Starting phenix.real_space_refine on Sun Dec 29 12:33:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dd8_27336/12_2024/8dd8_27336.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dd8_27336/12_2024/8dd8_27336.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dd8_27336/12_2024/8dd8_27336.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dd8_27336/12_2024/8dd8_27336.map" model { file = "/net/cci-nas-00/data/ceres_data/8dd8_27336/12_2024/8dd8_27336.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dd8_27336/12_2024/8dd8_27336.cif" } resolution = 3.4 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= 1.000 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: 4 Type Number sf(0) Gaussians S 75 5.16 5 C 6683 2.51 5 N 1810 2.21 5 O 1924 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 10492 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8265 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1011, 8265 Classifications: {'peptide': 1011} Link IDs: {'PCIS': 1, 'PTRANS': 46, 'TRANS': 963} Chain breaks: 3 Chain: "B" Number of atoms: 2227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 261, 2227 Classifications: {'peptide': 261} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 256} Chain breaks: 2 Time building chain proxies: 6.89, per 1000 atoms: 0.66 Number of scatterers: 10492 At special positions: 0 Unit cell: (89.024, 109.824, 137.28, 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 75 16.00 O 1924 8.00 N 1810 7.00 C 6683 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.72 Conformation dependent library (CDL) restraints added in 1.3 seconds 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2434 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 10 sheets defined 48.6% alpha, 11.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 41 through 54 removed outlier: 3.660A pdb=" N GLU A 48 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N ARG A 54 " --> pdb=" O PHE A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 62 Processing helix chain 'A' and resid 107 through 122 removed outlier: 3.540A pdb=" N LYS A 111 " --> pdb=" O ASN A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 130 Processing helix chain 'A' and resid 133 through 154 removed outlier: 3.580A pdb=" N GLN A 137 " --> pdb=" O ASP A 133 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU A 144 " --> pdb=" O ARG A 140 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N ASN A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 167 Processing helix chain 'A' and resid 178 through 183 removed outlier: 3.726A pdb=" N ASN A 183 " --> pdb=" O LYS A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 233 removed outlier: 3.888A pdb=" N ARG A 230 " --> pdb=" O ARG A 226 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N SER A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N MET A 232 " --> pdb=" O LYS A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 248 removed outlier: 3.747A pdb=" N VAL A 243 " --> pdb=" O LYS A 240 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N LEU A 244 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU A 245 " --> pdb=" O CYS A 242 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N GLN A 247 " --> pdb=" O LEU A 244 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N GLY A 248 " --> pdb=" O GLU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 269 Processing helix chain 'A' and resid 270 through 280 Processing helix chain 'A' and resid 290 through 297 removed outlier: 3.501A pdb=" N LEU A 297 " --> pdb=" O LEU A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 330 No H-bonds generated for 'chain 'A' and resid 328 through 330' Processing helix chain 'A' and resid 488 through 496 Processing helix chain 'A' and resid 526 through 537 removed outlier: 3.705A pdb=" N GLN A 530 " --> pdb=" O ASN A 526 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ARG A 537 " --> pdb=" O ALA A 533 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 554 Processing helix chain 'A' and resid 556 through 563 removed outlier: 3.631A pdb=" N VAL A 559 " --> pdb=" O HIS A 556 " (cutoff:3.500A) Proline residue: A 562 - end of helix Processing helix chain 'A' and resid 564 through 572 Processing helix chain 'A' and resid 577 through 589 removed outlier: 3.668A pdb=" N ASP A 589 " --> pdb=" O CYS A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 594 through 599 Processing helix chain 'A' and resid 600 through 603 Processing helix chain 'A' and resid 608 through 623 Processing helix chain 'A' and