Starting phenix.real_space_refine on Wed Aug 5 15:48:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ehr_48062/08_2026/9ehr_48062.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ehr_48062/08_2026/9ehr_48062.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ehr_48062/08_2026/9ehr_48062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ehr_48062/08_2026/9ehr_48062.map" model { file = "/net/cci-nas-00/data/ceres_data/9ehr_48062/08_2026/9ehr_48062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ehr_48062/08_2026/9ehr_48062.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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 131 5.49 5 Mg 2 5.21 5 S 18 5.16 5 C 6030 2.51 5 N 1781 2.21 5 O 2266 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10228 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 7441 Number of conformers: 1 Conformer: "" Number of residues, atoms: 893, 7441 Classifications: {'peptide': 893} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 24, 'TRANS': 868} Chain breaks: 5 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 33 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 1987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1987 Classifications: {'RNA': 94} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 8, 'rna3p_pur': 39, 'rna3p_pyr': 43} Link IDs: {'rna2p': 11, 'rna3p': 82} Chain: "C" Number of atoms: 612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 612 Classifications: {'DNA': 30} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 29} Chain: "D" Number of atoms: 186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 186 Classifications: {'DNA': 9} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 8} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 2.33, per 1000 atoms: 0.23 Number of scatterers: 10228 At special positions: 0 Unit cell: (77.4876, 109.982, 143.31, 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 18 16.00 P 131 15.00 Mg 2 11.99 O 2266 8.00 N 1781 7.00 C 6030 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: 0.62 Conformation dependent library (CDL) restraints added in 282.2 milliseconds 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1728 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 9 sheets defined 49.7% alpha, 10.9% beta 52 base pairs and 94 stacking pairs defined. Time for finding SS restraints: 1.25 Creating SS restraints... Processing helix chain 'A' and resid 52 through 82 removed outlier: 3.802A pdb=" N LYS A 72 " --> pdb=" O LYS A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 88 through 100 Processing helix chain 'A' and resid 311 through 325 removed outlier: 4.256A pdb=" N GLU A 325 " --> pdb=" O ASN A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 342 Processing helix chain 'A' and resid 349 through 362 Processing helix chain 'A' and resid 364 through 373 removed outlier: 3.990A pdb=" N LEU A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 384 through 399 Processing helix chain 'A' and resid 416 through 431 removed outlier: 3.833A pdb=" N THR A 429 " --> pdb=" O LYS A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 438 Processing helix chain 'A' and resid 466 through 474 Processing helix chain 'A' and resid 476 through 486 Processing helix chain 'A' and resid 487 through 494 Processing helix chain 'A' and resid 496 through 504 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.750A pdb=" N SER A 525 " --> pdb=" O GLN A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 543 Processing helix chain 'A' and resid 545 through 549 removed outlier: 3.739A pdb=" N ASP A 549 " --> pdb=" O LYS A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 565 Processing helix chain 'A' and resid 579 through 587 Processing helix chain 'A' and resid 606 through 623 Processing helix chain 'A' and resid 649 through 