" O ASN D 580 " ideal model delta sigma weight residual 121.06 117.85 3.21 1.16e+00 7.43e-01 7.68e+00 ... (remaining 9583 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.22: 3918 17.22 - 34.44: 280 34.44 - 51.66: 47 51.66 - 68.89: 14 68.89 - 86.11: 1 Dihedral angle restraints: 4260 sinusoidal: 1805 harmonic: 2455 Sorted by residual: 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 93.00 125.76 -32.76 1 1.00e+01 1.00e-02 1.53e+01 dihedral pdb=" CA ILE D 223 " pdb=" C ILE D 223 " pdb=" N GLU D 224 " pdb=" CA GLU D 224 " ideal model delta harmonic sigma weight residual 180.00 162.77 17.23 0 5.00e+00 4.00e-02 1.19e+01 dihedral pdb=" N VAL D 581 " pdb=" CA VAL D 581 " pdb=" CB VAL D 581 " pdb=" CG1 VAL D 581 " ideal model delta sinusoidal sigma weight residual -60.00 -115.06 55.06 3 1.50e+01 4.44e-03 9.32e+00 ... (remaining 4257 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 858 0.056 - 0.112: 152 0.112 - 0.167: 20 0.167 - 0.223: 5 0.223 - 0.279: 1 Chirality restraints: 1036 Sorted by residual: chirality pdb=" CA VAL A 551 " pdb=" N VAL A 551 " pdb=" C VAL A 551 " pdb=" CB VAL A 551 " both_signs ideal model delta sigma weight residual False 2.44 2.72 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA ASN D 53 " pdb=" N ASN D 53 " pdb=" C ASN D 53 " pdb=" CB ASN D 53 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB VAL A 539 " pdb=" CA VAL A 539 " pdb=" CG1 VAL A 539 " pdb=" CG2 VAL A 539 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.36e-01 ... (remaining 1033 not shown) Planarity restraints: 1237 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU D 145 " -0.038 5.00e-02 4.00e+02 5.81e-02 5.40e+00 pdb=" N PRO D 146 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO D 146 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO D 146 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 262 " 0.026 5.00e-02 4.00e+02 3.92e-02 2.45e+00 pdb=" N PRO D 263 " -0.068 5.00e-02 4.00e+02 pdb=" CA PRO D 263 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 263 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 32 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.33e+00 pdb=" C PHE D 32 " 0.026 2.00e-02 2.50e+03 pdb=" O PHE D 32 " -0.010 2.00e-02 2.50e+03 pdb=" N ASN D 33 " -0.009 2.00e-02 2.50e+03 ... (remaining 1234 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1596 2.79 - 3.32: 6369 3.32 - 3.84: 10763 3.84 - 4.37: 12074 4.37 - 4.90: 21571 Nonbonded interactions: 52373 Sorted by model distance: nonbonded pdb=" O PHE D 327 " pdb=" OG SER D 331 " model vdw 2.261 2.440 nonbonded pdb=" O ASP D 431 " pdb=" OG1 THR D 434 " model vdw 2.289 2.440 nonbonded pdb=" O ASN A 439 " pdb=" OG SER A 443 " model vdw 2.295 2.440 nonbonded pdb=" OD1 ASP A 442 " pdb=" OH TYR A 451 " model vdw 2.329 2.440 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.333 2.440 ... (remaining 52368 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=0.50 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: 2.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 9.150 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 28.120 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 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 0.041 7055 Z= 0.224 Angle : 0.558 6.131 9588 Z= 0.308 Chirality : 0.046 0.279 1036 Planarity : 0.004 0.058 1230 Dihedral : 11.822 86.106 2660 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.54 % Allowed : 7.05 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.15 (0.29), residues: 830 helix: 1.00 (0.27), residues: 385 sheet: -0.19 (0.63), residues: 57 loop : -0.73 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 436 HIS 0.003 0.000 HIS D 374 PHE 0.010 0.001 PHE D 369 TYR 0.015 0.001 TYR D 385 ARG 0.003 0.000 ARG D 514 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 129 time to evaluate : 0.752 Fit side-chains REVERT: D 168 TRP cc_start: 0.7965 (t-100) cc_final: 0.7462 (t-100) REVERT: D 223 ILE cc_start: 0.7665 (mt) cc_final: 0.6864 (mt) REVERT: D 300 GLN cc_start: 0.6498 (mm110) cc_final: 0.6021 (tm-30) REVERT: D 547 SER cc_start: 0.7753 (t) cc_final: 0.7487 (t) REVERT: A 428 ASP cc_start: 0.5576 (p0) cc_final: 0.5333 (p0) REVERT: A 578 ASP cc_start: 0.6644 (t0) cc_final: 0.6176 (t70) outliers start: 4 outliers final: 0 residues processed: 132 average time/residue: 0.2158 time to fit residues: 37.0104 Evaluate side-chains 88 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 70 optimal weight: 0.5980 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 42 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 25 optimal weight: 0.0370 chunk 39 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 75 optimal weight: 0.9980 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 345 HIS A 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7055 Z= 0.244 Angle : 0.596 12.363 9588 Z= 0.295 Chirality : 0.043 0.187 1036 Planarity : 0.004 0.054 1230 Dihedral : 6.411 58.695 1055 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 2.17 % Allowed : 11.25 % Favored : 86.