resid 624 through 631 Processing helix chain 'A' and resid 631 through 638 Processing helix chain 'A' and resid 647 through 658 Processing helix chain 'A' and resid 660 through 674 removed outlier: 3.725A pdb=" N PHE A 666 " --> pdb=" O ARG A 662 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLU A 674 " --> pdb=" O HIS A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 695 Processing helix chain 'A' and resid 697 through 723 removed outlier: 4.487A pdb=" N HIS A 701 " --> pdb=" O MET A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 727 through 740 Processing helix chain 'A' and resid 741 through 748 Processing helix chain 'A' and resid 807 through 828 Processing helix chain 'A' and resid 857 through 863 removed outlier: 4.021A pdb=" N LYS A 863 " --> pdb=" O GLN A 859 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 885 Processing helix chain 'A' and resid 886 through 888 No H-bonds generated for 'chain 'A' and resid 886 through 888' Processing helix chain 'A' and resid 889 through 912 Processing helix chain 'A' and resid 957 through 965 Processing helix chain 'A' and resid 974 through 994 Processing helix chain 'A' and resid 994 through 1006 removed outlier: 3.979A pdb=" N PHE A 998 " --> pdb=" O HIS A 994 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1026 removed outlier: 3.808A pdb=" N ILE A1019 " --> pdb=" O SER A1015 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N TYR A1021 " --> pdb=" O ASP A1017 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE A1022 " --> pdb=" O ASP A1018 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU A1026 " --> pdb=" O ILE A1022 " (cutoff:3.500A) Processing helix chain 'A' and resid 1031 through 1048 removed outlier: 3.545A pdb=" N LEU A1036 " --> pdb=" O GLU A1032 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 347 Processing helix chain 'B' and resid 385 through 389 removed outlier: 4.005A pdb=" N GLY B 388 " --> pdb=" O HIS B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 411 Processing helix chain 'B' and resid 446 through 448 No H-bonds generated for 'chain 'B' and resid 446 through 448' Processing helix chain 'B' and resid 449 through 504 removed outlier: 3.796A pdb=" N ASN B 453 " --> pdb=" O LEU B 449 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR B 454 " --> pdb=" O HIS B 450 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N GLN B 455 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE B 456 " --> pdb=" O TYR B 452 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLN B 457 " --> pdb=" O ASN B 453 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLU B 458 " --> pdb=" O THR B 454 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N LYS B 459 " --> pdb=" O GLN B 455 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLU B 462 " --> pdb=" O GLU B 458 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA B 483 " --> pdb=" O MET B 479 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE B 484 " --> pdb=" O LYS B 480 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N GLU B 485 " --> pdb=" O ARG B 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 565 removed outlier: 3.872A pdb=" N MET B 525 " --> pdb=" O ILE B 521 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N HIS B 526 " --> pdb=" O GLN B 522 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LYS B 530 " --> pdb=" O HIS B 526 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU B 531 " --> pdb=" O ASN B 527 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU B 547 " --> pdb=" O ARG B 543 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N LYS B 550 " --> pdb=" O GLU B 546 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N GLN B 552 " --> pdb=" O ASP B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 566 through 575 removed outlier: 3.699A pdb=" N LYS B 575 " --> pdb=" O ILE B 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 576 through 578 No H-bonds generated for 'chain 'B' and resid 576 through 578' Processing helix chain 'B' and resid 593 through 598 removed outlier: 4.263A pdb=" N LEU B 598 " --> pdb=" O LEU B 594 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 36 removed outlier: 3.709A pdb=" N MET A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU A 34 " --> pdb=" O VAL A 22 " (cutoff:3.500A) removed outlier: 5.590A pdb=" N VAL A 101 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N PHE A 98 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N VAL A 73 " --> pdb=" O PHE A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 212 