Starting phenix.real_space_refine on Sat Jul 20 06:04:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1l_36794/07_2024/8k1l_36794_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1l_36794/07_2024/8k1l_36794.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1l_36794/07_2024/8k1l_36794.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1l_36794/07_2024/8k1l_36794.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1l_36794/07_2024/8k1l_36794_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k1l_36794/07_2024/8k1l_36794_neut.cif" } resolution = 3.44 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.037 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 Al 1 5.89 5 S 69 5.16 5 C 6420 2.51 5 N 1671 2.21 5 O 1861 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 870": "OD1" <-> "OD2" Residue "A ARG 983": "NH1" <-> "NH2" Residue "A ARG 984": "NH1" <-> "NH2" Residue "B ASP 93": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 10026 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 979, 7657 Classifications: {'peptide': 979} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 44, 'TRANS': 934} Chain: "B" Number of atoms: 2364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2364 Classifications: {'peptide': 292} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 274} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'ALF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.40, per 1000 atoms: 0.54 Number of scatterers: 10026 At special positions: 0 Unit cell: (88.736, 103.776, 166.192, 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) S 69 16.00 Al 1 13.00 F 4 9.00 O 1861 8.00 N 1671 7.00 C 6420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS B 165 " - pdb=" SG CYS B 177 " distance=2.03 Simple disulfide: pdb=" SG CYS B 188 " - pdb=" SG CYS B 202 " distance=2.03 Simple disulfide: pdb=" SG CYS B 254 " - pdb=" SG CYS B 311 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.08 Conformation dependent library (CDL) restraints added in 1.9 seconds 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2356 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 9 sheets defined 47.7% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 24 through 33 Processing helix chain 'A' and resid 41 through 52 Processing helix chain 'A' and resid 64 through 73 removed outlier: 3.528A pdb=" N LYS A 68 " --> pdb=" O PRO A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 99 Processing helix chain 'A' and resid 105 through 128 removed outlier: 4.114A pdb=" N TYR A 125 " --> pdb=" O GLY A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 138 Processing helix chain 'A' and resid 150 through 153 Processing helix chain 'A' and resid 212 through 216 removed outlier: 3.895A pdb=" N THR A 216 " --> pdb=" O PRO A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 253 Processing helix chain 'A' and resid 259 through 284 Processing helix chain 'A' and resid 284 through 289 removed outlier: 3.958A pdb=" N PHE A 288 " --> pdb=" O ALA A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 removed outlier: 3.923A pdb=" N GLY A 303 " --> pdb=" O ILE A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 330 removed outlier: 3.589A pdb=" N LYS A 330 " --> pdb=" O LYS A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 345 removed outlier: 3.756A pdb=" N GLU A 342 " --> pdb=" O GLU A 339 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR A 343 " --> pdb=" O ALA A 340 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU A 344 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 405 Processing helix chain 'A' and resid 427 through 442 Processing helix chain 'A' and resid 444 through 451 Processing helix chain 'A' and resid 485 through 491 removed outlier: 4.084A pdb=" N GLU A 491 " --> pdb=" O GLU A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 523 removed outlier: 3.674A pdb=" N MET A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 595 through 607 Processing helix chain 'A' and resid 615 through 624 Processing helix chain 'A' and resid 641 through 647 removed outlier: 3.594A pdb=" N ASP A 647 " --> pdb=" O ASN A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 660 removed outlier: 3.528A pdb=" N TYR A 660 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 669 through 682 removed outlier: 3.849A pdb=" N LEU A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 703 Processing helix chain 'A' and resid 714 through 720 Processing helix chain 'A' and resid 731 through 755 removed outlier: 3.521A pdb=" N