Starting phenix.real_space_refine on Tue Aug 6 15:38:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1f_18809/08_2024/8r1f_18809.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1f_18809/08_2024/8r1f_18809.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1f_18809/08_2024/8r1f_18809.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1f_18809/08_2024/8r1f_18809.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1f_18809/08_2024/8r1f_18809.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1f_18809/08_2024/8r1f_18809.cif" } resolution = 3.67 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= -0.001 sd= 0.059 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: 6 Type Number sf(0) Gaussians Zn 3 6.06 5 S 56 5.16 5 C 5305 2.51 5 N 1431 2.21 5 O 1571 1.98 5 H 8263 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 16629 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 11110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 681, 11110 Classifications: {'peptide': 681} Link IDs: {'PTRANS': 28, 'TRANS': 652} Chain breaks: 1 Chain: "B" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2365 Classifications: {'peptide': 142} Link IDs: {'PTRANS': 7, 'TRANS': 134} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "C" Number of atoms: 3151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 3151 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 15, 'TRANS': 186} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12835 SG CYS B 110 56.475 36.607 79.155 1.00176.24 S ATOM 12878 SG CYS B 113 55.532 34.457 81.709 1.00179.11 S ATOM 13405 SG CYS B 143 55.194 38.288 82.316 1.00194.25 S ATOM 13429 SG CYS B 146 58.574 36.731 82.368 1.00210.49 S ATOM 11605 SG CYS B 37 56.648 19.590 79.458 1.00183.23 S ATOM 11652 SG CYS B 40 59.322 17.617 80.885 1.00176.19 S ATOM 12158 SG CYS B 70 58.332 21.223 82.276 1.00180.55 S ATOM 12202 SG CYS B 73 60.186 20.867 79.074 1.00173.90 S ATOM 14814 SG CYS C 176 16.452 40.292 92.297 1.00246.45 S ATOM 15777 SG CYS C 238 18.788 39.517 89.134 1.00228.58 S ATOM 15823 SG CYS C 242 20.345 40.437 92.437 1.00243.62 S Time building chain proxies: 7.44, per 1000 atoms: 0.45 Number of scatterers: 16629 At special positions: 0 Unit cell: (118.44, 109.62, 109.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 3 29.99 S 56 16.00 O 1571 8.00 N 1431 7.00 C 5305 6.00 H 8263 1.00 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 - 3.50 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 Time building additional restraints: 12.27 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 201 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 110 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 113 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 143 " pdb="ZN ZN B 201 " - pdb=" SG CYS B 146 " pdb=" ZN B 202 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 37 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 73 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 40 " pdb="ZN ZN B 202 " - pdb=" SG CYS B 70 " pdb=" ZN C 401 " pdb="ZN ZN C 401 " - pdb=" ND1 HIS C 179 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 238 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 242 " pdb="ZN ZN C 401 " - pdb=" SG CYS C 176 " Number of angles added : 15 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1952 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 9 sheets defined 56.4% alpha, 11.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 129 through 143 removed outlier: 3.874A pdb=" N ILE A 136 " --> pdb=" O LYS A 132 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LEU A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 158 Processing helix chain 'A' and resid 159 through 167 removed outlier: 4.206A pdb=" N PHE A 167 " --> pdb=" O LEU A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 235 through 247 Processing helix chain 'A' and resid 249 through 274 removed outlier: 3.536A pdb=" N ALA A 255 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N TYR A 262 " --> pdb=" O ASN A 258 " (cutoff:3.500A) Proline residue: A 265 - end of helix removed outlier: 3.535A pdb=" N CYS A 269 " --> pdb=" O PRO A 265 " (cutoff:3.500A) Processing helix chain 'A' and resid 275 through 280 removed outlier: 3.573A pdb=" N ARG A 279 " --> pdb=" O ASN A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 283 No H-bonds generated for 'chain 'A' and resid 281 through 283' Processing helix chain 'A' and resid 284 through 292 Processing helix chain 'A' and resid 293 through 297 removed outlier: 3.703A pdb=" N LEU A 296 " --> pdb=" O ASN A 293 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N HIS A 297 " --> pdb=" O ARG A 294 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 293 through 297' Processing helix chain 'A' and resid 298 through 304 removed outlier: 4.301A pdb=" N MET A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 314 Processing helix chain 'A' and resid 317 through 329 Processing helix chain 'A' and resid 332 through 354 removed outlier: 3.533A pdb=" N LEU A 346 " --> pdb=" O THR A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 364 Processing helix chain 'A' and resid 365 through 386 Processing helix chain 'A' and resid 403 through 413 Processing helix chain 'A' and resid 426 through 433 Processing helix