Starting phenix.real_space_refine on Thu Jul 2 16:53:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7y1l_33565/07_2026/7y1l_33565.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y1l_33565/07_2026/7y1l_33565.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.73 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y1l_33565/07_2026/7y1l_33565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y1l_33565/07_2026/7y1l_33565.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7y1l_33565/07_2026/7y1l_33565.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7y1l_33565/07_2026/7y1l_33565.cif" model { file = "/net/cci-nas-00/data/ceres_data/7y1l_33565/07_2026/7y1l_33565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y1l_33565/07_2026/7y1l_33565.cif" } resolution = 3.73 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 6 5.49 5 Mg 2 5.21 5 S 36 5.16 5 C 5816 2.51 5 N 1516 2.21 5 O 1579 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8955 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8858 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1189, 8858 Classifications: {'peptide': 1189} Incomplete info: {'truncation_to_alanine': 152} Link IDs: {'PTRANS': 35, 'TRANS': 1153} Chain breaks: 7 Unresolved non-hydrogen bonds: 541 Unresolved non-hydrogen angles: 669 Unresolved non-hydrogen dihedrals: 429 Unresolved non-hydrogen chiralities: 30 Planarities with less than four sites: {'PHE:plan': 2, 'ASP:plan': 28, 'GLU:plan': 29, 'ARG:plan': 8, 'ASN:plan1': 8, 'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 341 Chain: "A" Number of atoms: 97 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 97 Unusual residues: {' MG': 2, 'ATP': 2, 'BJX': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 2.56, per 1000 atoms: 0.29 Number of scatterers: 8955 At special positions: 0 Unit cell: (76.728, 100.914, 133.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 6 15.00 Mg 2 11.99 O 1579 8.00 N 1516 7.00 C 5816 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: 1.15 Conformation dependent library (CDL) restraints added in 428.1 milliseconds 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2246 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 6 sheets defined 72.6% alpha, 8.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 216 through 228 Processing helix chain 'A' and resid 228 through 238 removed outlier: 3.893A pdb=" N ASN A 232 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N THR A 233 " --> pdb=" O TRP A 229 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N LEU A 234 " --> pdb=" O TRP A 230 " (cutoff:3.500A) Processing helix chain 'A' and resid 252 through 255 Processing helix chain 'A' and resid 256 through 274 removed outlier: 3.813A pdb=" N LYS A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 312 removed outlier: 3.691A pdb=" N ALA A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ARG A 295 " --> pdb=" O ARG A 291 " (cutoff:3.500A) Proline residue: A 296 - end of helix Processing helix chain 'A' and resid 312 through 324 removed outlier: 3.910A pdb=" N LEU A 316 " --> pdb=" O PHE A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 348 removed outlier: 3.622A pdb=" N GLU A 346 " --> pdb=" O GLU A 343 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N ALA A 348 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 395 Processing helix chain 'A' and resid 405 through 416 Processing helix chain 'A' and resid 416 through 450 Proline residue: A 429 - end of helix removed outlier: 3.942A pdb=" N TRP A 432 " --> pdb=" O CYS A 428 " (cutoff:3.500A) Proline residue: A 435 - end of helix Processing helix chain 'A' and resid 452 through 462 removed outlier: 4.420A pdb=" N GLY A 456 " --> pdb=" O SER A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 497 removed outlier: 3.533A pdb=" N ILE A 466 " --> pdb=" O LEU A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 506 Processing helix chain 'A' and resid 507 through 558 removed outlier: 3.647A pdb=" N THR A 528 " --> pdb=" O SER A 524 " (cutoff:3.500A) Proline residue: A 544 - end of helix Processing helix chain 'A' and resid 564 through 607 removed outlier: 4.442A pdb=" N THR A 580 " --> pdb=" O HIS A 576 " (cutoff:3.500A) Proline residue: A 581 - end of helix removed outlier: 4.178A pdb=" N SER A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N THR A 587 " --> pdb=" O PHE A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 715 Processing helix chain 'A' and resid 761 through 768 Processing helix chain 'A' and resid 773 through 784 Processing helix chain 'A' and resid 786 through 793 Processing helix chain 'A' and resid 809 through 824 Processing helix chain 'A' and resid 839 through 850 Processing helix chain 'A' and resid 852 through 859 removed outlier: 3.581A pdb=" N ASP A 858 " --> pdb=" O PHE A 854 " (cutoff:3.500A) Processing helix chain 'A' and resid 891 through 899 Processing helix chain 'A' and resid 899 through 912 removed outlier: 3.546A pdb=" N LYS A 907 " --> pdb=" O TYR A 903 " (cutoff:3.500A) Processing helix chain 'A' and resid 925 through 937 Processing helix chain 'A' and resid 974 through 986 removed outlier: 3.810A pdb=" N GLY A 985 " --> pdb=" O TYR A 981 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY A 986 " --> pdb=" O LEU A 982 " (cutoff:3.500A) Processing helix chain 'A' and resid 986 through 1017 removed outlier: 4.092A pdb=" N GLU A1017 " --> pdb=" O THR A1013 " (cutoff:3.500A) Processing helix chain 'A' and resid 1028 through 1074 Processing helix chain 'A' and