Starting phenix.real_space_refine on Mon Jul 28 15:53:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wuc_21910/07_2025/6wuc_21910.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wuc_21910/07_2025/6wuc_21910.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6wuc_21910/07_2025/6wuc_21910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wuc_21910/07_2025/6wuc_21910.map" model { file = "/net/cci-nas-00/data/ceres_data/6wuc_21910/07_2025/6wuc_21910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wuc_21910/07_2025/6wuc_21910.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 434 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 6582 2.51 5 N 1738 2.21 5 O 1919 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10284 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1471 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain: "I" Number of atoms: 5777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 5777 Classifications: {'peptide': 713} Link IDs: {'PTRANS': 32, 'TRANS': 680} Chain breaks: 2 Chain: "K" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1903 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain: "W" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 432 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain breaks: 2 Chain: "T" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 701 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain breaks: 1 Time building chain proxies: 6.33, per 1000 atoms: 0.62 Number of scatterers: 10284 At special positions: 0 Unit cell: (92.4, 150.975, 132.825, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 45 16.00 O 1919 8.00 N 1738 7.00 C 6582 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 1.1 seconds 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2468 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 1 sheets defined 69.7% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'H' and resid 3 through 39 removed outlier: 3.849A pdb=" N LEU H 35 " --> pdb=" O ASP H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 66 removed outlier: 3.783A pdb=" N LEU H 52 " --> pdb=" O THR H 48 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 72 Processing helix chain 'H' and resid 82 through 94 removed outlier: 3.517A pdb=" N ASN H 88 " --> pdb=" O THR H 84 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLU H 91 " --> pdb=" O GLN H 87 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N GLU H 92 " --> pdb=" O ASN H 88 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N SER H 93 " --> pdb=" O LEU H 89 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ASN H 94 " --> pdb=" O LEU H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 106 removed outlier: 3.566A pdb=" N LEU H 101 " --> pdb=" O ASP H 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 134 removed outlier: 3.516A pdb=" N GLN H 113 " --> pdb=" O SER H 109 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER H 126 " --> pdb=" O ASP H 122 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N LYS H 127 " --> pdb=" O GLU H 123 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 156 removed outlier: 3.561A pdb=" N GLN H 151 " --> pdb=" O THR H 147 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 173 removed outlier: 3.829A pdb=" N THR H 160 " --> pdb=" O LYS H 156 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE H 161 " --> pdb=" O GLU H 157 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN H 162 " --> pdb=" O ASN H 158 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N SER H 172 " --> pdb=" O LEU H 168 " (cutoff:3.500A) Processing helix chain 'I' and resid 1 through 14 Processing helix chain 'I' and resid 22 through 36 removed outlier: 3.739A pdb=" N LYS I 36 " --> pdb=" O TYR I 32 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 55 Processing helix chain 'I' and resid 59 through 70 Processing helix chain 'I' and resid 78 through 87 removed outlier: 3.932A pdb=" N LEU I 82 " --> pdb=" O THR I 78 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU I 83 " --> pdb=" O LYS I 79 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU I 84 " --> pdb=" O GLU I 80 " (cutoff:3.500A) Processing helix chain 'I' and resid 93 through 97 removed outlier: 3.927A pdb=" N ARG I 97 " --> pdb=" O VAL I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 117 Processing helix chain 'I' and resid 118 through 121 Processing helix chain 'I' and resid 127 through 139 removed outlier: 3.832A pdb=" N SER I 134 " --> pdb=" O ASN I 130 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LEU I 137 " --> pdb=" O SER I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 140 through 142 No H-bonds generated for 'chain 'I' and resid 140 through 142' Processing helix chain 'I' and resid 143 through 147 removed outlier: 4.412A pdb=" N LYS I 147 " --> pdb=" O PHE I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 148 through 157 removed outlier: 4.147A pdb=" N LEU I 152 " --> pdb=" O TRP I 148 " (cutoff:3.500A) Processing helix chain 'I' and resid 159 through 163 Processing helix chain 'I' and resid 164 through 176 removed outlier: 3.813A pdb=" N LEU I 168 " --> pdb=" O LYS I 164 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE I 170 " --> pdb=" O TRP I 166 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG I 173 " --> pdb=" O SER I 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 177 through 181 removed outlier: 3.987A pdb=" N TYR I 180 " --> pdb=" O HIS I 177 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ARG I 181 " --> pdb=" O PRO I 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 177 through 181' Processing helix chain 'I' and resid 183 through 199 removed outlier: 4.014A pdb=" N LEU I 189 " --> pdb=" O GLY I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 201 through 209 removed outlier: 3.519A pdb=" N ILE I 209 " --> pdb=" O THR I 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 218 through 223 Processing helix chain 'I' and resid 227 through 242 Processing helix chain 'I' and resid 247 through 265 Processing helix chain 'I' and resid 295 through 302 Processing helix chain 'I' and resid 311 through 316 Processing helix chain 'I' and resid 354 through 369 removed outlier: 3.513A pdb=" N ALA I 369 " --> pdb=" O LYS I 365 " (cutoff:3.500A) Processing helix chain 'I' and resid 374 through 387 removed outlier: 3.729A