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.12 (0.29), residues: 830 helix: 0.91 (0.26), residues: 392 sheet: -0.02 (0.63), residues: 58 loop : -0.72 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 436 HIS 0.002 0.001 HIS D 540 PHE 0.020 0.002 PHE A 486 TYR 0.021 0.002 TYR D 385 ARG 0.004 0.001 ARG D 582 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 91 time to evaluate : 0.827 Fit side-chains revert: symmetry clash REVERT: D 225 ASP cc_start: 0.8228 (OUTLIER) cc_final: 0.8004 (m-30) REVERT: D 300 GLN cc_start: 0.6085 (mm110) cc_final: 0.5697 (tm-30) REVERT: A 428 ASP cc_start: 0.5439 (p0) cc_final: 0.5223 (p0) REVERT: A 584 ILE cc_start: 0.6483 (OUTLIER) cc_final: 0.6255 (tt) outliers start: 16 outliers final: 3 residues processed: 101 average time/residue: 0.1932 time to fit residues: 26.4497 Evaluate side-chains 86 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain A residue 584 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 41 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 75 optimal weight: 0.1980 chunk 81 optimal weight: 0.0040 chunk 67 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 25 optimal weight: 0.7980 chunk 60 optimal weight: 0.0970 overall best weight: 0.2990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 345 HIS A 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7055 Z= 0.168 Angle : 0.531 8.716 9588 Z= 0.264 Chirality : 0.040 0.169 1036 Planarity : 0.004 0.052 1230 Dihedral : 5.872 56.245 1055 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.49 % Allowed : 13.14 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.30 (0.29), residues: 830 helix: 1.08 (0.27), residues: 391 sheet: 0.01 (0.62), residues: 58 loop : -0.65 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 436 HIS 0.002 0.001 HIS D 374 PHE 0.025 0.001 PHE A 486 TYR 0.014 0.001 TYR D 385 ARG 0.002 0.000 ARG D 582 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.711 Fit side-chains REVERT: D 225 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7912 (m-30) REVERT: A 370 ASN cc_start: 0.6061 (OUTLIER) cc_final: 0.5769 (p0) REVERT: A 428 ASP cc_start: 0.5348 (p0) cc_final: 0.5078 (p0) REVERT: A 584 ILE cc_start: 0.6555 (OUTLIER) cc_final: 0.6332 (tt) outliers start: 11 outliers final: 3 residues processed: 105 average time/residue: 0.1765 time to fit residues: 25.6107 Evaluate side-chains 91 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 584 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.6980 chunk 56 optimal weight: 0.0970 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 HIS A 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 7055 Z= 0.256 Angle : 0.587 8.243 9588 Z= 0.296 Chirality : 0.043 0.185 1036 Planarity : 0.004 0.054 1230 Dihedral : 5.750 59.732 1055 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.90 % Allowed : 13.96 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.07 (0.29), residues: 830 helix: 0.97 (0.27), residues: 387 sheet: 0.11 (0.62), residues: 58 loop : -0.89 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP D 168 HIS 0.002 0.001 HIS D 374 PHE 0.018 0.002 PHE D 327 TYR 0.022 0.002 TYR D 385 ARG 0.004 0.000 ARG D 514 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: D 225 ASP cc_start: 0.8132 (OUTLIER) cc_final: 0.7902 (m-30) REVERT: D 270 MET cc_start: 0.7356 (tpp) cc_final: 0.7000 (tpp) REVERT: A 370 ASN cc_start: 0.6193 (OUTLIER) cc_final: 0.5911 (p0) REVERT: A 428 ASP cc_start: 0.5658 (p0) cc_final: 0.5177 (p0) REVERT: A 584 ILE cc_start: 0.6554 (OUTLIER) cc_final: 0.6342 (tt) outliers start: 14 outliers final: 4 residues processed: 101 average time/residue: 0.1634 time to fit residues: 23.1207 Evaluate side-chains 91 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 84 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 225 ASP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 584 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 45 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 59 optimal weight: 0.3980 chunk 33 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 72 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 345 HIS A 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7055 Z= 0.268 Angle : 0.587 8.350 9588 Z= 0.299 Chirality : 0.043 0.188 1036 Planarity : 0.004 0.052 1230 Dihedral : 5.621 59.304 1055 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 2.44 % Allowed : 13.28 % Favored : 84.