Starting phenix.real_space_refine on Wed Sep 25 14:04:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wuc_21910/09_2024/6wuc_21910.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wuc_21910/09_2024/6wuc_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wuc_21910/09_2024/6wuc_21910.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wuc_21910/09_2024/6wuc_21910.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wuc_21910/09_2024/6wuc_21910.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wuc_21910/09_2024/6wuc_21910.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 434 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 45 5.16 5 C 6582 2.51 5 N 1738 2.21 5 O 1919 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 57 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10284 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 1471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 1471 Classifications: {'peptide': 179} Link IDs: {'PTRANS': 5, 'TRANS': 173} Chain: "I" Number of atoms: 5777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 713, 5777 Classifications: {'peptide': 713} Link IDs: {'PTRANS': 32, 'TRANS': 680} Chain breaks: 2 Chain: "K" Number of atoms: 1903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 1903 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 6, 'TRANS': 228} Chain: "W" Number of atoms: 432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 432 Classifications: {'peptide': 55} Link IDs: {'TRANS': 54} Chain breaks: 2 Chain: "T" Number of atoms: 701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 701 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 2, 'TRANS': 81} Chain breaks: 1 Time building chain proxies: 5.77, per 1000 atoms: 0.56 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=0, symmetry=0 Time building additional restraints: 2.69 Conformation dependent library (CDL) restraints added in 1.1 seconds 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2468 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 1 sheets defined 69.7% alpha, 0.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.81 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: 2.78 Time building geometry restraints manager: 3.10 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: 1.35 - 2.06: 11 2.06 - 2.77: 2098 2.77 - 3.48: 14602 3.48 - 4.19: 24002 4.19 - 4.90: 43997 Nonbonded interactions: 84710 Sorted by model distance: nonbonded pdb=" NH2 ARG W 64 " pdb=" CB ALA W 80 " model vdw 1.351 3.540 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=" CZ ARG W 64 " pdb=" CB ALA W 80 " model vdw 1.677 3.690 nonbonded pdb=" OG1 THR I 656 " pdb=" O GLY I 685 " model vdw 1.769 3.040 ... (remaining 84705 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: 1.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 23.570 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.620 ------------------------------------------------------------------------------- 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 0.034 10479 Z= 0.251 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 : 1.351 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.99 % Favored : 90.37 % Rotamer: Outliers : 2.97 % Allowed : 8.41 % Favored : 88.62 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.18 (0.21), residues: 1246 helix: -1.25 (0.16), residues: 839 sheet: None (None), residues: 0 loop : -3.87 (0.25), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 136 HIS 0.005 0.001 HIS H 41 PHE 0.016 0.001 PHE I 660 TYR 0.014 0.001 TYR I 281 ARG 0.004 0.000 ARG I 395 *********************** 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 fitting. rotamer outliers: 35 poor density : 206 time to evaluate : 1.156 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: 0.2371 time to fit residues: 76.8653 Evaluate side-chains 160 residues out of total 1177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 149 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 291 TRP Chi-restraints excluded: chain I residue 484 THR Chi-restraints excluded: chain I residue 509 THR Chi-restraints excluded: chain I residue 513 ILE Chi-restraints excluded: chain I residue 618 LEU Chi-restraints excluded: chain I residue 686 TRP Chi-restraints excluded: chain I residue 725 LEU Chi-restraints excluded: chain K residue 140 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 37 optimal weight: 0.4980 chunk 59 optimal weight: 0.7980 chunk 72 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 19 HIS H 39 HIS H 60 GLN H 102 GLN H 107 GLN I 46 GLN I 107 GLN I 116 HIS ** I 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 221 HIS I 276 GLN I 305 GLN I 371 