resid 1076 through 1083 removed outlier: 4.050A pdb=" N PHE A1080 " --> pdb=" O PRO A1076 " (cutoff:3.500A) Processing helix chain 'A' and resid 1084 through 1094 removed outlier: 3.591A pdb=" N ILE A1088 " --> pdb=" O PRO A1084 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N PHE A1092 " --> pdb=" O ILE A1088 " (cutoff:3.500A) Processing helix chain 'A' and resid 1094 through 1102 Processing helix chain 'A' and resid 1102 through 1128 Processing helix chain 'A' and resid 1130 through 1176 removed outlier: 4.419A pdb=" N ALA A1134 " --> pdb=" O VAL A1130 " (cutoff:3.500A) Proline residue: A1137 - end of helix Proline residue: A1166 - end of helix Processing helix chain 'A' and resid 1177 through 1185 Processing helix chain 'A' and resid 1186 through 1237 Processing helix chain 'A' and resid 1240 through 1282 removed outlier: 4.062A pdb=" N THR A1255 " --> pdb=" O ALA A1251 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASN A1256 " --> pdb=" O LEU A1252 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N TYR A1257 " --> pdb=" O THR A1253 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ASN A1259 " --> pdb=" O THR A1255 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TRP A1260 " --> pdb=" O ASN A1256 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N VAL A1262 " --> pdb=" O LEU A1258 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A1274 " --> pdb=" O VAL A1270 " (cutoff:3.500A) Processing helix chain 'A' and resid 1301 through 1305 removed outlier: 4.322A pdb=" N GLU A1305 " --> pdb=" O TRP A1302 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1356 Processing helix chain 'A' and resid 1377 through 1384 Processing helix chain 'A' and resid 1399 through 1404 Processing helix chain 'A' and resid 1410 through 1421 Processing helix chain 'A' and resid 1423 through 1430 Processing helix chain 'A' and resid 1432 through 1435 Processing helix chain 'A' and resid 1439 through 1443 removed outlier: 3.967A pdb=" N GLU A1443 " --> pdb=" O GLU A1440 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1462 removed outlier: 3.550A pdb=" N LYS A1462 " --> pdb=" O ALA A1458 " (cutoff:3.500A) Processing helix chain 'A' and resid 1476 through 1490 Processing helix chain 'A' and resid 1502 through 1507 removed outlier: 3.896A pdb=" N ILE A1506 " --> pdb=" O ARG A1502 " (cutoff:3.500A) Processing helix chain 'A' and resid 1525 through 1533 Processing helix chain 'A' and resid 1535 through 1543 Processing sheet with id=AA1, first strand: chain 'A' and resid 684 through 687 removed outlier: 5.313A pdb=" N SER A 685 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE A 675 " --> pdb=" O SER A 685 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 684 through 687 removed outlier: 5.313A pdb=" N SER A 685 " --> pdb=" O PHE A 675 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N PHE A 675 " --> pdb=" O SER A 685 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N VAL A 670 " --> pdb=" O TYR A 726 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N TYR A 726 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N ASN A 672 " --> pdb=" O LYS A 724 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N LYS A 724 " --> pdb=" O ASN A 672 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 748 through 751 removed outlier: 6.100A pdb=" N ALA A 749 " --> pdb=" O PHE A 830 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N ASP A 832 " --> pdb=" O ALA A 749 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N ALA A 751 " --> pdb=" O ASP A 832 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N VAL A 829 " --> pdb=" O VAL A 863 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N VAL A 865 " --> pdb=" O VAL A 829 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU A 831 " --> pdb=" O VAL A 865 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N THR A 697 " --> pdb=" O LEU A 864 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1325 through 1332 removed outlier: 6.308A pdb=" N LYS A1326 " --> pdb=" O CYS A1314 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N CYS A1314 " --> pdb=" O LYS A1326 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N VAL A1328 " --> pdb=" O ASP A1312 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N LEU A1313 " --> pdb=" O ASP A1363 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASP A1363 " --> pdb=" O LEU A1313 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL A1315 " --> pdb=" O ILE A1361 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N ILE A1361 " --> pdb=" O VAL A1315 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1465 through 1469 removed outlier: 6.205A pdb=" N LYS A1337 " --> pdb=" O LEU A1511 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ILE A1513 " --> pdb=" O LYS A1337 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLY A1339 " --> pdb=" O ILE A1513 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N MET A1515 " --> pdb=" O GLY A1339 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N CYS A1341 " --> pdb=" O MET A1515 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLU A1522 " --> pdb=" O VAL A1514 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LYS A1516 " --> pdb=" O ILE A1520 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ILE A1520 " --> pdb=" O LYS A1516 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1397 through 1398 654 hydrogen bonds defined for protein. 