chain 'A' and resid 435 through 437 No H-bonds generated for 'chain 'A' and resid 435 through 437' Processing helix chain 'A' and resid 445 through 450 Processing helix chain 'A' and resid 451 through 458 Processing helix chain 'A' and resid 459 through 469 Processing helix chain 'A' and resid 476 through 484 Proline residue: A 481 - end of helix Processing helix chain 'A' and resid 485 through 516 Processing helix chain 'A' and resid 531 through 547 Processing helix chain 'A' and resid 549 through 553 Processing helix chain 'A' and resid 568 through 584 Processing helix chain 'A' and resid 585 through 588 Processing helix chain 'A' and resid 608 through 625 removed outlier: 3.982A pdb=" N PHE A 612 " --> pdb=" O THR A 608 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 642 removed outlier: 4.114A pdb=" N TYR A 638 " --> pdb=" O PRO A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 647 through 649 No H-bonds generated for 'chain 'A' and resid 647 through 649' Processing helix chain 'A' and resid 650 through 655 removed outlier: 3.815A pdb=" N SER A 654 " --> pdb=" O ASP A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 668 removed outlier: 3.592A pdb=" N SER A 661 " --> pdb=" O VAL A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 671 through 677 Processing helix chain 'A' and resid 699 through 703 Processing helix chain 'A' and resid 709 through 723 Processing helix chain 'A' and resid 726 through 742 removed outlier: 3.684A pdb=" N ALA A 732 " --> pdb=" O LYS A 728 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL A 740 " --> pdb=" O GLY A 736 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 750 Processing helix chain 'A' and resid 751 through 761 removed outlier: 3.656A pdb=" N LEU A 757 " --> pdb=" O GLU A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 766 through 774 Processing helix chain 'A' and resid 784 through 797 Processing helix chain 'A' and resid 798 through 811 Processing helix chain 'A' and resid 819 through 823 Processing helix chain 'A' and resid 854 through 869 Processing helix chain 'B' and resid 18 through 26 Processing helix chain 'B' and resid 45 through 55 Processing helix chain 'B' and resid 70 through 85 Processing helix chain 'B' and resid 92 through 100 Processing helix chain 'B' and resid 102 through 106 Processing helix chain 'B' and resid 118 through 128 Processing helix chain 'B' and resid 143 through 148 Processing helix chain 'C' and resid 104 through 108 removed outlier: 3.873A pdb=" N TYR C 107 " --> pdb=" O GLN C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 169 Processing helix chain 'C' and resid 176 through 181 Processing helix chain 'C' and resid 277 through 292 Processing sheet with id=AA1, first strand: chain 'A' and resid 387 through 388 removed outlier: 6.553A pdb=" N GLU A 387 " --> pdb=" O ARG A 440 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 522 through 527 Processing sheet with id=AA3, first strand: chain 'A' and resid 590 through 593 removed outlier: 3.673A pdb=" N LEU A 598 " --> pdb=" O ASP A 593 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 681 through 685 Processing sheet with id=AA5, first strand: chain 'A' and resid 775 through 777 removed outlier: 6.606A pdb=" N GLU A 775 " --> pdb=" O ILE A 827 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N LYS A 829 " --> pdb=" O GLU A 775 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ASP A 777 " --> pdb=" O LYS A 829 " (cutoff:3.500A) removed outlier: 8.110A pdb=" N GLY A 831 " --> pdb=" O ASP A 777 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE A 826 " --> pdb=" O LEU A 847 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N LEU A 849 " --> pdb=" O ILE A 826 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N ALA A 828 " --> pdb=" O LEU A 849 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLU A 851 " --> pdb=" O ALA A 828 " (cutoff:3.500A) removed outlier: 8.555A pdb=" N ASN A 830 " --> pdb=" O GLU A 851 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 36 through 37 removed outlier: 6.334A pdb=" N GLU B 36 " --> pdb=" O ALA B 68 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 86 through 91 removed outlier: 3.780A pdb=" N TYR B 88 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG B 109 " --> pdb=" O GLY B 141 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 110 through 113 removed outlier: 4.516A pdb=" N HIS C 233 " --> pdb=" O GLU C 198 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 124 through 127 removed outlier: 4.211A pdb=" N ILE C 251 " --> pdb=" O VAL C 272 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ALA C 161 " --> pdb=" O HIS C 214 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N HIS C 214 " --> pdb=" O ALA C 161 " (cutoff:3.500A) 422 hydrogen bonds defined for protein. 1176 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: 5.51 Time building geometry restraints manager: 12.