GLN I 398 GLN I 543 ASN I 703 HIS K 100 GLN K 212 ASN W 38 GLN W 77 HIS W 83 GLN T 280 HIS T 302 GLN T 322 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10479 Z= 0.202 Angle : 0.600 9.358 14178 Z= 0.312 Chirality : 0.040 0.220 1649 Planarity : 0.004 0.047 1781 Dihedral : 5.995 69.287 1367 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.75 % Favored : 91.25 % Rotamer: Outliers : 2.63 % Allowed : 11.64 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.24), residues: 1246 helix: -0.03 (0.18), residues: 854 sheet: None (None), residues: 0 loop : -3.44 (0.28), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP T 298 HIS 0.004 0.001 HIS T 280 PHE 0.012 0.001 PHE K 62 TYR 0.023 0.001 TYR I 76 ARG 0.004 0.000 ARG I 240 *********************** 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 fitting. rotamer outliers: 31 poor density : 168 time to evaluate : 1.162 Fit side-chains revert: symmetry clash REVERT: H 17 LYS cc_start: 0.8292 (tttm) cc_final: 0.8040 (ttmm) REVERT: I 65 TYR cc_start: 0.8051 (t80) cc_final: 0.7785 (t80) REVERT: I 108 SER cc_start: 0.8337 (t) cc_final: 0.8050 (p) REVERT: I 173 ARG cc_start: 0.8178 (ttm170) cc_final: 0.7927 (ttm110) REVERT: I 420 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8596 (mp) REVERT: I 633 ILE cc_start: 0.8543 (tt) cc_final: 0.8332 (pt) REVERT: I 695 ASP cc_start: 0.7910 (m-30) cc_final: 0.7666 (m-30) REVERT: K 84 GLN cc_start: 0.8255 (tm-30) cc_final: 0.8026 (tt0) REVERT: W 41 ASN cc_start: 0.8611 (m110) cc_final: 0.8358 (m-40) outliers start: 31 outliers final: 14 residues processed: 194 average time/residue: 0.2176 time to fit residues: 60.7758 Evaluate side-chains 155 residues out of total 1177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain I residue 62 THR Chi-restraints excluded: chain I residue 143 SER Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 420 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 466 LEU Chi-restraints excluded: chain I residue 473 VAL Chi-restraints excluded: chain I residue 509 THR Chi-restraints excluded: chain I residue 686 TRP Chi-restraints excluded: chain I residue 722 LEU Chi-restraints excluded: chain I residue 725 LEU Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain W residue 83 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 112 optimal weight: 10.0000 chunk 121 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 111 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 88 ASN I 46 GLN I 141 GLN I 195 GLN I 276 GLN K 30 GLN K 49 ASN K 100 GLN K 176 ASN W 51 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 10479 Z= 0.356 Angle : 0.649 13.935 14178 Z= 0.332 Chirality : 0.043 0.186 1649 Planarity : 0.004 0.047 1781 Dihedral : 5.712 42.784 1357 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.59 % Favored : 91.33 % Rotamer: Outliers : 3.74 % Allowed : 12.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.24), residues: 1246 helix: 0.22 (0.18), residues: 858 sheet: None (None), residues: 0 loop : -3.16 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 424 HIS 0.004 0.001 HIS H 41 PHE 0.025 0.002 PHE K 62 TYR 0.019 0.002 TYR I 76 ARG 0.006 0.001 ARG I 506 *********************** 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 192 residues out of total 1177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 148 time to evaluate : 1.092 Fit side-chains REVERT: H 17 LYS cc_start: 0.8366 (tttm) cc_final: 0.8114 (ttmm) REVERT: I 65 TYR cc_start: 0.8184 (t80) cc_final: 0.7930 (t80) REVERT: I 173 ARG cc_start: 0.8112 (ttm170) cc_final: 0.7773 (ttm110) REVERT: I 420 ILE cc_start: 0.9077 (OUTLIER) cc_final: 0.8657 (mp) REVERT: I 466 LEU cc_start: 0.8511 (OUTLIER) cc_final: 0.8132 (mm) REVERT: I 550 ASP cc_start: 0.8438 (p0) cc_final: 0.8183 (p0) REVERT: K 84 GLN cc_start: 0.8252 (tm-30) cc_final: 0.8002 (tt0) REVERT: K 147 GLU cc_start: 0.7279 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: W 41 ASN cc_start: 0.8566 (m110) cc_final: 0.8321 (m-40) outliers start: 44 outliers final: 28 residues processed: 180 average time/residue: 0.2125 time to fit residues: 54.7585 Evaluate side-chains 167 residues out of total 1177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 136 time to evaluate : 1.090 ------------------------------------------------------------------------------- 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 93 THR 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 291 TRP 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 103 MET 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 161 VAL Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 225 THR 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 