removed outlier: 4.005A pdb=" N GLN A 205 " --> pdb=" O VAL A 196 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N LEU A 285 " --> pdb=" O ILE A 191 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N VAL A 193 " --> pdb=" O LEU A 285 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU A 287 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N TRP A 195 " --> pdb=" O LEU A 287 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N ALA A 289 " --> pdb=" O TRP A 195 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N MET A 288 " --> pdb=" O ILE A 251 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 326 removed outlier: 6.084A pdb=" N LYS A 325 " --> pdb=" O LYS A 485 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 382 through 392 removed outlier: 6.853A pdb=" N TRP A 383 " --> pdb=" O CYS A 340 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N CYS A 340 " --> pdb=" O TRP A 383 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N LEU A 334 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N GLU A 474 " --> pdb=" O LEU A 339 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA A 341 " --> pdb=" O CYS A 472 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N CYS A 472 " --> pdb=" O ALA A 341 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N GLY A 439 " --> pdb=" O PHE A 477 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 365 through 366 removed outlier: 3.594A pdb=" N GLU A 365 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A 353 " --> pdb=" O VAL A 409 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 365 through 366 removed outlier: 3.594A pdb=" N GLU A 365 " --> pdb=" O HIS A 362 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N SER A 408 " --> pdb=" O PRO A 421 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 751 through 752 Processing sheet with id=AA8, first strand: chain 'A' and resid 770 through 771 removed outlier: 6.857A pdb=" N VAL A 845 " --> pdb=" O ILE A 841 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 854 through 856 Processing sheet with id=AB1, first strand: chain 'B' and resid 377 through 381 removed outlier: 3.655A pdb=" N ASN B 377 " --> pdb=" O LYS B 374 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR B 354 " --> pdb=" O ARG B 373 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1338 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: 3.77 Time building geometry restraints manager: 3.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3437 1.35 - 1.46: 2385 1.46 - 1.58: 4776 1.58 - 1.70: 0 1.70 - 1.82: 117 Bond restraints: 10715 Sorted by residual: bond pdb=" CB CYS A 901 " pdb=" SG CYS A 901 " ideal model delta sigma weight residual 1.808 1.772 0.036 3.30e-02 9.18e+02 1.21e+00 bond pdb=" CG1 ILE A1022 " pdb=" CD1 ILE A1022 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.14e+00 bond pdb=" CG LEU A 327 " pdb=" CD1 LEU A 327 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.14e+00 bond pdb=" CA ILE A 197 " pdb=" CB ILE A 197 " ideal model delta sigma weight residual 1.540 1.553 -0.013 1.36e-02 5.41e+03 8.60e-01 bond pdb=" CG LEU A 929 " pdb=" CD2 LEU A 929 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.32e-01 ... (remaining 10710 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 14261 2.18 - 4.35: 153 4.35 - 6.53: 28 6.53 - 8.70: 4 8.70 - 10.88: 1 Bond angle restraints: 14447 Sorted by residual: angle pdb=" CB MET A 489 " pdb=" CG MET A 489 " pdb=" SD MET A 489 " ideal model delta sigma weight residual 112.70 123.58 -10.88 3.00e+00 1.11e-01 1.32e+01 angle pdb=" C LYS B 419 " pdb=" N LEU B 420 " pdb=" CA LEU B 420 " ideal model delta sigma weight residual 121.54 126.93 -5.39 1.91e+00 2.74e-01 7.97e+00 angle pdb=" C VAL A 196 " pdb=" N ILE A 197 " pdb=" CA ILE A 197 " ideal model delta sigma weight residual 121.97 126.99 -5.02 1.80e+00 3.09e-01 7.77e+00 angle pdb=" N SER A 199 " pdb=" CA SER A 199 " pdb=" C SER A 199 " ideal model delta sigma weight residual 108.07 110.28 -2.21 8.90e-01 1.26e+00 6.17e+00 angle pdb=" C LEU A 234 " pdb=" N SER A 235 " pdb=" CA SER A 235 " ideal model delta sigma weight residual 121.54 126.24 -4.70 1.91e+00 2.74e-01 6.07e+00 ... (remaining 14442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.67: 5632 16.67 - 33.35: 716 33.35 - 50.02: 157 50.02 - 66.69: 32 66.69 - 83.36: 16 Dihedral angle restraints: 6553 sinusoidal: 2801 harmonic: 3752 Sorted by residual: dihedral pdb=" CA ALA A 775 " pdb=" C ALA A 775 " pdb=" N LYS A 776 " pdb=" CA LYS A 776 " ideal model delta harmonic sigma weight residual 