Starting phenix.real_space_refine on Wed Sep 17 18:42:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6wuc_21910/09_2025/6wuc_21910.cif Found real_map, /net/cci-nas-00/data/ceres_data/6wuc_21910/09_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_21910/09_2025/6wuc_21910.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6wuc_21910/09_2025/6wuc_21910.map" model { file = "/net/cci-nas-00/data/ceres_data/6wuc_21910/09_2025/6wuc_21910.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6wuc_21910/09_2025/6wuc_21910.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.40, per 1000 atoms: 0.23 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: 0.86 Conformation dependent library (CDL) restraints added in 302.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.26 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: 1.32 Time building geometry restraints manager: 1.11 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: 2.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 10.100 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.810 ------------------------------------------------------------------------------- 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 : 17.85 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.004 0.000 ARG I 395 TYR 0.014 0.001 TYR I 281 PHE 0.016 0.001 PHE I 660 TRP 0.007 0.001 TRP I 136 HIS 0.005 0.001 HIS H 41 Details of bonding type rmsd covalent geometry : bond 0.00392 (10479) covalent geometry : angle 0.72644 (14178) hydrogen bonds : bond 0.16295 ( 554) hydrogen bonds : angle 6.43979 ( 1632) 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 : 0.368 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: 0.1048 time to fit residues: 33.8870 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 : 0.346 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 123 optimal weight: 0.6980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** 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 390 ASN 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 T 335 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.161794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.125823 restraints weight = 13126.745| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 2.03 r_work: 0.3287 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3154 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10480 Z= 0.155 Angle : 0.618 10.342 14178 Z= 0.320 Chirality : 0.041 0.222 1649 Planarity : 0.004 0.051 1781 Dihedral : 6.079 71.160 1367 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 2.80 % Allowed : 11.98 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.67 (0.23), residues: 1246 helix: -0.08 (0.18), residues: 856 sheet: None (None), residues: 0 loop : -3.45 (0.28), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 240 TYR 0.025 0.001 TYR I 76 PHE 0.012 0.001 PHE I 660 TRP 0.010 0.001 TRP T 298 HIS 0.004 0.001 HIS H 41 Details of bonding type rmsd covalent geometry : bond 0.00366 (10479) covalent geometry : angle 0.61800 (14178) hydrogen bonds : bond 0.04187 ( 554) hydrogen bonds : angle 4.12893 ( 1632) Misc. bond : bond 0.00095 ( 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 199 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 166 time to evaluate : 0.443 Fit side-chains REVERT: H 17 LYS cc_start: 0.8449 (tttm) cc_final: 0.8194 (ttmm) REVERT: I 65 TYR cc_start: 0.8415 (t80) cc_final: 0.8181 (t80) REVERT: I 108 SER cc_start: 0.8615 (t) cc_final: 0.8310 (p) REVERT: I 173 ARG cc_start: 0.8571 (ttm170) cc_final: 0.8355 (ttm110) REVERT: I 256 ASP cc_start: 0.8336 (m-30) cc_final: 0.8062 (m-30) REVERT: I 317 LYS cc_start: 0.8101 (mtmt) cc_final: 0.7592 (pttp) REVERT: I 420 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8794 (mp) REVERT: I 633 ILE cc_start: 0.8789 (tt) cc_final: 0.8483 (pt) REVERT: I 695 ASP cc_start: 0.8539 (m-30) cc_final: 0.8306 (m-30) REVERT: K 84 GLN cc_start: 0.8525 (tm-30) cc_final: 0.8249 (tt0) REVERT: K 229 LYS cc_start: 0.7537 (OUTLIER) cc_final: 0.7234 (mmmt) REVERT: K 232 ASP cc_start: 0.8713 (p0) cc_final: 0.8334 (t0) REVERT: K 235 GLU cc_start: 0.7881 (tp30) cc_final: 0.7636 (tp30) REVERT: W 41 ASN cc_start: 0.8650 (m110) cc_final: 0.8362 (m-40) REVERT: W 83 GLN cc_start: 0.6916 (OUTLIER) cc_final: 0.6093 (pp30) outliers start: 33 outliers final: 13 residues processed: 194 average time/residue: 0.1018 time to fit residues: 28.1275 Evaluate side-chains 157 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.411 ------------------------------------------------------------------------------- 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 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 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 110 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 chunk 120 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 88 ASN H 107 GLN I 46 GLN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 GLN K 30 GLN K 100 GLN K 176 ASN W 51 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.164427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.127870 restraints weight = 13155.133| |-----------------------------------------------------------------------------| r_work (start): 0.3430 rms_B_bonded: 2.12 r_work: 0.3242 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10480 Z= 0.165 Angle : 0.604 12.523 14178 Z= 0.310 Chirality : 0.041 0.187 1649 Planarity : 0.004 0.047 1781 Dihedral : 5.572 40.069 1359 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 3.65 % Allowed : 12.66 % Favored : 83.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.05 (0.24), residues: 1246 helix: 0.34 (0.18), residues: 858 sheet: None (None), residues: 0 loop : -3.10 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 240 TYR 0.016 0.001 TYR I 76 PHE 0.019 0.002 PHE K 62 TRP 0.009 0.001 TRP T 298 HIS 0.004 0.001 HIS H 41 Details of bonding type rmsd covalent geometry : bond 0.00399 (10479) covalent geometry : angle 0.60400 (14178) hydrogen bonds : bond 0.04038 ( 554) hydrogen bonds : angle 3.91918 ( 1632) Misc. bond : bond 0.00073 ( 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: 43 poor density : 153 time to evaluate : 0.442 Fit side-chains REVERT: H 17 LYS cc_start: 0.8517 (tttm) cc_final: 0.8263 (ttmm) REVERT: H 34 TYR cc_start: 0.8708 (t80) cc_final: 0.8448 (t80) REVERT: I 65 TYR cc_start: 0.8451 (t80) cc_final: 0.8227 (t80) REVERT: I 108 SER cc_start: 0.8607 (t) cc_final: 0.8300 (p) REVERT: I 420 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8829 (mp) REVERT: I 466 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8607 (mm) REVERT: I 549 ASP cc_start: 0.8023 (t70) cc_final: 0.7800 (t70) REVERT: I 550 ASP cc_start: 0.8694 (p0) cc_final: 0.8428 (p0) REVERT: I 633 ILE cc_start: 0.8814 (tt) cc_final: 0.8607 (pt) REVERT: I 695 ASP cc_start: 0.8625 (m-30) cc_final: 0.8376 (m-30) REVERT: K 58 ARG cc_start: 0.7992 (ttm170) cc_final: 0.7303 (ttp80) REVERT: K 84 GLN cc_start: 0.8563 (tm-30) cc_final: 0.8262 (tt0) REVERT: K 147 GLU cc_start: 0.7818 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: K 229 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7289 (mmmt) REVERT: K 232 ASP cc_start: 0.8795 (p0) cc_final: 0.8367 (t0) REVERT: W 41 ASN cc_start: 0.8567 (m110) cc_final: 0.8215 (m-40) outliers start: 43 outliers final: 24 residues processed: 184 average time/residue: 0.0989 time to fit residues: 26.1300 Evaluate side-chains 172 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 144 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 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 466 LEU 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 54 THR Chi-restraints excluded: chain K residue 105 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 225 THR Chi-restraints excluded: chain K residue 229 LYS Chi-restraints excluded: chain K residue 236 THR 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 43 optimal weight: 0.0980 chunk 62 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 18 optimal weight: 0.0570 chunk 27 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 88 ASN ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 