111 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 119 optimal weight: 8.9990 chunk 59 optimal weight: 0.9980 chunk 107 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 88 ASN I 276 GLN ** I 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 188 HIS W 51 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10479 Z= 0.188 Angle : 0.571 13.850 14178 Z= 0.292 Chirality : 0.039 0.173 1649 Planarity : 0.004 0.044 1781 Dihedral : 5.438 39.729 1356 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 3.06 % Allowed : 14.36 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.25), residues: 1246 helix: 0.62 (0.18), residues: 860 sheet: None (None), residues: 0 loop : -2.90 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 291 HIS 0.008 0.001 HIS H 39 PHE 0.024 0.001 PHE K 62 TYR 0.022 0.001 TYR I 38 ARG 0.004 0.000 ARG I 240 *********************** 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 182 residues out of total 1177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 146 time to evaluate : 1.245 Fit side-chains REVERT: H 17 LYS cc_start: 0.8318 (tttm) cc_final: 0.8053 (ttmm) REVERT: H 154 VAL cc_start: 0.8814 (OUTLIER) cc_final: 0.8313 (t) REVERT: I 65 TYR cc_start: 0.8066 (t80) cc_final: 0.7814 (t80) REVERT: I 535 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8229 (mp) REVERT: I 695 ASP cc_start: 0.7908 (m-30) cc_final: 0.7676 (m-30) REVERT: K 147 GLU cc_start: 0.7257 (OUTLIER) cc_final: 0.7038 (mp0) REVERT: W 41 ASN cc_start: 0.8461 (m110) cc_final: 0.8203 (m110) outliers start: 36 outliers final: 14 residues processed: 175 average time/residue: 0.2120 time to fit residues: 54.0600 Evaluate side-chains 153 residues out of total 1177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 136 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain I residue 58 ILE Chi-restraints excluded: chain I residue 209 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 473 VAL Chi-restraints excluded: chain I residue 509 THR Chi-restraints excluded: chain I residue 535 LEU Chi-restraints excluded: chain I residue 618 LEU Chi-restraints excluded: chain I residue 686 TRP Chi-restraints excluded: chain I residue 722 LEU Chi-restraints excluded: chain I residue 725 LEU Chi-restraints excluded: chain K residue 126 THR Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain T residue 327 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 89 optimal weight: 0.6980 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 5.9990 chunk 82 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 107 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 276 GLN I 390 ASN ** I 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10479 Z= 0.268 Angle : 0.608 13.964 14178 Z= 0.309 Chirality : 0.041 0.156 1649 Planarity : 0.004 0.045 1781 Dihedral : 5.483 39.940 1356 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 3.91 % Allowed : 14.44 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.25), residues: 1246 helix: 0.71 (0.18), residues: 861 sheet: None (None), residues: 0 loop : -2.84 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 686 HIS 0.003 0.001 HIS I 487 PHE 0.024 0.002 PHE K 62 TYR 0.020 0.001 TYR I 38 ARG 0.005 0.000 ARG I 240 *********************** 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 185 residues out of total 1177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 139 time to evaluate : 1.166 Fit side-chains REVERT: H 17 LYS cc_start: 0.8325 (tttm) cc_final: 0.8072 (ttmm) REVERT: H 154 VAL cc_start: 0.8823 (OUTLIER) cc_final: 0.8566 (t) REVERT: I 65 TYR cc_start: 0.8124 (t80) cc_final: 0.7876 (t80) REVERT: I 420 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8639 (mp) REVERT: I 535 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8209 (mp) REVERT: I 550 ASP cc_start: 0.8361 (p0) cc_final: 0.8133 (p0) REVERT: K 147 GLU cc_start: 0.7247 (OUTLIER) cc_final: 0.7024 (mp0) REVERT: K 239 THR cc_start: 0.7655 (OUTLIER) cc_final: 0.7434 (t) REVERT: W 41 ASN cc_start: 0.8447 (m110) cc_final: 0.8121 (m-40) outliers start: 46 outliers final: 24 residues processed: 179 average time/residue: 0.2115 time to fit residues: 56.0712 Evaluate side-chains 161 residues out of total 1177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 132 time to evaluate : 1.134 ------------------------------------------------------------------------------- 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 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 535 LEU Chi-restraints excluded: chain I residue 618 LEU Chi-restraints excluded: chain I residue 686 TRP Chi-restraints excluded: chain I residue 722 LEU Chi-restraints excluded: chain I residue 725 LEU Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 105 LEU Chi-restraints excluded: chain K residue 126 THR Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain K residue 180 LEU Chi-restraints excluded: chain K residue 225 THR 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 40 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 119 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 46 GLN I 276 GLN ** I 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10479 Z= 0.230 Angle : 0.597 14.077 14178 Z= 0.302 Chirality : 0.041 0.157 1649 Planarity : 0.004 0.044 1781 Dihedral : 5.401 38.847 1356 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.99 % Favored : 91.01 % Rotamer: Outliers : 3.74 % Allowed : 14.61 % Favored : 81.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.25), residues: 1246 helix: 0.86 (0.18), residues: 862 sheet: None (None), residues: 0 loop : -2.83 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 166 HIS 0.003 0.001 HIS H 39 PHE 0.023 0.002 PHE K 62 TYR 0.017 0.001 TYR I 38 ARG 0.005 0.000 ARG I 240 *********************** 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 186 residues out of total 1177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 142 time to evaluate : 1.065 Fit side-chains REVERT: H 17 LYS cc_start: 0.8309 (tttm) cc_final: 0.8056 (ttmm) REVERT: H 154 VAL cc_start: 0.8833 (OUTLIER) cc_final: 0.8332 (t) REVERT: I 76 TYR cc_start: 0.8628 (OUTLIER) cc_final: 0.7946 (m-80) REVERT: I 420 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8605 (mp) REVERT: I 513 ILE cc_start: 0.8306 (OUTLIER) cc_final: 0.8102 (pt) REVERT: K 147 GLU cc_start: 0.7241 (OUTLIER) cc_final: 0.7012 (mp0) REVERT: K 239 THR cc_start: 0.7641 (OUTLIER) cc_final: 0.7432 (t) REVERT: W 41 ASN cc_start: 0.8431 (m110) cc_final: 0.8142 (m-40) outliers start: 44 outliers final: 24 residues processed: 180 average time/residue: 0.2065 time to fit residues: 54.0327 Evaluate side-chains 164 residues out of total 1177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 134 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 12 ILE Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 128 LEU Chi-restraints excluded: chain H residue 139 THR Chi-restraints excluded: chain H residue 154 VAL Chi-restraints excluded: chain I residue 58 ILE 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 420 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 473 VAL Chi-restraints excluded: chain I residue 485 LEU 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 711 TYR Chi-restraints excluded: chain I residue 722 LEU Chi-restraints excluded: chain I residue 725 LEU Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 105 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 225 THR 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 115 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 87 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 119 optimal weight: 5.9990 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 4.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 276 GLN ** I 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10479 Z= 0.195 Angle : 0.583 12.656 14178 Z= 0.295 Chirality : 0.040 0.161 1649 Planarity : 0.003 0.044 1781 Dihedral : 5.284 38.524 1356 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.67 % Favored : 91.33 % Rotamer: Outliers : 3.31 % Allowed : 15.12 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.25), residues: 1246 helix: 1.09 (0.18), residues: 857 sheet: None (None), residues: 0 loop : -2.75 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 166 HIS 0.003 0.001 HIS H 41 PHE 0.019 0.001 PHE K 62 TYR 0.018 0.001 TYR I 38 ARG 0.007 0.000 ARG I 240 *********************** 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 180 residues out of total 1177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 141 time to evaluate : 1.245 Fit side-chains REVERT: H 17 LYS cc_start: 0.8300 (tttm) cc_final: 0.8053 (ttmm) REVERT: I 76 TYR cc_start: 0.8547 (OUTLIER) cc_final: 0.7881 (m-80) REVERT: I 420 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8601 (mp) REVERT: K 147 GLU cc_start: 0.7236 (OUTLIER) cc_final: 0.7006 (mp0) REVERT: K 226 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.7278 (ptpp) REVERT: K 239 THR cc_start: 0.7645 (OUTLIER) cc_final: 0.7428 (t) REVERT: W 41 ASN cc_start: 0.8415 (m110) cc_final: 0.8130 (m-40) outliers start: 39 outliers final: 24 residues processed: 175 average time/residue: 0.2189 time to fit residues: 55.2366 Evaluate side-chains 167 residues out of total 1177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 138 time to evaluate : 