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.07 (0.28), residues: 830 helix: 0.84 (0.26), residues: 387 sheet: -0.11 (0.60), residues: 63 loop : -0.92 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP D 168 HIS 0.003 0.001 HIS D 374 PHE 0.019 0.002 PHE D 327 TYR 0.022 0.002 TYR D 385 ARG 0.004 0.000 ARG D 514 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 83 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: D 270 MET cc_start: 0.7339 (tpp) cc_final: 0.6994 (tpp) REVERT: A 370 ASN cc_start: 0.6211 (OUTLIER) cc_final: 0.5911 (p0) REVERT: A 405 ASP cc_start: 0.7476 (m-30) cc_final: 0.7241 (m-30) REVERT: A 584 ILE cc_start: 0.6545 (OUTLIER) cc_final: 0.6338 (tt) outliers start: 18 outliers final: 8 residues processed: 98 average time/residue: 0.1968 time to fit residues: 27.2219 Evaluate side-chains 91 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 370 ASN Chi-restraints excluded: chain A residue 584 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 72 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 47 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 80 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 chunk 77 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7055 Z= 0.289 Angle : 0.602 8.443 9588 Z= 0.308 Chirality : 0.045 0.340 1036 Planarity : 0.004 0.041 1230 Dihedral : 5.676 59.082 1055 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.76 % Allowed : 14.77 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.22 (0.28), residues: 830 helix: 0.72 (0.26), residues: 388 sheet: 0.09 (0.63), residues: 58 loop : -1.07 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP D 168 HIS 0.003 0.001 HIS D 374 PHE 0.021 0.002 PHE D 327 TYR 0.024 0.002 TYR D 385 ARG 0.004 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 90 time to evaluate : 0.771 Fit side-chains revert: symmetry clash REVERT: D 270 MET cc_start: 0.7408 (tpp) cc_final: 0.7114 (tpp) REVERT: A 405 ASP cc_start: 0.7447 (m-30) cc_final: 0.7187 (m-30) outliers start: 13 outliers final: 9 residues processed: 103 average time/residue: 0.1674 time to fit residues: 23.9051 Evaluate side-chains 94 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 410 LEU Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 0.5980 chunk 45 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 67 optimal weight: 0.0470 chunk 44 optimal weight: 0.1980 chunk 79 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 36 optimal weight: 0.3980 chunk 49 optimal weight: 0.0980 chunk 31 optimal weight: 2.9990 overall best weight: 0.2478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 450 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7314 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7055 Z= 0.166 Angle : 0.550 8.908 9588 Z= 0.275 Chirality : 0.042 0.347 1036 Planarity : 0.004 0.048 1230 Dihedral : 5.190 56.135 1055 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.36 % Allowed : 14.63 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.10 (0.29), residues: 830 helix: 1.04 (0.27), residues: 386 sheet: -0.14 (0.61), residues: 63 loop : -0.88 (0.30), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP D 168 HIS 0.003 0.001 HIS D 535 PHE 0.015 0.001 PHE D 504 TYR 0.012 0.001 TYR D 385 ARG 0.004 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 86 time to evaluate : 0.781 Fit side-chains REVERT: D 62 MET cc_start: 0.7414 (mtm) cc_final: 0.7205 (mtm) REVERT: D 190 MET cc_start: 0.8060 (tmm) cc_final: 0.7811 (tmm) REVERT: D 270 MET cc_start: 0.7417 (tpp) cc_final: 0.7213 (tpp) outliers start: 10 outliers final: 7 residues processed: 95 average time/residue: 0.1693 time to fit residues: 22.4385 Evaluate side-chains 89 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 47 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 50 optimal weight: 0.0970 chunk 54 optimal weight: 0.8980 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 72 optimal weight: 0.9980 chunk 76 optimal weight: 0.0970 chunk 69 optimal weight: 0.7980 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7363 moved from start: 0.2401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 7055 Z= 0.228 Angle : 0.588 8.850 9588 Z= 0.297 Chirality : 0.043 0.329 1036 Planarity : 0.004 0.051 1230 Dihedral : 5.345 58.782 1055 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.49 % Allowed : 15.04 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: -0.02 (0.28), residues: 830 helix: 0.95 (0.27), residues: 388 sheet: -0.35 (0.65), residues: 56 loop : -0.94 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP D 168 HIS 0.002 0.001 HIS D 535 PHE 0.016 0.001 PHE A 486 TYR 0.019 0.001 TYR D 385 ARG 0.005 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.794 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 96 average time/residue: 0.1707 time to fit residues: 22.7679 Evaluate side-chains 93 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.787 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 203 TRP Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain D residue 608 THR Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 74 optimal weight: 0.7980 chunk 76 optimal weight: 0.2980 chunk 44 optimal weight: 0.0670 chunk 32 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 67 optimal weight: 0.1980 chunk 70 optimal weight: 0.3980 chunk 48 optimal weight: 