pdb=" N VAL I 378 " --> pdb=" O THR I 374 " (cutoff:3.500A) Proline residue: I 380 - end of helix Processing helix chain 'I' and resid 389 through 401 removed outlier: 3.961A pdb=" N ARG I 395 " --> pdb=" O LYS I 391 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE I 397 " --> pdb=" O SER I 393 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLN I 398 " --> pdb=" O SER I 394 " (cutoff:3.500A) Processing helix chain 'I' and resid 403 through 409 removed outlier: 3.847A pdb=" N LEU I 408 " --> pdb=" O LYS I 404 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASP I 409 " --> pdb=" O TYR I 405 " (cutoff:3.500A) Processing helix chain 'I' and resid 409 through 421 removed outlier: 3.560A pdb=" N LEU I 413 " --> pdb=" O ASP I 409 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LYS I 415 " --> pdb=" O LEU I 411 " (cutoff:3.500A) Processing helix chain 'I' and resid 431 through 448 removed outlier: 3.659A pdb=" N PHE I 435 " --> pdb=" O GLY I 431 " (cutoff:3.500A) Processing helix chain 'I' and resid 457 through 475 removed outlier: 3.895A pdb=" N ASP I 475 " --> pdb=" O ASN I 471 " (cutoff:3.500A) Processing helix chain 'I' and resid 478 through 491 removed outlier: 3.584A pdb=" N THR I 484 " --> pdb=" O ALA I 480 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N HIS I 487 " --> pdb=" O LEU I 483 " (cutoff:3.500A) Processing helix chain 'I' and resid 511 through 525 removed outlier: 3.724A pdb=" N SER I 515 " --> pdb=" O ALA I 511 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR I 520 " --> pdb=" O LEU I 516 " (cutoff:3.500A) Processing helix chain 'I' and resid 531 through 535 Processing helix chain 'I' and resid 541 through 547 Processing helix chain 'I' and resid 550 through 563 Processing helix chain 'I' and resid 575 through 589 removed outlier: 3.794A pdb=" N MET I 580 " --> pdb=" O LYS I 576 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN I 581 " --> pdb=" O PHE I 577 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ASN I 582 " --> pdb=" O VAL I 578 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE I 585 " --> pdb=" O GLN I 581 " (cutoff:3.500A) Processing helix chain 'I' and resid 607 through 615 removed outlier: 4.370A pdb=" N PHE I 611 " --> pdb=" O SER I 607 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS I 612 " --> pdb=" O PRO I 608 " (cutoff:3.500A) Processing helix chain 'I' and resid 639 through 655 removed outlier: 3.681A pdb=" N ILE I 644 " --> pdb=" O SER I 640 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR I 652 " --> pdb=" O ARG I 648 " (cutoff:3.500A) Processing helix chain 'I' and resid 666 through 677 removed outlier: 3.533A pdb=" N ASN I 671 " --> pdb=" O GLU I 667 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N HIS I 677 " --> pdb=" O PHE I 673 " (cutoff:3.500A) Processing helix chain 'I' and resid 677 through 684 Processing helix chain 'I' and resid 692 through 705 Processing helix chain 'I' and resid 711 through 723 removed outlier: 3.958A pdb=" N ALA I 715 " --> pdb=" O TYR I 711 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N LYS I 723 " --> pdb=" O PHE I 719 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 39 Processing helix chain 'K' and resid 52 through 57 Processing helix chain 'K' and resid 69 through 129 removed outlier: 3.945A pdb=" N THR K 75 " --> pdb=" O GLY K 71 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU K 81 " --> pdb=" O ASN K 77 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA K 83 " --> pdb=" O LEU K 79 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU K 88 " --> pdb=" O GLN K 84 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VAL K 98 " --> pdb=" O ASN K 94 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ASP K 99 " --> pdb=" O ASP K 95 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N LYS K 101 " --> pdb=" O SER K 97 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ASP K 129 " --> pdb=" O MET K 125 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 159 Processing helix chain 'K' and resid 170 through 187 removed outlier: 3.631A pdb=" N LEU K 174 " --> pdb=" O SER K 170 " (cutoff:3.500A) Processing helix chain 'K' and resid 193 through 197 Processing helix chain 'K' and resid 201 through 211 removed outlier: 4.074A pdb=" N TYR K 205 " --> pdb=" O THR K 201 " (cutoff:3.500A) Processing helix chain 'W' and resid 16 through 22 Processing helix chain 'W' and resid 37 through 68 Processing helix chain 'W' and resid 78 through 83 Processing helix chain 'T' and resid 275 through 282 removed outlier: 3.769A pdb=" N THR T 282 " --> pdb=" O LEU T 278 " (cutoff:3.500A) Processing helix chain 'T' and resid 282 through 287 Processing helix chain 'T' and resid 296 through 317 Processing helix chain 'T' and resid 323 through 332 removed outlier: 3.900A pdb=" N MET T 331 " --> pdb=" O SER T 327 " (cutoff:3.500A) Processing helix chain 'T' and resid 336 through 348 removed outlier: 3.726A pdb=" N MET T 340 " --> pdb=" O ASN T 336 " (cutoff:3.500A) Processing helix chain 'T' and resid 349 through 361 removed outlier: 3.986A pdb=" N ARG T 355 " --> pdb=" O GLU T 351 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR T 359 " --> pdb=" O ARG T 355 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 214 through 215 554 hydrogen bonds defined for protein. 1632 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: 3.20 Time building geometry restraints manager: 3.