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 8245 1.03 - 1.23: 29 1.23 - 1.42: 3574 1.42 - 1.62: 4872 1.62 - 1.82: 83 Bond restraints: 16803 Sorted by residual: bond pdb=" N VAL A 234 " pdb=" H VAL A 234 " ideal model delta sigma weight residual 0.860 0.963 -0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" N MET B 8 " pdb=" CA MET B 8 " ideal model delta sigma weight residual 1.458 1.498 -0.040 1.90e-02 2.77e+03 4.42e+00 bond pdb=" CD ARG A 500 " pdb=" NE ARG A 500 " ideal model delta sigma weight residual 1.458 1.429 0.029 1.40e-02 5.10e+03 4.18e+00 bond pdb=" CG ARG A 500 " pdb=" CD ARG A 500 " ideal model delta sigma weight residual 1.520 1.468 0.052 3.00e-02 1.11e+03 3.01e+00 bond pdb=" CA ASP A 389 " pdb=" CB ASP A 389 " ideal model delta sigma weight residual 1.526 1.552 -0.026 1.53e-02 4.27e+03 2.82e+00 ... (remaining 16798 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.58: 533 106.58 - 113.45: 19273 113.45 - 120.31: 5710 120.31 - 127.18: 4759 127.18 - 134.05: 69 Bond angle restraints: 30344 Sorted by residual: angle pdb=" CB ARG A 500 " pdb=" CG ARG A 500 " pdb=" CD ARG A 500 " ideal model delta sigma weight residual 111.30 101.93 9.37 2.30e+00 1.89e-01 1.66e+01 angle pdb=" C GLU A 135 " pdb=" CA GLU A 135 " pdb=" CB GLU A 135 " ideal model delta sigma weight residual 110.46 103.06 7.40 1.94e+00 2.66e-01 1.46e+01 angle pdb=" C PHE A 256 " pdb=" CA PHE A 256 " pdb=" CB PHE A 256 " ideal model delta sigma weight residual 110.88 105.73 5.15 1.57e+00 4.06e-01 1.07e+01 angle pdb=" CA TYR A 146 " pdb=" CB TYR A 146 " pdb=" CG TYR A 146 " ideal model delta sigma weight residual 113.90 108.05 5.85 1.80e+00 3.09e-01 1.06e+01 angle pdb=" N LEU A 458 " pdb=" CA LEU A 458 " pdb=" C LEU A 458 " ideal model delta sigma weight residual 109.76 114.44 -4.68 1.59e+00 3.96e-01 8.67e+00 ... (remaining 30339 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.96: 7143 15.96 - 31.93: 452 31.93 - 47.89: 157 47.89 - 63.85: 133 63.85 - 79.82: 31 Dihedral angle restraints: 7916 sinusoidal: 4351 harmonic: 3565 Sorted by residual: dihedral pdb=" CD ARG A 500 " pdb=" NE ARG A 500 " pdb=" CZ ARG A 500 " pdb=" NH1 ARG A 500 " ideal model delta sinusoidal sigma weight residual 0.00 42.03 -42.03 1 1.00e+01 1.00e-02 2.47e+01 dihedral pdb=" CA SER B 147 " pdb=" C SER B 147 " pdb=" N ARG B 148 " pdb=" CA ARG B 148 " ideal model delta harmonic sigma weight residual 180.00 160.95 19.05 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" C ASN A 699 " pdb=" N ASN A 699 " pdb=" CA ASN A 699 " pdb=" CB ASN A 699 " ideal model delta harmonic sigma weight residual -122.60 -131.47 8.87 0 2.50e+00 1.60e-01 1.26e+01 ... (remaining 7913 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 768 0.056 - 0.111: 353 0.111 - 0.167: 117 0.167 - 0.222: 18 0.222 - 0.278: 4 Chirality restraints: 1260 Sorted by residual: chirality pdb=" CA ASN A 699 " pdb=" N ASN A 699 " pdb=" C ASN A 699 " pdb=" CB ASN A 699 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.93e+00 chirality pdb=" CA ILE B 34 " pdb=" N ILE B 34 " pdb=" C ILE B 34 " pdb=" CB ILE B 34 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ARG C 248 " pdb=" N ARG C 248 " pdb=" C ARG C 248 " pdb=" CB ARG C 248 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1257 not shown) Planarity restraints: 2472 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 500 " 0.874 9.50e-02 1.11e+02 2.92e-01 9.43e+01 pdb=" NE ARG A 500 " -0.023 2.00e-02 2.50e+03 pdb=" CZ ARG A 500 " -0.052 2.00e-02 2.50e+03 pdb=" NH1 ARG A 500 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 500 " 0.008 2.00e-02 2.50e+03 pdb="HH11 ARG A 500 " -0.008 2.00e-02 2.50e+03 pdb="HH12 ARG A 500 " 0.008 2.00e-02 2.50e+03 pdb="HH21 ARG A 500 " 0.002 2.00e-02 2.50e+03 pdb="HH22 ARG A 500 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 734 " -0.426 9.50e-02 1.11e+02 1.42e-01 2.16e+01 pdb=" NE ARG A 734 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG A 734 " 0.009 2.00e-02 2.50e+03 pdb=" NH1 ARG A 734 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG A 734 " -0.001 2.00e-02 2.50e+03 pdb="HH11 ARG A 734 " 0.009 2.00e-02 2.50e+03 pdb="HH12 ARG A 734 " -0.004 2.00e-02 2.50e+03 pdb="HH21 ARG A 734 " -0.001 2.00e-02 2.50e+03 pdb="HH22 ARG A 734 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 256 " -0.045 2.00e-02 2.50e+03 1.95e-02 1.14e+01 pdb=" CG PHE A 256 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 256 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE A 256 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE A 256 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 256 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 256 " -0.008 2.00e-02 2.50e+03 pdb=" HD1 PHE A 256 " 0.007 2.00e-02 2.50e+03 pdb=" HD2 PHE A 256 " 0.007 2.00e-02 2.50e+03 pdb=" HE1 PHE A 256 " -0.004 2.00e-02 2.50e+03 pdb=" HE2 PHE A 256 " -0.005 2.00e-02 2.50e+03 pdb=" HZ PHE A 256 " -0.007 2.00e-02 2.50e+03 ... (remaining 2469 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.26: 1706 2.26 - 2.85: 38212 2.85 - 3.43: 42591 3.43 - 4.02: 58195 4.02 - 4.60: 90108 Nonbonded interactions: 230812 Sorted by model distance: nonbonded pdb=" OE2 GLU A 130 " pdb=" HH TYR A 134 " model vdw 1.677 2.450 nonbonded pdb=" O PRO C 152 " pdb=" HG1 THR C 155 " model vdw 1.693 2.450 nonbonded pdb=" HH TYR A 668 " pdb=" OD2 ASP A 675 " model vdw 1.703 2.450 nonbonded pdb=" O PRO B 16 " pdb=" HH TYR B 61 " model vdw 1.708 2.450 nonbonded pdb=" HG SER C 95 " pdb=" O THR C 211 " model vdw 1.726 2.450 ... (remaining 230807 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 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: 1.050 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: 0.220 Extract box with map and model: 0.540 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 55.250 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5340 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 : 0.008 0.053 8540 Z= 0.483 Angle : 0.979 9.367 11541 Z= 0.572 Chirality : 0.068 0.278 1260 Planarity : 0.016 0.377 1501 Dihedral : 11.490 79.816 3271 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 0.