180.00 162.32 17.68 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA ASP B 560 " pdb=" CB ASP B 560 " pdb=" CG ASP B 560 " pdb=" OD1 ASP B 560 " ideal model delta sinusoidal sigma weight residual -30.00 -87.52 57.52 1 2.00e+01 2.50e-03 1.11e+01 dihedral pdb=" CA ASP B 367 " pdb=" C ASP B 367 " pdb=" N TYR B 368 " pdb=" CA TYR B 368 " ideal model delta harmonic sigma weight residual 180.00 163.47 16.53 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 6550 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1059 0.039 - 0.078: 372 0.078 - 0.118: 104 0.118 - 0.157: 22 0.157 - 0.196: 1 Chirality restraints: 1558 Sorted by residual: chirality pdb=" CB ILE A 197 " pdb=" CA ILE A 197 " pdb=" CG1 ILE A 197 " pdb=" CG2 ILE A 197 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.62e-01 chirality pdb=" CA VAL A 216 " pdb=" N VAL A 216 " pdb=" C VAL A 216 " pdb=" CB VAL A 216 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.74e-01 chirality pdb=" CG LEU A 956 " pdb=" CB LEU A 956 " pdb=" CD1 LEU A 956 " pdb=" CD2 LEU A 956 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.73e-01 ... (remaining 1555 not shown) Planarity restraints: 1854 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 16 " 0.042 5.00e-02 4.00e+02 6.29e-02 6.32e+00 pdb=" N PRO A 17 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO A 17 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 17 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 216 " 0.040 5.00e-02 4.00e+02 6.11e-02 5.98e+00 pdb=" N PRO A 217 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO A 217 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO A 217 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS A 420 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO A 421 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 421 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 421 " -0.026 5.00e-02 4.00e+02 ... (remaining 1851 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1145 2.75 - 3.29: 10361 3.29 - 3.82: 17182 3.82 - 4.36: 20438 4.36 - 4.90: 35207 Nonbonded interactions: 84333 Sorted by model distance: nonbonded pdb=" OE2 GLU A 970 " pdb=" OG1 THR A 972 " model vdw 2.211 3.040 nonbonded pdb=" O GLN B 497 " pdb=" OG1 THR B 500 " model vdw 2.221 3.040 nonbonded pdb=" OD1 ASN A 157 " pdb=" OG SER A 161 " model vdw 2.279 3.040 nonbonded pdb=" OD2 ASP A 138 " pdb=" OH TYR A 432 " model vdw 2.291 3.040 nonbonded pdb=" NH2 ARG A 916 " pdb=" O ASP A 933 " model vdw 2.292 3.120 ... (remaining 84328 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.350 Find NCS groups from input model: 0.130 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: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10715 Z= 0.221 Angle : 0.600 10.879 14447 Z= 0.300 Chirality : 0.044 0.196 1558 Planarity : 0.004 0.063 1854 Dihedral : 15.623 83.365 4119 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.97 % Favored : 95.95 % Rotamer: Outliers : 0.00 % Allowed : 0.17 % Favored : 99.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.65 (0.22), residues: 1258 helix: 0.30 (0.22), residues: 520 sheet: -0.20 (0.43), residues: 141 loop : -1.11 (0.23), residues: 597 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 780 HIS 0.015 0.001 HIS A 47 PHE 0.012 0.001 PHE A 954 TYR 0.014 0.001 TYR B 508 ARG 0.003 0.000 ARG A 93 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 1.220 Fit side-chains REVERT: A 216 VAL cc_start: 0.8536 (t) cc_final: 0.8292 (t) REVERT: A 599 MET cc_start: 0.8163 (ttp) cc_final: 0.7946 (ttp) REVERT: A 961 LEU cc_start: 0.7271 (mm) cc_final: 0.6972 (mt) outliers start: 0 outliers final: 0 residues processed: 103 average time/residue: 0.2299 time to fit residues: 34.7442 Evaluate side-chains 89 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 38 optimal weight: 0.0060 chunk 60 optimal weight: 0.7980 chunk 74 optimal weight: 2.9990 chunk 115 optimal weight: 4.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 676 HIS ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1044 ASN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A1048 HIS ** B 526 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10715 Z= 0.225 Angle : 0.538 7.317 14447 Z= 0.283 Chirality : 0.043 0.156 1558 Planarity : 0.004 0.059 1854 Dihedral : 4.137 17.542 1393 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.34 % Favored : 96.58 % Rotamer: Outliers : 0.34 % Allowed : 5.56 % Favored : 94.