652 Processing helix chain 'A' and resid 663 through 666 Processing helix chain 'A' and resid 667 through 676 Processing helix chain 'A' and resid 679 through 688 Processing helix chain 'A' and resid 691 through 699 Processing helix chain 'A' and resid 792 through 804 Processing helix chain 'A' and resid 814 through 823 Processing helix chain 'A' and resid 1282 through 1292 Processing helix chain 'A' and resid 1293 through 1296 removed outlier: 3.506A pdb=" N VAL A1296 " --> pdb=" O LEU A1293 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1293 through 1296' Processing helix chain 'A' and resid 1308 through 1319 removed outlier: 3.573A pdb=" N LEU A1312 " --> pdb=" O THR A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1333 through 1346 removed outlier: 3.676A pdb=" N ASN A1346 " --> pdb=" O ILE A1342 " (cutoff:3.500A) Processing helix chain 'A' and resid 1347 through 1350 Processing helix chain 'A' and resid 1355 through 1364 Processing helix chain 'A' and resid 1375 through 1384 removed outlier: 3.567A pdb=" N VAL A1379 " --> pdb=" O SER A1375 " (cutoff:3.500A) Processing helix chain 'A' and resid 1385 through 1388 Processing helix chain 'A' and resid 1398 through 1410 Processing helix chain 'A' and resid 1416 through 1425 Processing helix chain 'A' and resid 1472 through 1476 Processing helix chain 'A' and resid 1536 through 1543 Processing helix chain 'A' and resid 1569 through 1577 removed outlier: 5.224A pdb=" N TYR A1575 " --> pdb=" O SER A1571 " (cutoff:3.500A) Processing helix chain 'A' and resid 1586 through 1595 Processing helix chain 'A' and resid 1608 through 1624 removed outlier: 3.859A pdb=" N GLY A1621 " --> pdb=" O MET A1617 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE A1622 " --> pdb=" O LYS A1618 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 463 through 465 Processing sheet with id=AA2, first strand: chain 'A' and resid 513 through 514 Processing sheet with id=AA3, first strand: chain 'A' and resid 630 through 635 removed outlier: 5.278A pdb=" N ARG A 646 " --> pdb=" O GLU A 631 " (cutoff:3.500A) removed outlier: 8.723A pdb=" N ARG A 633 " --> pdb=" O THR A 644 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N THR A 644 " --> pdb=" O ARG A 633 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ASP A 635 " --> pdb=" O ASN A 642 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ASN A 642 " --> pdb=" O ASP A 635 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 1442 through 1446 removed outlier: 3.663A pdb=" N LEU A1443 " --> pdb=" O VAL A1371 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ARG A1370 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 8.816A pdb=" N ILE A1244 " --> pdb=" O ARG A1370 " (cutoff:3.500A) removed outlier: 13.869A pdb=" N LYS A1372 " --> pdb=" O ASP A1242 " (cutoff:3.500A) removed outlier: 18.065A pdb=" N ASP A1242 " --> pdb=" O LYS A1372 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLY A1243 " --> pdb=" O ASN A1469 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN A1469 " --> pdb=" O GLY A1243 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ILE A1467 " --> pdb=" O TYR A1245 " (cutoff:3.500A) removed outlier: 8.111A pdb=" N GLU A1247 " --> pdb=" O TYR A1465 " (cutoff:3.500A) removed outlier: 11.074A pdb=" N TYR A1465 " --> pdb=" O GLU A1247 " (cutoff:3.500A) removed outlier: 18.124A pdb=" N TYR A1249 " --> pdb=" O PHE A1463 " (cutoff:3.500A) removed outlier: 22.690A pdb=" N PHE A1463 " --> pdb=" O TYR A1249 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 1270 through 1273 removed outlier: 4.681A pdb=" N VAL A1261 " --> pdb=" O ILE A1273 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 1276 through 1277 Processing sheet with id=AA7, first strand: chain 'A' and resid 1390 through 1391 Processing sheet with id=AA8, first strand: chain 'A' and