Starting phenix.real_space_refine on Sat Dec 28 23:45:15 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y1l_33565/12_2024/7y1l_33565.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y1l_33565/12_2024/7y1l_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_33565/12_2024/7y1l_33565.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y1l_33565/12_2024/7y1l_33565.map" model { file = "/net/cci-nas-00/data/ceres_data/7y1l_33565/12_2024/7y1l_33565.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y1l_33565/12_2024/7y1l_33565.cif" } resolution = 3.73 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= 0.002 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: {'GLN:plan1': 9, 'HIS:plan': 3, 'TYR:plan': 2, 'ASN:plan1': 8, 'ASP:plan': 28, 'PHE:plan': 2, 'GLU:plan': 29, 'ARG:plan': 8} 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: 5.67, per 1000 atoms: 0.63 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: 2.90 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 1.07 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: 3.47 Time building geometry restraints manager: 3.14 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: 5302 31.03 - 62.06: 101 62.06 - 93.10: 9 93.10 - 124.13: 0 124.13 - 155.16: 1 Dihedral angle restraints: 5413 sinusoidal: 1950 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 5410 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: 1.660 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: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 24.340 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 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= 0.293 Angle : 0.587 7.748 12466 Z= 0.344 Chirality : 0.043 0.322 1519 Planarity : 0.004 0.068 1519 Dihedral : 12.439 155.161 3167 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.44 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 (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: 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 TRP 0.053 0.001 TRP A 229 HIS 0.005 0.001 HIS A1504 PHE 0.014 0.001 PHE A1149 TYR 0.026 0.001 TYR A 228 ARG 0.003 0.000 ARG A1218 *********************** 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 : 0.868 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: 0.9098 (tp) REVERT: A 814 GLN cc_start: 0.8797 (pt0) cc_final: 0.8183 (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: 0.6011 (t) REVERT: A 1426 MET cc_start: 0.9063 (mmm) cc_final: 0.8846 (tpp) outliers start: 9 outliers final: 3 residues processed: 176 average time/residue: 0.1613 time to fit residues: 43.1556 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 : 0.971 ------------------------------------------------------------------------------- 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 99 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 49 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 60 optimal weight: 0.0010 chunk 47 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 68 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 HIS A 867 HIS A1186 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9137 Z= 0.177 Angle : 0.570 7.749 12466 Z= 0.283 Chirality : 0.041 0.175 1519 Planarity : 0.003 0.041 1519 Dihedral : 9.694 123.038 1359 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 1.37 % Allowed : 10.62 % Favored : 88.01 % 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: 2.83 (0.25), residues: 1173 helix: 2.55 (0.18), residues: 805 sheet: 0.82 (0.64), residues: 68 loop : 0.28 (0.37), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 230 HIS 0.006 0.001 HIS A1504 PHE 0.016 0.001 PHE A 569 TYR 0.012 0.001 TYR A1331 ARG 0.004 0.000 ARG A 970 *********************** 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 174 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 162 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 228 TYR cc_start: 0.9027 (m-80) cc_final: 0.8162 (m-80) REVERT: A 434 MET cc_start: 0.8516 (tpp) cc_final: 0.8032 (mmm) REVERT: A 814 GLN cc_start: 0.8854 (pt0) cc_final: 0.8388 (tt0) REVERT: A 975 TRP cc_start: 0.8628 (m100) cc_final: 0.8110 (m100) REVERT: A 1044 PHE cc_start: 0.8349 (t80) cc_final: 0.7982 (t80) REVERT: A 1091 ARG cc_start: 0.8148 (mmt-90) cc_final: 0.7920 (mmt180) REVERT: A 1123 MET cc_start: 0.8608 (tpp) cc_final: 0.8405 (tpp) outliers start: 12 outliers final: 8 residues processed: 168 average time/residue: 0.1579 time to fit residues: 40.2727 Evaluate side-chains 135 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 