Starting phenix.real_space_refine on Fri Jun 28 22:35:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1f_18809/06_2024/8r1f_18809.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1f_18809/06_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_18809/06_2024/8r1f_18809.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1f_18809/06_2024/8r1f_18809.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1f_18809/06_2024/8r1f_18809.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r1f_18809/06_2024/8r1f_18809.pdb" } 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5370/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: 7.66, per 1000 atoms: 0.46 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: 11.83 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: 1.14 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: 5.79 Time building geometry restraints manager: 12.61 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 1.850 nonbonded pdb=" O PRO C 152 " pdb=" HG1 THR C 155 " model vdw 1.693 1.850 nonbonded pdb=" HH TYR A 668 " pdb=" OD2 ASP A 675 " model vdw 1.703 1.850 nonbonded pdb=" O PRO B 16 " pdb=" HH TYR B 61 " model vdw 1.708 1.850 nonbonded pdb=" HG SER C 95 " pdb=" O THR C 211 " model vdw 1.726 1.850 ... (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 ========== 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: 1.280 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: 0.240 Extract box with map and model: 4.090 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 55.420 Find NCS groups from input model: 0.260 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: 0.010 Load rotamer database and sin/cos tables:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.000 ------------------------------------------------------------------------------- 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 : 1.342 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: 0.5536 time to fit residues: 181.7273 Evaluate side-chains 159 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 158 time to evaluate : 1.392 ------------------------------------------------------------------------------- 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: 0.2980 chunk 26 optimal weight: 0.2980 chunk 52 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 6.9990 chunk 59 optimal weight: 8.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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** A 795 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5390 moved from start: 0.3171 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= 0.203 Angle : 0.589 5.952 11541 Z= 0.315 Chirality : 0.040 0.139 1260 Planarity : 0.005 0.062 1501 Dihedral : 4.664 56.097 1146 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.17 % Allowed : 8.20 % Favored : 90.63 % 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: 0.59 (0.26), residues: 1017 helix: 0.72 (0.23), residues: 484 sheet: -0.11 (0.48), residues: 117 loop : 0.37 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 791 HIS 0.004 0.001 HIS C 168 PHE 0.019 0.002 PHE A 730 TYR 0.018 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 170 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 159 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: 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: 0.5635 (mm) cc_final: 0.5274 (mt) REVERT: A 303 GLU cc_start: 0.6789 (tt0) cc_final: 0.6296 (tp30) REVERT: A 470 GLU cc_start: 0.5489 (tt0) cc_final: 0.5251 (mm-30) REVERT: A 511 TYR cc_start: 0.6335 (OUTLIER) cc_final: 0.6041 (t80) REVERT: A 556 TYR cc_start: 0.6713 (t80) cc_final: 0.6105 (t80) REVERT: A 558 GLU cc_start: 0.6634 (mt-10) cc_final: 0.6319 (mm-30) REVERT: A 559 PHE cc_start: 0.6491 (m-80) cc_final: 0.6129 (m-80) REVERT: A 589 MET cc_start: 0.6649 (mtp) cc_final: 0.6236 (mtp) REVERT: A 591 THR cc_start: 0.5441 (p) cc_final: 0.4806 (m) REVERT: A 757 LEU cc_start: 0.6606 (mt) cc_final: 0.6350 (tt) REVERT: B 58 CYS cc_start: 0.7217 (m) cc_final: 0.6352 (t) REVERT: B 72 LYS cc_start: 0.9004 (pttm) cc_final: 