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.21 % Allowed : 2.66 % Favored : 97.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.70 (0.25), residues: 1017 helix: -0.82 (0.20), residues: 482 sheet: -0.21 (0.47), residues: 118 loop : 0.21 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.004 TRP A 791 HIS 0.013 0.003 HIS C 233 PHE 0.051 0.005 PHE A 256 TYR 0.030 0.004 TYR A 494 ARG 0.037 0.001 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 256 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 254 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 GLU cc_start: 0.6539 (tt0) cc_final: 0.6319 (tp30) REVERT: A 313 MET cc_start: 0.7243 (ttm) cc_final: 0.6893 (ttm) REVERT: A 389 ASP cc_start: 0.6868 (m-30) cc_final: 0.5336 (p0) REVERT: A 415 GLU cc_start: 0.7134 (mt-10) cc_final: 0.6837 (mp0) REVERT: A 470 GLU cc_start: 0.5170 (tt0) cc_final: 0.4952 (mm-30) REVERT: A 556 TYR cc_start: 0.7071 (t80) cc_final: 0.6333 (t80) REVERT: A 558 GLU cc_start: 0.6763 (mt-10) cc_final: 0.6402 (mm-30) REVERT: A 559 PHE cc_start: 0.6303 (m-80) cc_final: 0.6009 (m-80) REVERT: A 591 THR cc_start: 0.5311 (p) cc_final: 0.4542 (m) REVERT: A 630 ASP cc_start: 0.6216 (p0) cc_final: 0.5757 (p0) REVERT: A 756 GLU cc_start: 0.6405 (tt0) cc_final: 0.6122 (tm-30) REVERT: A 757 LEU cc_start: 0.6630 (mt) cc_final: 0.6278 (tt) REVERT: B 47 ARG cc_start: 0.7264 (tpp80) cc_final: 0.7057 (tpp80) REVERT: B 58 CYS cc_start: 0.7062 (m) cc_final: 0.6222 (t) REVERT: B 61 TYR cc_start: 0.6486 (m-80) cc_final: 0.5270 (m-80) REVERT: B 72 LYS cc_start: 0.9120 (pttm) cc_final: 0.8878 (pttm) REVERT: B 90 LEU cc_start: 0.4983 (mt) cc_final: 0.4625 (mp) REVERT: B 129 LYS cc_start: 0.7730 (mttt) cc_final: 0.6998 (mmmt) REVERT: C 100 GLN cc_start: 0.7958 (pt0) cc_final: 0.7682 (pt0) REVERT: C 137 LEU cc_start: 0.7216 (tp) cc_final: 0.6625 (tp) REVERT: C 163 TYR cc_start: 0.4948 (m-80) cc_final: 0.4259 (m-80) REVERT: C 165 GLN cc_start: 0.8806 (mt0) cc_final: 0.8296 (mt0) REVERT: C 196 ARG cc_start: 0.7032 (mtt180) cc_final: 0.6282 (ttp-110) REVERT: C 271 GLU cc_start: 0.7220 (tt0) cc_final: 0.6909 (tt0) outliers start: 2 outliers final: 1 residues processed: 256 average time/residue: 0.5748 time to fit residues: 190.5571 Evaluate side-chains 159 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 209 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 42 optimal weight: 0.0980 chunk 26 optimal weight: 0.0970 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 59 optimal weight: 10.0000 chunk 92 optimal weight: 0.6980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 795 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5388 moved from start: 0.3351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8540 Z= 0.192 Angle : 0.587 5.222 11541 Z= 0.312 Chirality : 0.040 0.140 1260 Planarity : 0.005 0.046 1501 Dihedral : 4.699 56.088 1146 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.17 % Allowed : 8.09 % Favored : 90.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.26), residues: 1017 helix: 0.75 (0.23), residues: 484 sheet: -0.12 (0.47), residues: 120 loop : 0.39 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 791 HIS 0.006 0.001 HIS C 168 PHE 0.019 0.002 PHE A 730 TYR 0.016 0.002 TYR A 624 ARG 0.008 0.001 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 172 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 161 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 239 ILE cc_start: 0.5627 (mm) cc_final: 0.5280 (mt) REVERT: A 303 GLU cc_start: 0.6805 (tt0) cc_final: 0.6342 (tp30) REVERT: A 415 GLU cc_start: 0.7366 (mt-10) cc_final: 0.6971 (mp0) REVERT: A 470 GLU cc_start: 0.6263 (tt0) cc_final: 0.6042 (mm-30) REVERT: A 511 TYR cc_start: 0.6343 (OUTLIER) cc_final: 0.6054 (t80) REVERT: A 556 TYR cc_start: 0.6702 (t80) cc_final: 0.6036 (t80) REVERT: A 558 GLU cc_start: 0.6828 (mt-10) cc_final: 0.6387 (mm-30) REVERT: A 559 PHE cc_start: 0.6496 (m-80) cc_final: 0.6126 (m-80) REVERT: A 589 MET cc_start: 0.6750 (mtp) cc_final: 0.6523 (mtp) REVERT: A 591 THR cc_start: 0.5348 (p) cc_final: 0.4869 (m) REVERT: A 756 GLU cc_start: 0.5970 (tt0) cc_final: 0.5728 (tm-30) REVERT: A 757 LEU cc_start: 0.6633 (mt) cc_final: 0.6387 (tt) REVERT: B 18 LYS cc_start: 0.6404 (mmtt) cc_final: 0.5907 (mmmt) REVERT: B 58 CYS cc_start: 0.7323 (m) cc_final: 0.6293 (t) REVERT: B 72 LYS cc_start: 0.9000 (pttm) cc_final: 0.8798 (pttm) REVERT: B 127 ASP cc_start: 0.7867 (m-30) cc_final: 0.7641 (m-30) REVERT: B 129 LYS cc_start: 0.7661 (mttt) cc_final: 0.7028 (mmmt) REVERT: C 100 GLN cc_start: 0.7787 (pt0) cc_final: 0.7541 (pt0) REVERT: C 109 PHE cc_start: 0.8264 (t80) cc_final: 0.7828 (t80) REVERT: C 287 GLU cc_start: 0.9056 (pt0) cc_final: 0.8771 (pt0) outliers start: 11 outliers final: 8 residues processed: 166 average time/residue: 0.5173 time to fit residues: 114.4667 Evaluate side-chains 143 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 134 time to evaluate : 1.