Starting phenix.real_space_refine on Mon Jul 28 13:27:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pm0_13508/07_2025/7pm0_13508.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pm0_13508/07_2025/7pm0_13508.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pm0_13508/07_2025/7pm0_13508.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pm0_13508/07_2025/7pm0_13508.map" model { file = "/net/cci-nas-00/data/ceres_data/7pm0_13508/07_2025/7pm0_13508.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pm0_13508/07_2025/7pm0_13508.cif" } resolution = 3.6 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Br 1 7.06 5 P 3 5.49 5 Mg 1 5.21 5 S 62 5.16 5 C 6482 2.51 5 N 1723 2.21 5 O 1897 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 10169 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1059 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1059 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain breaks: 2 Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 37 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 31 Chain: "A" Number of atoms: 6130 Number of conformers: 1 Conformer: "" Number of residues, atoms: 751, 6130 Classifications: {'peptide': 751} Link IDs: {'PTRANS': 27, 'TRANS': 723} Chain breaks: 3 Chain: "C" Number of atoms: 2900 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2900 Classifications: {'peptide': 371} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 351} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 80 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 80 Unusual residues: {' MG': 1, '9UE': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 6.97, per 1000 atoms: 0.69 Number of scatterers: 10169 At special positions: 0 Unit cell: (104.5, 132, 152.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Br 1 34.99 S 62 16.00 P 3 15.00 Mg 1 11.99 O 1897 8.00 N 1723 7.00 C 6482 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: 2.92 Conformation dependent library (CDL) restraints added in 1.5 seconds 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2374 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 15 sheets defined 56.5% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.42 Creating SS restraints... Processing helix chain 'B' and resid 5 through 19 Processing helix chain 'B' and resid 29 through 39 removed outlier: 4.204A pdb=" N GLY B 33 " --> pdb=" O TYR B 29 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N ASP B 34 " --> pdb=" O SER B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 53 Processing helix chain 'B' and resid 56 through 63 Processing helix chain 'B' and resid 67 through 79 Proline residue: B 72 - end of helix Processing helix chain 'B' and resid 87 through 95 Processing helix chain 'B' and resid 105 through 116 Processing helix chain 'B' and resid 121 through 130 Processing helix chain 'B' and resid 140 through 150 Processing helix chain 'A' and resid 73 through 77 Processing helix chain 'A' and resid 81 through 95 Processing helix chain 'A' and resid 116 through 119 removed outlier: 4.482A pdb=" N TYR A 119 " --> pdb=" O LEU A 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 116 through 119' Processing helix chain 'A' and resid 120 through 129 removed outlier: 3.612A pdb=" N ILE A 124 " --> pdb=" O GLY A 120 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLY A 129 " --> pdb=" O ASN A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 135 removed outlier: 3.670A pdb=" N MET A 135 " --> pdb=" O MET A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 153 removed outlier: 3.724A pdb=" N VAL A 142 " --> pdb=" O HIS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 167 Processing helix chain 'A' and resid 168 through 185 Processing helix chain 'A' and resid 191 through 207 Proline residue: A 201 - end of helix Processing helix chain 'A' and resid 245 through 250 Processing helix chain 'A' and resid 259 through 269 removed outlier: 4.370A pdb=" N TYR A 263 " --> pdb=" O TYR A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 278 removed outlier: 6.081A pdb=" N GLU A 273 " --> pdb=" O ALA A 270 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N THR A 276 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 290 removed outlier: 4.301A pdb=" N GLN A 290 " --> pdb=" O HIS A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 315 removed outlier: 3.778A pdb=" N ASN A 307 " --> pdb=" O LYS A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 337 removed outlier: 3.675A pdb=" N MET A 323 " --> pdb=" O ASP A 319 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 365 Processing helix chain 'A' and resid 367 through 375 Processing helix chain 'A' and resid 392 through 424 Processing helix chain 'A' and resid 448 through 480 removed outlier: 3.857A pdb=" N MET A 478 " --> pdb=" O GLN A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 492 through 501 removed outlier: 3.589A pdb=" N LEU A 498 " --> pdb=" O PRO A 494 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 