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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 (0.23), residues: 1258 helix: 0.82 (0.22), residues: 550 sheet: -0.30 (0.42), residues: 141 loop : -1.04 (0.25), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 780 HIS 0.015 0.001 HIS A1048 PHE 0.010 0.001 PHE A 666 TYR 0.017 0.001 TYR B 508 ARG 0.004 0.000 ARG B 358 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 98 time to evaluate : 1.395 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 99 average time/residue: 0.2247 time to fit residues: 32.9842 Evaluate side-chains 89 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 531 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 0.4980 chunk 95 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 115 optimal weight: 7.9990 chunk 124 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 92 optimal weight: 0.0770 overall best weight: 1.0540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10715 Z= 0.230 Angle : 0.519 7.257 14447 Z= 0.270 Chirality : 0.043 0.155 1558 Planarity : 0.004 0.060 1854 Dihedral : 4.108 17.931 1393 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.13 % Favored : 95.79 % Rotamer: Outliers : 0.43 % Allowed : 9.32 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.21 (0.23), residues: 1258 helix: 0.90 (0.22), residues: 558 sheet: -0.42 (0.42), residues: 141 loop : -1.11 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 780 HIS 0.003 0.001 HIS A 665 PHE 0.011 0.001 PHE A 666 TYR 0.020 0.001 TYR B 508 ARG 0.003 0.000 ARG B 358 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 1.181 Fit side-chains REVERT: A 34 LEU cc_start: 0.7791 (mm) cc_final: 0.7541 (mt) REVERT: A 599 MET cc_start: 0.8072 (ttp) cc_final: 0.7748 (ttp) outliers start: 5 outliers final: 4 residues processed: 95 average time/residue: 0.2731 time to fit residues: 38.5786 Evaluate side-chains 94 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 90 time to evaluate : 2.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 531 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 7.9990 chunk 86 optimal weight: 0.9990 chunk 59 optimal weight: 0.5980 chunk 12 optimal weight: 0.0570 chunk 55 optimal weight: 1.9990 chunk 77 optimal weight: 0.6980 chunk 115 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 109 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 47 HIS ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10715 Z= 0.171 Angle : 0.488 7.112 14447 Z= 0.255 Chirality : 0.041 0.158 1558 Planarity : 0.003 0.059 1854 Dihedral : 4.005 17.704 1393 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.82 % Favored : 96.10 % Rotamer: Outliers : 0.43 % Allowed : 11.54 % Favored : 88.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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 (0.23), residues: 1258 helix: 1.13 (0.22), residues: 551 sheet: -0.34 (0.42), residues: 139 loop : -1.05 (0.25), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 780 HIS 0.004 0.001 HIS A 665 PHE 0.016 0.001 PHE B 456 TYR 0.017 0.001 TYR B 508 ARG 0.002 0.000 ARG B 358 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 94 time to evaluate : 1.329 Fit side-chains REVERT: A 34 LEU cc_start: 0.7797 (mm) cc_final: 0.7544 (mt) REVERT: A 232 MET cc_start: 0.6274 (ptp) cc_final: 0.5698 (ptm) outliers start: 5 outliers final: 3 residues processed: 96 average time/residue: 0.2208 time to fit residues: 31.8969 Evaluate side-chains 92 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 89 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 556 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 1 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 104 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 chunk 62 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 917 HIS ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 10715 Z= 0.350 Angle : 0.584 6.912 14447 Z= 0.300 Chirality : 0.045 0.187 1558 Planarity : 0.004 0.060 1854 Dihedral : 4.260 18.130 1393 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.61 % Favored : 95.31 % Rotamer: Outliers : 0.60 % Allowed : 13.76 % Favored : 85.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.26 (0.23), residues: 1258 helix: 0.90 (0.22), residues: 557 sheet: -0.65 (0.42), residues: 141 loop : -1.12 (0.25), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 780 HIS 0.005 0.001 HIS A 160 PHE 0.017 0.002 PHE A 666 TYR 0.016 0.002 TYR B 508 ARG 0.004 0.000 ARG A 401 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 1.430 Fit side-chains REVERT: A 161 SER cc_start: 0.8759 (OUTLIER) cc_final: 0.8503 (p) REVERT: A 232 MET cc_start: 0.6428 (ptp) cc_final: 0.5955 (ptm) outliers start: 7 outliers final: 5 residues processed: 93 average time/residue: 0.2304 time to fit residues: 31.7027 Evaluate side-chains 88 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 556 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 0.0570 chunk 110 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 122 optimal weight: 5.9990 chunk 102 optimal weight: 0.1980 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 40 optimal weight: 4.