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 289 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 63 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 82 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 91 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5464 moved from start: 0.4229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 8540 Z= 0.294 Angle : 0.600 5.105 11541 Z= 0.321 Chirality : 0.041 0.147 1260 Planarity : 0.005 0.057 1501 Dihedral : 4.823 58.323 1146 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.92 % Allowed : 9.90 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.26), residues: 1017 helix: 0.58 (0.23), residues: 487 sheet: -0.30 (0.48), residues: 118 loop : 0.46 (0.32), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 139 HIS 0.005 0.001 HIS C 168 PHE 0.027 0.002 PHE A 467 TYR 0.022 0.002 TYR B 86 ARG 0.007 0.001 ARG B 84 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 GLU cc_start: 0.7316 (tt0) cc_final: 0.6580 (tp30) REVERT: A 307 PRO cc_start: 0.4903 (Cg_exo) cc_final: 0.4679 (Cg_endo) REVERT: A 415 GLU cc_start: 0.7187 (mt-10) cc_final: 0.6918 (mp0) REVERT: A 470 GLU cc_start: 0.6480 (tt0) cc_final: 0.6183 (mm-30) REVERT: A 511 TYR cc_start: 0.6362 (OUTLIER) cc_final: 0.6044 (t80) REVERT: A 556 TYR cc_start: 0.6260 (t80) cc_final: 0.5826 (t80) REVERT: A 558 GLU cc_start: 0.6950 (mt-10) cc_final: 0.6654 (mm-30) REVERT: A 559 PHE cc_start: 0.6745 (m-80) cc_final: 0.6488 (m-80) REVERT: A 591 THR cc_start: 0.5646 (p) cc_final: 0.4980 (m) REVERT: A 597 LYS cc_start: 0.6942 (tttp) cc_final: 0.6371 (tppt) REVERT: A 753 GLU cc_start: 0.7029 (mp0) cc_final: 0.5988 (tp30) REVERT: A 757 LEU cc_start: 0.6588 (mt) cc_final: 0.6306 (tt) REVERT: B 58 CYS cc_start: 0.7334 (m) cc_final: 0.6324 (t) REVERT: B 63 ASP cc_start: 0.5876 (m-30) cc_final: 0.5654 (m-30) REVERT: B 72 LYS cc_start: 0.8956 (pttm) cc_final: 0.8744 (pttm) REVERT: B 127 ASP cc_start: 0.7734 (m-30) cc_final: 0.7439 (m-30) REVERT: B 129 LYS cc_start: 0.7727 (mttt) cc_final: 0.7015 (mmmt) REVERT: C 100 GLN cc_start: 0.7731 (pt0) cc_final: 0.7475 (pt0) REVERT: C 107 TYR cc_start: 0.8434 (m-80) cc_final: 0.8107 (m-80) REVERT: C 160 MET cc_start: 0.5726 (ttp) cc_final: 0.5479 (ttp) REVERT: C 206 LEU cc_start: 0.4426 (mp) cc_final: 0.3682 (tt) REVERT: C 287 GLU cc_start: 0.9041 (pt0) cc_final: 0.8721 (pt0) outliers start: 18 outliers final: 12 residues processed: 151 average time/residue: 0.5207 time to fit residues: 104.7309 Evaluate side-chains 141 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 631 VAL Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain A residue 741 THR Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 289 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.9990 chunk 48 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 44 optimal weight: 0.4980 chunk 62 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 55 optimal weight: 0.0980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5445 moved from start: 0.4738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8540 Z= 0.174 Angle : 0.513 5.057 11541 Z= 0.269 Chirality : 0.038 0.136 1260 Planarity : 0.004 0.045 1501 Dihedral : 4.546 58.996 1146 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.92 % Allowed : 11.29 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.27), residues: 1017 helix: 0.92 (0.23), residues: 488 sheet: -0.27 (0.49), residues: 116 loop : 0.59 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 139 HIS 0.003 0.001 HIS A 392 PHE 0.014 0.002 PHE A 730 TYR 0.013 0.001 TYR B 86 ARG 0.005 0.000 ARG A 500 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 GLU cc_start: 0.7388 (tt0) cc_final: 0.6462 (tp30) REVERT: A 401 ILE cc_start: 0.8263 (mt) cc_final: 0.7958 (pt) REVERT: A 415 GLU cc_start: 0.7189 (mt-10) cc_final: 0.6931 (mp0) REVERT: A 438 ASP cc_start: 0.6757 (OUTLIER) cc_final: 0.6421 (t0) REVERT: A 470 GLU cc_start: 0.6868 (tt0) cc_final: 0.6311 (mm-30) REVERT: A 511 TYR cc_start: 0.6410 (OUTLIER) cc_final: 0.6077 (t80) REVERT: A 556 TYR cc_start: 0.6264 (t80) cc_final: 0.5624 (t80) REVERT: A 558 GLU cc_start: 0.6891 (mt-10) cc_final: 0.6516 (mm-30) REVERT: A 559 PHE cc_start: 0.6737 (m-80) cc_final: 0.6426 (m-80) REVERT: A 591 THR cc_start: 0.5391 (p) cc_final: 0.4740 (m) REVERT: A 597 LYS cc_start: 0.7218 (tttp) cc_final: 0.6523 (tppt) REVERT: A 630 ASP cc_start: 0.6550 (p0) cc_final: 0.6205 (t70) REVERT: A 753 GLU cc_start: 0.6863 (mp0) cc_final: 0.5847 (tp30) REVERT: A 757 LEU cc_start: 0.6698 (mt) cc_final: 0.6333 (tt) REVERT: B 58 CYS cc_start: 0.7334 (m) cc_final: 0.6303 (t) REVERT: B 127 ASP cc_start: 0.7795 (m-30) cc_final: 0.7488 (m-30) REVERT: B 129 LYS cc_start: 0.7673 (mttt) cc_final: 0.7015 (mmmt) REVERT: B 132 PHE cc_start: 0.5605 (m-80) cc_final: 0.5091 (m-10) REVERT: C 100 GLN cc_start: 0.7778 (pt0) cc_final: 0.7564 (pt0) REVERT: C 107 TYR cc_start: 0.8424 (m-80) cc_final: 0.8204 (m-80) REVERT: C 206 LEU cc_start: 0.4359 (mp) cc_final: 0.3575 (tt) REVERT: C 287 GLU cc_start: 0.9073 (pt0) cc_final: 0.8832 (pt0) outliers start: 18 outliers final: 13 residues processed: 153 average time/residue: 0.4744 time to fit residues: 98.1557 