127 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 476 GLU 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 Chi-restraints excluded: chain A residue 1388 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 chunk 115 optimal weight: 20.0000 chunk 95 optimal weight: 20.0000 chunk 106 optimal weight: 5.9990 chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 0.4980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 9137 Z= 0.247 Angle : 0.568 7.353 12466 Z= 0.282 Chirality : 0.041 0.185 1519 Planarity : 0.003 0.047 1519 Dihedral : 9.373 131.243 1357 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.40 % Allowed : 13.47 % 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 (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: 2.75 (0.25), residues: 1173 helix: 2.50 (0.18), residues: 802 sheet: 0.82 (0.63), residues: 68 loop : 0.24 (0.36), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1302 HIS 0.007 0.001 HIS A1504 PHE 0.019 0.001 PHE A1362 TYR 0.014 0.001 TYR A1205 ARG 0.004 0.000 ARG A 363 *********************** 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 158 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 1.061 Fit side-chains revert: symmetry clash REVERT: A 228 TYR cc_start: 0.9081 (m-80) cc_final: 0.8239 (m-80) REVERT: A 363 ARG cc_start: 0.8105 (mmt90) cc_final: 0.7368 (mtt90) REVERT: A 434 MET cc_start: 0.8573 (tpp) cc_final: 0.7973 (mmm) REVERT: A 517 GLU cc_start: 0.8807 (tp30) cc_final: 0.8252 (tp30) REVERT: A 814 GLN cc_start: 0.8862 (pt0) cc_final: 0.8381 (tt0) REVERT: A 1044 PHE cc_start: 0.8406 (t80) cc_final: 0.8031 (t80) REVERT: A 1091 ARG cc_start: 0.8176 (mmt-90) cc_final: 0.7955 (mmt180) REVERT: A 1115 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9032 (mm) REVERT: A 1302 TRP cc_start: 0.8214 (t60) cc_final: 0.7813 (t60) outliers start: 21 outliers final: 14 residues processed: 147 average time/residue: 0.1650 time to fit residues: 37.1166 Evaluate side-chains 139 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 1.093 ------------------------------------------------------------------------------- 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 718 MET Chi-restraints excluded: chain A residue 822 LEU Chi-restraints excluded: chain A residue 886 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 1160 ASP Chi-restraints excluded: chain A residue 1226 ILE 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 106 optimal weight: 10.0000 chunk 80 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 114 optimal weight: 20.0000 chunk 56 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 HIS A1379 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2058 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= 0.207 Angle : 0.543 7.631 12466 Z= 0.271 Chirality : 0.040 0.168 1519 Planarity : 0.003 0.048 1519 Dihedral : 9.107 131.701 1357 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.74 % Allowed : 14.50 % Favored : 82.76 % 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: 2.71 (0.25), residues: 1173 helix: 2.46 (0.18), residues: 805 sheet: 0.83 (0.62), residues: 68 loop : 0.21 (0.36), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A1302 HIS 0.007 0.001 HIS A1504 PHE 0.024 0.001 PHE A1356 TYR 0.014 0.001 TYR A1205 ARG 0.003 0.000 ARG A 363 *********************** 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 163 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 139 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: A 228 TYR cc_start: 0.9055 (m-80) cc_final: 0.8242 (m-80) REVERT: A 363 ARG cc_start: 0.7953 (mmt90) cc_final: 0.7195 (mtt90) REVERT: A 434 MET cc_start: 0.8557 (tpp) cc_final: 0.7939 (mmm) REVERT: A 517 GLU cc_start: 0.8800 (tp30) cc_final: 0.8263 (tp30) REVERT: A 523 LEU cc_start: 0.9026 (OUTLIER) cc_final: 0.8563 (pp) REVERT: A 814 GLN cc_start: 0.8857 (pt0) cc_final: 0.8397 (tt0) REVERT: A 1044 PHE cc_start: 0.8389 (t80) cc_final: 0.7984 (t80) REVERT: A 1091 ARG cc_start: 0.8155 (mmt-90) cc_final: 0.7935 (mmt180) outliers start: 24 outliers final: 18 residues processed: 153 average time/residue: 0.1584 time to fit residues: 36.9495 Evaluate side-chains 145 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 886 VAL Chi-restraints excluded: chain A residue 1069 LEU 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 1179 THR 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 94 optimal weight: 9.9990 chunk 64 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 97 