resid 1491 through 1496 Processing sheet with id=AA9, first strand: chain 'A' and resid 1531 through 1533 removed outlier: 3.899A pdb=" N ILE A1547 " --> pdb=" O VAL A1533 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LYS A1562 " --> pdb=" O ALA A1545 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N ILE A1547 " --> pdb=" O ARG A1560 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N ARG A1560 " --> pdb=" O ILE A1547 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR A1549 " --> pdb=" O LYS A1558 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N LYS A1558 " --> pdb=" O TYR A1549 " (cutoff:3.500A) 320 hydrogen bonds defined for protein. 915 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 131 hydrogen bonds 246 hydrogen bond angles 0 basepair planarities 52 basepair parallelities 94 stacking parallelities Total time for adding SS restraints: 2.41 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2287 1.33 - 1.46: 3080 1.46 - 1.58: 5052 1.58 - 1.70: 261 1.70 - 1.82: 26 Bond restraints: 10706 Sorted by residual: bond pdb=" C1' DC C 24 " pdb=" N1 DC C 24 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.28e+01 bond pdb=" C1' DT D 4 " pdb=" N1 DT D 4 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.06e+01 bond pdb=" C1' DT C 19 " pdb=" N1 DT C 19 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.05e+01 bond pdb=" C1' DC C 1 " pdb=" N1 DC C 1 " ideal model delta sigma weight residual 1.468 1.511 -0.043 1.40e-02 5.10e+03 9.27e+00 bond pdb=" C1' DC C 20 " pdb=" N1 DC C 20 " ideal model delta sigma weight residual 1.468 1.507 -0.039 1.40e-02 5.10e+03 7.85e+00 ... (remaining 10701 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 14431 2.43 - 4.86: 532 4.86 - 7.29: 66 7.29 - 9.72: 20 9.72 - 12.16: 6 Bond angle restraints: 15055 Sorted by residual: angle pdb=" O5' G B 90 " pdb=" C5' G B 90 " pdb=" C4' G B 90 " ideal model delta sigma weight residual 109.40 116.36 -6.96 8.00e-01 1.56e+00 7.57e+01 angle pdb=" C1' U B 66 " pdb=" N1 U B 66 " pdb=" C2 U B 66 " ideal model delta sigma weight residual 117.70 126.85 -9.15 1.20e+00 6.94e-01 5.81e+01 angle pdb=" N1 U B 66 " pdb=" C2 U B 66 " pdb=" O2 U B 66 " ideal model delta sigma weight residual 122.80 128.03 -5.23 7.00e-01 2.04e+00 5.58e+01 angle pdb=" C3' U B 66 " pdb=" O3' U B 66 " pdb=" P U B 67 " ideal model delta sigma weight residual 119.70 127.99 -8.29 1.20e+00 6.94e-01 4.78e+01 angle pdb=" O2 U B 66 " pdb=" C2 U B 66 " pdb=" N3 U B 66 " ideal model delta sigma weight residual 122.20 117.47 4.73 7.00e-01 2.04e+00 4.57e+01 ... (remaining 15050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.59: 6038 32.59 - 65.18: 402 65.18 - 97.77: 52 97.77 - 130.36: 0 130.36 - 162.95: 3 Dihedral angle restraints: 6495 sinusoidal: 3833 harmonic: 2662 Sorted by residual: dihedral pdb=" O4' U B 57 " pdb=" C1' U B 57 " pdb=" N1 U B 57 " pdb=" C2 U B 57 " ideal model delta sinusoidal sigma weight residual 200.00 48.36 151.64 1 1.50e+01 4.44e-03 8.02e+01 dihedral pdb=" CD ARG A 824 " pdb=" NE ARG A 824 " pdb=" CZ ARG A 824 " pdb=" NH1 ARG A 824 " ideal model delta sinusoidal sigma weight residual 0.00 -74.01 74.01 1 1.00e+01 1.00e-02 6.96e+01 dihedral pdb=" CA ASP A1569 " pdb=" C ASP A1569 " pdb=" N ASP A1570 " pdb=" CA ASP A1570 " ideal model delta harmonic sigma weight residual 180.00 -153.15 -26.85 0 5.00e+00 4.00e-02 2.88e+01 ... (remaining 6492 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1194 0.056 - 0.112: 358 0.112 - 0.169: 148 0.169 - 0.225: 12 0.225 - 0.281: 10 Chirality restraints: 1722 Sorted by residual: chirality pdb=" C4' G B 90 " pdb=" C5' G B 90 " pdb=" O4' G B 90 " pdb=" C3' G B 90 " both_signs ideal model delta sigma weight residual False -2.50 -2.22 -0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" C1' A B 71 " pdb=" O4' A B 71 " pdb=" C2' A B 71 " pdb=" N9 A B 71 " both_signs ideal model delta sigma weight residual False 2.47 2.20 0.27 2.00e-01 2.50e+01 1.85e+00 chirality pdb=" C3' U B 66 " pdb=" C4' U B 66 " pdb=" O3' U B 66 " pdb=" C2' U B 66 " both_signs ideal model delta sigma weight residual False -2.74 -2.49 -0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 1719 not shown) Planarity restraints: 1442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 824 " 0.901 9.50e-02 1.11e+02 4.05e-01 1.11e+02 pdb=" NE ARG A 824 " -0.076 2.00e-02 2.50e+03 pdb=" CZ ARG A 824 " 0.048 2.00e-02 2.50e+03 pdb=" NH1 ARG A 824 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A 824 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' U B 80 " -0.035 2.00e-02 2.50e+03 2.57e-02 1.48e+01 pdb=" N1 U B 80 " 0.063 2.00e-02 2.50e+03 pdb=" C2 U B 80 " -0.023 2.00e-02 2.50e+03 pdb=" O2 U B 80 " 0.008 2.00e-02 2.50e+03 pdb=" N3 U B 80 " 0.003 2.00e-02 2.50e+03 pdb=" C4 U B 80 " -0.003 2.00e-02 2.50e+03 pdb=" O4 U B 80 " -0.006 2.00e-02 2.50e+03 pdb=" C5 U B 80 " -0.005 2.00e-02 2.50e+03 pdb=" C6 U B 80 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 81 " -0.042 2.00e-02 2.50e+03 2.11e-02 1.33e+01 pdb=" N9 G B 81 " 0.055 2.00e-02 2.50e+03 pdb=" C8 G B 81 " 0.003 2.00e-02 2.50e+03 pdb=" N7 G B 81 " 0.005 2.00e-02 2.50e+03 pdb=" C5 G B 81 " -0.006 2.00e-02 2.50e+03 pdb=" C6 G B 81 " -0.014 2.00e-02 2.50e+03 pdb=" O6 G B 81 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G B 81 " 0.006 2.00e-02 2.50e+03 pdb=" C2 G B 81 " 0.007 2.00e-02 2.50e+03 pdb=" N2 G B 81 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G B 81 " 0.004 2.00e-02 2.50e+03 pdb=" C4 G B 81 " -0.011 2.00e-02 2.50e+03 ... (remaining 1439 not shown) Histogram of nonbonded interaction distances: 2.51 - 2.99: 4655 2.99 - 3.47: 10131 3.47 - 3.94: 18946 3.94 - 4.42: 21301 4.42 - 4.90: 31164 Nonbonded interactions: 86197 Sorted by model distance: nonbonded pdb=" OP2 C B 46 " pdb="MG MG B 102 " model vdw 2.511 2.170 nonbonded pdb=" O4' U B 66 " pdb=" C6 U B 66 " model vdw 2.527 2.672 nonbonded pdb=" O4' C B 34 " pdb=" C6 C B 34 " model vdw 2.542 2.672 nonbonded pdb=" O4' C B 18 " pdb=" C6 C B 18 " model vdw 2.553 2.672 nonbonded pdb=" N1 G B 62 " pdb=" C4 G B 62 " model vdw 2.584 2.672 ... (remaining 86192 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.940 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: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.040 Find NCS groups from input model: 0.040 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: 0.010 Load rotamer database and sin/cos tables:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 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 0.088 10706 Z= 0.348 Angle : 1.059 12.156 15055 Z= 0.736 Chirality : 0.063 0.281 1722 Planarity : 0.012 0.405 1442 Dihedral : 19.364 162.946 4767 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 0.85 % Allowed : 16.83 % Favored : 82.32 % Cbeta Deviations : 0.12 % 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: 0.08 (0.26), residues: 881 helix: 0.16 (0.25), residues: 400 sheet: 0.36 (0.55), residues: 75 loop : 0.08 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.059 0.002 ARG A 824 TYR 0.063 0.002 TYR A 480 PHE 0.044 0.003 PHE A 540 TRP 0.027 0.003 TRP A 477 HIS 0.005 0.001 HIS A 341 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.35 (10706) covalent geometry : angle 1.05880 / 0.74 (15055) hydrogen bonds : bond 0.13437 / 9.37 ( 451) hydrogen bonds : angle 5.92010 / 4.33 ( 1161) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.200 Fit side-chains revert: symmetry clash REVERT: A 325 GLU cc_start: 0.7447 (tp30) cc_final: 0.7127 (tp30) REVERT: A 498 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8043 (tm-30) REVERT: A 500 ASP cc_start: 0.8628 (m-30) cc_final: 0.8397 (m-30) REVERT: A 502 LYS cc_start: 