0.8801 (pttm) REVERT: B 90 LEU cc_start: 0.5238 (mt) cc_final: 0.4840 (mt) REVERT: B 129 LYS cc_start: 0.7664 (mttt) cc_final: 0.7025 (mmmt) REVERT: C 100 GLN cc_start: 0.7838 (pt0) cc_final: 0.7580 (pt0) REVERT: C 109 PHE cc_start: 0.8322 (t80) cc_final: 0.7806 (t80) REVERT: C 163 TYR cc_start: 0.4493 (m-80) cc_final: 0.4140 (m-80) REVERT: C 255 ILE cc_start: 0.7448 (mt) cc_final: 0.7222 (mt) REVERT: C 287 GLU cc_start: 0.9049 (pt0) cc_final: 0.8814 (pt0) outliers start: 11 outliers final: 8 residues processed: 163 average time/residue: 0.5045 time to fit residues: 109.0037 Evaluate side-chains 140 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 131 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 666 LEU Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain B residue 32 ASP 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: 0.0060 chunk 28 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 63 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 100 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 91 optimal weight: 7.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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: 0.5414 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8540 Z= 0.186 Angle : 0.524 5.389 11541 Z= 0.275 Chirality : 0.038 0.138 1260 Planarity : 0.005 0.052 1501 Dihedral : 4.446 57.647 1146 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.38 % Allowed : 9.90 % Favored : 88.71 % 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: 1.08 (0.23), residues: 487 sheet: -0.26 (0.49), residues: 115 loop : 0.55 (0.32), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 146 HIS 0.002 0.001 HIS C 168 PHE 0.015 0.002 PHE A 730 TYR 0.018 0.001 TYR A 502 ARG 0.009 0.000 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 149 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 136 time to evaluate : 1.400 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: symmetry clash REVERT: A 303 GLU cc_start: 0.7036 (tt0) cc_final: 0.6493 (tp30) REVERT: A 478 MET cc_start: 0.7599 (mtp) cc_final: 0.7207 (mtp) REVERT: A 511 TYR cc_start: 0.6353 (OUTLIER) cc_final: 0.6086 (t80) REVERT: A 556 TYR cc_start: 0.6303 (t80) cc_final: 0.5801 (t80) REVERT: A 559 PHE cc_start: 0.6537 (m-80) cc_final: 0.6185 (m-80) REVERT: A 589 MET cc_start: 0.6470 (mtp) cc_final: 0.6195 (mtp) REVERT: A 591 THR cc_start: 0.5353 (p) cc_final: 0.4718 (m) REVERT: A 667 GLU cc_start: 0.7825 (pp20) cc_final: 0.7607 (pp20) REVERT: A 757 LEU cc_start: 0.6690 (mt) cc_final: 0.6321 (tt) REVERT: B 58 CYS cc_start: 0.7039 (m) cc_final: 0.6247 (t) REVERT: B 72 LYS cc_start: 0.8956 (pttm) cc_final: 0.8729 (pttm) REVERT: B 127 ASP cc_start: 0.7750 (m-30) cc_final: 0.7488 (m-30) REVERT: B 129 LYS cc_start: 0.7654 (mttt) cc_final: 0.7014 (mmmt) REVERT: C 100 GLN cc_start: 0.7759 (pt0) cc_final: 0.7503 (pt0) REVERT: C 160 MET cc_start: 0.5760 (ttp) cc_final: 0.5521 (ttp) REVERT: C 206 LEU cc_start: 0.4132 (mp) cc_final: 0.3469 (tt) REVERT: C 287 GLU cc_start: 0.9037 (pt0) cc_final: 0.8829 (pt0) outliers start: 13 outliers final: 8 residues processed: 143 average time/residue: 0.4717 time to fit residues: 91.1983 Evaluate side-chains 132 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 511 TYR 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 23 CYS Chi-restraints excluded: chain C residue 209 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.9980 chunk 48 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 93 optimal weight: 7.9990 chunk 98 optimal weight: 2.9990 chunk 88 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 82 optimal weight: 8.