1935 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: 2.00 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1360 1.31 - 1.43: 2411 1.43 - 1.56: 5277 1.56 - 1.68: 31 1.68 - 1.81: 58 Bond restraints: 9137 Sorted by residual: bond pdb=" C16 BJX A1605 " pdb=" N1 BJX A1605 " ideal model delta sigma weight residual 1.344 1.453 -0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" CA MET A 231 " pdb=" C MET A 231 " ideal model delta sigma weight residual 1.522 1.588 -0.065 1.36e-02 5.41e+03 2.30e+01 bond pdb=" CA ARG A1542 " pdb=" C ARG A1542 " ideal model delta sigma weight residual 1.523 1.584 -0.061 1.30e-02 5.92e+03 2.20e+01 bond pdb=" CA ASN A 232 " pdb=" CB ASN A 232 " ideal model delta sigma weight residual 1.528 1.599 -0.070 1.56e-02 4.11e+03 2.02e+01 bond pdb=" CA VAL A1541 " pdb=" C VAL A1541 " ideal model delta sigma weight residual 1.524 1.579 -0.055 1.22e-02 6.72e+03 2.00e+01 ... (remaining 9132 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 12211 1.55 - 3.10: 169 3.10 - 4.65: 51 4.65 - 6.20: 25 6.20 - 7.75: 10 Bond angle restraints: 12466 Sorted by residual: angle pdb=" C ILE A 321 " pdb=" CA ILE A 321 " pdb=" CB ILE A 321 " ideal model delta sigma weight residual 111.97 104.22 7.75 1.28e+00 6.10e-01 3.66e+01 angle pdb=" C VAL A 322 " pdb=" CA VAL A 322 " pdb=" CB VAL A 322 " ideal model delta sigma weight residual 112.14 105.00 7.14 1.35e+00 5.49e-01 2.79e+01 angle pdb=" N TRP A 229 " pdb=" CA TRP A 229 " pdb=" CB TRP A 229 " ideal model delta sigma weight residual 110.12 117.70 -7.58 1.47e+00 4.63e-01 2.66e+01 angle pdb=" O ILE A 318 " pdb=" C ILE A 318 " pdb=" N SER A 319 " ideal model delta sigma weight residual 121.87 126.38 -4.51 9.70e-01 1.06e+00 2.16e+01 angle pdb=" N ILE A 321 " pdb=" CA ILE A 321 " pdb=" CB ILE A 321 " ideal model delta sigma weight residual 110.55 115.94 -5.39 1.17e+00 7.31e-01 2.12e+01 ... (remaining 12461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.03: 5269 31.03 - 62.06: 67 62.06 - 93.10: 4 93.10 - 124.13: 0 124.13 - 155.16: 1 Dihedral angle restraints: 5341 sinusoidal: 1878 harmonic: 3463 Sorted by residual: dihedral pdb=" O BJX A1605 " pdb=" C16 BJX A1605 " pdb=" C17 BJX A1605 " pdb=" C18 BJX A1605 " ideal model delta sinusoidal sigma weight residual 10.31 -144.85 155.16 1 3.00e+01 1.11e-03 2.03e+01 dihedral pdb=" CA GLN A 323 " pdb=" C GLN A 323 " pdb=" N ARG A 324 " pdb=" CA ARG A 324 " ideal model delta harmonic sigma weight residual 180.00 158.87 21.13 0 5.00e+00 4.00e-02 1.79e+01 dihedral pdb=" CA ASP A1100 " pdb=" C ASP A1100 " pdb=" N GLN A1101 " pdb=" CA GLN A1101 " ideal model delta harmonic sigma weight residual 180.00 -163.50 -16.50 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 5338 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1371 0.064 - 0.129: 129 0.129 - 0.193: 10 0.193 - 0.257: 1 0.257 - 0.322: 8 Chirality restraints: 1519 Sorted by residual: chirality pdb=" CA ILE A 321 " pdb=" N ILE A 321 " pdb=" C ILE A 321 " pdb=" CB ILE A 321 " both_signs ideal model delta sigma weight residual False 2.43 2.75 -0.32 2.00e-01 2.50e+01 2.59e+00 chirality pdb=" CA VAL A1541 " pdb=" N VAL A1541 " pdb=" C VAL A1541 " pdb=" CB VAL A1541 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.22e+00 chirality pdb=" C2' ATP A1603 " pdb=" C1' ATP A1603 " pdb=" C3' ATP A1603 " pdb=" O2' ATP A1603 " both_signs ideal model delta sigma weight residual False -2.68 -2.97 0.29 2.00e-01 2.50e+01 2.14e+00 ... (remaining 1516 not shown) Planarity restraints: 1519 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 227 " 0.020 2.00e-02 2.50e+03 4.11e-02 1.69e+01 pdb=" C THR A 227 " -0.071 2.00e-02 2.50e+03 pdb=" O THR A 227 " 0.027 2.00e-02 2.50e+03 pdb=" N TYR A 228 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 229 " 0.032 2.00e-02 2.50e+03 2.00e-02 1.00e+01 pdb=" CG TRP A 229 " -0.053 2.00e-02 2.50e+03 pdb=" CD1 TRP A 229 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 TRP A 229 " 0.005 2.00e-02 2.50e+03 pdb=" NE1 TRP A 229 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TRP A 229 " 0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP A 229 " -0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 229 " 0.005 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 229 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 229 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 580 " -0.035 5.00e-02 4.00e+02 5.36e-02 4.59e+00 pdb=" N PRO A 581 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 581 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 581 " -0.030 5.00e-02 4.00e+02 ... (remaining 1516 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1124 2.74 - 3.28: 10067 3.28 - 3.82: 15369 3.82 - 4.36: 16713 4.36 - 4.90: 29355 Nonbonded interactions: 72628 Sorted by model distance: nonbonded pdb=" OE1 GLN A 753 " pdb="MG MG A1602 " model vdw 2.202 2.170 nonbonded pdb=" OD2 ASP A1008 " pdb=" OH TYR A1250 " model vdw 2.207 3.040 nonbonded pdb=" ND2 ASN A 430 " pdb=" O BJX A1605 " model vdw 2.212 3.120 nonbonded pdb=" OD1 ASN A 232 " pdb=" NE1 TRP A1214 " model vdw 2.216 3.120 nonbonded pdb="MG MG A1601 " pdb=" O3B ATP A1604 " model vdw 2.220 2.170 ... (remaining 72623 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.610 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 11.690 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 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 0.109 9137 Z= 0.290 Angle : 0.587 7.748 12466 Z= 0.344 Chirality : 0.043 0.322 1519 Planarity : 0.004 0.068 1519 Dihedral : 11.091 155.161 3095 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 1.03 % Allowed : 4.45 % Favored : 94.