515 removed outlier: 4.027A pdb=" N LYS A 514 " --> pdb=" O ASP A 510 " (cutoff:3.500A) Processing helix chain 'A' and resid 521 through 532 removed outlier: 3.777A pdb=" N GLN A 525 " --> pdb=" O ASP A 521 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS A 526 " --> pdb=" O THR A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 569 Processing helix chain 'A' and resid 573 through 582 removed outlier: 3.829A pdb=" N LEU A 580 " --> pdb=" O GLN A 576 " (cutoff:3.500A) Processing helix chain 'A' and resid 587 through 593 removed outlier: 4.066A pdb=" N PHE A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 634 Processing helix chain 'A' and resid 635 through 652 Processing helix chain 'A' and resid 674 through 685 removed outlier: 3.584A pdb=" N GLN A 680 " --> pdb=" O LYS A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 696 removed outlier: 3.666A pdb=" N ALA A 696 " --> pdb=" O ARG A 692 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 712 removed outlier: 3.800A pdb=" N ARG A 710 " --> pdb=" O GLU A 706 " (cutoff:3.500A) Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 723 through 736 Processing helix chain 'A' and resid 738 through 740 No H-bonds generated for 'chain 'A' and resid 738 through 740' Processing helix chain 'A' and resid 754 through 792 Processing helix chain 'C' and resid 55 through 62 Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.899A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.929A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 Processing helix chain 'C' and resid 181 through 196 removed outlier: 3.859A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.643A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 233 removed outlier: 3.541A pdb=" N GLU C 226 " --> pdb=" O ASP C 222 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 260 removed outlier: 3.791A pdb=" N ARG C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) Proline residue: C 258 - end of helix Processing helix chain 'C' and resid 261 through 262 No H-bonds generated for 'chain 'C' and resid 261 through 262' Processing helix chain 'C' and resid 263 through 268 Processing helix chain 'C' and resid 273 through 285 Processing helix chain 'C' and resid 288 through 296 removed outlier: 4.286A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 305 Processing helix chain 'C' and resid 308 through 321 Processing helix chain 'C' and resid 332 through 336 removed outlier: 4.475A pdb=" N LYS C 336 " --> pdb=" O PRO C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 350 through 355 Processing helix chain 'C' and resid 359 through 366 removed outlier: 3.570A pdb=" N ALA C 365 " --> pdb=" O GLU C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 375 removed outlier: 4.177A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE C 375 " --> pdb=" O HIS C 371 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 26 through 28 Processing sheet with id=AA2, first strand: chain 'A' and resid 12 through 16 removed outlier: 3.653A pdb=" N LEU A 40 " --> pdb=" O LEU A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 101 through 103 Processing sheet with id=AA4, first strand: chain 'A' and resid 234 through 242 removed outlier: 3.988A pdb=" N GLY A 236 " --> pdb=" O GLY A 227 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 431 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N GLN A 157 " --> pdb=" O PHE A 432 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 208 through 209 Processing sheet with id=AA6, first strand: chain 'A' and resid 341 through 344 removed outlier: 5.539A pdb=" N SER A 342 " --> pdb=" O ALA A 349 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ALA A 349 " --> pdb=" O SER A 342 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ASP A 344 " --> pdb=" O SER A 347 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 377 through 381 Processing sheet with id=AA8, first strand: chain 'A' and resid 538 through 539 Processing sheet with id=AA9, first strand: chain 'A' and resid 700 through 703 removed outlier: 3.589A pdb=" N SER A 700 " --> pdb=" O PHE A 751 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.550A pdb=" N LYS C 18 " --> pdb=" O ASP C 11 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU C 107 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.524A pdb=" N THR C 66 " --> pdb=" O ARG C 37 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.349A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 528 hydrogen bonds defined for protein. 1458 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: 4.84 Time building geometry restraints manager: 3.