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 0 optimal weight: 1.9990 chunk 58 optimal weight: 9.9990 chunk 102 optimal weight: 3.9990 chunk 28 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 9137 Z= 0.241 Angle : 0.553 9.530 12466 Z= 0.278 Chirality : 0.040 0.199 1519 Planarity : 0.003 0.047 1519 Dihedral : 8.960 135.210 1357 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.85 % Allowed : 15.75 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.65 (0.24), residues: 1173 helix: 2.44 (0.18), residues: 799 sheet: 0.89 (0.62), residues: 68 loop : 0.14 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1302 HIS 0.007 0.001 HIS A1504 PHE 0.019 0.001 PHE A 988 TYR 0.015 0.001 TYR A1205 ARG 0.003 0.000 ARG A1218 *********************** 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 158 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: A 228 TYR cc_start: 0.9071 (m-80) cc_final: 0.8238 (m-80) REVERT: A 434 MET cc_start: 0.8566 (tpp) cc_final: 0.8048 (mmm) REVERT: A 517 GLU cc_start: 0.8819 (tp30) cc_final: 0.8148 (tp30) REVERT: A 523 LEU cc_start: 0.9039 (OUTLIER) cc_final: 0.8564 (pp) REVERT: A 814 GLN cc_start: 0.8852 (pt0) cc_final: 0.8399 (tt0) REVERT: A 1044 PHE cc_start: 0.8405 (t80) cc_final: 0.8010 (t80) REVERT: A 1091 ARG cc_start: 0.8193 (mmt-90) cc_final: 0.7960 (mmt180) REVERT: A 1302 TRP cc_start: 0.8342 (t60) cc_final: 0.7829 (t60) outliers start: 25 outliers final: 21 residues processed: 147 average time/residue: 0.1544 time to fit residues: 35.4563 Evaluate side-chains 146 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 1.038 ------------------------------------------------------------------------------- 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 495 ILE 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 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 1160 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 114 optimal weight: 0.3980 chunk 94 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 37 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9137 Z= 0.183 Angle : 0.532 10.479 12466 Z= 0.263 Chirality : 0.039 0.197 1519 Planarity : 0.003 0.047 1519 Dihedral : 8.783 135.282 1357 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 2.85 % Allowed : 17.24 % Favored : 79.91 % 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: 2.72 (0.24), residues: 1173 helix: 2.49 (0.18), residues: 799 sheet: 1.14 (0.61), residues: 68 loop : 0.12 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1302 HIS 0.008 0.001 HIS A1504 PHE 0.029 0.001 PHE A 988 TYR 0.016 0.001 TYR A1205 ARG 0.008 0.000 ARG A 363 *********************** 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 160 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 135 time to evaluate : 0.991 Fit side-chains revert: symmetry clash REVERT: A 228 TYR cc_start: 0.9025 (m-80) cc_final: 0.8244 (m-80) REVERT: A 363 ARG cc_start: 0.8052 (mmt90) cc_final: 0.7802 (mtt90) REVERT: A 402 MET cc_start: 0.7933 (ttp) cc_final: 0.7677 (ptm) REVERT: A 434 MET cc_start: 0.8503 (tpp) cc_final: 0.7939 (mmm) REVERT: A 517 GLU cc_start: 0.8802 (tp30) cc_final: 0.8114 (tp30) REVERT: A 523 LEU cc_start: 0.9019 (OUTLIER) cc_final: 0.8544 (pp) REVERT: A 814 GLN cc_start: 0.8856 (pt0) cc_final: 0.8416 (tt0) REVERT: A 1044 PHE cc_start: 0.8379 (t80) cc_final: 0.7999 (t80) REVERT: A 1091 ARG cc_start: 0.8178 (mmt-90) cc_final: 0.7925 (mmt180) outliers start: 25 outliers final: 18 residues processed: 150 average time/residue: 0.1494 time to fit residues: 35.0814 Evaluate side-chains 139 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 509 HIS Chi-restraints excluded: chain A residue 523 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 1160 ASP 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 110 optimal weight: 9.9990 chunk 12 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 chunk 96 optimal weight: 4.9990 chunk 63 optimal weight: 0.9980 chunk 113 optimal weight: 6.9990 chunk 71 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 52 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9137 Z= 0.169 Angle : 0.535 11.280 12466 Z= 0.269 Chirality : 0.040 0.303 1519 Planarity : 0.003 0.042 1519 Dihedral : 8.681 137.067 1357 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.74 % Allowed : 17.92 % Favored : 79.34 % 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: 2.67 (0.24), residues: 1173 helix: 2.46 (0.18), residues: 795 sheet: 1.27 (0.61), residues: 68 loop : 0.07 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A1302 