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3307 1.34 - 1.46: 1319 1.46 - 1.57: 5778 1.57 - 1.69: 0 1.69 - 1.81: 75 Bond restraints: 10479 Sorted by residual: bond pdb=" CA ASP I 351 " pdb=" C ASP I 351 " ideal model delta sigma weight residual 1.521 1.491 0.031 1.19e-02 7.06e+03 6.65e+00 bond pdb=" CA GLU I 373 " pdb=" C GLU I 373 " ideal model delta sigma weight residual 1.524 1.553 -0.030 1.26e-02 6.30e+03 5.55e+00 bond pdb=" N GLU I 373 " pdb=" CA GLU I 373 " ideal model delta sigma weight residual 1.459 1.483 -0.024 1.20e-02 6.94e+03 4.08e+00 bond pdb=" N SER H 178 " pdb=" CA SER H 178 " ideal model delta sigma weight residual 1.457 1.483 -0.026 1.29e-02 6.01e+03 3.99e+00 bond pdb=" N THR K 236 " pdb=" CA THR K 236 " ideal model delta sigma weight residual 1.460 1.438 0.022 1.20e-02 6.94e+03 3.37e+00 ... (remaining 10474 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.45: 13962 2.45 - 4.91: 186 4.91 - 7.36: 28 7.36 - 9.81: 1 9.81 - 12.27: 1 Bond angle restraints: 14178 Sorted by residual: angle pdb=" N GLU I 373 " pdb=" CA GLU I 373 " pdb=" C GLU I 373 " ideal model delta sigma weight residual 111.14 120.15 -9.01 1.08e+00 8.57e-01 6.96e+01 angle pdb=" N ILE I 518 " pdb=" CA ILE I 518 " pdb=" C ILE I 518 " ideal model delta sigma weight residual 110.72 104.23 6.49 1.01e+00 9.80e-01 4.13e+01 angle pdb=" N HIS T 280 " pdb=" CA HIS T 280 " pdb=" C HIS T 280 " ideal model delta sigma weight residual 111.36 117.83 -6.47 1.09e+00 8.42e-01 3.52e+01 angle pdb=" N ILE I 541 " pdb=" CA ILE I 541 " pdb=" C ILE I 541 " ideal model delta sigma weight residual 110.72 116.67 -5.95 1.01e+00 9.80e-01 3.48e+01 angle pdb=" N LEU T 293 " pdb=" CA LEU T 293 " pdb=" C LEU T 293 " ideal model delta sigma weight residual 108.39 96.12 12.27 2.10e+00 2.27e-01 3.41e+01 ... (remaining 14173 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 5935 17.82 - 35.64: 367 35.64 - 53.46: 88 53.46 - 71.28: 10 71.28 - 89.10: 14 Dihedral angle restraints: 6414 sinusoidal: 2652 harmonic: 3762 Sorted by residual: dihedral pdb=" CA GLY I 663 " pdb=" C GLY I 663 " pdb=" N ILE I 664 " pdb=" CA ILE I 664 " ideal model delta harmonic sigma weight residual 180.00 155.28 24.72 0 5.00e+00 4.00e-02 2.44e+01 dihedral pdb=" CA ILE I 209 " pdb=" C ILE I 209 " pdb=" N THR I 210 " pdb=" CA THR I 210 " ideal model delta harmonic sigma weight residual 180.00 158.18 21.82 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" N SER H 178 " pdb=" C SER H 178 " pdb=" CA SER H 178 " pdb=" CB SER H 178 " ideal model delta harmonic sigma weight residual 122.80 132.95 -10.15 0 2.50e+00 1.60e-01 1.65e+01 ... (remaining 6411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 1523 0.073 - 0.146: 109 0.146 - 0.219: 9 0.219 - 0.292: 5 0.292 - 0.365: 3 Chirality restraints: 1649 Sorted by residual: chirality pdb=" CA SER H 178 " pdb=" N SER H 178 " pdb=" C SER H 178 " pdb=" CB SER H 178 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CA LYS I 723 " pdb=" N LYS I 723 " pdb=" C LYS I 723 " pdb=" CB LYS I 723 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CA LEU T 293 " pdb=" N LEU T 293 " pdb=" C LEU T 293 " pdb=" CB LEU T 293 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 1646 not shown) Planarity restraints: 1781 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP I 540 " 0.018 2.00e-02 2.50e+03 3.58e-02 1.28e+01 pdb=" C ASP I 540 " -0.062 2.00e-02 2.50e+03 pdb=" O ASP I 540 " 0.024 2.00e-02 2.50e+03 pdb=" N ILE I 541 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU I 680 " -0.016 2.00e-02 2.50e+03 3.20e-02 1.03e+01 pdb=" C GLU I 680 " 0.055 2.00e-02 2.50e+03 pdb=" O GLU I 680 " -0.021 2.00e-02 2.50e+03 pdb=" N ILE I 681 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL K 161 " 0.041 5.00e-02 4.00e+02 6.23e-02 6.21e+00 pdb=" N PRO K 162 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO K 162 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO K 162 " 0.032 5.00e-02 4.00e+02 ... (remaining 1778 not shown) Histogram of nonbonded interaction distances: 1.43 - 2.12: 10 2.12 - 2.82: 3158 2.82 - 3.51: 14433 3.51 - 4.21: 23971 4.21 - 4.90: 43135 Nonbonded interactions: 84707 Sorted by model distance: nonbonded pdb=" O CYS I 462 " pdb=" CD2 LEU I 466 " model vdw 1.431 3.460 nonbonded pdb=" NH1 ARG W 64 " pdb=" O ALA W 80 " model vdw 1.475 3.120 nonbonded pdb=" OG1 THR I 656 " pdb=" O GLY I 685 " model vdw 1.769 3.040 nonbonded pdb=" SD MET I 1 " pdb=" CZ TYR I 38 " model vdw 1.852 3.620 nonbonded pdb=" NH1 ARG W 64 " pdb=" C ALA W 80 " model vdw 1.891 3.350 ... (remaining 84702 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 26.740 Find NCS groups from input model: 0.130 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:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 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 0.079 10480 Z= 0.220 Angle : 0.726 12.266 14178 Z= 0.468 Chirality : 0.046 0.365 1649 Planarity : 0.004 0.062 1781 Dihedral : 13.184 89.096 3946 Min Nonbonded Distance : 1.431 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.99 % Favored : 90.37 % Rotamer: Outliers : 2.97 % Allowed : 8.41 % Favored : 88.62 % Cbeta Deviations : 0.08 % 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: -3.18 (0.21), residues: 1246 helix: -1.25 (0.16), residues: 839 sheet: None (None), residues: 0 loop : -3.87 (0.25), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 136 HIS 0.005 0.001 HIS H 41 PHE 0.016 0.001 PHE I 660 TYR 0.014 0.001 TYR I 281 ARG 0.004 0.000 ARG I 395 Details of bonding type rmsd hydrogen bonds : bond 0.16295 ( 554) hydrogen bonds : angle 6.43979 ( 1632) covalent geometry : bond 0.00392 (10479) covalent geometry : angle 0.72644 (14178) Misc. bond : bond 0.07941 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 206 time to evaluate : 1.101 Fit side-chains revert: symmetry clash REVERT: H 17 LYS cc_start: 0.8284 (tttm) cc_final: 0.8070 (ttmm) REVERT: I 65 TYR cc_start: 0.8059 (t80) cc_final: 0.7610 (t80) REVERT: I 108 SER cc_start: 0.8377 (t) cc_final: 0.8092 (p) REVERT: I 158 THR cc_start: 0.8401 (p) cc_final: 0.8002 (p) REVERT: I 256 ASP cc_start: 0.7803 (m-30) cc_final: 0.7521 (m-30) REVERT: I 260 SER cc_start: 0.8750 (p) cc_final: 0.8526 (m) REVERT: I 313 ASP cc_start: 0.7670 (t0) cc_final: 0.7019 (t70) REVERT: I 315 MET cc_start: 0.7342 (ptt) cc_final: 0.7058 (ptt) REVERT: I 489 MET cc_start: 0.8719 (mmp) cc_final: 0.8349 (mmp) REVERT: I 521 GLN cc_start: 0.7902 (tp40) cc_final: 0.7104 (tm-30) REVERT: I 586 MET cc_start: 0.7884 (tpp) cc_final: 0.7592 (tpt) REVERT: W 41 ASN cc_start: 0.8673 (m110) cc_final: 0.8385 (m-40) outliers start: 35 outliers final: 11 residues processed: 234 average time/residue: 0.2347 time to fit residues: 75.9998 Evaluate side-chains 160 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 291 TRP Chi-restraints excluded: chain I residue 484 THR Chi-restraints excluded: chain I residue 509 THR Chi-restraints excluded: chain I residue 513 ILE Chi-restraints excluded: chain I residue 618 LEU Chi-restraints excluded: chain I residue 686 TRP Chi-restraints excluded: chain I residue 725 LEU Chi-restraints excluded: chain K residue 140 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 59 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 19 HIS H 39 HIS H 60 GLN H 102 GLN H 107 GLN I 46 GLN