0.8446 (tptp) cc_final: 0.7909 (tppp) REVERT: A 618 ARG cc_start: 0.7603 (tmm-80) cc_final: 0.7178 (ttm170) REVERT: A 629 MET cc_start: 0.8414 (mmt) cc_final: 0.8017 (ttt) REVERT: A 808 LYS cc_start: 0.8292 (mtmm) cc_final: 0.7674 (mmmt) REVERT: A 1520 LYS cc_start: 0.8970 (pptt) cc_final: 0.8747 (ptpp) REVERT: A 1540 ARG cc_start: 0.9453 (mmm-85) cc_final: 0.9220 (mmm-85) outliers start: 7 outliers final: 6 residues processed: 62 average time/residue: 0.4365 time to fit residues: 29.4375 Evaluate side-chains 62 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 56 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 1502 SER Chi-restraints excluded: chain A residue 1592 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 8.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.4980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 20.0000 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 0.5980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 476 ASN A 643 ASN A1490 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.130801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.090573 restraints weight = 18287.765| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 2.27 r_work: 0.3193 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.0781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10706 Z= 0.167 Angle : 0.602 6.636 15055 Z= 0.345 Chirality : 0.044 0.378 1722 Planarity : 0.004 0.042 1442 Dihedral : 20.037 166.214 2860 Min Nonbonded Distance : 2.328 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.20 % Allowed : 13.29 % Favored : 84.51 % 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: 0.75 (0.28), residues: 881 helix: 0.83 (0.26), residues: 409 sheet: 0.47 (0.52), residues: 89 loop : 0.33 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 824 TYR 0.043 0.002 TYR A 480 PHE 0.018 0.002 PHE A 540 TRP 0.011 0.002 TRP A1459 HIS 0.008 0.001 HIS A1579 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.17 (10706) covalent geometry : angle 0.60180 / 0.34 (15055) hydrogen bonds : bond 0.05258 / 3.55 ( 451) hydrogen bonds : angle 4.53317 / 3.28 ( 1161) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.252 Fit side-chains revert: symmetry clash REVERT: A 500 ASP cc_start: 0.8659 (m-30) cc_final: 0.8428 (m-30) REVERT: A 543 ASP cc_start: 0.7903 (m-30) cc_final: 0.6734 (t0) REVERT: A 629 MET cc_start: 0.8458 (mmt) cc_final: 0.8042 (ttt) REVERT: A 808 LYS cc_start: 0.8278 (mtmm) cc_final: 0.7641 (mmmt) REVERT: A 1257 GLU cc_start: 0.8780 (mp0) cc_final: 0.8507 (mm-30) REVERT: A 1304 ILE cc_start: 0.8932 (pt) cc_final: 0.8614 (pp) REVERT: A 1540 ARG cc_start: 0.9426 (mmm-85) cc_final: 0.9181 (mmm-85) REVERT: A 1592 GLU cc_start: 0.8781 (OUTLIER) cc_final: 0.8207 (mp0) REVERT: A 1617 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8717 (tmm) outliers start: 18 outliers final: 8 residues processed: 70 average time/residue: 0.4834 time to fit residues: 36.9202 Evaluate side-chains 57 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 470 LEU Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 1431 THR Chi-restraints excluded: chain A residue 1471 SER Chi-restraints excluded: chain A residue 1517 VAL Chi-restraints excluded: chain A residue 1592 GLU Chi-restraints excluded: chain A residue 1617 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 38 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 77 optimal weight: 0.0970 chunk 57 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 0.0010 chunk 49 optimal weight: 6.9990 overall best weight: 1.