THR A 735 " --> pdb=" O ALA A 731 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N TYR A 753 " --> pdb=" O LYS A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 770 Proline residue: A 764 - end of helix Processing helix chain 'A' and resid 778 through 787 removed outlier: 3.507A pdb=" N CYS A 784 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ILE A 785 " --> pdb=" O THR A 781 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 790 No H-bonds generated for 'chain 'A' and resid 788 through 790' Processing helix chain 'A' and resid 791 through 797 Processing helix chain 'A' and resid 798 through 800 No H-bonds generated for 'chain 'A' and resid 798 through 800' Processing helix chain 'A' and resid 819 through 827 Processing helix chain 'A' and resid 828 through 850 removed outlier: 3.520A pdb=" N MET A 833 " --> pdb=" O GLN A 829 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 841 " --> pdb=" O GLY A 837 " (cutoff:3.500A) Processing helix chain 'A' and resid 852 through 857 removed outlier: 3.654A pdb=" N PHE A 857 " --> pdb=" O PRO A 853 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 865 removed outlier: 3.568A pdb=" N GLU A 864 " --> pdb=" O ARG A 860 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER A 865 " --> pdb=" O LYS A 861 " (cutoff:3.500A) Processing helix chain 'A' and resid 880 through 912 removed outlier: 4.186A pdb=" N THR A 905 " --> pdb=" O ILE A 901 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASP A 906 " --> pdb=" O VAL A 902 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N THR A 912 " --> pdb=" O ILE A 908 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 921 Processing helix chain 'A' and resid 924 through 942 Processing helix chain 'A' and resid 964 through 984 Processing helix chain 'A' and resid 988 through 993 Processing helix chain 'B' and resid 59 through 90 Processing helix chain 'B' and resid 138 through 149 Processing helix chain 'B' and resid 153 through 159 removed outlier: 3.854A pdb=" N SER B 158 " --> pdb=" O THR B 154 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 185 Processing helix chain 'B' and resid 189 through 196 removed outlier: 5.673A pdb=" N PHE B 194 " --> pdb=" O GLU B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 229 through 242 Processing helix chain 'B' and resid 243 through 248 Processing helix chain 'B' and resid 258 through 265 removed outlier: 4.223A pdb=" N GLU B 263 " --> pdb=" O ALA B 259 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 147 through 148 removed outlier: 3.963A pdb=" N PHE A 147 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLY A 233 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ARG A 232 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE A 234 " --> pdb=" O ARG A 181 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N ASP A 179 " --> pdb=" O ILE A 236 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 189 through 190 Processing sheet with id=AA3, first strand: chain 'A' and resid 333 through 335 removed outlier: 6.889A pdb=" N VAL A 687 " --> pdb=" O ILE A 705 " (cutoff:3.500A) removed outlier: 8.003A pdb=" N VAL A 707 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N VAL A 689 " --> pdb=" O VAL A 707 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N MET A 709 " --> pdb=" O VAL A 689 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL A 588 " --> pdb=" O ILE A 663 " (cutoff:3.500A) removed outlier: 8.373A pdb=" N PHE A 665 " --> pdb=" O VAL A 588 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N MET A 590 " --> pdb=" O PHE A 665 " (cutoff:3.500A) removed outlier: 5.854A pdb=" N ALA A 638 " --> pdb=" O VAL A 664 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 373 through 376 removed outlier: 3.609A pdb=" N VAL A 375 " --> pdb=" O MET A 368 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N HIS A 367 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 9.921A pdb=" N LEU A 558 " --> pdb=" O GLU A 534 " (cutoff:3.500A) removed outlier: 8.673A pdb=" N GLU A 534 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N PHE A 560 " --> pdb=" O ASP A 532 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N ASP A 532 " --> pdb=" O PHE A 560 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR A 478 " --> pdb=" O LEU A 535 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N LYS A 483 " --> pdb=" O GLN A 466 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN A 466 " --> pdb=" O LYS A 483 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N VAL A 