2.560 ------------------------------------------------------------------------------- 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 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 485 LEU 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 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 57 LEU Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain K residue 226 LYS Chi-restraints excluded: chain K residue 239 THR Chi-restraints excluded: chain T residue 327 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 0.2980 chunk 47 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 75 optimal weight: 0.0870 chunk 81 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 108 optimal weight: 0.5980 overall best weight: 0.5160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 276 GLN ** I 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 51 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10479 Z= 0.167 Angle : 0.582 14.745 14178 Z= 0.293 Chirality : 0.039 0.173 1649 Planarity : 0.003 0.043 1781 Dihedral : 5.131 37.999 1356 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 2.72 % Allowed : 16.31 % Favored : 80.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.25), residues: 1246 helix: 1.28 (0.19), residues: 856 sheet: None (None), residues: 0 loop : -2.75 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 291 HIS 0.006 0.001 HIS H 39 PHE 0.024 0.001 PHE T 311 TYR 0.013 0.001 TYR I 38 ARG 0.007 0.000 ARG I 240 *********************** 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 186 residues out of total 1177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 154 time to evaluate : 1.182 Fit side-chains REVERT: I 76 TYR cc_start: 0.8433 (OUTLIER) cc_final: 0.7831 (m-80) REVERT: I 420 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8588 (mp) REVERT: K 5 LYS cc_start: 0.6492 (pttm) cc_final: 0.5970 (mttm) REVERT: K 147 GLU cc_start: 0.7248 (OUTLIER) cc_final: 0.6984 (mp0) REVERT: K 226 LYS cc_start: 0.7597 (OUTLIER) cc_final: 0.7219 (ptpp) REVERT: W 41 ASN cc_start: 0.8410 (m110) cc_final: 0.8140 (m-40) outliers start: 32 outliers final: 20 residues processed: 182 average time/residue: 0.2116 time to fit residues: 55.8066 Evaluate side-chains 167 residues out of total 1177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 143 time to evaluate : 1.101 ------------------------------------------------------------------------------- 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 58 ILE Chi-restraints excluded: chain I residue 76 TYR Chi-restraints excluded: chain I residue 209 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 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 48 VAL Chi-restraints excluded: chain K residue 54 THR 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 225 THR Chi-restraints excluded: chain K residue 226 LYS Chi-restraints excluded: chain T residue 327 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 7.9990 chunk 104 optimal weight: 2.9990 chunk 111 optimal weight: 0.0980 chunk 67 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 276 GLN ** I 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 195 ASN W 41 ASN W 51 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10479 Z= 0.263 Angle : 0.625 12.631 14178 Z= 0.315 Chirality : 0.042 0.184 1649 Planarity : 0.004 0.052 1781 Dihedral : 5.275 39.528 1356 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.15 % Favored : 90.85 % Rotamer: Outliers : 3.31 % Allowed : 16.48 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.25), residues: 1246 helix: 1.15 (0.18), residues: 860 sheet: None (None), residues: 0 loop : -2.73 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 113 HIS 0.006 0.001 HIS H 39 PHE 0.021 0.002 PHE K 62 TYR 0.016 0.001 TYR I 281 ARG 0.007 0.000 ARG I 240 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2492 Ramachandran restraints generated. 1246 Oldfield, 0 Emsley, 1246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 139 time to evaluate : 1.336 Fit side-chains REVERT: H 17 LYS cc_start: 0.8379 (tttm) cc_final: 0.8129 (ttmm) REVERT: I 76 TYR cc_start: 0.8580 (OUTLIER) cc_final: 0.7829 (m-80) REVERT: I 420 ILE cc_start: 0.9041 (OUTLIER) cc_final: 0.8617 (mp) REVERT: K 5 LYS cc_start: 0.6638 (pttm) cc_final: 0.6106 (mttm) REVERT: K 147 GLU cc_start: 0.7269 (OUTLIER) cc_final: 0.7025 (mp0) REVERT: K 226 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.7277 (ptpp) outliers start: 39 outliers final: 23 residues processed: 174 average time/residue: 0.2122 time to fit residues: 53.3865 Evaluate side-chains 166 residues out of total 1177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 139 