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 2916 1.33 - 1.47: 2821 1.47 - 1.60: 4544 1.60 - 1.73: 3 1.73 - 1.87: 102 Bond restraints: 10386 Sorted by residual: bond pdb=" O4 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.568 1.508 0.060 2.00e-02 2.50e+03 9.05e+00 bond pdb=" O3 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.569 1.509 0.060 2.00e-02 2.50e+03 9.01e+00 bond pdb=" O2 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.567 1.508 0.059 2.00e-02 2.50e+03 8.72e+00 bond pdb=" O1 PO4 C 402 " pdb=" P PO4 C 402 " ideal model delta sigma weight residual 1.565 1.507 0.058 2.00e-02 2.50e+03 8.28e+00 bond pdb=" CE1 HIC C 73 " pdb=" NE2 HIC C 73 " ideal model delta sigma weight residual 1.347 1.402 -0.055 2.00e-02 2.50e+03 7.50e+00 ... (remaining 10381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 13845 2.88 - 5.76: 164 5.76 - 8.65: 12 8.65 - 11.53: 6 11.53 - 14.41: 1 Bond angle restraints: 14028 Sorted by residual: angle pdb=" C20 9UE C 404 " pdb=" C8 9UE C 404 " pdb=" C7 9UE C 404 " ideal model delta sigma weight residual 118.25 103.84 14.41 3.00e+00 1.11e-01 2.31e+01 angle pdb=" CB MET C 82 " pdb=" CG MET C 82 " pdb=" SD MET C 82 " ideal model delta sigma weight residual 112.70 101.23 11.47 3.00e+00 1.11e-01 1.46e+01 angle pdb=" C6 9UE C 404 " pdb=" N 9UE C 404 " pdb=" C7 9UE C 404 " ideal model delta sigma weight residual 128.90 117.78 11.12 3.00e+00 1.11e-01 1.37e+01 angle pdb=" CA TYR A 711 " pdb=" CB TYR A 711 " pdb=" CG TYR A 711 " ideal model delta sigma weight residual 113.90 107.26 6.64 1.80e+00 3.09e-01 1.36e+01 angle pdb=" C1' ADP C 401 " pdb=" C2' ADP C 401 " pdb=" C3' ADP C 401 " ideal model delta sigma weight residual 111.00 100.01 10.99 3.00e+00 1.11e-01 1.34e+01 ... (remaining 14023 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 6139 35.63 - 71.26: 98 71.26 - 106.89: 31 106.89 - 142.52: 6 142.52 - 178.14: 12 Dihedral angle restraints: 6286 sinusoidal: 2602 harmonic: 3684 Sorted by residual: dihedral pdb=" O1B ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PB ADP C 401 " pdb=" PA ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 62.63 -122.63 1 2.00e+01 2.50e-03 3.69e+01 dihedral pdb=" C5' ADP C 401 " pdb=" O5' ADP C 401 " pdb=" PA ADP C 401 " pdb=" O2A ADP C 401 " ideal model delta sinusoidal sigma weight residual 300.00 178.49 121.51 1 2.00e+01 2.50e-03 3.65e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 58.88 -118.88 1 2.00e+01 2.50e-03 3.56e+01 ... (remaining 6283 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1338 0.080 - 0.160: 178 0.160 - 0.241: 7 0.241 - 0.321: 3 0.321 - 0.401: 2 Chirality restraints: 1528 Sorted by residual: chirality pdb=" C3 9UE C 404 " pdb=" O 9UE C 404 " pdb=" C2 9UE C 404 " pdb=" C35 9UE C 404 " both_signs ideal model delta sigma weight residual False 2.21 2.61 -0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" C10 9UE C 404 " pdb=" C18 9UE C 404 " pdb=" C9 9UE C 404 " pdb=" N2 9UE C 404 " both_signs ideal model delta sigma weight residual False -2.32 -2.71 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" C8 9UE C 404 " pdb=" C20 9UE C 404 " pdb=" C7 9UE C 404 " pdb=" N1 9UE C 404 " both_signs ideal model delta sigma weight residual False 2.15 2.44 -0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 1525 not shown) Planarity restraints: 1797 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 248 " -0.137 9.50e-02 1.11e+02 7.89e-02 3.27e+01 pdb=" NE ARG A 248 " 0.040 2.00e-02 2.50e+03 pdb=" CZ ARG A 248 " -0.094 2.00e-02 2.50e+03 pdb=" NH1 ARG A 248 " 0.033 2.00e-02 2.50e+03 pdb=" NH2 ARG A 248 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 213 " 0.371 9.50e-02 1.11e+02 1.70e-01 3.26e+01 pdb=" NE ARG A 213 " 0.001 2.00e-02 2.50e+03 pdb=" CZ ARG A 213 " -0.073 2.00e-02 2.50e+03 pdb=" NH1 ARG A 213 " 0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG A 213 " 0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 254 " -0.341 9.50e-02 1.11e+02 1.57e-01 3.07e+01 pdb=" NE ARG C 254 " -0.003 2.00e-02 2.50e+03 pdb=" CZ ARG C 254 " 0.074 2.00e-02 2.50e+03 pdb=" NH1 ARG C 254 " -0.020 2.00e-02 2.50e+03 pdb=" NH2 ARG C 254 " -0.036 2.00e-02 2.50e+03 ... (remaining 1794 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 57 2.58 - 3.16: 8781 3.16 - 3.74: 15049 3.74 - 4.32: 21210 4.32 - 4.90: 35236 Nonbonded interactions: 80333 Sorted by model distance: nonbonded pdb=" O3 PO4 C 402 " pdb="MG MG C 403 " model vdw 2.002 2.170 nonbonded pdb=" O3B ADP C 401 " pdb="MG MG C 403 " model vdw 2.008 2.170 nonbonded pdb=" OH TYR A 456 " pdb=" OE1 GLU A 500 " model vdw 2.089 3.040 nonbonded pdb=" O GLU B 118 " pdb=" NH2 ARG A 779 " model vdw 2.207 3.120 nonbonded pdb=" NH2 ARG B 37 " pdb=" O PRO B 43 " model vdw 2.211 3.120 ... (remaining 80328 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 24.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.110 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 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 : 0.005 0.092 10386 Z= 0.251 Angle : 0.868 14.410 14028 Z= 0.494 Chirality : 0.054 0.401 1528 Planarity : 0.010 0.170 1797 Dihedral : 18.285 178.144 3912 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: -1.27 (0.20), residues: 1242 helix: -1.40 (0.17), residues: 592 sheet: 0.10 (0.37), residues: 157 loop : -0.13 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 374 HIS 0.014 0.002 HIS A 418 PHE 0.036 0.002 PHE A 707 TYR 0.036 0.007 TYR A 113 ARG 0.096 0.011 ARG A 248 Details of bonding type rmsd hydrogen bonds : bond 0.15643 ( 526) hydrogen bonds : angle 7.02482 ( 1458) covalent geometry : bond 0.00544 (10386) covalent geometry : angle 0.86843 (14028) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 176 time to evaluate : 1.