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.25), residues: 1173 helix: 2.33 (0.18), residues: 794 sheet: 1.23 (0.67), residues: 68 loop : 0.20 (0.37), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1218 TYR 0.026 0.001 TYR A 228 PHE 0.014 0.001 PHE A1149 TRP 0.053 0.001 TRP A 229 HIS 0.005 0.001 HIS A1504 Details of bonding type rmsd/Z covalent geometry : bond 0.00468 / 0.29 ( 9137) covalent geometry : angle 0.58722 / 0.34 (12466) hydrogen bonds : bond 0.13021 / 8.80 ( 652) hydrogen bonds : angle 5.81291 / 4.42 ( 1935) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 169 time to evaluate : 0.353 Fit side-chains revert: symmetry clash REVERT: A 228 TYR cc_start: 0.9049 (m-80) cc_final: 0.8114 (m-80) REVERT: A 434 MET cc_start: 0.8460 (tpp) cc_final: 0.7850 (mmm) REVERT: A 523 LEU cc_start: 0.9038 (mm) cc_final: 0.8570 (pp) REVERT: A 786 LEU cc_start: 0.9339 (tp) cc_final: 0.9096 (tp) REVERT: A 814 GLN cc_start: 0.8797 (pt0) cc_final: 0.8181 (tt0) REVERT: A 1044 PHE cc_start: 0.8345 (t80) cc_final: 0.8078 (t80) REVERT: A 1091 ARG cc_start: 0.8267 (mmt-90) cc_final: 0.8035 (mmt180) REVERT: A 1367 VAL cc_start: 0.6280 (t) cc_final: 0.6010 (t) REVERT: A 1426 MET cc_start: 0.9063 (mmm) cc_final: 0.8845 (tpp) outliers start: 9 outliers final: 3 residues processed: 176 average time/residue: 0.0713 time to fit residues: 19.5562 Evaluate side-chains 128 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 125 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 1160 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.0570 chunk 49 optimal weight: 8.9990 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.0770 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 9.9990 overall best weight: 0.5258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 576 HIS A 867 HIS A1186 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.117462 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.090065 restraints weight = 21320.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.089233 restraints weight = 12150.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.090015 restraints weight = 9211.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.090735 restraints weight = 6863.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.090896 restraints weight = 6037.798| |-----------------------------------------------------------------------------| r_work (final): 0.3298 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9137 Z= 0.133 Angle : 0.565 7.700 12466 Z= 0.280 Chirality : 0.040 0.176 1519 Planarity : 0.003 0.041 1519 Dihedral : 6.417 122.582 1287 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.14 % Allowed : 10.96 % Favored : 87.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.88 (0.25), residues: 1173 helix: 2.58 (0.18), residues: 805 sheet: 0.88 (0.64), residues: 68 loop : 0.31 (0.38), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 860 TYR 0.012 0.001 TYR A1331 PHE 0.016 0.001 PHE A 569 TRP 0.011 0.001 TRP A 230 HIS 0.007 0.001 HIS A1504 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.13 ( 9137) covalent geometry : angle 0.56515 / 0.28 (12466) hydrogen bonds : bond 0.04694 / 3.10 ( 652) hydrogen bonds : angle 4.56348 / 3.46 ( 1935) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 0.423 Fit side-chains revert: symmetry clash REVERT: A 228 TYR cc_start: 0.8993 (m-80) cc_final: 0.8131 (m-80) REVERT: A 243 ILE cc_start: 0.9220 (mm) cc_final: 0.8972 (mm) REVERT: A 434 MET cc_start: 0.8523 (tpp) cc_final: 0.8012 (mmm) REVERT: A 814 GLN cc_start: 0.8823 (pt0) cc_final: 0.8443 (tt0) REVERT: A 975 TRP cc_start: 0.8658 (m100) cc_final: 0.8127 (m100) REVERT: A 1044 PHE cc_start: 0.8517 (t80) cc_final: 0.8142 (t80) REVERT: A 1091 ARG cc_start: 0.8158 (mmt-90) cc_final: 0.7909 (mmt180) outliers start: 10 outliers final: 5 residues processed: 168 average time/residue: 0.0727 time to fit residues: 18.7485 Evaluate side-chains 135 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 1128 THR Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1160 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 12 optimal weight: 2.9990 chunk 37 optimal weight: 0.0870 chunk 99 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 43 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 93 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 107 optimal weight: 4.9990 overall best weight: 1.0560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.116916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.089773 restraints weight = 21480.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.087546 restraints weight = 12351.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.088692 restraints weight = 9496.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.090377 restraints weight = 6751.