HIS 0.008 0.001 HIS A1504 PHE 0.030 0.001 PHE A 988 TYR 0.018 0.001 TYR A1205 ARG 0.006 0.000 ARG A 363 *********************** 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 154 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 1.045 Fit side-chains revert: symmetry clash REVERT: A 228 TYR cc_start: 0.8988 (m-80) cc_final: 0.8210 (m-80) REVERT: A 363 ARG cc_start: 0.7965 (mmt90) cc_final: 0.7724 (mtt90) REVERT: A 402 MET cc_start: 0.7925 (ttp) cc_final: 0.7644 (ptm) REVERT: A 434 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8053 (mmm) REVERT: A 517 GLU cc_start: 0.8788 (tp30) cc_final: 0.8102 (tp30) REVERT: A 523 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8535 (pp) REVERT: A 814 GLN cc_start: 0.8862 (pt0) cc_final: 0.8431 (tt0) REVERT: A 1044 PHE cc_start: 0.8384 (t80) cc_final: 0.8018 (t80) REVERT: A 1302 TRP cc_start: 0.8282 (t60) cc_final: 0.7919 (t60) outliers start: 24 outliers final: 18 residues processed: 144 average time/residue: 0.1549 time to fit residues: 35.1989 Evaluate side-chains 141 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 121 time to evaluate : 1.049 ------------------------------------------------------------------------------- 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 577 ILE 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 1258 LEU Chi-restraints excluded: chain A residue 1259 ASN Chi-restraints excluded: chain A residue 1361 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 67 optimal weight: 0.1980 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 89 optimal weight: 0.5980 chunk 103 optimal weight: 7.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 576 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9137 Z= 0.163 Angle : 0.533 11.733 12466 Z= 0.264 Chirality : 0.039 0.194 1519 Planarity : 0.003 0.036 1519 Dihedral : 8.560 139.572 1355 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.40 % Allowed : 18.04 % Favored : 79.57 % 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: 2.67 (0.24), residues: 1173 helix: 2.47 (0.18), residues: 798 sheet: 1.37 (0.61), residues: 68 loop : -0.02 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1302 HIS 0.008 0.001 HIS A1504 PHE 0.022 0.001 PHE A 988 TYR 0.012 0.001 TYR A1205 ARG 0.004 0.000 ARG A 363 *********************** 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 161 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 140 time to evaluate : 1.031 Fit side-chains revert: symmetry clash REVERT: A 228 TYR cc_start: 0.9019 (m-80) cc_final: 0.8189 (m-80) REVERT: A 235 ILE cc_start: 0.9333 (mm) cc_final: 0.8738 (mt) REVERT: A 363 ARG cc_start: 0.7921 (mmt90) cc_final: 0.7645 (mtt90) REVERT: A 402 MET cc_start: 0.7896 (ttp) cc_final: 0.7626 (ptm) REVERT: A 434 MET cc_start: 0.8583 (OUTLIER) cc_final: 0.8158 (mmm) REVERT: A 517 GLU cc_start: 0.8784 (tp30) cc_final: 0.8102 (tp30) REVERT: A 523 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8530 (pp) REVERT: A 814 GLN cc_start: 0.8846 (pt0) cc_final: 0.8381 (tt0) REVERT: A 1044 PHE cc_start: 0.8361 (t80) cc_final: 0.7988 (t80) REVERT: A 1302 TRP cc_start: 0.8297 (t60) cc_final: 0.7971 (t60) outliers start: 21 outliers final: 17 residues processed: 153 average time/residue: 0.1481 time to fit residues: 36.1152 Evaluate side-chains 143 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.988 ------------------------------------------------------------------------------- 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 105 optimal weight: 1.9990 chunk 63 optimal weight: 0.7980 chunk 46 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 95 optimal weight: 20.0000 chunk 100 optimal weight: 0.3980 chunk 69 optimal weight: 0.0770 chunk 112 optimal weight: 0.6980 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1240 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9137 Z= 0.164 Angle : 0.551 12.060 12466 Z= 0.271 Chirality : 0.039 0.195 1519 Planarity : 0.003 0.034 1519 Dihedral : 8.486 141.265 1355 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.51 % Allowed : 18.95 % Favored : 78.54 % 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: 2.72 (0.24), residues: 1173 helix: 2.52 (0.18), residues: 797 sheet: 1.42 (0.61), residues: 68 loop : -0.01 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1302 HIS 0.007 0.001 HIS A1504 PHE 0.027 0.001 PHE A1356 TYR 0.014 0.001 TYR A1205 ARG 0.005 0.000 ARG A 363 *********************** 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 158 