0.6980 chunk 78 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 overall best weight: 0.3118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.2449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7055 Z= 0.181 Angle : 0.566 8.777 9588 Z= 0.284 Chirality : 0.042 0.319 1036 Planarity : 0.004 0.053 1230 Dihedral : 5.157 56.803 1055 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.22 % Allowed : 15.04 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.10 (0.29), residues: 830 helix: 1.05 (0.27), residues: 386 sheet: -0.42 (0.64), residues: 56 loop : -0.84 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP D 168 HIS 0.003 0.001 HIS D 535 PHE 0.015 0.001 PHE A 486 TYR 0.013 0.001 TYR D 385 ARG 0.005 0.000 ARG A 328 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.818 Fit side-chains REVERT: A 386 LYS cc_start: 0.6825 (mmtm) cc_final: 0.5671 (pttt) outliers start: 9 outliers final: 8 residues processed: 89 average time/residue: 0.1794 time to fit residues: 22.2723 Evaluate side-chains 89 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 324 THR Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain D residue 361 CYS Chi-restraints excluded: chain A residue 335 LEU Chi-restraints excluded: chain A residue 350 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 54 optimal weight: 0.2980 chunk 82 optimal weight: 5.9990 chunk 76 optimal weight: 0.0770 chunk 65 optimal weight: 0.5980 chunk 6 optimal weight: 0.0770 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 0.1980 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 0.0370 chunk 20 optimal weight: 0.0030 chunk 60 optimal weight: 0.1980 overall best weight: 0.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7251 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 7055 Z= 0.150 Angle : 0.558 11.596 9588 Z= 0.275 Chirality : 0.041 0.314 1036 Planarity : 0.004 0.055 1230 Dihedral : 4.921 55.042 1055 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.68 % Allowed : 15.45 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.36 (0.29), residues: 830 helix: 1.33 (0.27), residues: 377 sheet: -0.59 (0.64), residues: 58 loop : -0.67 (0.31), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D 168 HIS 0.003 0.001 HIS D 535 PHE 0.017 0.001 PHE D 504 TYR 0.009 0.001 TYR D 127 ARG 0.004 0.000 ARG A 328 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 0.751 Fit side-chains REVERT: D 50 TYR cc_start: 0.6911 (t80) cc_final: 0.6556 (t80) REVERT: D 190 MET cc_start: 0.7987 (tmm) cc_final: 0.7782 (tmm) REVERT: D 323 MET cc_start: 0.7111 (mmm) cc_final: 0.6444 (mmm) REVERT: A 386 LYS cc_start: 0.6836 (mmtm) cc_final: 0.5710 (pttt) outliers start: 5 outliers final: 5 residues processed: 86 average time/residue: 0.1894 time to fit residues: 22.1383 Evaluate side-chains 84 residues out of total 736 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 81 GLN Chi-restraints excluded: chain D residue 148 LEU Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 347 THR Chi-restraints excluded: chain A residue 335 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 83 random chunks: chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 0.2980 chunk 65 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 47 optimal weight: 0.0270 chunk 75 optimal weight: 0.7980 overall best weight: 0.5238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 370 ASN ** 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 = 0.4179 r_free = 0.4179 target = 0.194761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.171292 restraints weight = 11182.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.171552 restraints weight = 20916.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.170615 restraints weight = 13336.594| |-----------------------------------------------------------------------------| r_work (final): 0.3917 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3917 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3917 r_free = 0.3917 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3917 r_free = 0.3917 target_work(ls_wunit_k1) = 0.169 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3917 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 7055 Z= 0.232 Angle : 0.593 10.239 9588 Z= 0.296 Chirality : 0.043 0.316 1036 Planarity : 0.004 0.059 1230 Dihedral : 5.209 58.277 1055 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.95 % Allowed : 15.31 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % 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: 0.10 (0.29), residues: 830 helix: 1.09 (0.27), residues: 386 sheet: -0.42 (0.65), residues: 56 loop : -0.89 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP D 168 HIS 0.003 0.001 HIS D 374 PHE 0.024 0.001 PHE D 603 TYR 0.020 0.001 TYR D 385 ARG 0.004 0.000 ARG A 328 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1781.45 seconds wall clock time: 32 minutes 37.64 seconds (1957.64 seconds total)