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 PHE cc_start: 0.8549 (m-80) cc_final: 0.8292 (m-10) REVERT: A 359 ILE cc_start: 0.9448 (mt) cc_final: 0.9241 (mm) REVERT: C 195 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7648 (mt-10) REVERT: C 227 MET cc_start: 0.8685 (tpp) cc_final: 0.8480 (tpt) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.3067 time to fit residues: 74.7157 Evaluate side-chains 101 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 1.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 105 optimal weight: 0.3980 chunk 94 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 50 optimal weight: 0.0000 chunk 97 optimal weight: 3.9990 chunk 37 optimal weight: 0.0980 chunk 59 optimal weight: 1.9990 chunk 72 optimal weight: 0.6980 chunk 113 optimal weight: 0.9990 overall best weight: 0.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN A 200 ASN ** A 464 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 497 ASN A 726 GLN C 41 GLN C 111 ASN C 115 ASN C 162 ASN C 296 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.082472 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.059674 restraints weight = 30029.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.061933 restraints weight = 14665.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.063453 restraints weight = 9182.499| |-----------------------------------------------------------------------------| r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10386 Z= 0.138 Angle : 0.687 9.474 14028 Z= 0.353 Chirality : 0.046 0.394 1528 Planarity : 0.004 0.051 1797 Dihedral : 18.294 166.236 1430 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Rotamer: Outliers : 1.11 % Allowed : 6.09 % Favored : 92.80 % 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: 1.07 (0.23), residues: 1242 helix: 0.91 (0.20), residues: 604 sheet: 0.87 (0.41), residues: 156 loop : 0.63 (0.28), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 374 HIS 0.009 0.001 HIS A 418 PHE 0.017 0.002 PHE A 707 TYR 0.014 0.002 TYR B 86 ARG 0.005 0.001 ARG C 177 Details of bonding type rmsd hydrogen bonds : bond 0.04410 ( 526) hydrogen bonds : angle 5.17421 ( 1458) covalent geometry : bond 0.00297 (10386) covalent geometry : angle 0.68688 (14028) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 PHE cc_start: 0.8636 (m-80) cc_final: 0.8395 (m-10) REVERT: B 105 MET cc_start: 0.9273 (mmp) cc_final: 0.8810 (tpp) REVERT: A 135 MET cc_start: 0.8756 (mmm) cc_final: 0.8496 (mmm) REVERT: A 416 VAL cc_start: 0.9216 (t) cc_final: 0.8971 (p) REVERT: C 59 GLN cc_start: 0.8408 (tm-30) cc_final: 0.8030 (tp-100) REVERT: C 192 ILE cc_start: 0.9099 (tt) cc_final: 0.8814 (tt) REVERT: C 195 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7833 (mt-10) REVERT: C 227 MET cc_start: 0.8586 (tpp) cc_final: 0.8247 (tpt) REVERT: C 236 LEU cc_start: 0.8173 (OUTLIER) cc_final: 0.7544 (tp) REVERT: C 353 GLN cc_start: 0.8835 (mm110) cc_final: 0.8594 (mm-40) outliers start: 12 outliers final: 3 residues processed: 132 average time/residue: 0.2450 time to fit residues: 47.7716 Evaluate side-chains 93 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 89 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain C residue 212 ILE Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 327 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 89 optimal weight: 0.7980 chunk 72 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 18 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 chunk 7 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 264 GLN A 410 ASN C 275 HIS C 371 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.081501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.058638 restraints weight = 30049.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.060855 restraints weight = 14755.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.062372 restraints weight = 9295.115| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.2747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10386 Z= 0.159 Angle : 0.639 11.589 14028 Z= 0.320 Chirality : 0.044 0.307 1528 Planarity : 0.004 0.055 1797 Dihedral : 17.531 166.479 1430 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Rotamer: Outliers : 1.11 % Allowed : 8.49 % Favored : 90.41 % 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: 1.44 (0.24), residues: 1242 helix: 1.28 (0.21), residues: 612 sheet: 1.02 (0.41), residues: 158 loop : 0.71 (0.29), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 374 HIS 0.009 0.001 HIS A 418 PHE 0.024 0.002 PHE B 4 TYR 0.014 0.001 TYR A 490 ARG 0.005 0.000 ARG B 64 Details of bonding type rmsd hydrogen bonds : bond 0.04152 ( 526) hydrogen bonds : angle 4.90956 ( 1458) covalent geometry : bond 0.00367 (10386) covalent geometry : angle 0.63941 (14028) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 1.