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 861 GLN ** A 920 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10715 Z= 0.166 Angle : 0.495 7.459 14447 Z= 0.255 Chirality : 0.042 0.163 1558 Planarity : 0.003 0.061 1854 Dihedral : 4.037 18.030 1393 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 0.77 % Allowed : 14.96 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: -0.06 (0.23), residues: 1258 helix: 1.11 (0.22), residues: 558 sheet: -0.48 (0.42), residues: 139 loop : -1.07 (0.25), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 780 HIS 0.005 0.001 HIS A 665 PHE 0.010 0.001 PHE A 50 TYR 0.016 0.001 TYR B 508 ARG 0.002 0.000 ARG B 358 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 1.351 Fit side-chains REVERT: A 232 MET cc_start: 0.6372 (ptp) cc_final: 0.5918 (ptm) REVERT: B 450 HIS cc_start: 0.5275 (m90) cc_final: 0.5000 (m90) outliers start: 9 outliers final: 5 residues processed: 97 average time/residue: 0.2245 time to fit residues: 32.3512 Evaluate side-chains 90 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 556 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 69 optimal weight: 0.0770 chunk 103 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 920 ASN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10715 Z= 0.176 Angle : 0.499 7.454 14447 Z= 0.256 Chirality : 0.042 0.165 1558 Planarity : 0.003 0.060 1854 Dihedral : 3.957 17.689 1393 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 0.94 % Allowed : 15.21 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.09 (0.24), residues: 1258 helix: 1.26 (0.22), residues: 555 sheet: -0.45 (0.42), residues: 139 loop : -1.00 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 780 HIS 0.005 0.001 HIS A 665 PHE 0.025 0.001 PHE B 456 TYR 0.017 0.001 TYR B 508 ARG 0.002 0.000 ARG B 358 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 1.289 Fit side-chains REVERT: A 123 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.7002 (ppp) REVERT: A 232 MET cc_start: 0.6360 (ptp) cc_final: 0.5947 (ptm) outliers start: 11 outliers final: 8 residues processed: 94 average time/residue: 0.2254 time to fit residues: 31.8085 Evaluate side-chains 93 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 84 time to evaluate : 1.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 895 ASP Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 556 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 0.8980 chunk 48 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 36 optimal weight: 0.0970 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 83 optimal weight: 9.9990 chunk 60 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 96 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1047 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10715 Z= 0.169 Angle : 0.496 7.964 14447 Z= 0.254 Chirality : 0.042 0.191 1558 Planarity : 0.003 0.060 1854 Dihedral : 3.943 17.702 1393 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.20 % Allowed : 15.38 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.16 (0.24), residues: 1258 helix: 1.33 (0.22), residues: 555 sheet: -0.38 (0.42), residues: 139 loop : -0.99 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 780 HIS 0.005 0.001 HIS A 665 PHE 0.024 0.001 PHE B 456 TYR 0.016 0.001 TYR B 508 ARG 0.002 0.000 ARG A 975 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 1.490 Fit side-chains REVERT: A 123 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.6993 (ppp) REVERT: A 232 MET cc_start: 0.6366 (ptp) cc_final: 0.5982 (ptm) outliers start: 14 outliers final: 8 residues processed: 101 average time/residue: 0.2472 time to fit residues: 37.6640 Evaluate side-chains 97 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain A residue 875 HIS Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 556 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 106 optimal weight: 0.1980 chunk 114 optimal weight: 6.9990 chunk 68 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 89 optimal weight: 0.1980 chunk 35 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 