276 GLN ** I 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 49 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 = 0.3941 r_free = 0.3941 target = 0.168567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.132444 restraints weight = 13024.725| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.96 r_work: 0.3344 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.2154 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= 0.110 Angle : 0.545 10.997 14178 Z= 0.280 Chirality : 0.039 0.153 1649 Planarity : 0.003 0.044 1781 Dihedral : 5.272 38.425 1358 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 3.14 % Allowed : 13.76 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.25), residues: 1246 helix: 0.77 (0.18), residues: 860 sheet: None (None), residues: 0 loop : -2.90 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 240 TYR 0.015 0.001 TYR I 38 PHE 0.023 0.001 PHE T 311 TRP 0.008 0.001 TRP T 298 HIS 0.004 0.000 HIS H 41 Details of bonding type rmsd covalent geometry : bond 0.00242 (10479) covalent geometry : angle 0.54526 (14178) hydrogen bonds : bond 0.03493 ( 554) hydrogen bonds : angle 3.68214 ( 1632) Misc. bond : bond 0.00027 ( 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 198 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 161 time to evaluate : 0.348 Fit side-chains REVERT: H 17 LYS cc_start: 0.8497 (tttm) cc_final: 0.8233 (ttmm) REVERT: H 34 TYR cc_start: 0.8663 (t80) cc_final: 0.8408 (t80) REVERT: H 154 VAL cc_start: 0.8735 (OUTLIER) cc_final: 0.8383 (t) REVERT: H 157 GLU cc_start: 0.7706 (tt0) cc_final: 0.7467 (tm-30) REVERT: I 108 SER cc_start: 0.8545 (t) cc_final: 0.8255 (p) REVERT: I 549 ASP cc_start: 0.7934 (t70) cc_final: 0.7721 (t70) REVERT: I 695 ASP cc_start: 0.8534 (m-30) cc_final: 0.8260 (m-30) REVERT: K 58 ARG cc_start: 0.7921 (ttm170) cc_final: 0.7329 (ttp80) REVERT: K 84 GLN cc_start: 0.8497 (tm-30) cc_final: 0.8246 (tt0) REVERT: K 128 MET cc_start: 0.7416 (ttp) cc_final: 0.6475 (tmm) REVERT: K 147 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: K 229 LYS cc_start: 0.7631 (OUTLIER) cc_final: 0.7320 (mmmt) REVERT: K 232 ASP cc_start: 0.8734 (p0) cc_final: 0.8262 (t0) REVERT: W 41 ASN cc_start: 0.8523 (m110) cc_final: 0.8187 (m-40) outliers start: 37 outliers final: 13 residues processed: 191 average time/residue: 0.0913 time to fit residues: 25.1570 Evaluate side-chains 161 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 145 time to evaluate : 0.409 ------------------------------------------------------------------------------- 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 209 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 44 optimal weight: 0.0060 chunk 115 optimal weight: 6.9990 chunk 96 optimal weight: 1.9990 chunk 69 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 32 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 chunk 95 optimal weight: 0.8980 overall best weight: 1.1802 ------------------------------------------------------------------------------- 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 = 0.3875 r_free = 0.3875 target = 0.162298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.125195 restraints weight = 13024.324| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 2.04 r_work: 0.3273 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 10480 Z= 0.151 Angle : 0.588 12.379 14178 Z= 0.299 Chirality : 0.041 0.174 1649 Planarity : 0.004 0.043 1781 Dihedral : 5.330 39.266 1356 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 3.74 % Allowed : 13.68 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.28 (0.25), residues: 1246 helix: 0.90 (0.18), residues: 866 sheet: None (None), residues: 0 loop : -2.81 (0.30), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 240 TYR 0.015 0.001 TYR I 281 PHE 0.020 0.001 PHE K 62 TRP 0.008 0.001 TRP I 113 HIS 0.008 0.001 HIS H 39 Details of bonding type rmsd covalent geometry : bond 0.00365 (10479) covalent geometry : angle 0.58847 (14178) hydrogen bonds : bond 0.03768 ( 554) hydrogen bonds : angle 3.72033 ( 1632) Misc. bond : bond 0.00008 ( 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 193 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 149 time to evaluate : 0.418 Fit side-chains REVERT: H 17 LYS cc_start: 0.8524 (tttm) cc_final: 0.8264 (ttmm) REVERT: H 34 TYR cc_start: 0.8722 (t80) cc_final: 0.8472 (t80) REVERT: H 154 VAL cc_start: 0.8756 (OUTLIER) cc_final: 0.8374 (t) REVERT: H 157 GLU cc_start: 0.7744 (tt0) cc_final: 0.7504 (tm-30) REVERT: I 76 TYR cc_start: 0.8726 (OUTLIER) cc_final: 0.8081 (m-80) REVERT: I 108 SER cc_start: 0.8597 (t) cc_final: 0.8285 (p) REVERT: I 173 ARG cc_start: 0.8482 (ttm170) cc_final: 0.8209 (ttm110) REVERT: I 420 ILE cc_start: 0.9197 (OUTLIER) cc_final: 0.8824 (mp) REVERT: I 549 ASP cc_start: 0.7919 (t70) cc_final: 0.7701 (t70) REVERT: I 695 ASP cc_start: 0.8579 (m-30) cc_final: 0.8340 (m-30) REVERT: K 58 ARG cc_start: 0.7976 (ttm170) cc_final: 0.7414 (ttp80) REVERT: K 84 GLN cc_start: 0.8547 (tm-30) cc_final: 0.8274 (tt0) REVERT: K 128 MET cc_start: 0.7303 (ttp) cc_final: 0.6478 (tmm) REVERT: K 147 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7538 (mp0) REVERT: K 229 LYS cc_start: 0.7706 (OUTLIER) cc_final: 0.7354 (mmmt) REVERT: K 232 ASP cc_start: 0.8754 (p0) cc_final: 0.8287 (t0) REVERT: W 41 ASN cc_start: 0.8457 (m110) cc_final: 0.8104 (m-40) outliers start: 44 outliers final: 21 residues processed: 185 average time/residue: 0.1005 time to fit residues: 26.7406 Evaluate side-chains 168 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.415 ------------------------------------------------------------------------------- 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 76 TYR Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 211 ILE 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 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 Chi-restraints excluded: chain K residue 239 THR 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 96 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 70 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 120 optimal weight: 0.3980 chunk 46 optimal weight: 0.7980 chunk 14 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.164947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.128018 restraints weight = 13143.488| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 2.04 r_work: 0.3308 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3169 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3169 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10480 Z= 0.120 Angle : 0.564 11.008 14178 Z= 0.287 Chirality : 0.039 0.156 1649 Planarity : 0.003 0.041 1781 Dihedral : 5.188 38.002 1356 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 3.65 % Allowed : 14.36 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.03 (0.25), residues: 1246 helix: 1.08 (0.18), residues: 867 sheet: None (None), residues: 0 loop : -2.72 (0.30), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 240 TYR 0.014 0.001 TYR I 38 PHE 0.022 0.001 PHE T 311 TRP 0.007 0.001 TRP I 166 HIS 0.006 0.001 HIS H 39 Details of bonding type rmsd covalent geometry : bond 0.00278 (10479) covalent geometry : angle 0.56387 (14178) hydrogen bonds : bond 0.03469 ( 554) hydrogen bonds : angle 3.63912 ( 1632) Misc. bond : bond 0.00012 ( 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 196 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 153 time to evaluate : 0.463 Fit side-chains REVERT: H 17 LYS cc_start: 0.8502 (tttm) cc_final: 0.8251 (ttmm) REVERT: H 21 GLU cc_start: 0.8214 (mm-30) cc_final: 0.7927 (mp0) REVERT: H 34 TYR cc_start: 0.8674 (t80) cc_final: 0.8393 (t80) REVERT: H 154 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8373 (t) REVERT: I 76 TYR cc_start: 0.8670 (OUTLIER) cc_final: 0.8108 (m-80) REVERT: I 108 SER cc_start: 0.8578 (t) cc_final: 0.8273 (p) REVERT: I 173 ARG cc_start: 0.8461 (ttm170) cc_final: 0.8223 (ttm110) REVERT: I 420 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8802 (mp) REVERT: I 549 ASP cc_start: 0.7811 (t70) cc_final: 0.7581 (t70) REVERT: I 695 ASP cc_start: 0.8521 (m-30) cc_final: 0.8256 (m-30) REVERT: K 58 ARG cc_start: 0.7947 (ttm170) cc_final: 0.7390 (ttp80) REVERT: K 84 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8274 (tt0) REVERT: K 147 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: K 190 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8841 (tt) REVERT: K 229 LYS cc_start: 0.7651 (OUTLIER) cc_final: 0.7348 (mmmt) REVERT: K 232 ASP cc_start: 0.8785 (p0) cc_final: 0.8263 (t0) REVERT: W 41 ASN cc_start: 0.8446 (m110) cc_final: 0.8109 (m-40) outliers start: 43 outliers final: 20 residues processed: 188 average time/residue: 0.0949 time to fit residues: 25.8308 Evaluate side-chains 168 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.380 ------------------------------------------------------------------------------- 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 209 ILE Chi-restraints excluded: chain I residue 211 ILE 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 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 147 GLU Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 190 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 104 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 110 optimal weight: 0.2980 chunk 40 optimal weight: 0.9980 chunk 119 optimal weight: 8.9990 chunk 76 optimal weight: 0.4980 chunk 88 optimal weight: 0.9980 chunk 37 optimal weight: 0.0270 chunk 91 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 26 optimal weight: 0.8980 overall best weight: 0.4838 ------------------------------------------------------------------------------- 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 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 195 ASN W 51 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.167937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.131780 restraints weight = 12938.701| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 2.04 r_work: 0.3338 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.2622 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 : 0.564 9.875 14178 Z= 0.287 Chirality : 0.039 0.165 1649 Planarity : 0.003 0.045 1781 Dihedral : 5.060 38.145 1356 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 3.06 % Allowed : 15.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.19 (0.25), residues: 1246 helix: 1.27 (0.19), residues: 864 sheet: None (None), residues: 0 loop : -2.67 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 240 TYR 0.012 0.001 TYR I 281 PHE 0.015 0.001 PHE K 62 TRP 0.007 0.001 TRP I 291 HIS 0.005 0.001 HIS H 39 Details of bonding type rmsd covalent geometry : bond 0.00249 (10479) covalent geometry : angle 0.56422 (14178) hydrogen bonds : bond 0.03375 ( 554) hydrogen bonds : angle 3.59433 ( 1632) Misc. bond : bond 0.00010 ( 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: 36 poor density : 148 time to evaluate : 0.364 Fit side-chains REVERT: H 34 TYR cc_start: 0.8594 (t80) cc_final: 0.8303 (t80) REVERT: H 154 VAL cc_start: 0.8672 (OUTLIER) cc_final: 0.8344 (t) REVERT: I 76 TYR cc_start: 0.8585 (OUTLIER) cc_final: 0.8016 (m-80) REVERT: I 108 SER cc_start: 0.8541 (t) cc_final: 0.8247 (p) REVERT: I 236 ARG cc_start: 0.8461 (ttp80) cc_final: 0.8193 (ttp80) REVERT: I 420 ILE cc_start: 0.9168 (OUTLIER) cc_final: 0.8788 (mp) REVERT: I 549 ASP cc_start: 0.7799 (t70) cc_final: 0.7558 (t70) REVERT: I 695 ASP cc_start: 0.8490 (m-30) cc_final: 0.8225 (m-30) REVERT: K 5 LYS cc_start: 0.6407 (pttm) cc_final: 0.5870 (mttm) REVERT: K 58 ARG cc_start: 0.7897 (ttm170) cc_final: 0.7305 (ttp80) REVERT: K 84 GLN cc_start: 0.8511 (tm-30) cc_final: 0.8261 (tt0) REVERT: K 147 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7494 (mp0) REVERT: K 190 LEU cc_start: 0.9036 (OUTLIER) cc_final: 0.8831 (tt) REVERT: K 229 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7389 (mmmt) REVERT: K 232 ASP cc_start: 0.8773 (p0) cc_final: 0.8234 (t0) REVERT: W 41 ASN cc_start: 0.8464 (m110) cc_final: 0.8142 (m-40) outliers start: 36 outliers final: 22 residues processed: 177 average time/residue: 0.0968 time to fit residues: 24.4613 Evaluate side-chains 171 