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 PHE cc_start: 0.8575 (m-80) cc_final: 0.8372 (m-10) REVERT: B 105 MET cc_start: 0.9278 (mmp) cc_final: 0.8840 (tpp) REVERT: B 110 ARG cc_start: 0.8851 (mmt180) cc_final: 0.8576 (tpt170) REVERT: A 135 MET cc_start: 0.8731 (mmm) cc_final: 0.8297 (mmm) REVERT: A 416 VAL cc_start: 0.9192 (t) cc_final: 0.8924 (p) REVERT: A 441 PHE cc_start: 0.8018 (m-80) cc_final: 0.7640 (t80) REVERT: A 507 ASP cc_start: 0.8219 (m-30) cc_final: 0.7946 (m-30) REVERT: C 59 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8272 (tp-100) REVERT: C 227 MET cc_start: 0.8610 (tpp) cc_final: 0.8250 (tpt) REVERT: C 236 LEU cc_start: 0.8123 (OUTLIER) cc_final: 0.7363 (tp) REVERT: C 353 GLN cc_start: 0.8850 (mm110) cc_final: 0.8611 (mm-40) outliers start: 12 outliers final: 5 residues processed: 109 average time/residue: 0.2426 time to fit residues: 39.5173 Evaluate side-chains 88 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 327 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 78 optimal weight: 0.2980 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 100 optimal weight: 0.0060 chunk 119 optimal weight: 1.9990 chunk 73 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 75 optimal weight: 0.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.082038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.059523 restraints weight = 29667.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.061744 restraints weight = 14454.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.063246 restraints weight = 9061.960| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10386 Z= 0.122 Angle : 0.593 10.723 14028 Z= 0.294 Chirality : 0.043 0.298 1528 Planarity : 0.004 0.056 1797 Dihedral : 16.832 166.261 1430 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.29 % Allowed : 9.59 % Favored : 89.11 % 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: 1.68 (0.24), residues: 1242 helix: 1.56 (0.21), residues: 614 sheet: 0.94 (0.40), residues: 165 loop : 0.77 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 484 HIS 0.007 0.001 HIS A 418 PHE 0.024 0.001 PHE B 19 TYR 0.011 0.001 TYR A 456 ARG 0.002 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.03690 ( 526) hydrogen bonds : angle 4.63398 ( 1458) covalent geometry : bond 0.00270 (10386) covalent geometry : angle 0.59252 (14028) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.9204 (mmp) cc_final: 0.8739 (tpp) REVERT: A 135 MET cc_start: 0.8690 (mmm) cc_final: 0.8288 (mmm) REVERT: A 305 MET cc_start: 0.8397 (tpt) cc_final: 0.7977 (tpt) REVERT: A 416 VAL cc_start: 0.9146 (t) cc_final: 0.8879 (p) REVERT: A 441 PHE cc_start: 0.7955 (m-80) cc_final: 0.7732 (t80) REVERT: C 227 MET cc_start: 0.8581 (tpp) cc_final: 0.8227 (tpt) REVERT: C 236 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.7864 (mm) outliers start: 14 outliers final: 9 residues processed: 112 average time/residue: 0.1934 time to fit residues: 32.9280 Evaluate side-chains 100 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 327 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 52 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 41 optimal weight: 0.2980 chunk 2 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 37 optimal weight: 0.1980 chunk 116 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 71 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.081531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.059171 restraints weight = 29627.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.061362 restraints weight = 14423.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.062857 restraints weight = 9039.751| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10386 Z= 0.134 Angle : 0.590 10.283 14028 Z= 0.289 Chirality : 0.043 0.340 1528 Planarity : 0.004 0.054 1797 Dihedral : 16.024 166.384 1430 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.57 % Allowed : 10.24 % Favored : 88.19 % 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: 1.82 (0.24), residues: 1242 helix: 1.69 (0.21), residues: 620 sheet: 1.10 (0.41), residues: 159 loop : 0.75 (0.30), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 484 HIS 0.010 0.001 HIS A 418 PHE 0.020 0.001 PHE B 19 TYR 0.012 0.001 TYR A 456 ARG 0.002 0.000 ARG A 327 Details of bonding type rmsd hydrogen bonds : bond 0.03623 ( 526) hydrogen bonds : angle 4.50959 ( 1458) covalent geometry : bond 0.00303 (10386) covalent geometry : angle 0.59006 (14028) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 96 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 ARG cc_start: 0.9033 (tpt170) cc_final: 0.8612 (mmt180) REVERT: A 135 MET cc_start: 0.8720 (mmm) cc_final: 0.8317 (mmm) REVERT: A 305 MET cc_start: 0.8388 (tpt) cc_final: 0.7985 (tpt) REVERT: A 363 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9173 (mm) REVERT: A 416 VAL cc_start: 0.9115 (t) cc_final: 0.8860 (p) REVERT: A 441 PHE cc_start: 0.7941 (m-80) cc_final: 0.7727 (t80) REVERT: A 507 ASP cc_start: 0.7726 (m-30) cc_final: 0.7167 (m-30) REVERT: C 227 MET cc_start: 0.8453 (tpp) cc_final: 0.8073 (tpt) REVERT: C 236 LEU cc_start: 0.8201 (OUTLIER) cc_final: 0.7907 (mm) outliers start: 17 outliers final: 9 residues processed: 109 average time/residue: 0.2258 time to fit residues: 36.8739 Evaluate side-chains 102 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 1.