113 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1047 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10715 Z= 0.194 Angle : 0.518 7.498 14447 Z= 0.264 Chirality : 0.042 0.203 1558 Planarity : 0.003 0.059 1854 Dihedral : 3.957 17.525 1393 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.21 % Favored : 95.71 % Rotamer: Outliers : 0.85 % Allowed : 15.56 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.19 (0.24), residues: 1258 helix: 1.34 (0.22), residues: 555 sheet: -0.38 (0.43), residues: 139 loop : -0.96 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 780 HIS 0.005 0.001 HIS A 665 PHE 0.026 0.001 PHE B 456 TYR 0.015 0.001 TYR B 508 ARG 0.001 0.000 ARG B 358 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 1.325 Fit side-chains REVERT: A 123 MET cc_start: 0.8712 (OUTLIER) cc_final: 0.7006 (ppp) REVERT: A 232 MET cc_start: 0.6428 (ptp) cc_final: 0.6042 (ptm) outliers start: 10 outliers final: 7 residues processed: 94 average time/residue: 0.2441 time to fit residues: 34.3490 Evaluate side-chains 96 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 1.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 556 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 3.9990 chunk 120 optimal weight: 5.9990 chunk 73 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 126 optimal weight: 7.9990 chunk 116 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 10 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 61 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10715 Z= 0.226 Angle : 0.535 7.573 14447 Z= 0.272 Chirality : 0.043 0.201 1558 Planarity : 0.003 0.059 1854 Dihedral : 4.028 17.725 1393 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.29 % Favored : 95.63 % Rotamer: Outliers : 0.94 % Allowed : 15.64 % Favored : 83.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.14 (0.24), residues: 1258 helix: 1.28 (0.22), residues: 555 sheet: -0.35 (0.43), residues: 138 loop : -0.98 (0.26), residues: 565 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 780 HIS 0.005 0.001 HIS A 665 PHE 0.026 0.001 PHE B 456 TYR 0.013 0.001 TYR B 508 ARG 0.002 0.000 ARG A 401 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2516 Ramachandran restraints generated. 1258 Oldfield, 0 Emsley, 1258 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 1.362 Fit side-chains REVERT: A 123 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.7028 (ppp) REVERT: A 232 MET cc_start: 0.6492 (ptp) cc_final: 0.6114 (ptm) outliers start: 11 outliers final: 7 residues processed: 96 average time/residue: 0.2213 time to fit residues: 31.9844 Evaluate side-chains 95 residues out of total 1170 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 87 time to evaluate : 1.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 TYR Chi-restraints excluded: chain A residue 121 ILE Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 281 ARG Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 364 MET Chi-restraints excluded: chain B residue 556 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 92 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 100 optimal weight: 0.9990 chunk 42 optimal weight: 0.0050 chunk 103 optimal weight: 1.9990 chunk 12 optimal weight: 0.0770 chunk 18 optimal weight: 3.9990 overall best weight: 0.5354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1044 ASN ** A1047 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.128433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.102276 restraints weight = 21625.968| |-----------------------------------------------------------------------------| r_work (start): 0.3494 rms_B_bonded: 2.38 r_work: 0.3217 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10715 Z= 0.160 Angle : 0.514 7.767 14447 Z= 0.262 Chirality : 0.042 0.201 1558 Planarity : 0.003 0.060 1854 Dihedral : 3.944 17.470 1393 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.05 % Favored : 95.87 % Rotamer: Outliers : 0.68 % Allowed : 15.64 % Favored : 83.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.92 % 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: 0.23 (0.24), residues: 1258 helix: 1.38 (0.22), residues: 556 sheet: -0.26 (0.43), residues: 138 loop : -0.97 (0.26), residues: 564 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 780 HIS 0.006 0.001 HIS A 665 PHE 0.026 0.001 PHE B 456 TYR 0.013 0.001 TYR B 508 ARG 0.002 0.000 ARG B 358 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2195.73 seconds wall clock time: 42 minutes 11.58 seconds (2531.58 seconds total)