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.090264 restraints weight = 5688.732| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 9137 Z= 0.142 Angle : 0.556 7.269 12466 Z= 0.273 Chirality : 0.040 0.207 1519 Planarity : 0.003 0.046 1519 Dihedral : 6.364 127.915 1285 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.94 % Allowed : 13.93 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.85 (0.25), residues: 1173 helix: 2.56 (0.18), residues: 803 sheet: 0.93 (0.64), residues: 68 loop : 0.27 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 363 TYR 0.014 0.001 TYR A1205 PHE 0.019 0.001 PHE A1362 TRP 0.015 0.001 TRP A1302 HIS 0.007 0.001 HIS A1504 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 9137) covalent geometry : angle 0.55628 / 0.27 (12466) hydrogen bonds : bond 0.04553 / 2.98 ( 652) hydrogen bonds : angle 4.42821 / 3.35 ( 1935) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 0.395 Fit side-chains revert: symmetry clash REVERT: A 228 TYR cc_start: 0.9076 (m-80) cc_final: 0.8226 (m-80) REVERT: A 434 MET cc_start: 0.8561 (tpp) cc_final: 0.7946 (mmm) REVERT: A 502 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8531 (mp) REVERT: A 517 GLU cc_start: 0.8779 (tp30) cc_final: 0.8293 (tp30) REVERT: A 814 GLN cc_start: 0.8836 (pt0) cc_final: 0.8434 (tt0) REVERT: A 822 LEU cc_start: 0.9383 (OUTLIER) cc_final: 0.9077 (mm) REVERT: A 1044 PHE cc_start: 0.8493 (t80) cc_final: 0.8096 (t80) REVERT: A 1111 THR cc_start: 0.9171 (p) cc_final: 0.8941 (t) REVERT: A 1302 TRP cc_start: 0.8235 (t60) cc_final: 0.7821 (t60) outliers start: 17 outliers final: 12 residues processed: 150 average time/residue: 0.0733 time to fit residues: 17.0767 Evaluate side-chains 138 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 502 LEU Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 886 VAL Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1160 ASP Chi-restraints excluded: chain A residue 1248 LEU Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1259 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 100 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 67 optimal weight: 0.0170 chunk 85 optimal weight: 2.9990 chunk 117 optimal weight: 0.6980 chunk 105 optimal weight: 9.9990 chunk 27 optimal weight: 6.9990 chunk 19 optimal weight: 0.0270 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 576 HIS A1379 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.118713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.091706 restraints weight = 21748.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.089749 restraints weight = 12133.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.090882 restraints weight = 9496.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.092480 restraints weight = 6623.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.092398 restraints weight = 5529.277| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9137 Z= 0.117 Angle : 0.533 8.926 12466 Z= 0.261 Chirality : 0.039 0.189 1519 Planarity : 0.003 0.047 1519 Dihedral : 6.209 127.309 1285 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 2.51 % Allowed : 15.18 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.84 (0.25), residues: 1173 helix: 2.59 (0.18), residues: 800 sheet: 1.00 (0.62), residues: 68 loop : 0.20 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1382 TYR 0.015 0.001 TYR A1205 PHE 0.017 0.001 PHE A 988 TRP 0.010 0.001 TRP A1302 HIS 0.007 0.001 HIS A1504 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.12 ( 9137) covalent geometry : angle 0.53279 / 0.26 (12466) hydrogen bonds : bond 0.04283 / 2.82 ( 652) hydrogen bonds : angle 4.24148 / 3.21 ( 1935) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 147 time to evaluate : 0.357 Fit side-chains revert: symmetry clash REVERT: A 228 TYR cc_start: 0.9033 (m-80) cc_final: 0.8260 (m-80) REVERT: A 434 MET cc_start: 0.8482 (tpp) cc_final: 0.7976 (mmm) REVERT: A 517 GLU cc_start: 0.8747 (tp30) cc_final: 0.8093 (tp30) REVERT: A 523 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8612 (pp) REVERT: A 814 GLN cc_start: 0.8820 (pt0) cc_final: 0.8416 (tt0) REVERT: A 822 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9087 (mm) REVERT: A 1044 PHE cc_start: 0.8496 (t80) cc_final: 0.8096 (t80) REVERT: A 1215 LEU cc_start: 0.8325 (tp) cc_final: 0.8080 (tp) outliers start: 22 outliers final: 12 residues processed: 160 average time/residue: 0.0627 time to fit residues: 16.3640 Evaluate side-chains 142 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 128 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1248 LEU Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1361 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 116 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 7 optimal weight: 0.7980 chunk 113 optimal weight: 6.9990 chunk 92 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 100 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 576 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.114055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.086654 restraints weight = 21722.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.084149 restraints weight = 12663.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.085373 restraints weight = 10030.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.086620 restraints weight = 6869.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.086702 restraints weight = 6061.331| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 9137 Z= 0.255 Angle : 0.623 9.061 12466 Z= 0.316 Chirality : 0.042 0.208 1519 Planarity : 0.004 0.046 1519 Dihedral : 6.634 133.730 1283 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.74 % Allowed : 16.44 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.24), residues: 1173 helix: 2.35 (0.18), residues: 795 sheet: 0.87 (0.62), residues: 68 loop : 0.14 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1382 TYR 0.011 0.001 TYR A 228 PHE 0.019 0.002 PHE A 988 TRP 0.014 0.001 TRP A1302 HIS 0.007 0.001 HIS A1001 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.25 ( 9137) covalent geometry : angle 0.62303 / 0.32 (12466) hydrogen bonds : bond 0.04848 / 3.18 ( 652) hydrogen bonds : angle 4.47814 / 3.37 ( 1935) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 