I 107 GLN I 116 HIS ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 221 HIS I 276 GLN I 305 GLN I 371 GLN I 398 GLN I 543 ASN I 703 HIS K 100 GLN K 212 ASN W 38 GLN W 77 HIS W 83 GLN T 280 HIS T 302 GLN T 322 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.165021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.129849 restraints weight = 12914.444| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.86 r_work: 0.3329 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10480 Z= 0.136 Angle : 0.600 9.158 14178 Z= 0.311 Chirality : 0.040 0.219 1649 Planarity : 0.004 0.052 1781 Dihedral : 6.002 69.091 1367 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 2.72 % Allowed : 11.64 % Favored : 85.64 % 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: -1.58 (0.24), residues: 1246 helix: -0.00 (0.18), residues: 853 sheet: None (None), residues: 0 loop : -3.42 (0.27), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP T 298 HIS 0.004 0.001 HIS T 280 PHE 0.013 0.001 PHE K 62 TYR 0.022 0.001 TYR I 76 ARG 0.004 0.000 ARG I 240 Details of bonding type rmsd hydrogen bonds : bond 0.03963 ( 554) hydrogen bonds : angle 4.07074 ( 1632) covalent geometry : bond 0.00313 (10479) covalent geometry : angle 0.59978 (14178) Misc. bond : bond 0.00107 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 168 time to evaluate : 1.475 Fit side-chains REVERT: H 17 LYS cc_start: 0.8491 (tttm) cc_final: 0.8246 (ttmm) REVERT: I 65 TYR cc_start: 0.8399 (t80) cc_final: 0.8164 (t80) REVERT: I 108 SER cc_start: 0.8541 (t) cc_final: 0.8260 (p) REVERT: I 256 ASP cc_start: 0.8329 (m-30) cc_final: 0.8090 (m-30) REVERT: I 317 LYS cc_start: 0.7998 (mtmt) cc_final: 0.7597 (pttp) REVERT: I 420 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8775 (mp) REVERT: I 586 MET cc_start: 0.8860 (tpp) cc_final: 0.8657 (tpt) REVERT: I 633 ILE cc_start: 0.8781 (tt) cc_final: 0.8510 (pt) REVERT: I 695 ASP cc_start: 0.8574 (m-30) cc_final: 0.8303 (m-30) REVERT: K 30 GLN cc_start: 0.8380 (tp40) cc_final: 0.8176 (tp-100) REVERT: K 84 GLN cc_start: 0.8523 (tm-30) cc_final: 0.8252 (tt0) REVERT: K 128 MET cc_start: 0.7098 (tmm) cc_final: 0.6830 (tmm) REVERT: K 229 LYS cc_start: 0.7594 (OUTLIER) cc_final: 0.7286 (mmmt) REVERT: K 232 ASP cc_start: 0.8715 (p0) cc_final: 0.8342 (t0) REVERT: K 235 GLU cc_start: 0.7776 (tp30) cc_final: 0.7554 (tp30) REVERT: W 41 ASN cc_start: 0.8666 (m110) cc_final: 0.8390 (m110) REVERT: W 51 GLN cc_start: 0.7932 (tt0) cc_final: 0.7699 (mt0) REVERT: W 83 GLN cc_start: 0.6891 (OUTLIER) cc_final: 0.6067 (pp30) outliers start: 32 outliers final: 14 residues processed: 194 average time/residue: 0.2452 time to fit residues: 69.0642 Evaluate side-chains 158 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 141 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 91 THR Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 466 LEU Chi-restraints excluded: chain I residue 473 VAL Chi-restraints excluded: chain I residue 509 THR Chi-restraints excluded: chain I residue 686 TRP Chi-restraints excluded: chain I residue 722 LEU Chi-restraints excluded: chain I residue 725 LEU Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 229 LYS Chi-restraints excluded: chain W residue 83 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 101 optimal weight: 9.9990 chunk 69 optimal weight: 0.0770 chunk 110 optimal weight: 0.9980 chunk 72 optimal weight: 4.9990 chunk 10 optimal weight: 0.0000 chunk 50 optimal weight: 0.0870 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 4.9990 chunk 89 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 overall best weight: 0.4120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 88 ASN I 46 GLN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 GLN K 49 ASN K 100 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.167437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.132012 restraints weight = 13057.217| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 1.89 r_work: 0.3360 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10480 Z= 0.111 Angle : 0.548 8.517 14178 Z= 0.285 Chirality : 0.039 0.181 1649 Planarity : 0.004 0.050 1781 Dihedral : 5.257 39.800 1357 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 2.80 % Allowed : 13.34 % Favored : 83.86 % 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: -0.76 (0.24), residues: 1246 helix: 0.59 (0.18), residues: 857 sheet: None (None), residues: 0 loop : -3.08 (0.29), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP T 298 HIS 0.004 0.001 HIS H 41 PHE 0.017 0.001 PHE K 62 TYR 0.013 0.001 TYR I 76 ARG 0.004 0.000 ARG I 240 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 554) hydrogen bonds : angle 3.75403 ( 1632) covalent geometry : bond 0.00243 (10479) covalent geometry : angle 0.54810 (14178) Misc. bond : bond 0.00117 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 163 time to evaluate : 1.423 Fit side-chains REVERT: H 17 LYS cc_start: 0.8495 (tttm) cc_final: 0.8253 (ttmm) REVERT: H 39 HIS cc_start: 0.7630 (m90) cc_final: 0.7346 (m170) REVERT: H 154 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8390 (t) REVERT: I 108 SER cc_start: 0.8518 (t) cc_final: 0.8256 (p) REVERT: I 535 LEU cc_start: 0.8625 (OUTLIER) cc_final: 0.8296 (mp) REVERT: I 695 ASP cc_start: 0.8550 (m-30) cc_final: 0.8273 (m-30) REVERT: K 84 GLN cc_start: 0.8473 (tm-30) cc_final: 0.8229 (tt0) REVERT: K 147 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7479 (mp0) REVERT: K 229 LYS cc_start: 0.7642 (OUTLIER) cc_final: 0.7334 (mmmt) REVERT: K 232 ASP cc_start: 0.8738 (p0) cc_final: 0.8274 (t0) REVERT: W 41 ASN cc_start: 0.8535 (m110) cc_final: 0.8214 (m110) REVERT: W 51 GLN cc_start: 0.7810 (tt0) cc_final: 0.7605 (mt0) outliers start: 33 outliers final: 15 residues processed: 186 average time/residue: 0.2901 time to fit residues: 77.8427 Evaluate side-chains 163 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 144 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 276 GLN Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 473 VAL Chi-restraints excluded: chain I residue 509 THR Chi-restraints excluded: chain I residue 535 LEU Chi-restraints excluded: chain I residue 618 LEU Chi-restraints excluded: chain I residue 686 TRP Chi-restraints excluded: chain I residue 722 LEU Chi-restraints excluded: chain I residue 725 LEU Chi-restraints excluded: chain K residue 126 THR Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 229 LYS Chi-restraints excluded: chain T residue 327 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 4.9990 chunk 43 optimal weight: 0.3980 chunk 105 optimal weight: 0.9980 chunk 117 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 GLN ** I 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.164750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.128599 restraints weight = 13002.515| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 2.01 r_work: 0.3308 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3171 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 10480 Z= 0.142 Angle : 0.564 10.648 14178 Z= 0.291 Chirality : 0.040 0.150 1649 Planarity : 0.004 0.043 1781 Dihedral : 5.271 39.686 1356 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 3.65 % Allowed : 13.17 % Favored : 83.