467 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU A 456 " --> pdb=" O VAL A 467 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL A 469 " --> pdb=" O VAL A 454 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 373 through 376 removed outlier: 3.609A pdb=" N VAL A 375 " --> pdb=" O MET A 368 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N HIS A 367 " --> pdb=" O SER A 565 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N CYS A 493 " --> pdb=" O LEU A 558 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE A 560 " --> pdb=" O CYS A 493 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR A 495 " --> pdb=" O PHE A 560 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLY A 562 " --> pdb=" O THR A 495 " (cutoff:3.500A) removed outlier: 9.240A pdb=" N LEU A 497 " --> pdb=" O GLY A 562 " (cutoff:3.500A) removed outlier: 12.386A pdb=" N MET A 564 " --> pdb=" O LEU A 497 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 409 through 410 removed outlier: 4.166A pdb=" N GLU A 409 " --> pdb=" O ASN A 425 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 871 through 872 Processing sheet with id=AA8, first strand: chain 'B' and resid 112 through 114 Processing sheet with id=AA9, first strand: chain 'B' and resid 127 through 130 removed outlier: 5.975A pdb=" N ILE B 128 " --> pdb=" O ARG B 334 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N MET B 335 " --> pdb=" O GLN B 305 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN B 305 " --> pdb=" O MET B 335 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TRP B 251 " --> pdb=" O TRP B 314 " (cutoff:3.500A) 453 hydrogen bonds defined for protein. 1293 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.35 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2575 1.33 - 1.45: 2001 1.45 - 1.58: 5566 1.58 - 1.70: 0 1.70 - 1.82: 115 Bond restraints: 10257 Sorted by residual: bond pdb=" F1 ALF A1001 " pdb="AL ALF A1001 " ideal model delta sigma weight residual 1.684 1.785 -0.101 2.00e-02 2.50e+03 2.53e+01 bond pdb=" F2 ALF A1001 " pdb="AL ALF A1001 " ideal model delta sigma weight residual 1.685 1.785 -0.100 2.00e-02 2.50e+03 2.50e+01 bond pdb=" F3 ALF A1001 " pdb="AL ALF A1001 " ideal model delta sigma weight residual 1.685 1.783 -0.098 2.00e-02 2.50e+03 2.40e+01 bond pdb=" F4 ALF A1001 " pdb="AL ALF A1001 " ideal model delta sigma weight residual 1.686 1.783 -0.097 2.00e-02 2.50e+03 2.36e+01 bond pdb=" N ILE A 180 " pdb=" CA ILE A 180 " ideal model delta sigma weight residual 1.458 1.492 -0.035 1.14e-02 7.69e+03 9.39e+00 ... (remaining 10252 not shown) Histogram of bond angle deviations from ideal: 89.83 - 107.85: 421 107.85 - 125.86: 13312 125.86 - 143.88: 164 143.88 - 161.89: 0 161.89 - 179.90: 2 Bond angle restraints: 13899 Sorted by residual: angle pdb=" F1 ALF A1001 " pdb="AL ALF A1001 " pdb=" F2 ALF A1001 " ideal model delta sigma weight residual 108.68 179.90 -71.22 3.00e+00 1.11e-01 5.64e+02 angle pdb=" F3 ALF A1001 " pdb="AL ALF A1001 " pdb=" F4 ALF A1001 " ideal model delta sigma weight residual 109.63 179.36 -69.73 3.00e+00 1.11e-01 5.40e+02 angle pdb=" F2 ALF A1001 " pdb="AL ALF A1001 " pdb=" F4 ALF A1001 " ideal model delta sigma weight residual 110.21 90.25 19.96 3.00e+00 1.11e-01 4.43e+01 angle pdb=" F1 ALF A1001 " pdb="AL ALF A1001 " pdb=" F3 ALF A1001 " ideal model delta sigma weight residual 109.69 89.90 19.79 3.00e+00 1.11e-01 4.35e+01 angle pdb=" F2 ALF A1001 " pdb="AL ALF A1001 " pdb=" F3 ALF A1001 " ideal model delta sigma weight residual 109.59 90.02 19.57 3.00e+00 1.11e-01 4.26e+01 ... (remaining 13894 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 5208 17.13 - 34.27: 722 34.27 - 51.40: 163 51.40 - 68.54: 38 68.54 - 85.67: 8 Dihedral angle restraints: 6139 sinusoidal: 2472 harmonic: 3667 Sorted by residual: dihedral pdb=" CB CYS B 188 " pdb=" SG CYS B 188 " pdb=" SG CYS B 202 " pdb=" CB CYS B 202 " ideal model delta sinusoidal sigma weight residual 93.00 159.64 -66.64 1 1.00e+01 1.00e-02 5.79e+01 dihedral pdb=" CA TYR B 280 " pdb=" C TYR B 280 " pdb=" N TYR B 281 " pdb=" CA TYR B 281 " ideal model delta harmonic sigma weight residual -180.00 -150.38 -29.62 0 5.00e+00 4.00e-02 3.51e+01 dihedral pdb=" CA SER A 406 " pdb=" C SER A 406 " pdb=" N ARG A 407 " pdb=" CA ARG A 407 " ideal model delta harmonic sigma weight residual 180.00 158.95 21.05 0 5.00e+00 4.00e-02 1.77e+01 ... (remaining 6136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 1239 0.052 - 0.103: 238 0.103 - 0.155: 51 0.155 - 0.206: 9 0.206 - 0.258: 3 Chirality