124 time to evaluate : 0.361 Fit side-chains REVERT: A 228 TYR cc_start: 0.9160 (m-80) cc_final: 0.8321 (m-80) REVERT: A 434 MET cc_start: 0.8625 (tpp) cc_final: 0.8404 (mmt) REVERT: A 517 GLU cc_start: 0.8844 (tp30) cc_final: 0.8194 (tp30) REVERT: A 523 LEU cc_start: 0.9065 (OUTLIER) cc_final: 0.8631 (pp) REVERT: A 814 GLN cc_start: 0.8821 (pt0) cc_final: 0.8446 (tt0) REVERT: A 822 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9138 (mm) REVERT: A 1044 PHE cc_start: 0.8575 (t80) cc_final: 0.8333 (t80) outliers start: 24 outliers final: 17 residues processed: 136 average time/residue: 0.0606 time to fit residues: 13.5820 Evaluate side-chains 137 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 118 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1187 GLU Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1246 LEU Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1361 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 87 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 71 optimal weight: 0.9990 chunk 57 optimal weight: 4.9990 chunk 73 optimal weight: 0.8980 chunk 82 optimal weight: 2.9990 chunk 117 optimal weight: 5.9990 chunk 102 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 576 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.116021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.088813 restraints weight = 21458.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.086517 restraints weight = 12159.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.087724 restraints weight = 9485.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.089154 restraints weight = 6581.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.089129 restraints weight = 5745.058| |-----------------------------------------------------------------------------| r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9137 Z= 0.151 Angle : 0.551 10.081 12466 Z= 0.272 Chirality : 0.039 0.171 1519 Planarity : 0.003 0.046 1519 Dihedral : 6.458 129.199 1283 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.63 % Allowed : 17.92 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.60 (0.24), residues: 1173 helix: 2.40 (0.18), residues: 795 sheet: 1.09 (0.62), residues: 68 loop : 0.12 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1382 TYR 0.013 0.001 TYR A1205 PHE 0.028 0.001 PHE A 988 TRP 0.016 0.001 TRP A1302 HIS 0.007 0.001 HIS A1504 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 9137) covalent geometry : angle 0.55056 / 0.27 (12466) hydrogen bonds : bond 0.04523 / 2.96 ( 652) hydrogen bonds : angle 4.30377 / 3.24 ( 1935) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 130 time to evaluate : 0.363 Fit side-chains revert: symmetry clash REVERT: A 228 TYR cc_start: 0.9060 (m-80) cc_final: 0.8234 (m-80) REVERT: A 434 MET cc_start: 0.8585 (tpp) cc_final: 0.8041 (mmm) REVERT: A 517 GLU cc_start: 0.8826 (tp30) cc_final: 0.8146 (tp30) REVERT: A 523 LEU cc_start: 0.9031 (OUTLIER) cc_final: 0.8564 (pp) REVERT: A 814 GLN cc_start: 0.8828 (pt0) cc_final: 0.8431 (tt0) REVERT: A 822 LEU cc_start: 0.9448 (OUTLIER) cc_final: 0.9157 (mm) REVERT: A 1044 PHE cc_start: 0.8536 (t80) cc_final: 0.8144 (t80) REVERT: A 1302 TRP cc_start: 0.8364 (t60) cc_final: 0.7837 (t60) outliers start: 23 outliers final: 19 residues processed: 144 average time/residue: 0.0579 time to fit residues: 13.7429 Evaluate side-chains 141 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1187 GLU Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1361 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 14 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 106 optimal weight: 7.9990 chunk 41 optimal weight: 8.9990 chunk 95 optimal weight: 20.0000 chunk 59 optimal weight: 9.9990 chunk 19 optimal weight: 0.0020 chunk 110 optimal weight: 7.9990 chunk 34 optimal weight: 0.6980 overall best weight: 1.1394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1444 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.116725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.089549 restraints weight = 21758.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.087245 restraints weight = 12216.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.088499 restraints weight = 9519.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.089769 restraints weight = 6520.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.089827 restraints weight = 5779.882| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9137 Z= 0.140 Angle : 0.556 10.961 12466 Z= 0.273 Chirality : 0.039 0.203 1519 Planarity : 0.003 0.041 1519 Dihedral : 6.418 129.891 1283 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.97 % Allowed : 18.61 % Favored : 78.