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.25), residues: 1246 helix: 0.78 (0.18), residues: 859 sheet: None (None), residues: 0 loop : -2.90 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 113 HIS 0.004 0.001 HIS H 41 PHE 0.020 0.001 PHE K 62 TYR 0.015 0.001 TYR H 34 ARG 0.004 0.000 ARG I 240 Details of bonding type rmsd hydrogen bonds : bond 0.03669 ( 554) hydrogen bonds : angle 3.71663 ( 1632) covalent geometry : bond 0.00339 (10479) covalent geometry : angle 0.56446 (14178) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 147 time to evaluate : 1.057 Fit side-chains REVERT: H 17 LYS cc_start: 0.8554 (tttm) cc_final: 0.8293 (ttmm) REVERT: H 154 VAL cc_start: 0.8734 (OUTLIER) cc_final: 0.8357 (t) REVERT: H 157 GLU cc_start: 0.7698 (tt0) cc_final: 0.7480 (tm-30) REVERT: I 108 SER cc_start: 0.8578 (t) cc_final: 0.8280 (p) REVERT: I 276 GLN cc_start: 0.4485 (OUTLIER) cc_final: 0.2609 (mp10) REVERT: I 420 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8788 (mp) REVERT: I 549 ASP cc_start: 0.7978 (t70) cc_final: 0.7750 (t70) REVERT: I 695 ASP cc_start: 0.8552 (m-30) cc_final: 0.8286 (m-30) REVERT: K 58 ARG cc_start: 0.7994 (ttm170) cc_final: 0.7375 (ttp80) REVERT: K 128 MET cc_start: 0.7337 (ttp) cc_final: 0.6380 (tmm) REVERT: K 147 GLU cc_start: 0.7765 (OUTLIER) cc_final: 0.7524 (mp0) REVERT: K 229 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7335 (mmmt) REVERT: K 232 ASP cc_start: 0.8772 (p0) cc_final: 0.8269 (t0) REVERT: W 41 ASN cc_start: 0.8504 (m110) cc_final: 0.8179 (m110) outliers start: 43 outliers final: 18 residues processed: 182 average time/residue: 0.2341 time to fit residues: 60.8882 Evaluate side-chains 157 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 276 GLN Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 473 VAL Chi-restraints excluded: chain I residue 509 THR Chi-restraints excluded: chain I residue 618 LEU Chi-restraints excluded: chain I residue 686 TRP Chi-restraints excluded: chain I residue 722 LEU Chi-restraints excluded: chain I residue 725 LEU Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 126 THR Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain K residue 229 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 39 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 58 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 68 optimal weight: 4.9990 chunk 31 optimal weight: 0.1980 chunk 119 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 46 GLN I 129 HIS ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 GLN ** I 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 176 ASN W 51 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.167437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.131374 restraints weight = 12996.086| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.03 r_work: 0.3313 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10480 Z= 0.127 Angle : 0.564 10.770 14178 Z= 0.286 Chirality : 0.039 0.176 1649 Planarity : 0.003 0.042 1781 Dihedral : 5.237 39.335 1356 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.35 % Favored : 91.65 % Rotamer: Outliers : 3.65 % Allowed : 14.19 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.25), residues: 1246 helix: 0.94 (0.18), residues: 867 sheet: None (None), residues: 0 loop : -2.80 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 113 HIS 0.006 0.001 HIS H 39 PHE 0.018 0.001 PHE K 62 TYR 0.016 0.001 TYR I 38 ARG 0.006 0.000 ARG I 236 Details of bonding type rmsd hydrogen bonds : bond 0.03542 ( 554) hydrogen bonds : angle 3.67730 ( 1632) covalent geometry : bond 0.00297 (10479) covalent geometry : angle 0.56370 (14178) Misc. bond : bond 0.00015 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 144 time to evaluate : 1.133 Fit side-chains REVERT: H 17 LYS cc_start: 0.8548 (tttm) cc_final: 0.7970 (ttmm) REVERT: H 21 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7803 (mp0) REVERT: H 154 VAL cc_start: 0.8751 (OUTLIER) cc_final: 0.8388 (t) REVERT: H 157 GLU cc_start: 0.7684 (tt0) cc_final: 0.7481 (tm-30) REVERT: I 108 SER cc_start: 0.8592 (t) cc_final: 0.8300 (p) REVERT: I 276 GLN cc_start: 0.4072 (OUTLIER) cc_final: 0.2355 (mp10) REVERT: I 420 ILE cc_start: 0.9161 (OUTLIER) cc_final: 0.8782 (mp) REVERT: I 535 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8321 (mp) REVERT: I 549 ASP cc_start: 0.7929 (t70) cc_final: 0.7704 (t70) REVERT: I 695 ASP cc_start: 0.8553 (m-30) cc_final: 0.8284 (m-30) REVERT: K 58 ARG cc_start: 0.7970 (ttm170) cc_final: 0.7363 (ttp80) REVERT: K 128 MET cc_start: 0.7346 (ttp) cc_final: 0.6462 (tmm) REVERT: K 147 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: K 229 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7320 (mmmt) REVERT: K 232 ASP cc_start: 0.8781 (p0) cc_final: 0.8252 (t0) REVERT: W 41 ASN cc_start: 0.8457 (m110) cc_final: 0.8096 (m-40) outliers start: 43 outliers final: 21 residues processed: 180 average time/residue: 0.2694 time to fit residues: 70.2696 Evaluate side-chains 165 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 1.