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 143 time to evaluate : 0.426 ------------------------------------------------------------------------------- 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 76 TYR Chi-restraints excluded: chain I residue 209 ILE 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 618 LEU Chi-restraints excluded: chain I residue 622 THR Chi-restraints excluded: chain I residue 686 TRP Chi-restraints excluded: chain I residue 711 TYR 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 57 LEU 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 190 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 66 optimal weight: 2.9990 chunk 112 optimal weight: 10.0000 chunk 82 optimal weight: 0.8980 chunk 48 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 1 optimal weight: 0.5980 chunk 70 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** K 195 ASN W 51 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3926 r_free = 0.3926 target = 0.167124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.129997 restraints weight = 12982.098| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 2.06 r_work: 0.3295 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10480 Z= 0.123 Angle : 0.574 10.386 14178 Z= 0.291 Chirality : 0.040 0.162 1649 Planarity : 0.003 0.046 1781 Dihedral : 5.048 38.473 1356 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.59 % Favored : 91.41 % Rotamer: Outliers : 2.80 % Allowed : 15.72 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.24 (0.25), residues: 1246 helix: 1.31 (0.18), residues: 864 sheet: None (None), residues: 0 loop : -2.64 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 236 TYR 0.013 0.001 TYR I 281 PHE 0.026 0.001 PHE T 311 TRP 0.007 0.001 TRP I 113 HIS 0.005 0.001 HIS H 39 Details of bonding type rmsd covalent geometry : bond 0.00286 (10479) covalent geometry : angle 0.57362 (14178) hydrogen bonds : bond 0.03411 ( 554) hydrogen bonds : angle 3.60671 ( 1632) Misc. bond : bond 0.00001 ( 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 178 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 145 time to evaluate : 0.416 Fit side-chains REVERT: H 21 GLU cc_start: 0.8216 (mm-30) cc_final: 0.7787 (mp0) REVERT: H 154 VAL cc_start: 0.8664 (OUTLIER) cc_final: 0.8427 (t) REVERT: I 76 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.8070 (m-80) REVERT: I 108 SER cc_start: 0.8595 (t) cc_final: 0.8296 (p) REVERT: I 420 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8788 (mp) REVERT: I 549 ASP cc_start: 0.7816 (t70) cc_final: 0.7585 (t70) REVERT: I 695 ASP cc_start: 0.8548 (m-30) cc_final: 0.8283 (m-30) REVERT: K 5 LYS cc_start: 0.6419 (pttm) cc_final: 0.5909 (mttm) REVERT: K 58 ARG cc_start: 0.7908 (ttm170) cc_final: 0.7287 (ttp80) REVERT: K 61 MET cc_start: 0.8441 (mtm) cc_final: 0.8140 (mtt) REVERT: K 147 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7536 (mp0) REVERT: K 229 LYS cc_start: 0.7673 (OUTLIER) cc_final: 0.7395 (mmmt) REVERT: K 232 ASP cc_start: 0.8795 (p0) cc_final: 0.8249 (t0) REVERT: W 41 ASN cc_start: 0.8486 (m110) cc_final: 0.8165 (m-40) outliers start: 33 outliers final: 21 residues processed: 172 average time/residue: 0.1037 time to fit residues: 25.4481 Evaluate side-chains 166 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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 76 TYR Chi-restraints excluded: chain I residue 115 VAL Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 282 VAL 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 622 THR Chi-restraints excluded: chain I residue 686 TRP Chi-restraints excluded: chain I residue 711 TYR 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 6 optimal weight: 0.7980 chunk 96 optimal weight: 0.8980 chunk 106 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 99 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 75 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 80 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3924 r_free = 0.3924 target = 0.166775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.129464 