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.5435 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8540 Z= 0.207 Angle : 0.518 6.060 11541 Z= 0.272 Chirality : 0.039 0.156 1260 Planarity : 0.004 0.044 1501 Dihedral : 4.461 57.972 1146 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.70 % Allowed : 10.76 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.27), residues: 1017 helix: 1.07 (0.23), residues: 488 sheet: -0.49 (0.49), residues: 115 loop : 0.58 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 139 HIS 0.005 0.001 HIS C 233 PHE 0.016 0.002 PHE A 467 TYR 0.013 0.001 TYR B 86 ARG 0.005 0.000 ARG B 84 *********************** 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 147 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 1.464 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: 0.7411 (tt0) cc_final: 0.6566 (tp30) REVERT: A 415 GLU cc_start: 0.7746 (mp0) cc_final: 0.7512 (mp0) REVERT: A 460 MET cc_start: 0.6170 (mmm) cc_final: 0.5719 (mmm) REVERT: A 470 GLU cc_start: 0.5822 (tt0) cc_final: 0.5472 (mm-30) REVERT: A 511 TYR cc_start: 0.6371 (OUTLIER) cc_final: 0.6098 (t80) REVERT: A 545 MET cc_start: 0.7385 (ttp) cc_final: 0.7174 (ttm) REVERT: A 559 PHE cc_start: 0.6602 (m-80) cc_final: 0.6352 (m-80) REVERT: A 591 THR cc_start: 0.5416 (p) cc_final: 0.4792 (m) REVERT: A 667 GLU cc_start: 0.7975 (pp20) cc_final: 0.7759 (pp20) REVERT: A 753 GLU cc_start: 0.6841 (mp0) cc_final: 0.5826 (tp30) REVERT: A 757 LEU cc_start: 0.6690 (mt) cc_final: 0.6355 (tt) REVERT: B 58 CYS cc_start: 0.7053 (m) cc_final: 0.6216 (t) REVERT: B 72 LYS cc_start: 0.8955 (pttm) cc_final: 0.8743 (pttm) REVERT: B 127 ASP cc_start: 0.7671 (m-30) cc_final: 0.7395 (m-30) REVERT: B 129 LYS cc_start: 0.7653 (mttt) cc_final: 0.7001 (mmmt) REVERT: C 100 GLN cc_start: 0.7708 (pt0) cc_final: 0.7470 (pt0) REVERT: C 107 TYR cc_start: 0.8428 (m-80) cc_final: 0.8168 (m-80) REVERT: C 140 THR cc_start: 0.5040 (OUTLIER) cc_final: 0.4694 (t) REVERT: C 206 LEU cc_start: 0.4392 (mp) cc_final: 0.3532 (tt) REVERT: C 233 HIS cc_start: 0.6606 (m-70) cc_final: 0.6325 (m90) REVERT: C 287 GLU cc_start: 0.9056 (pt0) cc_final: 0.8821 (pt0) REVERT: C 292 LYS cc_start: 0.8570 (mttt) cc_final: 0.8351 (mttp) outliers start: 16 outliers final: 11 residues processed: 141 average time/residue: 0.4650 time to fit residues: 88.9319 Evaluate side-chains 142 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 129 time to evaluate : 1.371 ------------------------------------------------------------------------------- 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 237 ASP Chi-restraints excluded: chain A residue 392 HIS 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 636 VAL Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain C residue 140 THR Chi-restraints excluded: chain C residue 209 ARG 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: 0.7980 chunk 40 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 88 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.5466 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8540 Z= 0.251 Angle : 0.539 6.580 11541 Z= 0.286 Chirality : 0.039 0.150 1260 Planarity : 0.005 0.050 1501 Dihedral : 4.569 58.474 1146 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.81 % Allowed : 10.97 % Favored : 87.22 % 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: 0.72 (0.27), residues: 1017 helix: 0.86 (0.23), residues: 488 sheet: -0.55 (0.49), residues: 113 loop : 0.55 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 139 HIS 0.004 0.001 HIS A 392 PHE 0.022 0.002 PHE A 467 TYR 0.015 0.002 TYR B 86 ARG 0.005 0.001 ARG A 500 *********************** 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: 17 poor density : 131 time to evaluate : 1.217 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: A 401 ILE cc_start: 0.8249 (mt) cc_final: 0.7942 (pt) REVERT: A 470 GLU cc_start: 0.6009 (tt0) cc_final: 0.5807 (mm-30) REVERT: A 478 MET cc_start: 0.7928 (mtp) cc_final: 0.7645 (mtp) REVERT: A 511 TYR cc_start: 0.6407 (OUTLIER) cc_final: 0.6136 (t80) REVERT: A 545 MET cc_start: 0.7396 (ttp) cc_final: 0.7169 (ttm) REVERT: A 556 TYR cc_start: 0.6322 (t80) cc_final: 0.6007 (t80) REVERT: A 572 LYS cc_start: 0.7478 (tttt) cc_final: 0.6871 (tptt) REVERT: A 723 ASN cc_start: 0.5391 (OUTLIER) cc_final: 0.2550 (m-40) REVERT: A 757 LEU cc_start: 0.6683 (mt) cc_final: 0.6301 (tt) REVERT: B 58 CYS cc_start: 0.7072 (m) cc_final: 0.6221 (t) REVERT: B 72 LYS cc_start: 0.8907 (pttm) cc_final: 0.8677 (pttm) REVERT: B 127 ASP cc_start: 0.7572 (m-30) cc_final: 0.7269 (m-30) REVERT: B 129 LYS cc_start: 0.7701 (mttt) cc_final: 0.7042 (mmmt) REVERT: C 107 TYR cc_start: 0.8338 (m-80) cc_final: 0.8122 (m-80) REVERT: C 206 LEU cc_start: 0.4350 (mp) cc_final: 0.3442 (tt) REVERT: C 233 HIS cc_start: 0.6942 (m-70) cc_final: 0.6727 (m90) REVERT: C 287 GLU cc_start: 0.9059 (pt0) cc_final: 0.8793 (pt0) REVERT: C 292 LYS cc_start: 0.8621 (mttt) cc_final: 0.8352 (mttp) outliers start: 17 outliers final: 13 residues processed: 142 average time/residue: 0.4570 time to fit residues: 89.1988 Evaluate side-chains 134 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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 392 HIS 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 636 VAL Chi-restraints excluded: chain A residue 723 ASN Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 32 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 95 optimal weight: 0.1980 chunk 11 optimal weight: 0.1980 chunk 56 optimal weight: 0.5980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.5432 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8540 Z= 0.142 Angle : 0.479 7.019 11541 Z= 0.246 Chirality : 0.037 0.139 1260 Planarity : 0.004 0.041 1501 Dihedral : 4.296 58.730 1146 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.28 % Allowed : 12.46 % Favored : 86.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.27), residues: 1017 helix: 1.27 (0.24), residues: 488 sheet: -0.51 (0.49), residues: 113 loop : 0.71 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 139 HIS 0.003 0.001 HIS B 125 PHE 0.015 0.001 PHE A 730 TYR 0.011 0.001 TYR A 494 ARG 0.003 0.000 ARG B 84 *********************** 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 135 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 123 time to evaluate : 1.251 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: A 401 ILE cc_start: 0.8345 (mt) cc_final: 0.8064 (pt) REVERT: A 470 GLU cc_start: 0.6041 (tt0) cc_final: 0.5608 (mm-30) REVERT: A 478 MET cc_start: 0.7930 (mtp) cc_final: 0.7546 (mtp) REVERT: A 511 TYR cc_start: 0.6428 (OUTLIER) cc_final: 0.6107 (t80) REVERT: A 545 MET cc_start: 0.7368 (ttp) cc_final: 0.7150 (ttm) REVERT: A 552 LYS cc_start: 0.8396 (mttp) cc_final: 0.8005 (mmtm) REVERT: A 556 TYR cc_start: 0.6230 (t80) cc_final: 0.5939 (t80) REVERT: A 572 LYS cc_start: 0.7518 (tttt) cc_final: 0.7047 (tptp) REVERT: A 597 LYS cc_start: 0.7051 (tttp) cc_final: 0.6536 (tptp) REVERT: B 58 CYS cc_start: 0.7177 (m) cc_final: 0.6241 (t) REVERT: B 72 LYS cc_start: 0.8895 (pttm) cc_final: 0.8656 (pttm) REVERT: B 127 ASP cc_start: 0.7698 (m-30) cc_final: 0.7435 (m-30) REVERT: B 129 LYS cc_start: 0.7710 (mttt) cc_final: 0.7020 (mmmt) REVERT: C 206 LEU cc_start: 0.4200 (mp) cc_final: 0.3268 (tt) REVERT: C 287 GLU cc_start: 0.9096 (pt0) cc_final: 0.8857 (pt0) outliers start: 12 outliers final: 10 residues processed: 130 average time/residue: 0.4925 time to fit residues: 85.9882 Evaluate side-chains 128 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 117 time to evaluate : 1.371 ------------------------------------------------------------------------------- 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 392 HIS 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 23 CYS Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 78 SER 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: 0.4980 chunk 83 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 59 optimal weight: 20.0000 chunk 45 optimal weight: 0.2980 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 0.0970 chunk 58 optimal weight: 4.9990 chunk 29 optimal weight: 0.1980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.5425 moved from start: 0.5269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8540 Z= 0.141 Angle : 0.472 7.246 11541 Z= 0.241 Chirality : 0.037 0.140 1260 Planarity : 0.004 0.037 1501 Dihedral : 4.168 59.006 1146 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.28 % Allowed : 12.57 % 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: 