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain I residue 276 GLN Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 473 VAL Chi-restraints excluded: chain I residue 509 THR Chi-restraints excluded: chain I residue 535 LEU Chi-restraints excluded: chain I residue 618 LEU Chi-restraints excluded: chain I residue 686 TRP Chi-restraints excluded: chain I residue 722 LEU Chi-restraints excluded: chain I residue 725 LEU Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 126 THR Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain K residue 229 LYS Chi-restraints excluded: chain T residue 327 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 118 optimal weight: 5.9990 chunk 61 optimal weight: 0.5980 chunk 113 optimal weight: 8.9990 chunk 102 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 72 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 46 GLN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 GLN ** I 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.163729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.127308 restraints weight = 12960.411| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 1.97 r_work: 0.3294 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3160 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10480 Z= 0.135 Angle : 0.566 11.158 14178 Z= 0.289 Chirality : 0.040 0.154 1649 Planarity : 0.003 0.041 1781 Dihedral : 5.227 38.673 1356 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 3.91 % Allowed : 13.85 % Favored : 82.24 % 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 (0.25), residues: 1246 helix: 1.06 (0.18), residues: 867 sheet: None (None), residues: 0 loop : -2.74 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 113 HIS 0.005 0.001 HIS H 39 PHE 0.021 0.001 PHE T 311 TYR 0.014 0.001 TYR I 38 ARG 0.006 0.000 ARG I 240 Details of bonding type rmsd hydrogen bonds : bond 0.03549 ( 554) hydrogen bonds : angle 3.64444 ( 1632) covalent geometry : bond 0.00322 (10479) covalent geometry : angle 0.56647 (14178) Misc. bond : bond 0.00005 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 144 time to evaluate : 1.114 Fit side-chains REVERT: H 154 VAL cc_start: 0.8731 (OUTLIER) cc_final: 0.8381 (t) REVERT: I 76 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.8031 (m-80) REVERT: I 108 SER cc_start: 0.8566 (t) cc_final: 0.8261 (p) REVERT: I 276 GLN cc_start: 0.4167 (OUTLIER) cc_final: 0.2667 (mp10) REVERT: I 420 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8789 (mp) REVERT: I 535 LEU cc_start: 0.8633 (OUTLIER) cc_final: 0.8295 (mp) REVERT: I 549 ASP cc_start: 0.7875 (t70) cc_final: 0.7641 (t70) REVERT: I 695 ASP cc_start: 0.8559 (m-30) cc_final: 0.8297 (m-30) REVERT: K 58 ARG cc_start: 0.7945 (ttm170) cc_final: 0.7400 (ttp80) REVERT: K 128 MET cc_start: 0.7346 (ttp) cc_final: 0.6471 (tmm) REVERT: K 147 GLU cc_start: 0.7778 (OUTLIER) cc_final: 0.7530 (mp0) REVERT: K 229 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7349 (mmmt) REVERT: K 232 ASP cc_start: 0.8779 (p0) cc_final: 0.8241 (t0) REVERT: W 41 ASN cc_start: 0.8460 (m110) cc_final: 0.8145 (m-40) outliers start: 46 outliers final: 23 residues processed: 184 average time/residue: 0.2135 time to fit residues: 56.6297 Evaluate side-chains 168 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 138 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain I residue 276 GLN Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain I residue 378 VAL Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 509 THR Chi-restraints excluded: chain I residue 535 LEU Chi-restraints excluded: chain I residue 618 LEU Chi-restraints excluded: chain I residue 686 TRP Chi-restraints excluded: chain I residue 722 LEU Chi-restraints excluded: chain I residue 725 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain K residue 229 LYS Chi-restraints excluded: chain K residue 239 THR Chi-restraints excluded: chain T residue 327 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 47 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 chunk 121 optimal weight: 0.0670 chunk 8 optimal weight: 0.8980 chunk 88 optimal weight: 0.6980 chunk 108 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 55 optimal weight: 0.6980 chunk 22 optimal weight: 0.2980 chunk 56 optimal weight: 0.8980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 46 GLN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 GLN ** I 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.167182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.130061 restraints weight = 13125.449| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.09 r_work: 0.3333 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3205 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3205 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10480 Z= 0.112 Angle : 0.562 10.141 14178 Z= 0.286 Chirality : 0.039 0.151 1649 Planarity : 0.003 0.041 1781 Dihedral : 5.089 37.958 1356 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.95 % Favored : 92.05 % Rotamer: Outliers : 3.14 % Allowed : 15.29 % Favored : 81.56 % 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: 0.18 (0.25), residues: 1246 helix: 1.25 (0.19), residues: 863 sheet: None (None), residues: 0 loop : -2.63 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 291 HIS 0.006 0.001 HIS H 39 PHE 0.017 0.001 PHE K 62 TYR 0.015 0.001 TYR I 38 ARG 0.007 0.000 ARG I 240 Details of bonding type rmsd hydrogen bonds : bond 0.03379 ( 554) hydrogen bonds : angle 3.60495 ( 1632) covalent geometry : bond 0.00254 (10479) covalent geometry : angle 0.56213 (14178) Misc. bond : bond 0.00011 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 147 time to evaluate : 1.245 Fit side-chains REVERT: H 21 GLU cc_start: 0.8211 (mm-30) cc_final: 0.7764 (mp0) REVERT: H 154 VAL cc_start: 0.8668 (OUTLIER) cc_final: 0.8348 (t) REVERT: I 76 TYR cc_start: 0.8534 (OUTLIER) cc_final: 0.8009 (m-80) REVERT: I 108 SER cc_start: 0.8559 (t) cc_final: 0.8269 (p) REVERT: I 276 GLN cc_start: 0.3700 (OUTLIER) cc_final: 0.2616 (mp10) REVERT: I 420 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8768 (mp) REVERT: I 535 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8303 (mp) REVERT: I 549 ASP cc_start: 0.7793 (t70) cc_final: 0.7557 (t70) REVERT: I 695 ASP cc_start: 0.8522 (m-30) cc_final: 0.8261 (m-30) REVERT: K 49 ASN cc_start: 0.7293 (p0) cc_final: 0.7011 (m-40) REVERT: K 58 ARG cc_start: 0.7896 (ttm170) cc_final: 0.7338 (ttp80) REVERT: K 128 MET cc_start: 0.7246 (ttp) cc_final: 0.6654 (tmm) REVERT: K 147 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7534 (mp0) REVERT: K 229 LYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7352 (mmmt) REVERT: K 232 ASP cc_start: 0.8781 (p0) cc_final: 0.8230 (t0) REVERT: W 41 ASN cc_start: 0.8468 (m110) cc_final: 0.8180 (m-40) outliers start: 37 outliers final: 22 residues processed: 177 average time/residue: 0.2183 time to fit residues: 55.9536 Evaluate side-chains 168 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 139 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 276 GLN Chi-restraints excluded: chain I residue 378 VAL Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 509 THR Chi-restraints excluded: chain I residue 535 LEU Chi-restraints excluded: chain I residue 618 LEU Chi-restraints excluded: chain I residue 622 THR Chi-restraints excluded: chain I residue 686 TRP Chi-restraints excluded: chain I residue 722 LEU Chi-restraints excluded: chain I residue 725 LEU Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 229 LYS Chi-restraints excluded: chain K residue 239 THR Chi-restraints excluded: chain T residue 327 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 82 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 62 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 63 optimal weight: 0.0980 chunk 81 optimal weight: 5.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 GLN ** I 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 195 ASN W 41 ASN W 51 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.166335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.128677 restraints weight = 13086.032| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 2.07 r_work: 0.3294 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10480 Z= 0.131 Angle : 0.574 10.757 14178 Z= 0.291 Chirality : 0.040 0.152 1649 Planarity : 0.003 0.040 1781 Dihedral : 5.108 38.658 1356 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 3.40 % Allowed : 15.21 % Favored : 81.39 % 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: 0.24 (0.25), residues: 1246 helix: 1.31 (0.19), residues: 863 sheet: None (None), residues: 0 loop : -2.63 (0.30), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 113 HIS 0.005 0.001 HIS H 39 PHE 0.026 0.001 PHE T 311 TYR 0.016 0.001 TYR H 34 ARG 0.007 0.000 ARG I 240 Details of bonding type rmsd hydrogen bonds : bond 0.03493 ( 554) hydrogen bonds : angle 3.61183 ( 1632) covalent geometry : bond 0.00312 (10479) covalent geometry : angle 0.57383 (14178) Misc. bond : bond 0.00000 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 145 time to evaluate : 2.154 Fit side-chains REVERT: H 21 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7800 (mp0) REVERT: H 154 VAL cc_start: 0.8645 (OUTLIER) cc_final: 0.8383 (t) REVERT: I 76 TYR cc_start: 0.8593 (OUTLIER) cc_final: 0.7991 (m-80) REVERT: I 108 SER cc_start: 0.8598 (t) cc_final: 0.8302 (p) REVERT: I 276 GLN cc_start: 0.3616 (OUTLIER) cc_final: 0.2927 (mp10) REVERT: I 420 ILE cc_start: 0.9165 (OUTLIER) cc_final: 0.8784 (mp) REVERT: I 535 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8302 (mp) REVERT: I 549 ASP cc_start: 0.7864 (t70) cc_final: 0.7629 (t70) REVERT: I 695 ASP cc_start: 0.8584 (m-30) cc_final: 0.8328 (m-30) REVERT: K 5 LYS cc_start: 0.6426 (pttm) cc_final: 0.5819 (mttm) REVERT: K 58 ARG cc_start: 0.7936 (ttm170) cc_final: 0.7296 (ttp80) REVERT: K 61 MET cc_start: 0.8463 (mtm) cc_final: 0.8141 (mtt) REVERT: K 128 MET cc_start: 0.7367 (ttp) cc_final: 0.6689 (tmm) REVERT: K 147 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: K 229 LYS cc_start: 0.7670 (OUTLIER) cc_final: 0.7382 (mmmt) REVERT: K 232 ASP cc_start: 0.8801 (p0) cc_final: 0.8236 (t0) REVERT: W 41 ASN cc_start: 0.8394 (m-40) cc_final: 0.8105 (m-40) outliers start: 40 outliers final: 24 residues processed: 178 average time/residue: 0.2644 time to fit residues: 67.7920 Evaluate side-chains 171 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 1.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 276 GLN Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain I residue 378 VAL Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 509 THR Chi-restraints excluded: chain I residue 535 LEU Chi-restraints excluded: chain I residue 618 LEU Chi-restraints excluded: chain I residue 622 THR Chi-restraints excluded: chain I residue 686 TRP Chi-restraints excluded: chain I residue 722 LEU Chi-restraints excluded: chain I residue 725 LEU Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 195 ASN Chi-restraints excluded: chain K residue 229 LYS Chi-restraints excluded: chain K residue 239 THR Chi-restraints excluded: chain T residue 327 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 91 optimal weight: 6.9990 chunk 70 optimal weight: 0.6980 chunk 115 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 93 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 60 optimal weight: 0.0050 chunk 110 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 46 GLN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 GLN ** I 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 195 ASN W 51 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.167508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.130290 restraints weight = 13038.193| |-----------------------------------------------------------------------------| r_work (start): 0.3493 rms_B_bonded: 2.08 r_work: 0.3320 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10480 Z= 0.115 Angle : 0.574 9.702 14178 Z= 0.292 Chirality : 0.040 0.151 1649 Planarity : 0.003 0.041 1781 Dihedral : 5.028 38.178 1356 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.80 % Allowed : 15.80 % Favored : 81.39 % 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: 0.36 (0.25), residues: 1246 helix: 1.41 (0.19), residues: 862 sheet: None (None), residues: 0 loop : -2.61 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 291 HIS 0.005 0.001 HIS H 39 PHE 0.017 0.001 PHE K 62 TYR 0.015 0.001 TYR H 34 ARG 0.007 0.000 ARG I 240 Details of bonding type rmsd hydrogen bonds : bond 0.03378 ( 554) hydrogen bonds : angle 3.60752 ( 1632) covalent geometry : bond 0.00261 (10479) covalent geometry : angle 0.57367 (14178) Misc. bond : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 1.630 Fit side-chains REVERT: H 21 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7765 (mp0) REVERT: I 76 TYR cc_start: 0.8519 (OUTLIER) cc_final: 0.7999 (m-80) REVERT: I 108 SER cc_start: 0.8589 (t) cc_final: 0.8295 (p) REVERT: I 276 GLN cc_start: 0.3679 (OUTLIER) cc_final: 0.3184 (mp10) REVERT: I 420 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8768 (mp) REVERT: I 535 LEU cc_start: 0.8588 (OUTLIER) cc_final: 0.8277 (mp) REVERT: I 549 ASP cc_start: 0.7844 (t70) cc_final: 0.7603 (t70) REVERT: I 695 ASP cc_start: 0.8531 (m-30) cc_final: 0.8269 (m-30) REVERT: K 5 LYS cc_start: 0.6385 (pttm) cc_final: 0.5882 (mttm) REVERT: K 58 ARG cc_start: 0.7911 (ttm170) cc_final: 0.7263 (ttp80) REVERT: K 61 MET cc_start: 0.8418 (mtm) cc_final: 0.8125 (mtt) REVERT: K 147 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: K 229 LYS cc_start: 0.7640 (OUTLIER) cc_final: 0.7353 (mmmt) REVERT: K 232 ASP cc_start: 0.8806 (p0) cc_final: 0.8219 (t0) outliers start: 33 outliers final: 22 residues processed: 171 average time/residue: 0.3538 time to fit residues: 88.2901 Evaluate side-chains 170 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 142 time to evaluate : 1.