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 496 ILE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 327 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 68 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 102 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 50 optimal weight: 0.0010 chunk 51 optimal weight: 1.9990 chunk 114 optimal weight: 0.9980 chunk 123 optimal weight: 2.9990 chunk 109 optimal weight: 0.9980 chunk 121 optimal weight: 0.5980 chunk 113 optimal weight: 0.3980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.082173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.059646 restraints weight = 29610.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.061884 restraints weight = 14268.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.063418 restraints weight = 8885.984| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10386 Z= 0.114 Angle : 0.580 9.495 14028 Z= 0.284 Chirality : 0.042 0.331 1528 Planarity : 0.004 0.056 1797 Dihedral : 15.664 166.552 1430 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer: Outliers : 1.66 % Allowed : 10.15 % Favored : 88.19 % 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: 1.84 (0.24), residues: 1242 helix: 1.77 (0.21), residues: 620 sheet: 0.89 (0.42), residues: 150 loop : 0.76 (0.30), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 484 HIS 0.008 0.001 HIS A 418 PHE 0.025 0.001 PHE B 96 TYR 0.011 0.001 TYR A 456 ARG 0.002 0.000 ARG A 327 Details of bonding type rmsd hydrogen bonds : bond 0.03442 ( 526) hydrogen bonds : angle 4.39852 ( 1458) covalent geometry : bond 0.00252 (10386) covalent geometry : angle 0.58038 (14028) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 98 time to evaluate : 1.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.9212 (mmp) cc_final: 0.8691 (tpp) REVERT: B 110 ARG cc_start: 0.8998 (tpt170) cc_final: 0.8636 (mmt180) REVERT: A 135 MET cc_start: 0.8752 (mmm) cc_final: 0.8448 (mmm) REVERT: A 363 LEU cc_start: 0.9428 (OUTLIER) cc_final: 0.9094 (mm) REVERT: A 364 MET cc_start: 0.8573 (mmm) cc_final: 0.8278 (mmt) REVERT: A 416 VAL cc_start: 0.9043 (t) cc_final: 0.8780 (p) REVERT: A 507 ASP cc_start: 0.7706 (m-30) cc_final: 0.6969 (m-30) REVERT: C 227 MET cc_start: 0.8422 (tpp) cc_final: 0.8158 (tpt) REVERT: C 236 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.7954 (mm) outliers start: 18 outliers final: 7 residues processed: 111 average time/residue: 0.2659 time to fit residues: 45.1109 Evaluate side-chains 102 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 1.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 327 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 82 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 119 optimal weight: 0.0970 chunk 71 optimal weight: 0.3980 chunk 98 optimal weight: 2.9990 chunk 1 optimal weight: 10.0000 chunk 37 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 775 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.081710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.059127 restraints weight = 30112.547| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.061325 restraints weight = 14729.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.062802 restraints weight = 9298.809| |-----------------------------------------------------------------------------| r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10386 Z= 0.130 Angle : 0.593 9.872 14028 Z= 0.290 Chirality : 0.043 0.314 1528 Planarity : 0.004 0.053 1797 Dihedral : 15.499 167.238 1430 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.11 % Allowed : 11.07 % Favored : 87.82 % 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: 1.78 (0.24), residues: 1242 helix: 1.83 (0.21), residues: 617 sheet: 0.72 (0.43), residues: 143 loop : 0.63 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 484 HIS 0.007 0.001 HIS A 418 PHE 0.028 0.001 PHE B 12 TYR 0.013 0.001 TYR A 658 ARG 0.003 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 526) hydrogen bonds : angle 4.38094 ( 1458) covalent geometry : bond 0.00293 (10386) covalent geometry : angle 0.59304 (14028) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 91 time to evaluate : 1.416 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.9185 (mmp) cc_final: 0.8657 (tpp) REVERT: B 110 ARG