restraints: 1540 Sorted by residual: chirality pdb=" CB ILE A 759 " pdb=" CA ILE A 759 " pdb=" CG1 ILE A 759 " pdb=" CG2 ILE A 759 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA ILE A 625 " pdb=" N ILE A 625 " pdb=" C ILE A 625 " pdb=" CB ILE A 625 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CG LEU B 76 " pdb=" CB LEU B 76 " pdb=" CD1 LEU B 76 " pdb=" CD2 LEU B 76 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.14e+00 ... (remaining 1537 not shown) Planarity restraints: 1786 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 622 " 0.616 9.50e-02 1.11e+02 2.76e-01 4.65e+01 pdb=" NE ARG A 622 " -0.038 2.00e-02 2.50e+03 pdb=" CZ ARG A 622 " -0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG A 622 " -0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG A 622 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 983 " -0.335 9.50e-02 1.11e+02 1.50e-01 1.38e+01 pdb=" NE ARG A 983 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 983 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 983 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 983 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 175 " -0.237 9.50e-02 1.11e+02 1.06e-01 6.95e+00 pdb=" NE ARG A 175 " 0.014 2.00e-02 2.50e+03 pdb=" CZ ARG A 175 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 175 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 175 " -0.008 2.00e-02 2.50e+03 ... (remaining 1783 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 195 2.63 - 3.20: 9671 3.20 - 3.77: 15847 3.77 - 4.33: 21704 4.33 - 4.90: 35452 Nonbonded interactions: 82869 Sorted by model distance: nonbonded pdb=" O ALA A 431 " pdb=" CE LYS A 435 " model vdw 2.067 3.440 nonbonded pdb=" OD2 ASP A 353 " pdb=" F2 ALF A1001 " model vdw 2.125 2.390 nonbonded pdb=" O ASP B 227 " pdb=" OD1 ASP B 227 " model vdw 2.146 3.040 nonbonded pdb=" O GLY A 312 " pdb=" OG1 THR A 316 " model vdw 2.179 2.440 nonbonded pdb=" OD1 ASP A 353 " pdb=" F3 ALF A1001 " model vdw 2.179 2.390 ... (remaining 82864 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 30.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 27.930 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 10257 Z= 0.288 Angle : 1.168 71.224 13899 Z= 0.518 Chirality : 0.046 0.258 1540 Planarity : 0.009 0.276 1786 Dihedral : 16.417 85.672 3774 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 0.37 % Allowed : 24.06 % Favored : 75.57 % 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: -1.16 (0.24), residues: 1267 helix: -0.05 (0.22), residues: 562 sheet: -1.08 (0.49), residues: 129 loop : -1.36 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 63 HIS 0.008 0.001 HIS B 187 PHE 0.011 0.001 PHE A 989 TYR 0.024 0.001 TYR B 281 ARG 0.004 0.001 ARG B 214 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 117 time to evaluate : 1.271 Fit side-chains REVERT: A 523 MET cc_start: 0.8016 (mpp) cc_final: 0.7549 (pmm) outliers start: 4 outliers final: 3 residues processed: 120 average time/residue: 0.2307 time to fit residues: 39.5098 Evaluate side-chains 115 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 112 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 627 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 4.9990 chunk 95 optimal weight: 0.8980 chunk 52 optimal weight: 0.0270 chunk 32 optimal weight: 0.5980 chunk 64 optimal weight: 0.8980 chunk 51 optimal weight: 7.9990 chunk 98 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 73 optimal weight: 0.9990 chunk 114 optimal weight: 5.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 985 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10257 Z= 0.207 Angle : 0.620 9.764 13899 Z= 0.315 Chirality : 0.042 0.246 1540 Planarity : 0.004 0.040 1786 Dihedral : 4.445 28.209 1373 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.60 % Favored : 94.32 % Rotamer: Outliers : 3.29 % Allowed : 22.32 % Favored : 74.38 % 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: -0.53 (0.24), residues: 1267 helix: 0.67 (0.22), residues: 569 sheet: -1.12 (0.45), residues: 140 loop : -1.17 (0.27), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 63 HIS 0.003 0.001 HIS B 187 PHE 0.012 0.001 PHE A 410 TYR 0.021 0.001 TYR A 465 ARG 0.006 0.001 ARG A 622 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 118 time to evaluate : 1.154 Fit side-chains REVERT: A 465 TYR cc_start: 0.7281 (p90) cc_final: 0.7069 (p90) REVERT: B 56 MET cc_start: 0.7363 (tpt) cc_final: 0.7035 (tpt) outliers start: 36 outliers final: 26 residues processed: 144 average time/residue: 0.2128 time to fit residues: 44.2513 Evaluate side-chains 135 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 109 time to evaluate : 1.