restraints weight = 12933.214| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 2.05 r_work: 0.3294 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.2700 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= 0.128 Angle : 0.599 13.000 14178 Z= 0.299 Chirality : 0.040 0.161 1649 Planarity : 0.004 0.048 1781 Dihedral : 5.055 38.699 1356 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 2.89 % Allowed : 15.80 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.25), residues: 1246 helix: 1.35 (0.18), residues: 864 sheet: None (None), residues: 0 loop : -2.64 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 240 TYR 0.014 0.001 TYR I 281 PHE 0.019 0.001 PHE K 62 TRP 0.008 0.001 TRP I 113 HIS 0.005 0.001 HIS H 39 Details of bonding type rmsd covalent geometry : bond 0.00302 (10479) covalent geometry : angle 0.59870 (14178) hydrogen bonds : bond 0.03457 ( 554) hydrogen bonds : angle 3.61909 ( 1632) Misc. bond : bond 0.00000 ( 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 176 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 142 time to evaluate : 0.338 Fit side-chains REVERT: H 21 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7781 (mp0) REVERT: H 34 TYR cc_start: 0.8610 (t80) cc_final: 0.8258 (t80) REVERT: I 76 TYR cc_start: 0.8635 (OUTLIER) cc_final: 0.8019 (m-80) REVERT: I 108 SER cc_start: 0.8613 (t) cc_final: 0.8316 (p) REVERT: I 420 ILE cc_start: 0.9172 (OUTLIER) cc_final: 0.8793 (mp) REVERT: I 549 ASP cc_start: 0.7845 (t70) cc_final: 0.7610 (t70) REVERT: I 695 ASP cc_start: 0.8518 (m-30) cc_final: 0.8252 (m-30) REVERT: K 5 LYS cc_start: 0.6485 (pttm) cc_final: 0.5963 (mttm) REVERT: K 58 ARG cc_start: 0.7977 (ttm170) cc_final: 0.7317 (ttp80) REVERT: K 61 MET cc_start: 0.8447 (mtm) cc_final: 0.8143 (mtt) REVERT: K 147 GLU cc_start: 0.7823 (OUTLIER) cc_final: 0.7555 (mp0) REVERT: K 226 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7442 (ptpp) REVERT: K 229 LYS cc_start: 0.7693 (OUTLIER) cc_final: 0.7399 (mmmt) REVERT: K 232 ASP cc_start: 0.8816 (p0) cc_final: 0.8257 (t0) REVERT: K 239 THR cc_start: 0.7944 (OUTLIER) cc_final: 0.7711 (t) REVERT: W 41 ASN cc_start: 0.8490 (m110) cc_final: 0.8163 (m-40) outliers start: 34 outliers final: 21 residues processed: 171 average time/residue: 0.0877 time to fit residues: 21.6446 Evaluate side-chains 168 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 76 TYR Chi-restraints excluded: chain I residue 209 ILE 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 622 THR Chi-restraints excluded: chain I residue 686 TRP Chi-restraints excluded: chain I residue 711 TYR 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 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 225 THR Chi-restraints excluded: chain K residue 226 LYS Chi-restraints excluded: chain K residue 229 LYS Chi-restraints excluded: chain K residue 239 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 19 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 44 optimal weight: 0.0870 chunk 21 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 110 optimal weight: 0.2980 chunk 55 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.166641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.129738 restraints weight = 13028.766| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.13 r_work: 0.3293 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.2820 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= 0.117 Angle : 0.587 13.466 14178 Z= 0.294 Chirality : 0.040 0.163 1649 Planarity : 0.003 0.049 1781 Dihedral : 4.968 38.186 1356 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 2.29 % Allowed : 16.57 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.41 (0.25), residues: 1246 helix: 1.46 (0.18), residues: 860 sheet: None (None), residues: 0 loop : -2.59 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 240 TYR 0.013 0.001 TYR I 281 PHE 0.030 0.001 PHE T 311 TRP 0.007 0.001 TRP I 291 HIS 0.005 0.001 HIS H 39 Details of bonding type rmsd covalent geometry : bond 0.00267 (10479) covalent geometry : angle 0.58741 (14178) hydrogen bonds : bond 0.03336 ( 554) hydrogen bonds : angle 3.58902 ( 1632) Misc. bond : bond 0.00005 ( 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 171 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 0.429 Fit side-chains REVERT: H 21 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7761 (mp0) REVERT: I 76 TYR cc_start: 0.8649 (OUTLIER) cc_final: 0.8069 (m-80) REVERT: I 108 SER cc_start: 0.8616 (t) cc_final: 0.8307 (p) REVERT: I 216 LYS cc_start: 0.7574 (mttm) cc_final: 0.7197 (ttpt) REVERT: I 420 ILE cc_start: 0.9189 (OUTLIER) cc_final: 0.8801 (mp) REVERT: I 549 ASP cc_start: 0.7883 (t70) cc_final: 0.7634 (t70) REVERT: I 650 LEU cc_start: 0.8171 (mt) cc_final: 0.7867 (mt) REVERT: I 695 ASP cc_start: 0.8505 (m-30) cc_final: 0.8253 (m-30) REVERT: K 5 LYS cc_start: 0.6540 (pttm) cc_final: 0.6048 (mttm) REVERT: K 58 ARG cc_start: 0.7937 (ttm170) cc_final: 0.7204 (ttp80) REVERT: K 61 MET cc_start: 0.8472 (mtm) cc_final: 0.8168 (mtt) REVERT: K 128 MET cc_start: 0.7294 (ttp) cc_final: 0.6997 (tmm) REVERT: K 147 GLU cc_start: 0.7856 (OUTLIER) cc_final: 0.7587 (mp0) REVERT: K 226 LYS cc_start: 0.7843 (OUTLIER) cc_final: 0.7427 (ptpp) REVERT: K 229 LYS cc_start: 0.7699 (OUTLIER) cc_final: 0.7400 (mmmt) REVERT: K 232 ASP cc_start: 0.8833 (p0) cc_final: 0.8250 (t0) REVERT: K 239 THR cc_start: 0.7933 (OUTLIER) cc_final: 0.7711 (t) REVERT: W 41 ASN cc_start: 0.8485 (m110) cc_final: 0.8176 (m-40) outliers start: 27 outliers final: 20 residues processed: 166 average time/residue: 0.1017 time to fit residues: 23.9457 Evaluate side-chains 166 residues out of total 1177 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 140 time to evaluate : 0.412 ------------------------------------------------------------------------------- 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 76 TYR Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 282 VAL 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 622 THR Chi-restraints excluded: chain I residue 686 TRP Chi-restraints excluded: chain I residue 711 TYR 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 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 226 LYS Chi-restraints excluded: chain K residue 229 LYS Chi-restraints excluded: chain K residue 239 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 10 optimal weight: 4.9990 chunk 94 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 92 optimal weight: 0.4980 chunk 69 optimal weight: 0.4980 chunk 89 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 41 optimal weight: 0.4980 chunk 119 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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 = 0.3920 r_free = 0.3920 target = 0.166509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.129462 restraints weight = 13180.262| |-----------------------------------------------------------------------------| r_work (start): 0.3474 rms_B_bonded: 2.16 r_work: 0.3297 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3159 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3159 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2866 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= 0.119 Angle : 0.592 13.217 14178 Z= 0.296 Chirality : 0.040 0.174 1649 Planarity : 0.004 0.046 1781 Dihedral : 4.935 38.480 1356 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.51 % Favored : 91.49 % Rotamer: Outliers : 2.55 % Allowed : 16.31 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.25), residues: 1246 helix: 1.50 (0.18), residues: 861 sheet: None (None), residues: 0 loop : -2.56 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 240 TYR 0.013 0.001 TYR I 281 PHE 0.017 0.001 PHE K 62 TRP 0.007 0.001 TRP I 166 HIS 0.005 0.001 HIS H 39 Details of bonding type rmsd covalent geometry : bond 0.00274 (10479) covalent geometry : angle 0.59165 (14178) hydrogen bonds : bond 0.03361 ( 554) hydrogen bonds : angle 3.57904 ( 1632) Misc. bond : bond 0.00003 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2909.22 seconds wall clock time: 50 minutes 34.80 seconds (3034.80 seconds total)