1.33 (0.27), residues: 1017 helix: 1.43 (0.24), residues: 488 sheet: -0.26 (0.51), residues: 105 loop : 0.74 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 139 HIS 0.002 0.000 HIS A 392 PHE 0.014 0.001 PHE A 730 TYR 0.011 0.001 TYR A 494 ARG 0.003 0.000 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 134 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 1.481 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 359 ARG cc_start: 0.8438 (ttp-110) cc_final: 0.8111 (tmm-80) REVERT: A 360 ASN cc_start: 0.6914 (t0) cc_final: 0.6418 (t0) REVERT: A 401 ILE cc_start: 0.8353 (mt) cc_final: 0.8080 (pt) REVERT: A 470 GLU cc_start: 0.6144 (tt0) cc_final: 0.5497 (mm-30) REVERT: A 511 TYR cc_start: 0.6405 (OUTLIER) cc_final: 0.6085 (t80) REVERT: A 552 LYS cc_start: 0.8398 (mttp) cc_final: 0.7998 (mmtm) REVERT: A 556 TYR cc_start: 0.6210 (t80) cc_final: 0.5944 (t80) REVERT: A 572 LYS cc_start: 0.7507 (tttt) cc_final: 0.6956 (tptp) REVERT: A 597 LYS cc_start: 0.7088 (tttp) cc_final: 0.6401 (tppt) REVERT: A 723 ASN cc_start: 0.5569 (OUTLIER) cc_final: 0.2480 (m-40) REVERT: B 18 LYS cc_start: 0.6140 (mmtt) cc_final: 0.5660 (mmmt) REVERT: B 58 CYS cc_start: 0.7221 (m) cc_final: 0.6219 (t) REVERT: B 72 LYS cc_start: 0.8789 (pttm) cc_final: 0.8508 (pttm) REVERT: B 127 ASP cc_start: 0.7774 (m-30) cc_final: 0.7549 (m-30) REVERT: B 129 LYS cc_start: 0.7602 (mttt) cc_final: 0.6957 (mmmt) REVERT: C 200 ASN cc_start: 0.7193 (m-40) cc_final: 0.6944 (m-40) REVERT: C 206 LEU cc_start: 0.4403 (mp) cc_final: 0.3489 (tt) REVERT: C 287 GLU cc_start: 0.9124 (pt0) cc_final: 0.8900 (pt0) outliers start: 12 outliers final: 10 residues processed: 130 average time/residue: 0.4682 time to fit residues: 82.5152 Evaluate side-chains 129 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 117 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 127 TYR Chi-restraints excluded: chain A residue 318 LEU 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 636 VAL Chi-restraints excluded: chain A residue 723 ASN Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain C residue 209 ARG 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: 9.9990 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 77 optimal weight: 0.2980 chunk 89 optimal weight: 3.9990 chunk 94 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5475 moved from start: 0.5486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8540 Z= 0.273 Angle : 0.549 7.864 11541 Z= 0.288 Chirality : 0.039 0.142 1260 Planarity : 0.005 0.049 1501 Dihedral : 4.445 58.845 1146 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 2.02 % Allowed : 12.46 % 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: 0.89 (0.27), residues: 1017 helix: 1.04 (0.23), residues: 482 sheet: -0.36 (0.51), residues: 105 loop : 0.53 (0.31), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 139 HIS 0.005 0.001 HIS B 125 PHE 0.016 0.002 PHE A 309 TYR 0.018 0.002 TYR B 86 ARG 0.005 0.001 ARG A 424 *********************** 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: 19 poor density : 118 time to evaluate : 1.379 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: 0.6844 (OUTLIER) cc_final: 0.6392 (tmm-80) REVERT: A 359 ARG cc_start: 0.8436 (ttp-110) cc_final: 0.8079 (tmm-80) REVERT: A 360 ASN cc_start: 0.6910 (t0) cc_final: 0.6417 (t0) REVERT: A 470 GLU cc_start: 0.6299 (tt0) cc_final: 0.5557 (mm-30) REVERT: A 478 MET cc_start: 0.7791 (mtp) cc_final: 0.7545 (mtp) REVERT: A 511 TYR cc_start: 0.6440 (OUTLIER) cc_final: 0.6094 (t80) REVERT: A 552 LYS cc_start: 0.8360 (mttp) cc_final: 0.7969 (mmtm) REVERT: A 556 TYR cc_start: 0.6073 (t80) cc_final: 0.5843 (t80) REVERT: A 572 LYS cc_start: 0.7554 (tttt) cc_final: 0.7001 (tptt) REVERT: A 597 LYS cc_start: 0.7305 (tttp) cc_final: 0.6681 (tppt) REVERT: A 723 ASN cc_start: 0.5397 (OUTLIER) cc_final: 0.2606 (m-40) REVERT: B 58 CYS cc_start: 0.7066 (m) cc_final: 0.6239 (t) REVERT: B 72 LYS cc_start: 0.8776 (pttm) cc_final: 0.8503 (pttm) REVERT: B 127 ASP cc_start: 0.7752 (m-30) cc_final: 0.7530 (m-30) REVERT: B 129 LYS cc_start: 