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 322 THR Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 624 ASN Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 991 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 309 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 63 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 0.6980 chunk 77 optimal weight: 0.0770 chunk 31 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 123 optimal weight: 0.8980 chunk 102 optimal weight: 0.2980 chunk 113 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 91 optimal weight: 0.6980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 985 ASN ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10257 Z= 0.175 Angle : 0.568 7.546 13899 Z= 0.286 Chirality : 0.041 0.241 1540 Planarity : 0.004 0.044 1786 Dihedral : 4.331 38.477 1373 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.37 % Favored : 94.55 % Rotamer: Outliers : 3.20 % Allowed : 22.51 % Favored : 74.29 % 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: -0.22 (0.24), residues: 1267 helix: 1.00 (0.22), residues: 561 sheet: -0.97 (0.44), residues: 140 loop : -1.06 (0.27), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 63 HIS 0.002 0.001 HIS A 414 PHE 0.023 0.001 PHE A 980 TYR 0.014 0.001 TYR A 465 ARG 0.003 0.000 ARG A 622 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 126 time to evaluate : 1.192 Fit side-chains REVERT: A 142 MET cc_start: 0.7695 (ppp) cc_final: 0.7466 (ppp) REVERT: A 517 TYR cc_start: 0.7940 (t80) cc_final: 0.7666 (t80) REVERT: B 55 PHE cc_start: 0.7417 (t80) cc_final: 0.6824 (t80) REVERT: B 56 MET cc_start: 0.7251 (tpt) cc_final: 0.6872 (tpt) outliers start: 35 outliers final: 22 residues processed: 152 average time/residue: 0.2129 time to fit residues: 47.0846 Evaluate side-chains 134 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 112 time to evaluate : 1.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 480 LEU Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 1.9990 chunk 86 optimal weight: 0.6980 chunk 59 optimal weight: 0.0770 chunk 12 optimal weight: 4.9990 chunk 54 optimal weight: 10.0000 chunk 76 optimal weight: 0.5980 chunk 115 optimal weight: 0.0060 chunk 121 optimal weight: 0.0170 chunk 60 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 overall best weight: 0.2792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 360 GLN A 372 GLN ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 10257 Z= 0.151 Angle : 0.541 9.415 13899 Z= 0.273 Chirality : 0.040 0.252 1540 Planarity : 0.004 0.046 1786 Dihedral : 4.185 39.007 1371 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.37 % Favored : 94.55 % Rotamer: Outliers : 3.39 % Allowed : 22.23 % Favored : 74.38 % 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: -0.11 (0.24), residues: 1267 helix: 1.10 (0.22), residues: 576 sheet: -0.86 (0.44), residues: 140 loop : -1.10 (0.27), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 63 HIS 0.003 0.000 HIS A 414 PHE 0.007 0.001 PHE A 410 TYR 0.011 0.001 TYR A 768 ARG 0.003 0.000 ARG A 422 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 122 time to evaluate : 1.168 Fit side-chains revert: symmetry clash REVERT: A 30 ARG cc_start: 0.7487 (mmp-170) cc_final: 0.7193 (mmm160) REVERT: A 142 MET cc_start: 0.7860 (ppp) cc_final: 0.7479 (ppp) REVERT: A 509 MET cc_start: 0.7338 (mmp) cc_final: 0.7094 (mmp) REVERT: A 517 TYR cc_start: 0.7895 (t80) cc_final: 0.7646 (t80) REVERT: A 633 ARG cc_start: 0.8094 (tmm160) cc_final: 0.7811 (ttp80) REVERT: B 55 PHE cc_start: 0.7379 (t80) cc_final: 0.6835 (t80) REVERT: B 56 MET cc_start: 0.7091 (tpt) cc_final: 0.6645 (tpt) outliers start: 37 outliers final: 27 residues processed: 150 average time/residue: 0.2111 time to fit residues: 45.9639 Evaluate side-chains 140 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 113 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 101 optimal weight: 3.9990 chunk 69 optimal weight: 0.0020 chunk 1 optimal weight: 0.4980 chunk 90 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 chunk 103 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 62 optimal weight: 0.8980 chunk 109 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 218 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10257 Z= 0.166 Angle : 0.537 9.475 13899 Z= 0.268 Chirality : 0.040 0.255 1540 Planarity : 0.004 0.047 1786 Dihedral : 4.125 39.676 1371 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.05 % Favored : 94.79 % Rotamer: Outliers : 3.29 % Allowed : 22.51 % Favored : 74.20 % 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: 0.02 (0.24), residues: 1267 helix: 1.21 (0.22), residues: 578 sheet: -0.44 (0.47), residues: 128 loop : -1.14 (0.27), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 63 HIS 0.002 0.001 HIS A 414 PHE 0.025 0.001 PHE A 145 TYR 0.013 0.001 TYR A 465 ARG 0.003 0.000 ARG A 741 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 121 time to evaluate : 1.294 Fit side-chains revert: symmetry clash REVERT: A 135 MET cc_start: 0.8602 (tpp) cc_final: 0.8335 (mmm) REVERT: A 368 MET cc_start: 0.6525 (mtm) cc_final: 0.6228 (mtm) REVERT: A 509 MET cc_start: 0.7334 (mmp) cc_final: 0.7115 (mmp) REVERT: A 517 TYR cc_start: 0.7882 (t80) cc_final: 0.7622 (t80) REVERT: A 633 ARG cc_start: 0.7999 (tmm160) cc_final: 0.7724 (ttp80) REVERT: B 55 PHE cc_start: 0.7293 (t80) cc_final: 0.6789 (t80) REVERT: B 56 MET cc_start: 0.6984 (tpt) cc_final: 0.6555 (tpt) outliers start: 36 outliers final: 27 residues processed: 149 average time/residue: 0.2212 time to fit residues: 48.3759 Evaluate side-chains 141 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 114 time to evaluate : 1.165 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 301 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 40 optimal weight: 9.9990 chunk 109 optimal weight: 9.9990 chunk 24 optimal weight: 0.7980 chunk 71 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 121 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10257 Z= 0.210 Angle : 0.552 10.319 13899 Z= 0.276 Chirality : 0.041 0.263 1540 Planarity : 0.004 0.047 1786 Dihedral : 4.162 41.019 1371 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.68 % Favored : 94.16 % Rotamer: Outliers : 3.84 % Allowed : 21.96 % Favored : 74.20 % 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: -0.01 (0.24), residues: 1267 helix: 1.18 (0.22), residues: 578 sheet: -0.41 (0.47), residues: 128 loop : -1.16 (0.26), residues: 561 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 63 HIS 0.002 0.001 HIS A 641 PHE 0.009 0.001 PHE A 665 TYR 0.015 0.001 TYR A 995 ARG 0.003 0.000 ARG A 741 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 121 time to evaluate : 1.324 Fit side-chains revert: symmetry clash REVERT: A 459 PHE cc_start: 0.2050 (OUTLIER) cc_final: 0.0432 (m-10) REVERT: A 517 TYR cc_start: 0.7847 (t80) cc_final: 0.7624 (t80) REVERT: A 531 CYS cc_start: 0.6102 (OUTLIER) cc_final: 0.5517 (m) REVERT: A 633 ARG cc_start: 0.8018 (tmm160) cc_final: 0.7775 (ttp80) REVERT: B 55 PHE cc_start: 0.7337 (t80) cc_final: 0.6831 (t80) REVERT: B 56 MET cc_start: 0.7018 (tpt) cc_final: 0.6601 (tpt) outliers start: 42 outliers final: 31 residues processed: 153 average time/residue: 0.2166 time to fit residues: 48.2290 Evaluate side-chains 146 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 113 time to evaluate : 1.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 343 THR Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 531 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 303 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 13 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 102 optimal weight: 0.4980 chunk 121 optimal weight: 0.0980 chunk 76 optimal weight: 0.0770 chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 75 optimal weight: 0.7980 chunk 48 optimal weight: 10.0000 overall best weight: 0.4738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10257 Z= 0.164 Angle : 0.553 10.993 13899 Z= 0.273 Chirality : 0.040 0.262 1540 Planarity : 0.004 0.048 1786 Dihedral : 4.120 44.770 1371 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.97 % Favored : 94.87 % Rotamer: Outliers : 3.39 % Allowed : 22.96 % Favored : 73.65 % 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: 0.07 (0.24), residues: 1267 helix: 1.27 (0.22), residues: 579 sheet: -0.38 (0.47), residues: 128 loop : -1.16 (0.26), residues: 560 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 63 HIS 0.003 0.001 HIS A 267 PHE 0.028 0.001 PHE A 145 TYR 0.012 0.001 TYR A 465 ARG 0.004 0.000 ARG A 448 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 123 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: A 52 TYR cc_start: 0.6143 (OUTLIER) cc_final: 0.5437 (p90) REVERT: A 175 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.6834 (ttp-170) REVERT: A 459 PHE cc_start: 0.1926 (OUTLIER) cc_final: 