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 276 GLN Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain I residue 378 VAL Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 509 THR Chi-restraints excluded: chain I residue 535 LEU Chi-restraints excluded: chain I residue 686 TRP Chi-restraints excluded: chain I residue 722 LEU Chi-restraints excluded: chain I residue 725 LEU Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 229 LYS Chi-restraints excluded: chain T residue 327 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 1.9990 chunk 61 optimal weight: 0.0010 chunk 87 optimal weight: 0.0000 chunk 97 optimal weight: 0.0870 chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 1 optimal weight: 0.8980 chunk 77 optimal weight: 0.0020 chunk 59 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 40 optimal weight: 0.5980 overall best weight: 0.0776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.169485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.132942 restraints weight = 13186.377| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.99 r_work: 0.3358 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 10480 Z= 0.108 Angle : 0.571 9.288 14178 Z= 0.288 Chirality : 0.039 0.202 1649 Planarity : 0.003 0.040 1781 Dihedral : 4.820 37.358 1356 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.70 % Favored : 92.30 % Rotamer: Outliers : 2.29 % Allowed : 15.97 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1246 helix: 1.57 (0.19), residues: 861 sheet: None (None), residues: 0 loop : -2.56 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP I 291 HIS 0.004 0.000 HIS H 39 PHE 0.030 0.001 PHE T 311 TYR 0.015 0.001 TYR H 34 ARG 0.007 0.000 ARG I 240 Details of bonding type rmsd hydrogen bonds : bond 0.03152 ( 554) hydrogen bonds : angle 3.55393 ( 1632) covalent geometry : bond 0.00229 (10479) covalent geometry : angle 0.57062 (14178) Misc. bond : bond 0.00013 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 157 time to evaluate : 1.105 Fit side-chains REVERT: H 21 GLU cc_start: 0.7914 (mm-30) cc_final: 0.7545 (mp0) REVERT: I 76 TYR cc_start: 0.8230 (OUTLIER) cc_final: 0.7998 (m-80) REVERT: I 108 SER cc_start: 0.8415 (t) cc_final: 0.8113 (p) REVERT: I 216 LYS cc_start: 0.7417 (mttm) cc_final: 0.7203 (ttpt) REVERT: I 420 ILE cc_start: 0.9080 (OUTLIER) cc_final: 0.8678 (mp) REVERT: I 535 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8214 (mp) REVERT: I 549 ASP cc_start: 0.7617 (t70) cc_final: 0.7362 (t70) REVERT: I 595 ASN cc_start: 0.8442 (p0) cc_final: 0.7903 (p0) REVERT: I 695 ASP cc_start: 0.8309 (m-30) cc_final: 0.8052 (m-30) REVERT: K 5 LYS cc_start: 0.6572 (pttm) cc_final: 0.6109 (mttm) REVERT: K 58 ARG cc_start: 0.7743 (ttm170) cc_final: 0.7267 (ttp80) REVERT: K 61 MET cc_start: 0.8304 (mtm) cc_final: 0.8064 (mtt) REVERT: K 147 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7394 (mp0) REVERT: K 226 LYS cc_start: 0.7789 (OUTLIER) cc_final: 0.7347 (ptpp) REVERT: K 232 ASP cc_start: 0.8612 (p0) cc_final: 0.8101 (t0) REVERT: K 239 THR cc_start: 0.7704 (OUTLIER) cc_final: 0.7482 (t) REVERT: T 323 GLU cc_start: 0.5690 (pm20) cc_final: 0.4174 (tm-30) outliers start: 27 outliers final: 15 residues processed: 179 average time/residue: 0.2381 time to fit residues: 60.9140 Evaluate side-chains 167 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 146 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain I residue 51 LEU Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain I residue 378 VAL Chi-restraints excluded: chain I residue 385 VAL Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 535 LEU Chi-restraints excluded: chain I residue 622 THR Chi-restraints excluded: chain I residue 686 TRP Chi-restraints excluded: chain I residue 722 LEU Chi-restraints excluded: chain K residue 33 ILE Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 226 LYS Chi-restraints excluded: chain K residue 239 THR Chi-restraints excluded: chain T residue 327 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 110 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 27 optimal weight: 0.1980 chunk 88 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 53 optimal weight: 0.0770 overall best weight: 0.7740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 41 ASN ** W 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.164790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.128089 restraints weight = 13008.740| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 2.12 r_work: 0.3301 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10480 Z= 0.128 Angle : 0.615 14.519 14178 Z= 0.304 Chirality : 0.041 0.203 1649 Planarity : 0.004 0.054 1781 Dihedral : 4.803 38.723 1353 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 2.55 % Allowed : 16.23 % Favored : 81.22 % 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: 0.54 (0.25), residues: 1246 helix: 1.56 (0.19), residues: 860 sheet: None (None), residues: 0 loop : -2.55 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 113 HIS 0.007 0.001 HIS H 39 PHE 0.018 0.001 PHE K 62 TYR 0.018 0.001 TYR H 34 ARG 0.008 0.000 ARG I 240 Details of bonding type rmsd hydrogen bonds : bond 0.03407 ( 554) hydrogen bonds : angle 3.58123 ( 1632) covalent geometry : bond 0.00302 (10479) covalent geometry : angle 0.61514 (14178) Misc. bond : bond 0.00004 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6956.32 seconds wall clock time: 127 minutes 46.06 seconds (7666.06 seconds total)