0.7662 (mttt) cc_final: 0.7002 (mmmt) REVERT: C 164 LYS cc_start: 0.6334 (tttt) cc_final: 0.6120 (ttmt) REVERT: C 200 ASN cc_start: 0.7337 (m-40) cc_final: 0.7115 (m-40) REVERT: C 206 LEU cc_start: 0.4439 (mp) cc_final: 0.3495 (tt) REVERT: C 287 GLU cc_start: 0.9068 (pt0) cc_final: 0.8797 (pt0) outliers start: 19 outliers final: 14 residues processed: 130 average time/residue: 0.5026 time to fit residues: 88.4653 Evaluate side-chains 131 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 1.366 ------------------------------------------------------------------------------- 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 392 HIS Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 534 ASP 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 723 ASN Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 32 ASP Chi-restraints excluded: chain B residue 78 SER 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: 0.9990 chunk 71 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 82 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 60 optimal weight: 9.9990 chunk 96 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5513 moved from start: 0.5877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 8540 Z= 0.378 Angle : 0.652 11.589 11541 Z= 0.346 Chirality : 0.042 0.154 1260 Planarity : 0.006 0.059 1501 Dihedral : 5.002 58.293 1146 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.92 % Allowed : 13.21 % Favored : 84.88 % 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: 0.04 (0.26), residues: 1017 helix: 0.27 (0.23), residues: 479 sheet: -0.60 (0.52), residues: 106 loop : 0.15 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 139 HIS 0.005 0.001 HIS A 392 PHE 0.022 0.003 PHE A 309 TYR 0.020 0.002 TYR B 86 ARG 0.008 0.001 ARG A 424 *********************** 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 136 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 118 time to evaluate : 1.347 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: 0.6912 (OUTLIER) cc_final: 0.6519 (ttp80) REVERT: A 360 ASN cc_start: 0.6712 (t0) cc_final: 0.6422 (t0) REVERT: A 511 TYR cc_start: 0.6437 (OUTLIER) cc_final: 0.6078 (t80) REVERT: A 524 ARG cc_start: 0.6701 (ttt180) cc_final: 0.6313 (ttm170) REVERT: A 552 LYS cc_start: 0.8340 (mttp) cc_final: 0.7992 (mmtm) REVERT: A 572 LYS cc_start: 0.7520 (tttt) cc_final: 0.6876 (tptt) REVERT: A 597 LYS cc_start: 0.7253 (tttp) cc_final: 0.6670 (tppt) REVERT: B 58 CYS cc_start: 0.7121 (m) cc_final: 0.6092 (t) REVERT: B 63 ASP cc_start: 0.6283 (m-30) cc_final: 0.5988 (t0) REVERT: B 72 LYS cc_start: 0.8749 (pttm) cc_final: 0.8472 (pttm) REVERT: B 127 ASP cc_start: 0.7610 (m-30) cc_final: 0.7326 (m-30) REVERT: B 129 LYS cc_start: 0.7691 (mttt) cc_final: 0.7032 (mmmt) REVERT: C 164 LYS cc_start: 0.6612 (tttt) cc_final: 0.6409 (ttmt) REVERT: C 169 MET cc_start: 0.8133 (ttp) cc_final: 0.7912 (tmm) REVERT: C 200 ASN cc_start: 0.7228 (m-40) cc_final: 0.6973 (m-40) REVERT: C 206 LEU cc_start: 0.4478 (mp) cc_final: 0.3524 (tt) REVERT: C 287 GLU cc_start: 0.9067 (pt0) cc_final: 0.8815 (pt0) outliers start: 18 outliers final: 15 residues processed: 130 average time/residue: 0.5225 time to fit residues: 89.9069 Evaluate side-chains 132 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 392 HIS Chi-restraints excluded: chain A residue 456 GLU Chi-restraints excluded: chain A residue 479 THR Chi-restraints excluded: chain A residue 511 TYR Chi-restraints excluded: chain A residue 534 ASP Chi-restraints excluded: chain A residue 560 GLU 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 723 ASN Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 78 SER 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: 3.9990 chunk 80 optimal weight: 0.0870 chunk 8 optimal weight: 0.9990 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 64 optimal weight: 9.9990 chunk 86 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 74 optimal weight: 0.9990 chunk 11 optimal weight: 0.2980 overall best weight: 0.5560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** 