Evaluate side-chains 142 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 289 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 0.0170 chunk 84 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 0.1980 chunk 19 optimal weight: 0.3980 overall best weight: 0.5222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5440 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8540 Z= 0.160 Angle : 0.497 6.125 11541 Z= 0.257 Chirality : 0.038 0.158 1260 Planarity : 0.004 0.042 1501 Dihedral : 4.383 59.567 1146 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.02 % Allowed : 11.40 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.27), residues: 1017 helix: 1.17 (0.23), residues: 488 sheet: -0.24 (0.49), residues: 116 loop : 0.65 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 139 HIS 0.003 0.001 HIS C 168 PHE 0.014 0.001 PHE A 730 TYR 0.012 0.001 TYR A 494 ARG 0.005 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 129 time to evaluate : 1.298 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.6681 (OUTLIER) cc_final: 0.6273 (ttp-110) REVERT: A 401 ILE cc_start: 0.8254 (mt) cc_final: 0.7935 (pt) REVERT: A 415 GLU cc_start: 0.7152 (mt-10) cc_final: 0.6875 (mp0) REVERT: A 438 ASP cc_start: 0.6757 (OUTLIER) cc_final: 0.6452 (t0) REVERT: A 470 GLU cc_start: 0.6937 (tt0) cc_final: 0.6310 (mm-30) REVERT: A 511 TYR cc_start: 0.6390 (OUTLIER) cc_final: 0.6067 (t80) REVERT: A 537 LEU cc_start: 0.4540 (OUTLIER) cc_final: 0.4262 (tt) REVERT: A 556 TYR cc_start: 0.6104 (t80) cc_final: 0.5430 (t80) REVERT: A 558 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6524 (mm-30) REVERT: A 559 PHE cc_start: 0.6678 (m-80) cc_final: 0.6338 (m-80) REVERT: A 591 THR cc_start: 0.5373 (p) cc_final: 0.4743 (m) REVERT: A 597 LYS cc_start: 0.7198 (tttp) cc_final: 0.6515 (tppt) REVERT: A 630 ASP cc_start: 0.6580 (p0) cc_final: 0.6299 (t70) REVERT: A 753 GLU cc_start: 0.6789 (mp0) cc_final: 0.5649 (tp30) REVERT: A 757 LEU cc_start: 0.6670 (mt) cc_final: 0.6325 (tt) REVERT: B 18 LYS cc_start: 0.6378 (mmtt) cc_final: 0.5893 (mmmt) REVERT: B 58 CYS cc_start: 0.7301 (m) cc_final: 0.6201 (t) REVERT: B 127 ASP cc_start: 0.8038 (m-30) cc_final: 0.7799 (m-30) REVERT: B 129 LYS cc_start: 0.7727 (mttt) cc_final: 0.7097 (mmmt) REVERT: C 140 THR cc_start: 0.5300 (OUTLIER) cc_final: 0.4999 (t) REVERT: C 200 ASN cc_start: 0.7120 (m110) cc_final: 0.6894 (m-40) REVERT: C 206 LEU cc_start: 0.4150 (mp) cc_final: 0.3306 (tt) REVERT: C 287 GLU cc_start: 0.9072 (pt0) cc_final: 0.8828 (pt0) outliers start: 19 outliers final: 12 residues processed: 141 average time/residue: 0.4894 time to fit residues: 92.4773 Evaluate side-chains 140 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 209 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 95 optimal weight: 7.9990 chunk 11 optimal weight: 0.3980 chunk 56 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 392 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5444 moved from start: 0.5177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8540 Z= 0.170 Angle : 0.491 5.395 11541 Z= 0.255 Chirality : 0.038 0.140 1260 Planarity : 0.004 0.052 1501 Dihedral : 4.329 59.891 1146 Min Nonbonded Distance : 2.321 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.02 % Allowed : 11.29 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.27), residues: 1017 helix: 1.28 (0.23), residues: 487 sheet: -0.15 (0.50), residues: 114 loop : 0.68 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 139 HIS 0.003 0.001 HIS C 168 PHE 0.014 0.001 PHE A 467 TYR 0.013 0.001 TYR B 86 ARG 0.006 0.000 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 150 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 131 time to evaluate : 1.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.6685 (OUTLIER) cc_final: 0.6263 (ttp-110) REVERT: A 401 ILE cc_start: 0.8365 (mt) cc_final: 0.8076 (pt) REVERT: A 438 ASP cc_start: 0.6801 (OUTLIER) cc_final: 0.6488 (t0) REVERT: A 463 ASP cc_start: 0.6334 (OUTLIER) cc_final: 0.5987 (t70) REVERT: A 470 GLU cc_start: 0.6949 (tt0) cc_final: 0.6391 (mm-30) REVERT: A 511 TYR cc_start: 0.6429 (OUTLIER) cc_final: 0.6049 (t80) REVERT: A 537 LEU cc_start: 0.4406 (OUTLIER) cc_final: 0.4098 (tt) REVERT: A 552 LYS cc_start: 0.8340 (mttp) cc_final: 0.7885 (mmtm) REVERT: A 556 TYR cc_start: 0.5804 (t80) cc_final: 0.5197 (t80) REVERT: A 558 GLU cc_start: 0.6725 (mt-10) cc_final: 0.6449 (mm-30) REVERT: A 591 THR cc_start: 0.5387 (p) cc_final: 0.4796 (m) REVERT: A 753 GLU cc_start: 0.6998 (mp0) cc_final: 0.5686 (tp30) REVERT: A 757 LEU cc_start: 0.6648 (mt) cc_final: 0.6297 (tt) REVERT: B 18 LYS cc_start: 0.6396 (mmtt) cc_final: 0.5903 (mmmt) REVERT: B 58 CYS cc_start: 0.7395 (m) cc_final: 0.6192 (t) REVERT: B 127 ASP cc_start: 0.8069 (m-30) cc_final: 0.7869 (m-30) REVERT: B 129 LYS cc_start: 0.7716 (mttt) cc_final: 0.7047 (mmmt) REVERT: C 140 THR cc_start: 0.5475 (OUTLIER) cc_final: 0.5026 (t) REVERT: C 206 LEU cc_start: 0.4348 (mp) cc_final: 0.3467 (tt) REVERT: C 287 GLU cc_start: 0.9064 (pt0) cc_final: 0.8786 (pt0) outliers start: 19 outliers final: 12 residues processed: 144 average time/residue: 0.4719 time to fit residues: 92.6364 Evaluate side-chains 142 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 438 ASP Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 