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.24), residues: 1173 helix: 2.38 (0.18), residues: 795 sheet: 1.20 (0.62), residues: 68 loop : 0.12 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1382 TYR 0.018 0.001 TYR A1205 PHE 0.032 0.001 PHE A 988 TRP 0.013 0.001 TRP A1302 HIS 0.008 0.001 HIS A1504 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 9137) covalent geometry : angle 0.55594 / 0.27 (12466) hydrogen bonds : bond 0.04433 / 2.92 ( 652) hydrogen bonds : angle 4.22724 / 3.19 ( 1935) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.227 Fit side-chains REVERT: A 228 TYR cc_start: 0.9046 (m-80) cc_final: 0.8250 (m-80) REVERT: A 434 MET cc_start: 0.8558 (OUTLIER) cc_final: 0.7946 (mmm) REVERT: A 517 GLU cc_start: 0.8807 (tp30) cc_final: 0.8117 (tp30) REVERT: A 523 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8552 (pp) REVERT: A 814 GLN cc_start: 0.8788 (pt0) cc_final: 0.8361 (tt0) REVERT: A 822 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9137 (mm) REVERT: A 1044 PHE cc_start: 0.8535 (t80) cc_final: 0.8296 (t80) outliers start: 26 outliers final: 20 residues processed: 146 average time/residue: 0.0494 time to fit residues: 11.9071 Evaluate side-chains 142 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 119 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1187 GLU Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1361 ILE Chi-restraints excluded: chain A residue 1444 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 0 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 82 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 576 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.116624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.088323 restraints weight = 21637.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.087470 restraints weight = 11899.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.088389 restraints weight = 9918.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.089183 restraints weight = 6898.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.089430 restraints weight = 6099.660| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 9137 Z= 0.134 Angle : 0.571 11.438 12466 Z= 0.276 Chirality : 0.039 0.203 1519 Planarity : 0.003 0.039 1519 Dihedral : 6.380 129.645 1283 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.85 % Allowed : 19.29 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.24), residues: 1173 helix: 2.35 (0.18), residues: 797 sheet: 1.29 (0.62), residues: 68 loop : 0.04 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1382 TYR 0.019 0.001 TYR A1205 PHE 0.032 0.001 PHE A 988 TRP 0.017 0.001 TRP A1302 HIS 0.008 0.001 HIS A1504 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.13 ( 9137) covalent geometry : angle 0.57119 / 0.28 (12466) hydrogen bonds : bond 0.04375 / 2.87 ( 652) hydrogen bonds : angle 4.23071 / 3.18 ( 1935) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.259 Fit side-chains revert: symmetry clash REVERT: A 228 TYR cc_start: 0.8990 (m-80) cc_final: 0.8223 (m-80) REVERT: A 434 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8007 (mmm) REVERT: A 517 GLU cc_start: 0.8853 (tp30) cc_final: 0.8165 (tp30) REVERT: A 523 LEU cc_start: 0.9021 (OUTLIER) cc_final: 0.8543 (pp) REVERT: A 814 GLN cc_start: 0.8776 (pt0) cc_final: 0.8355 (tt0) REVERT: A 822 LEU cc_start: 0.9426 (OUTLIER) cc_final: 0.9142 (mm) REVERT: A 1044 PHE cc_start: 0.8624 (t80) cc_final: 0.8385 (t80) REVERT: A 1302 TRP cc_start: 0.8390 (t60) cc_final: 0.8013 (t60) outliers start: 25 outliers final: 20 residues processed: 142 average time/residue: 0.0536 time to fit residues: 12.4634 Evaluate side-chains 143 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 120 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1187 GLU Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1361 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 53 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 11 optimal weight: 0.0870 chunk 95 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 69 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.1760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 576 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.116285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.088789 restraints weight = 21602.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.086566 restraints weight = 12520.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.087735 restraints weight = 9892.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.089354 restraints weight = 6751.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.089312 restraints weight = 5512.846| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 9137 Z= 0.143 Angle : 0.567 11.440 12466 Z= 0.277 Chirality : 0.039 0.207 1519 Planarity : 0.003 0.035 1519 Dihedral : 6.399 131.115 1283 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.97 % Allowed : 18.84 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.24), residues: 1173 helix: 2.38 (0.18), residues: 797 sheet: 1.33 (0.62), residues: 68 loop : 0.02 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 256 TYR 0.023 0.001 TYR A1205 PHE 0.035 0.001 PHE A 988 TRP 0.015 0.001 TRP A1302 HIS 0.007 0.001 HIS A1504 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 9137) covalent geometry : angle 0.56708 / 0.28 (12466) hydrogen bonds : bond 0.04389 / 2.87 ( 652) hydrogen bonds : angle 4.19507 / 3.15 ( 1935) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.282 Fit side-chains REVERT: A 228 TYR cc_start: 0.9044 (m-80) cc_final: 0.8259 (m-80) REVERT: A 434 MET cc_start: 0.8596 (OUTLIER) cc_final: 0.8027 (mmm) REVERT: A 517 GLU cc_start: 0.8821 (tp30) cc_final: 0.8133 (tp30) REVERT: A 523 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8548 (pp) REVERT: A 814 GLN cc_start: 0.8755 (pt0) cc_final: 0.8320 (tt0) REVERT: A 822 LEU cc_start: 0.9468 (OUTLIER) cc_final: 0.9172 (mm) REVERT: A 1044 PHE cc_start: 0.8562 (t80) cc_final: 0.8327 (t80) REVERT: A 1302 TRP cc_start: 0.8360 (t60) cc_final: 0.7997 (t60) outliers start: 26 outliers final: 20 residues processed: 138 average time/residue: 0.0565 time to fit residues: 12.7705 Evaluate side-chains 140 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 117 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 455 VAL Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 604 GLU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1187 GLU Chi-restraints excluded: chain A residue 1226 ILE Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1361 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 39 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 100 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 60 optimal weight: 10.0000 chunk 82 optimal weight: 0.9990 chunk 110 optimal weight: 8.9990 chunk 49 optimal weight: 0.0070 chunk 71 optimal weight: 1.9990 chunk 21 optimal weight: 0.0570 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.117952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.090856 restraints weight = 21517.