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 1.034 Fit side-chains REVERT: A 228 TYR cc_start: 0.9001 (m-80) cc_final: 0.8198 (m-80) REVERT: A 235 ILE cc_start: 0.9299 (mm) cc_final: 0.8667 (mt) REVERT: A 363 ARG cc_start: 0.7897 (mmt90) cc_final: 0.7641 (mtt90) REVERT: A 402 MET cc_start: 0.7900 (ttp) cc_final: 0.7685 (ptm) REVERT: A 434 MET cc_start: 0.8601 (OUTLIER) cc_final: 0.8169 (mmm) REVERT: A 517 GLU cc_start: 0.8772 (tp30) cc_final: 0.8094 (tp30) REVERT: A 523 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8525 (pp) REVERT: A 814 GLN cc_start: 0.8856 (pt0) cc_final: 0.8389 (tt0) REVERT: A 1044 PHE cc_start: 0.8356 (t80) cc_final: 0.7984 (t80) REVERT: A 1302 TRP cc_start: 0.8303 (t60) cc_final: 0.7989 (t60) outliers start: 22 outliers final: 17 residues processed: 150 average time/residue: 0.1472 time to fit residues: 34.8618 Evaluate side-chains 150 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 0.930 ------------------------------------------------------------------------------- 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 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 68 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 77 optimal weight: 0.7980 chunk 117 optimal weight: 6.9990 chunk 108 optimal weight: 10.0000 chunk 93 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 0.0070 chunk 74 optimal weight: 0.6980 chunk 99 optimal weight: 5.9990 overall best weight: 1.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9137 Z= 0.220 Angle : 0.579 12.316 12466 Z= 0.285 Chirality : 0.040 0.206 1519 Planarity : 0.003 0.042 1519 Dihedral : 8.566 144.808 1355 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 2.17 % Allowed : 20.21 % Favored : 77.63 % 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: 2.69 (0.24), residues: 1173 helix: 2.50 (0.18), residues: 797 sheet: 1.11 (0.60), residues: 68 loop : 0.01 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A1302 HIS 0.007 0.001 HIS A1504 PHE 0.037 0.001 PHE A 988 TYR 0.021 0.001 TYR A1205 ARG 0.005 0.000 ARG A 363 ********************** 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 147 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 128 time to evaluate : 0.991 Fit side-chains REVERT: A 228 TYR cc_start: 0.9037 (m-80) cc_final: 0.8210 (m-80) REVERT: A 363 ARG cc_start: 0.8069 (mmt90) cc_final: 0.7780 (mtt90) REVERT: A 434 MET cc_start: 0.8648 (OUTLIER) cc_final: 0.8107 (mmm) REVERT: A 517 GLU cc_start: 0.8816 (tp30) cc_final: 0.8140 (tp30) REVERT: A 523 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8553 (pp) REVERT: A 814 GLN cc_start: 0.8859 (pt0) cc_final: 0.8381 (tt0) REVERT: A 1044 PHE cc_start: 0.8396 (t80) cc_final: 0.8018 (t80) REVERT: A 1302 TRP cc_start: 0.8368 (t60) cc_final: 0.8100 (t60) outliers start: 19 outliers final: 17 residues processed: 139 average time/residue: 0.1484 time to fit residues: 32.8803 Evaluate side-chains 144 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 1.089 ------------------------------------------------------------------------------- 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 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 28 optimal weight: 5.9990 chunk 86 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 93 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 5 optimal weight: 0.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.117273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.090402 restraints weight = 21369.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.088665 restraints weight = 11985.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.089733 restraints weight = 9213.490| |-----------------------------------------------------------------------------| r_work (final): 0.3273 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9137 Z= 0.207 Angle : 0.580 12.360 12466 Z= 0.284 Chirality : 0.040 0.216 1519 Planarity : 0.003 0.041 1519 Dihedral : 8.511 143.333 1355 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.17 % Allowed : 20.66 % Favored : 77.17 % 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: 2.67 (0.24), residues: 1173 helix: 2.49 (0.18), residues: 798 sheet: 1.08 (0.61), residues: 68 loop : -0.02 (0.34), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1302 HIS 0.007 0.001 HIS A1504 PHE 0.025 0.001 PHE A1356 TYR 0.019 0.001 TYR A1205 ARG 0.005 0.000 ARG A 363 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1727.72 seconds wall clock time: 32 minutes 29.26 seconds (1949.26 seconds total)