463 ASP Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 209 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 83 optimal weight: 3.9990 chunk 98 optimal weight: 0.9980 chunk 61 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 45 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5473 moved from start: 0.5427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8540 Z= 0.237 Angle : 0.528 7.242 11541 Z= 0.278 Chirality : 0.039 0.140 1260 Planarity : 0.005 0.043 1501 Dihedral : 4.475 59.849 1146 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 2.02 % Allowed : 11.82 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.27), residues: 1017 helix: 1.05 (0.23), residues: 487 sheet: -0.13 (0.51), residues: 108 loop : 0.53 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 139 HIS 0.004 0.001 HIS C 168 PHE 0.023 0.002 PHE A 467 TYR 0.019 0.001 TYR B 86 ARG 0.006 0.001 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 123 time to evaluate : 1.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.6789 (OUTLIER) cc_final: 0.6449 (ttp80) REVERT: A 470 GLU cc_start: 0.6920 (tt0) cc_final: 0.6174 (mm-30) REVERT: A 511 TYR cc_start: 0.6402 (OUTLIER) cc_final: 0.6067 (t80) REVERT: A 552 LYS cc_start: 0.8284 (mttp) cc_final: 0.7860 (mmtm) REVERT: A 556 TYR cc_start: 0.5719 (t80) cc_final: 0.5131 (t80) REVERT: A 572 LYS cc_start: 0.7601 (tttt) cc_final: 0.7026 (tptp) REVERT: B 58 CYS cc_start: 0.7377 (m) cc_final: 0.6268 (t) REVERT: B 127 ASP cc_start: 0.8072 (m-30) cc_final: 0.7856 (m-30) REVERT: B 129 LYS cc_start: 0.7634 (mttt) cc_final: 0.6973 (mmmt) REVERT: C 169 MET cc_start: 0.8284 (ttm) cc_final: 0.7944 (ttp) REVERT: C 200 ASN cc_start: 0.7934 (m-40) cc_final: 0.7645 (m110) REVERT: C 206 LEU cc_start: 0.4253 (mp) cc_final: 0.3284 (tt) REVERT: C 287 GLU cc_start: 0.9065 (pt0) cc_final: 0.8788 (pt0) outliers start: 19 outliers final: 14 residues processed: 135 average time/residue: 0.4881 time to fit residues: 89.0529 Evaluate side-chains 134 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 118 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain C residue 209 ARG Chi-restraints excluded: chain C residue 289 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 66 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 0.0040 chunk 77 optimal weight: 0.0170 chunk 89 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 85 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 0.0770 overall best weight: 0.8192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN C 193 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5464 moved from start: 0.5582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8540 Z= 0.196 Angle : 0.509 7.957 11541 Z= 0.266 Chirality : 0.038 0.141 1260 Planarity : 0.004 0.044 1501 Dihedral : 4.414 59.939 1146 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.70 % Allowed : 12.14 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.27), residues: 1017 helix: 1.12 (0.23), residues: 487 sheet: -0.11 (0.50), residues: 108 loop : 0.52 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 139 HIS 0.004 0.001 HIS C 168 PHE 0.017 0.002 PHE A 467 TYR 0.014 0.001 TYR C 103 ARG 0.004 0.000 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 1.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.6756 (OUTLIER) cc_final: 0.6430 (ttp80) REVERT: A 415 GLU cc_start: 0.6838 (mt-10) cc_final: 0.6284 (mp0) REVERT: A 470 GLU cc_start: 0.7061 (tt0) cc_final: 0.6114 (mm-30) REVERT: A 511 TYR cc_start: 0.6431 (OUTLIER) cc_final: 0.6081 (t80) REVERT: A 552 LYS cc_start: 0.8362 (mttp) cc_final: 0.7967 (mmtm) REVERT: A 556 TYR cc_start: 0.6103 (t80) cc_final: 0.5856 (t80) REVERT: A 572 LYS cc_start: 0.7486 (tttt) cc_final: 0.6992 (tptp) REVERT: B 58 CYS cc_start: 0.7368 (m) cc_final: 0.6275 (t) REVERT: B 129 LYS cc_start: 0.7630 (mttt) cc_final: 0.6965 (mmmt) REVERT: C 200 ASN cc_start: 0.7983 (m-40) cc_final: 0.7623 (m110) REVERT: C 206 LEU cc_start: 0.4191 (mp) cc_final: 0.3226 (tt) REVERT: C 287 GLU cc_start: 0.9060 (pt0) cc_final: 0.8792 (pt0) outliers start: 16 outliers final: 13 residues processed: 129 average time/residue: 0.5025 time to fit residues: 87.6518 Evaluate side-chains 131 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 116 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain C residue 209 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.4980 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 82 optimal weight: 10.0000 chunk 86 optimal weight: 1.9990 chunk 91 optimal weight: 9.9990 chunk 60 optimal weight: 9.9990 chunk 96 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5484 moved from start: 0.5745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8540 Z= 0.246 Angle : 0.544 8.113 11541 Z= 0.286 Chirality : 0.039 0.140 1260 Planarity : 0.005 0.046 1501 Dihedral : 4.533 59.682 1146 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.70 % Allowed : 12.78 % Favored : 85.