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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 58 ILE 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 420 ILE Chi-restraints excluded: chain I residue 443 ILE Chi-restraints excluded: chain I residue 485 LEU 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 711 TYR Chi-restraints excluded: chain I residue 722 LEU Chi-restraints excluded: chain I residue 725 LEU Chi-restraints excluded: chain K residue 48 VAL Chi-restraints excluded: chain K residue 54 THR Chi-restraints excluded: chain K residue 57 LEU Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain K residue 195 ASN Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain K residue 226 LYS Chi-restraints excluded: chain T residue 327 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 7.9990 chunk 71 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 123 optimal weight: 4.9990 chunk 113 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 75 optimal weight: 0.0570 chunk 60 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.9100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 276 GLN ** I 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 195 ASN W 51 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10479 Z= 0.206 Angle : 0.620 16.104 14178 Z= 0.310 Chirality : 0.041 0.171 1649 Planarity : 0.004 0.049 1781 Dihedral : 5.225 38.728 1356 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 3.06 % Allowed : 16.99 % Favored : 79.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.25), residues: 1246 helix: 1.23 (0.18), residues: 860 sheet: None (None), residues: 0 loop : -2.69 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 166 HIS 0.004 0.001 HIS H 39 PHE 0.029 0.002 PHE T 311 TYR 0.014 0.001 TYR I 281 ARG 0.008 0.000 ARG I 240 ********************** 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 177 residues out of total 1177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 141 time to evaluate : 1.144 Fit side-chains REVERT: H 17 LYS cc_start: 0.8366 (tttm) cc_final: 0.8115 (ttmm) REVERT: I 76 TYR cc_start: 0.8559 (OUTLIER) cc_final: 0.7898 (m-80) REVERT: I 420 ILE cc_start: 0.9016 (OUTLIER) cc_final: 0.8592 (mp) REVERT: K 5 LYS cc_start: 0.6594 (pttm) cc_final: 0.6109 (mttm) REVERT: K 147 GLU cc_start: 0.7282 (OUTLIER) cc_final: 0.7039 (mp0) REVERT: K 226 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7274 (ptpp) outliers start: 36 outliers final: 26 residues processed: 171 average time/residue: 0.2369 time to fit residues: 58.0260 Evaluate side-chains 166 residues out of total 1177 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 136 time to evaluate : 1.121 ------------------------------------------------------------------------------- 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 206 GLU 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 485 LEU 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 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 57 LEU Chi-restraints excluded: chain K residue 103 MET Chi-restraints excluded: chain K residue 147 GLU Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain K residue 195 ASN Chi-restraints excluded: chain K residue 225 THR Chi-restraints excluded: chain K residue 226 LYS Chi-restraints excluded: chain T residue 327 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 41 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 86 optimal weight: 0.0870 overall best weight: 0.9560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 276 GLN ** I 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 195 ASN W 41 ASN W 51 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.163607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.126244 restraints weight = 13059.886| |-----------------------------------------------------------------------------| r_work (start): 0.3429 rms_B_bonded: 2.12 r_work: 0.3247 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10479 Z= 0.211 Angle : 0.611 11.976 14178 Z= 0.308 Chirality : 0.041 0.189 1649 Planarity : 0.004 0.053 1781 Dihedral : 5.195 38.632 1356 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.83 % Favored : 91.17 % Rotamer: Outliers : 2.63 % Allowed : 17.25 % Favored : 80.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1246 helix: 1.27 (0.18), residues: 860 sheet: None (None), residues: 0 loop : -2.66 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 166 HIS 0.007 0.001 HIS H 39 PHE 0.019 0.001 PHE K 62 TYR 0.015 0.001 TYR I 281 ARG 0.008 0.000 ARG I 240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2406.60 seconds wall clock time: 43 minutes 42.83 seconds (2622.83 seconds total)