0.0340 (m-10) REVERT: A 531 CYS cc_start: 0.6107 (OUTLIER) cc_final: 0.5520 (m) REVERT: A 633 ARG cc_start: 0.7959 (tmm160) cc_final: 0.7725 (ttp80) REVERT: B 55 PHE cc_start: 0.7298 (t80) cc_final: 0.6879 (t80) REVERT: B 56 MET cc_start: 0.6963 (tpt) cc_final: 0.6553 (tpt) outliers start: 37 outliers final: 31 residues processed: 151 average time/residue: 0.2165 time to fit residues: 46.9279 Evaluate side-chains 149 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 114 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 531 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 813 VAL Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 303 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 72 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 23 optimal weight: 5.9990 chunk 77 optimal weight: 0.7980 chunk 82 optimal weight: 0.5980 chunk 60 optimal weight: 6.9990 chunk 11 optimal weight: 0.4980 chunk 95 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 116 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10257 Z= 0.256 Angle : 0.583 11.507 13899 Z= 0.292 Chirality : 0.042 0.267 1540 Planarity : 0.004 0.084 1786 Dihedral : 4.285 48.477 1371 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.00 % Favored : 93.84 % Rotamer: Outliers : 3.75 % Allowed : 23.33 % Favored : 72.92 % 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: -0.08 (0.24), residues: 1267 helix: 1.08 (0.22), residues: 584 sheet: -0.38 (0.46), residues: 128 loop : -1.19 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 251 HIS 0.003 0.001 HIS A 641 PHE 0.012 0.001 PHE A 268 TYR 0.013 0.001 TYR A 768 ARG 0.008 0.000 ARG A 741 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 120 time to evaluate : 1.032 Fit side-chains revert: symmetry clash REVERT: A 142 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7018 (ppp) REVERT: A 149 ILE cc_start: 0.8127 (mt) cc_final: 0.7808 (mt) REVERT: A 175 ARG cc_start: 0.8447 (OUTLIER) cc_final: 0.6793 (ttp-170) REVERT: A 459 PHE cc_start: 0.2041 (OUTLIER) cc_final: 0.0374 (m-10) REVERT: A 531 CYS cc_start: 0.6055 (OUTLIER) cc_final: 0.5455 (m) REVERT: B 55 PHE cc_start: 0.7437 (t80) cc_final: 0.7025 (t80) REVERT: B 56 MET cc_start: 0.7075 (tpt) cc_final: 0.6706 (tpt) REVERT: B 209 LYS cc_start: 0.9059 (OUTLIER) cc_final: 0.8745 (ptpp) outliers start: 41 outliers final: 31 residues processed: 152 average time/residue: 0.2067 time to fit residues: 45.4953 Evaluate side-chains 151 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 115 time to evaluate : 1.040 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 531 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 303 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 113 optimal weight: 0.9990 chunk 116 optimal weight: 3.9990 chunk 68 optimal weight: 0.6980 chunk 49 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 102 optimal weight: 0.0060 chunk 107 optimal weight: 2.9990 chunk 112 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 119 optimal weight: 0.9980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10257 Z= 0.192 Angle : 0.581 12.543 13899 Z= 0.286 Chirality : 0.042 0.265 1540 Planarity : 0.004 0.074 1786 Dihedral : 4.249 51.465 1371 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.52 % Favored : 94.40 % Rotamer: Outliers : 3.84 % Allowed : 23.70 % Favored : 72.46 % 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: 0.03 (0.24), residues: 1267 helix: 1.18 (0.22), residues: 583 sheet: -0.30 (0.46), residues: 127 loop : -1.15 (0.26), residues: 557 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 63 HIS 0.003 0.001 HIS A 267 PHE 0.029 0.001 PHE A 145 TYR 0.013 0.001 TYR A 768 ARG 0.003 0.000 ARG A 741 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 117 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.6162 (OUTLIER) cc_final: 0.5633 (p90) REVERT: A 142 MET cc_start: 0.7954 (OUTLIER) cc_final: 0.6704 (ppp) REVERT: A 459 PHE cc_start: 0.1877 (OUTLIER) cc_final: 0.0240 (m-10) REVERT: A 517 TYR cc_start: 0.7471 (t80) cc_final: 0.7213 (t80) REVERT: A 531 CYS cc_start: 0.6012 (OUTLIER) cc_final: 0.5360 (m) REVERT: B 55 PHE cc_start: 0.7383 (t80) cc_final: 0.7031 (t80) REVERT: B 56 MET cc_start: 0.7086 (tpt) cc_final: 0.6711 (tpt) outliers start: 42 outliers final: 35 residues processed: 147 average time/residue: 0.2156 time to fit residues: 46.3180 Evaluate side-chains 153 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 114 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 142 