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.26), residues: 1017 helix: 1.00 (0.23), residues: 480 sheet: -0.11 (0.51), residues: 107 loop : 0.41 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 139 HIS 0.003 0.001 HIS A 392 PHE 0.022 0.002 PHE A 467 TYR 0.018 0.002 TYR B 86 ARG 0.005 0.000 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 137 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.6698 (OUTLIER) cc_final: 0.6370 (ttp80) REVERT: A 415 GLU cc_start: 0.6688 (mt-10) cc_final: 0.6221 (mp0) REVERT: A 470 GLU cc_start: 0.6937 (tt0) cc_final: 0.6118 (mm-30) REVERT: A 511 TYR cc_start: 0.6385 (OUTLIER) cc_final: 0.6068 (t80) REVERT: A 552 LYS cc_start: 0.8371 (mttp) cc_final: 0.7996 (mmtm) REVERT: A 556 TYR cc_start: 0.5972 (t80) cc_final: 0.5714 (t80) REVERT: A 572 LYS cc_start: 0.7619 (tttt) cc_final: 0.7034 (tptt) REVERT: B 58 CYS cc_start: 0.7371 (m) cc_final: 0.6145 (t) REVERT: B 129 LYS cc_start: 0.7604 (mttt) cc_final: 0.6942 (mmmt) REVERT: C 200 ASN cc_start: 0.7979 (m-40) cc_final: 0.7600 (m110) REVERT: C 206 LEU cc_start: 0.4084 (mp) cc_final: 0.3129 (tt) REVERT: C 287 GLU cc_start: 0.9046 (pt0) cc_final: 0.8775 (pt0) outliers start: 16 outliers final: 12 residues processed: 129 average time/residue: 0.5021 time to fit residues: 87.0805 Evaluate side-chains 134 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 120 time to evaluate : 1.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 318 LEU Chi-restraints excluded: chain A residue 450 ILE Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 595 SER Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain C residue 209 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 4.9990 chunk 93 optimal weight: 7.9990 chunk 80 optimal weight: 0.4980 chunk 8 optimal weight: 0.9980 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 24 optimal weight: 0.0570 chunk 74 optimal weight: 0.4980 chunk 11 optimal weight: 0.2980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5445 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8540 Z= 0.151 Angle : 0.503 8.976 11541 Z= 0.261 Chirality : 0.038 0.143 1260 Planarity : 0.004 0.039 1501 Dihedral : 4.319 59.877 1146 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.38 % Allowed : 13.21 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.27), residues: 1017 helix: 1.38 (0.24), residues: 480 sheet: 0.03 (0.51), residues: 105 loop : 0.59 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 139 HIS 0.002 0.001 HIS C 168 PHE 0.013 0.001 PHE A 730 TYR 0.016 0.001 TYR C 103 ARG 0.004 0.000 ARG A 417 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2034 Ramachandran restraints generated. 1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 144 is missing expected H atoms. Skipping. Residue SER 145 is missing expected H atoms. Skipping. Residue SER 147 is missing expected H atoms. Skipping. Evaluate side-chains 135 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 151 ARG cc_start: 0.6637 (OUTLIER) cc_final: 0.6180 (ttp-110) REVERT: A 415 GLU cc_start: 0.6657 (mt-10) cc_final: 0.6182 (mp0) REVERT: A 470 GLU cc_start: 0.7158 (tt0) cc_final: 0.6877 (tt0) REVERT: A 478 MET cc_start: 0.7641 (mtp) cc_final: 0.7365 (mtp) REVERT: A 511 TYR cc_start: 0.6430 (OUTLIER) cc_final: 0.6080 (t80) REVERT: A 537 LEU cc_start: 0.3759 (OUTLIER) cc_final: 0.3422 (tt) REVERT: A 552 LYS cc_start: 0.8371 (mttp) cc_final: 0.7979 (mmtm) REVERT: A 556 TYR cc_start: 0.6060 (t80) cc_final: 0.5835 (t80) REVERT: A 572 LYS cc_start: 0.7563 (tttt) cc_final: 0.7108 (tptp) REVERT: B 58 CYS cc_start: 0.7438 (m) cc_final: 0.6284 (t) REVERT: B 129 LYS cc_start: 0.7552 (mttt) cc_final: 0.6962 (mmmt) REVERT: C 200 ASN cc_start: 0.7981 (m-40) cc_final: 0.7601 (m110) REVERT: C 206 LEU cc_start: 0.4116 (mp) cc_final: 0.3140 (tt) REVERT: C 287 GLU cc_start: 0.9059 (pt0) cc_final: 0.8782 (pt0) outliers start: 13 outliers final: 8 residues processed: 129 average time/residue: 0.5014 time to fit residues: 87.5681 Evaluate side-chains 130 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 119 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 151 ARG Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 537 LEU Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 636 VAL Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain C residue 209 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 58 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 chunk 54 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4657 r_free = 0.4657 target = 0.215010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.181419 restraints weight = 38246.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.185061 restraints weight = 21437.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.187979 restraints weight = 14533.783| |-----------------------------------------------------------------------------| r_work (final): 0.4371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8540 Z= 0.189 Angle : 0.516 8.322 11541 Z= 0.270 Chirality : 0.038 0.141 1260 Planarity : 0.004 0.050 1501 Dihedral : 4.328 59.995 1146 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.38 % Allowed : 13.53 % Favored : 85.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.27), residues: 1017 helix: 1.34 (0.24), residues: 480 sheet: 0.00 (0.50), residues: 107 loop : 0.56 (0.32), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 139 HIS 0.003 0.001 HIS C 168 PHE 0.015 0.001 PHE A 467 TYR 0.016 0.001 TYR C 103 ARG 0.007 0.000 ARG C 282 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4040.06 seconds wall clock time: 70 minutes 57.20 seconds (4257.20 seconds total)