cc_start: 0.8996 (tpt170) cc_final: 0.8656 (mmt180) REVERT: A 135 MET cc_start: 0.8748 (mmm) cc_final: 0.8406 (mmm) REVERT: A 305 MET cc_start: 0.8503 (tpt) cc_final: 0.8134 (tpp) REVERT: A 363 LEU cc_start: 0.9375 (OUTLIER) cc_final: 0.9059 (mm) REVERT: A 364 MET cc_start: 0.8496 (mmm) cc_final: 0.8219 (mmt) REVERT: A 416 VAL cc_start: 0.9076 (t) cc_final: 0.8808 (p) REVERT: A 507 ASP cc_start: 0.7771 (m-30) cc_final: 0.7099 (m-30) REVERT: C 227 MET cc_start: 0.8450 (tpp) cc_final: 0.8182 (tpt) REVERT: C 236 LEU cc_start: 0.8256 (OUTLIER) cc_final: 0.8001 (mm) outliers start: 12 outliers final: 8 residues processed: 98 average time/residue: 0.3089 time to fit residues: 44.0445 Evaluate side-chains 97 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 327 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 55 optimal weight: 0.4980 chunk 99 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 93 optimal weight: 0.7980 chunk 82 optimal weight: 2.9990 chunk 94 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 15 optimal weight: 2.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.081538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.058785 restraints weight = 30112.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.060995 restraints weight = 14881.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.062498 restraints weight = 9415.635| |-----------------------------------------------------------------------------| r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10386 Z= 0.137 Angle : 0.587 9.879 14028 Z= 0.289 Chirality : 0.042 0.305 1528 Planarity : 0.004 0.053 1797 Dihedral : 15.586 168.656 1430 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 1.29 % Allowed : 11.81 % Favored : 86.90 % 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: 1.76 (0.24), residues: 1242 helix: 1.85 (0.21), residues: 615 sheet: 0.66 (0.43), residues: 143 loop : 0.57 (0.29), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 484 HIS 0.007 0.001 HIS A 418 PHE 0.018 0.001 PHE B 96 TYR 0.012 0.001 TYR A 456 ARG 0.003 0.000 ARG A 789 Details of bonding type rmsd hydrogen bonds : bond 0.03452 ( 526) hydrogen bonds : angle 4.38397 ( 1458) covalent geometry : bond 0.00311 (10386) covalent geometry : angle 0.58738 (14028) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 91 time to evaluate : 2.834 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.9185 (mmp) cc_final: 0.8639 (tpp) REVERT: B 110 ARG cc_start: 0.9003 (tpt170) cc_final: 0.8654 (mmt180) REVERT: A 135 MET cc_start: 0.8709 (mmm) cc_final: 0.8338 (mmm) REVERT: A 305 MET cc_start: 0.8487 (tpt) cc_final: 0.8001 (tpt) REVERT: A 363 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9060 (mm) REVERT: A 364 MET cc_start: 0.8449 (mmm) cc_final: 0.8245 (mmt) REVERT: A 416 VAL cc_start: 0.9096 (t) cc_final: 0.8836 (p) REVERT: A 507 ASP cc_start: 0.7807 (m-30) cc_final: 0.7256 (m-30) REVERT: C 236 LEU cc_start: 0.8247 (OUTLIER) cc_final: 0.7987 (mm) outliers start: 14 outliers final: 11 residues processed: 99 average time/residue: 0.2455 time to fit residues: 37.5485 Evaluate side-chains 100 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 87 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 89 TYR Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 426 THR Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 44 MET Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain C residue 327 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 116 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 70 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 38 optimal weight: 0.8980 chunk 50 optimal weight: 0.0870 chunk 48 optimal weight: 0.6980 chunk 84 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.082181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.059537 restraints weight = 30315.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.061761 restraints weight = 14979.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.063278 restraints weight = 9441.264| |-----------------------------------------------------------------------------| r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.3896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10386 Z= 0.113 Angle : 0.591 10.802 14028 Z= 0.288 Chirality : 0.042 0.283 1528 Planarity : 0.004 0.051 1797 Dihedral : 15.731 170.007 1430 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 1.29 % Allowed : 11.99 % Favored : 86.72 % 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: 1.81 (0.24), residues: 1242 helix: 1.87 (0.21), residues: 623 sheet: 0.64 (0.43), residues: 143 loop : 0.61 (0.29), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP A 484 HIS 0.006 0.001 HIS A 418 PHE 0.018 0.001 PHE B 96 TYR 0.012 0.001 TYR A 456 ARG 0.004 0.000 ARG A 789 Details of bonding type rmsd hydrogen bonds : bond 0.03371 ( 526) hydrogen bonds : angle 4.37617 ( 1458) covalent geometry : bond 0.00253 (10386) covalent geometry : angle 0.59143 (14028) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.9194 (mmp) cc_final: 0.8639 (tpp) REVERT: B 110 ARG cc_start: 0.9000 (tpt170) cc_final: 0.8650 (mmt180) REVERT: A 135 MET cc_start: 0.8709 (mmm) cc_final: 0.8384 (mmm) REVERT: A 305 MET cc_start: 0.8476 (tpt) cc_final: 0.7949 (tpt) REVERT: A 363 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9053 (mp) REVERT: A 416 VAL cc_start: 0.9054 (t) cc_final: 0.8772 (p) REVERT: A 507 ASP cc_start: 0.7785 (m-30) cc_final: 0.7234 (m-30) REVERT: C 283 MET cc_start: 0.8767 (mmm) cc_final: 0.8523 (mmm) outliers start: 14 outliers final: 8 residues processed: 99 average time/residue: 0.2138 time to fit residues: 32.0941 Evaluate side-chains 96 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 363 LEU Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 327 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 54 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 chunk 50 optimal weight: 0.7980 chunk 56 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 124 optimal weight: 0.0070 chunk 36 optimal weight: 0.9980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.081782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.059232 restraints weight = 30278.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.061425 restraints weight = 14787.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.062930 restraints weight = 9291.207| |-----------------------------------------------------------------------------| r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10386 Z= 0.129 Angle : 0.597 10.484 14028 Z= 0.295 Chirality : 0.042 0.281 1528 Planarity : 0.004 0.052 1797 Dihedral : 15.977 171.832 1430 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.64 % Favored : 99.36 % Rotamer: Outliers : 1.01 % Allowed : 11.99 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.82 (0.24), residues: 1242 helix: 1.87 (0.21), residues: 621 sheet: 0.77 (0.42), residues: 152 loop : 0.59 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 484 HIS 0.006 0.001 HIS A 418 PHE 0.019 0.001 PHE B 96 TYR 0.013 0.001 TYR A 456 ARG 0.004 0.000 ARG A 789 Details of bonding type rmsd hydrogen bonds : bond 0.03423 ( 526) hydrogen bonds : angle 4.39218 ( 1458) covalent geometry : bond 0.00293 (10386) covalent geometry : angle 0.59690 (14028) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2484 Ramachandran restraints generated. 1242 Oldfield, 0 Emsley, 1242 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 105 MET cc_start: 0.9196 (mmp) cc_final: 0.8636 (tpp) REVERT: B 110 ARG cc_start: 0.8992 (tpt170) cc_final: 0.8561 (mmt180) REVERT: A 135 MET cc_start: 0.8688 (mmm) cc_final: 0.8296 (mmm) REVERT: A 305 MET cc_start: 0.8518 (tpt) cc_final: 0.7994 (tpt) REVERT: A 507 ASP cc_start: 0.7817 (m-30) cc_final: 0.7128 (m-30) REVERT: A 788 MET cc_start: 0.8999 (ptp) cc_final: 0.8691 (pmm) REVERT: C 227 MET cc_start: 0.8707 (tpt) cc_final: 0.8449 (tpt) REVERT: C 283 MET cc_start: 0.8773 (mmm) cc_final: 0.8560 (mmm) outliers start: 11 outliers final: 9 residues processed: 95 average time/residue: 0.2112 time to fit residues: 30.7735 Evaluate side-chains 92 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 147 HIS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 441 PHE Chi-restraints excluded: chain A residue 765 ASP Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 260 THR Chi-restraints excluded: chain C residue 327 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 42 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 61 optimal weight: 0.1980 chunk 122 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 60 optimal weight: 0.0060 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.081241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.058518 restraints weight = 30335.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.060727 restraints weight = 14943.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.062216 restraints weight = 9389.773| |-----------------------------------------------------------------------------| r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10386 Z= 0.146 Angle : 0.601 11.324 14028 Z= 0.297 Chirality : 0.042 0.263 1528 Planarity : 0.004 0.052 1797 Dihedral : 16.010 171.262 1430 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.11 % Allowed : 12.27 % Favored : 86.62 % 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: 1.77 (0.24), residues: 1242 helix: 1.83 (0.21), residues: 623 sheet: 0.76 (0.42), residues: 152 loop : 0.56 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 484 HIS 0.006 0.001 HIS A 418 PHE 0.019 0.001 PHE B 96 TYR 0.013 0.001 TYR A 456 ARG 0.003 0.000 ARG A 41 Details of bonding type rmsd hydrogen bonds : bond 0.03563 ( 526) hydrogen bonds : angle 4.40387 ( 1458) covalent geometry : bond 0.00334 (10386) covalent geometry : angle 0.60137 (14028) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3906.02 seconds wall clock time: 71 minutes 53.42 seconds (4313.42 seconds total)