MET Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 515 ASN Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 531 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 789 THR Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 303 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 73 optimal weight: 0.3980 chunk 56 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 115 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 61 optimal weight: 5.9990 chunk 79 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10257 Z= 0.195 Angle : 0.581 13.011 13899 Z= 0.286 Chirality : 0.042 0.262 1540 Planarity : 0.004 0.072 1786 Dihedral : 4.248 54.568 1371 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.08 % Favored : 93.84 % Rotamer: Outliers : 3.48 % Allowed : 24.06 % Favored : 72.46 % 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: 0.06 (0.24), residues: 1267 helix: 1.20 (0.22), residues: 585 sheet: -0.31 (0.46), residues: 127 loop : -1.14 (0.26), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 63 HIS 0.003 0.001 HIS A 267 PHE 0.012 0.001 PHE A 268 TYR 0.013 0.001 TYR A 768 ARG 0.007 0.000 ARG A 633 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2534 Ramachandran restraints generated. 1267 Oldfield, 0 Emsley, 1267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 116 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 TYR cc_start: 0.6103 (OUTLIER) cc_final: 0.5583 (p90) REVERT: A 531 CYS cc_start: 0.5994 (OUTLIER) cc_final: 0.5362 (m) REVERT: B 55 PHE cc_start: 0.7388 (t80) cc_final: 0.6963 (t80) REVERT: B 56 MET cc_start: 0.7082 (tpt) cc_final: 0.6499 (tpt) REVERT: B 209 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8732 (ptpp) outliers start: 38 outliers final: 33 residues processed: 144 average time/residue: 0.2147 time to fit residues: 44.6639 Evaluate side-chains 151 residues out of total 1093 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 115 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 TYR Chi-restraints excluded: chain A residue 70 CYS Chi-restraints excluded: chain A residue 97 TYR Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 164 VAL Chi-restraints excluded: chain A residue 170 VAL Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 250 LEU Chi-restraints excluded: chain A residue 424 VAL Chi-restraints excluded: chain A residue 459 PHE Chi-restraints excluded: chain A residue 482 MET Chi-restraints excluded: chain A residue 523 MET Chi-restraints excluded: chain A residue 531 CYS Chi-restraints excluded: chain A residue 623 LEU Chi-restraints excluded: chain A residue 639 VAL Chi-restraints excluded: chain A residue 705 ILE Chi-restraints excluded: chain A residue 716 VAL Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 759 ILE Chi-restraints excluded: chain A residue 780 VAL Chi-restraints excluded: chain A residue 819 ASN Chi-restraints excluded: chain A residue 844 VAL Chi-restraints excluded: chain A residue 880 THR Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 926 THR Chi-restraints excluded: chain B residue 67 THR Chi-restraints excluded: chain B residue 168 ASP Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 202 CYS Chi-restraints excluded: chain B residue 209 LYS Chi-restraints excluded: chain B residue 291 THR Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 303 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 0.8980 chunk 92 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 0.0870 chunk 100 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 2.9990 chunk 87 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.130102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.095880 restraints weight = 18989.603| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.57 r_work: 0.3237 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10257 Z= 0.188 Angle : 0.582 13.198 13899 Z= 0.285 Chirality : 0.042 0.260 1540 Planarity : 0.004 0.072 1786 Dihedral : 4.240 56.849 1370 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.60 % Favored : 94.32 % Rotamer: Outliers : 3.48 % Allowed : 24.15 % Favored : 72.37 % 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: 0.11 (0.24), residues: 1267 helix: 1.26 (0.22), residues: 578 sheet: -0.27 (0.47), residues: 127 loop : -1.11 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 63 HIS 0.003 0.001 HIS A 267 PHE 0.030 0.001 PHE A 145 TYR 0.024 0.001 TYR A 517 ARG 0.003 0.000 ARG A 741 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2572.48 seconds wall clock time: 47 minutes 9.39 seconds (2829.39 seconds total)