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: 0.5457 moved from start: 0.5859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8540 Z= 0.168 Angle : 0.515 9.065 11541 Z= 0.265 Chirality : 0.038 0.141 1260 Planarity : 0.004 0.048 1501 Dihedral : 4.508 58.588 1146 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.70 % Allowed : 13.95 % Favored : 84.35 % 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: 0.66 (0.26), residues: 1017 helix: 0.86 (0.23), residues: 481 sheet: -0.36 (0.53), residues: 105 loop : 0.36 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 139 HIS 0.005 0.001 HIS A 392 PHE 0.015 0.001 PHE A 730 TYR 0.012 0.001 TYR A 494 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 136 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 1.622 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: 0.6811 (OUTLIER) cc_final: 0.6359 (ttp-110) REVERT: A 360 ASN cc_start: 0.6979 (t0) cc_final: 0.6698 (t0) REVERT: A 470 GLU cc_start: 0.6232 (tt0) cc_final: 0.5838 (mm-30) REVERT: A 511 TYR cc_start: 0.6482 (OUTLIER) cc_final: 0.6098 (t80) REVERT: A 552 LYS cc_start: 0.8466 (mttp) cc_final: 0.8155 (mmtm) REVERT: A 572 LYS cc_start: 0.7299 (tttt) cc_final: 0.6693 (tptp) REVERT: A 597 LYS cc_start: 0.7303 (tttp) cc_final: 0.6648 (tppt) REVERT: A 723 ASN cc_start: 0.5339 (OUTLIER) cc_final: 0.2504 (m-40) REVERT: B 58 CYS cc_start: 0.7109 (m) cc_final: 0.6181 (t) REVERT: B 63 ASP cc_start: 0.6609 (m-30) cc_final: 0.6145 (t0) REVERT: B 72 LYS cc_start: 0.8767 (pttm) cc_final: 0.8476 (pttm) REVERT: B 127 ASP cc_start: 0.7713 (m-30) cc_final: 0.7489 (m-30) REVERT: B 129 LYS cc_start: 0.7661 (mttt) cc_final: 0.6977 (mmmt) REVERT: C 169 MET cc_start: 0.8118 (ttp) cc_final: 0.7843 (tmm) REVERT: C 200 ASN cc_start: 0.7236 (m-40) cc_final: 0.6973 (m-40) REVERT: C 206 LEU cc_start: 0.4144 (mp) cc_final: 0.3248 (tt) REVERT: C 287 GLU cc_start: 0.9118 (pt0) cc_final: 0.8887 (pt0) outliers start: 16 outliers final: 10 residues processed: 130 average time/residue: 0.5209 time to fit residues: 90.5722 Evaluate side-chains 130 residues out of total 942 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 1.274 ------------------------------------------------------------------------------- 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 534 ASP 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 723 ASN Chi-restraints excluded: chain A residue 739 MET Chi-restraints excluded: chain B residue 23 CYS Chi-restraints excluded: chain B residue 78 SER 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: 0.9990 chunk 81 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 4 optimal weight: 0.2980 chunk 58 optimal weight: 4.9990 chunk 92 optimal weight: 0.9990 chunk 54 optimal weight: 0.4980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 100 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4636 r_free = 0.4636 target = 0.212315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.176813 restraints weight = 38166.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.180919 restraints weight = 23455.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.185116 restraints weight = 15432.027| |-----------------------------------------------------------------------------| r_work (final): 0.4350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.5975 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= 0.195 Angle : 0.525 8.785 11541 Z= 0.272 Chirality : 0.038 0.140 1260 Planarity : 0.004 0.047 1501 Dihedral : 4.455 58.638 1146 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 1.60 % Allowed : 14.06 % Favored : 84.35 % 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: 0.78 (0.26), residues: 1017 helix: 1.00 (0.23), residues: 481 sheet: -0.32 (0.53), residues: 105 loop : 0.37 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 139 HIS 0.005 0.001 HIS A 392 PHE 0.014 0.002 PHE A 730 TYR 0.012 0.001 TYR B 86 ARG 0.005 0.000 ARG A 417 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3869.99 seconds wall clock time: 67 minutes 58.09 seconds (4078.09 seconds total)