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.088414 restraints weight = 13090.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.089614 restraints weight = 10220.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.091035 restraints weight = 7059.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.091024 restraints weight = 6079.844| |-----------------------------------------------------------------------------| r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9137 Z= 0.116 Angle : 0.560 11.822 12466 Z= 0.269 Chirality : 0.039 0.202 1519 Planarity : 0.003 0.035 1519 Dihedral : 6.252 129.841 1283 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.28 % Allowed : 19.75 % Favored : 77.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.24), residues: 1173 helix: 2.40 (0.18), residues: 797 sheet: 1.35 (0.61), residues: 68 loop : -0.01 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 256 TYR 0.025 0.001 TYR A1205 PHE 0.025 0.001 PHE A 988 TRP 0.016 0.001 TRP A1302 HIS 0.008 0.001 HIS A1504 Details of bonding type rmsd/Z covalent geometry : bond 0.00247 / 0.12 ( 9137) covalent geometry : angle 0.56013 / 0.27 (12466) hydrogen bonds : bond 0.04189 / 2.75 ( 652) hydrogen bonds : angle 4.13391 / 3.10 ( 1935) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2346 Ramachandran restraints generated. 1173 Oldfield, 0 Emsley, 1173 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 0.454 Fit side-chains revert: symmetry clash REVERT: A 228 TYR cc_start: 0.8980 (m-80) cc_final: 0.8173 (m-80) REVERT: A 434 MET cc_start: 0.8563 (OUTLIER) cc_final: 0.8099 (mmm) REVERT: A 517 GLU cc_start: 0.8797 (tp30) cc_final: 0.8124 (tp30) REVERT: A 523 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8520 (pp) REVERT: A 814 GLN cc_start: 0.8761 (pt0) cc_final: 0.8322 (tt0) REVERT: A 822 LEU cc_start: 0.9452 (OUTLIER) cc_final: 0.9168 (mm) REVERT: A 1044 PHE cc_start: 0.8544 (t80) cc_final: 0.8176 (t80) REVERT: A 1302 TRP cc_start: 0.8356 (t60) cc_final: 0.8042 (t60) outliers start: 20 outliers final: 17 residues processed: 149 average time/residue: 0.0583 time to fit residues: 14.2161 Evaluate side-chains 150 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 425 LEU Chi-restraints excluded: chain A residue 434 MET Chi-restraints excluded: chain A residue 509 HIS Chi-restraints excluded: chain A residue 523 LEU Chi-restraints excluded: chain A residue 715 LEU Chi-restraints excluded: chain A residue 718 MET Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 971 THR Chi-restraints excluded: chain A residue 1003 VAL Chi-restraints excluded: chain A residue 1069 LEU Chi-restraints excluded: chain A residue 1115 LEU Chi-restraints excluded: chain A residue 1135 LEU Chi-restraints excluded: chain A residue 1159 LEU Chi-restraints excluded: chain A residue 1179 THR Chi-restraints excluded: chain A residue 1187 GLU Chi-restraints excluded: chain A residue 1258 LEU Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1361 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 111 optimal weight: 30.0000 chunk 21 optimal weight: 0.5980 chunk 81 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 79 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 chunk 115 optimal weight: 8.9990 chunk 78 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 576 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.117588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.089473 restraints weight = 21302.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.088314 restraints weight = 12254.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.089464 restraints weight = 9986.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.090818 restraints weight = 6887.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.090896 restraints weight = 5992.882| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8456 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9137 Z= 0.128 Angle : 0.568 11.784 12466 Z= 0.274 Chirality : 0.040 0.305 1519 Planarity : 0.003 0.035 1519 Dihedral : 6.229 132.008 1283 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.28 % Allowed : 20.21 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.24), residues: 1173 helix: 2.42 (0.18), residues: 797 sheet: 1.26 (0.60), residues: 68 loop : -0.01 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1218 TYR 0.021 0.001 TYR A1205 PHE 0.036 0.001 PHE A 988 TRP 0.014 0.001 TRP A1302 HIS 0.008 0.001 HIS A1504 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 ( 9137) covalent geometry : angle 0.56757 / 0.27 (12466) hydrogen bonds : bond 0.04221 / 2.77 ( 652) hydrogen bonds : angle 4.12162 / 3.09 ( 1935) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1390.57 seconds wall clock time: 24 minutes 52.86 seconds (1492.86 seconds total)