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 476 ASN A 643 ASN A1490 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.128734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.087515 restraints weight = 18267.537| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.29 r_work: 0.3171 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10706 Z= 0.166 Angle : 0.568 7.441 15055 Z= 0.327 Chirality : 0.043 0.384 1722 Planarity : 0.003 0.035 1442 Dihedral : 19.989 169.162 2856 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.32 % Allowed : 12.68 % Favored : 85.00 % 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: 1.03 (0.28), residues: 881 helix: 1.12 (0.26), residues: 414 sheet: 0.40 (0.52), residues: 89 loop : 0.45 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 824 TYR 0.046 0.001 TYR A 480 PHE 0.017 0.002 PHE A1420 TRP 0.011 0.001 TRP A 87 HIS 0.006 0.001 HIS A1579 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.17 (10706) covalent geometry : angle 0.56765 / 0.33 (15055) hydrogen bonds : bond 0.04788 / 3.23 ( 451) hydrogen bonds : angle 4.26923 / 3.07 ( 1161) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 54 time to evaluate : 0.384 Fit side-chains REVERT: A 543 ASP cc_start: 0.7729 (m-30) cc_final: 0.6542 (t0) REVERT: A 629 MET cc_start: 0.8481 (mmt) cc_final: 0.8121 (ttt) REVERT: A 808 LYS cc_start: 0.8210 (mtmm) cc_final: 0.7578 (mmmt) REVERT: A 1304 ILE cc_start: 0.8993 (pt) cc_final: 0.8691 (pp) REVERT: A 1540 ARG cc_start: 0.9461 (mmm-85) cc_final: 0.9106 (mmm-85) REVERT: A 1569 ASP cc_start: 0.8628 (t70) cc_final: 0.8382 (t0) REVERT: A 1592 GLU cc_start: 0.8715 (OUTLIER) cc_final: 0.7699 (mp0) REVERT: A 1617 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8714 (tmm) outliers start: 19 outliers final: 12 residues processed: 69 average time/residue: 0.4224 time to fit residues: 32.0227 Evaluate side-chains 64 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 50 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1431 THR Chi-restraints excluded: chain A residue 1458 THR Chi-restraints excluded: chain A residue 1471 SER Chi-restraints excluded: chain A residue 1577 MET Chi-restraints excluded: chain A residue 1592 GLU Chi-restraints excluded: chain A residue 1617 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 81 optimal weight: 0.7980 chunk 96 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 chunk 55 optimal weight: 0.9980 chunk 67 optimal weight: 0.0040 chunk 0 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 42 optimal weight: 0.9980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 798 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.129959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.088268 restraints weight = 18341.385| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.32 r_work: 0.3186 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3186 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10706 Z= 0.129 Angle : 0.520 7.462 15055 Z= 0.304 Chirality : 0.041 0.379 1722 Planarity : 0.003 0.034 1442 Dihedral : 19.981 171.164 2856 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.07 % Allowed : 13.29 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.20 (0.28), residues: 881 helix: 1.34 (0.26), residues: 415 sheet: 0.39 (0.52), residues: 89 loop : 0.44 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 824 TYR 0.043 0.001 TYR A 480 PHE 0.024 0.001 PHE A 540 TRP 0.010 0.001 TRP A 477 HIS 0.005 0.001 HIS A1579 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.13 (10706) covalent geometry : angle 0.52022 / 0.30 (15055) hydrogen bonds : bond 0.04329 / 2.91 ( 451) hydrogen bonds : angle 4.08645 / 2.93 ( 1161) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 55 time to evaluate : 0.248 Fit side-chains REVERT: A 543 ASP cc_start: 0.7707 (m-30) cc_final: 0.6475 (t0) REVERT: A 629 MET cc_start: 0.8419 (mmt) cc_final: 0.8115 (ttt) REVERT: A 808 LYS cc_start: 0.8201 (mtmm) cc_final: 0.7585 (mmmt) REVERT: A 1304 ILE cc_start: 0.9011 (pt) cc_final: 0.8712 (pp) REVERT: A 1518 ASP cc_start: 0.8108 (m-30) cc_final: 0.7847 (m-30) REVERT: A 1540 ARG cc_start: 0.9474 (mmm-85) cc_final: 0.9120 (mmm-85) REVERT: A 1569 ASP cc_start: 0.8661 (t70) cc_final: 0.8390 (t0) REVERT: A 1617 MET cc_start: 0.9027 (OUTLIER) cc_final: 0.8768 (tmm) outliers start: 17 outliers final: 11 residues processed: 68 average time/residue: 0.4496 time to fit residues: 33.0826 Evaluate side-chains 64 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1471 SER Chi-restraints excluded: chain A residue 1517 VAL Chi-restraints excluded: chain A residue 1577 MET Chi-restraints excluded: chain A residue 1592 GLU Chi-restraints excluded: chain A residue 1617 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 22 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 95 optimal weight: 9.9990 chunk 31 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 32 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 chunk 47 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 89 optimal weight: 30.0000 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 798 GLN A 810 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.129337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.089290 restraints weight = 18356.181| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 2.24 r_work: 0.3173 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3043 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10706 Z= 0.151 Angle : 0.525 7.718 15055 Z= 0.304 Chirality : 0.041 0.375 1722 Planarity : 0.003 0.032 1442 Dihedral : 19.926 172.847 2856 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.68 % Favored : 99.32 % Rotamer: Outliers : 2.32 % Allowed : 13.78 % Favored : 83.90 % 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: 1.35 (0.29), residues: 881 helix: 1.55 (0.26), residues: 414 sheet: 0.25 (0.51), residues: 89 loop : 0.48 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 102 TYR 0.042 0.001 TYR A 480 PHE 0.020 0.002 PHE A 607 TRP 0.009 0.001 TRP A 79 HIS 0.004 0.001 HIS A1579 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (10706) covalent geometry : angle 0.52498 / 0.30 (15055) hydrogen bonds : bond 0.04457 / 3.01 ( 451) hydrogen bonds : angle 4.04229 / 2.89 ( 1161) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 49 time to evaluate : 0.344 Fit side-chains REVERT: A 543 ASP cc_start: 0.7765 (m-30) cc_final: 0.6467 (t0) REVERT: A 629 MET cc_start: 0.8512 (mmt) cc_final: 0.8146 (ttt) REVERT: A 1304 ILE cc_start: 0.9046 (pt) cc_final: 0.8748 (pp) REVERT: A 1540 ARG cc_start: 0.9482 (mmm-85) cc_final: 0.9089 (mmm-85) REVERT: A 1569 ASP cc_start: 0.8747 (t70) cc_final: 0.8372 (t0) REVERT: A 1592 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8134 (mp0) REVERT: A 1617 MET cc_start: 0.9188 (OUTLIER) cc_final: 0.8899 (tmm) outliers start: 19 outliers final: 12 residues processed: 63 average time/residue: 0.5139 time to fit residues: 35.3452 Evaluate side-chains 57 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 540 PHE Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1458 THR Chi-restraints excluded: chain A residue 1471 SER Chi-restraints excluded: chain A residue 1577 MET Chi-restraints excluded: chain A residue 1592 GLU Chi-restraints excluded: chain A residue 1617 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 98 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 45 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 43 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 798 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.127417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.086158 restraints weight = 18400.605| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.28 r_work: 0.3144 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.1722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10706 Z= 0.181 Angle : 0.542 8.027 15055 Z= 0.312 Chirality : 0.042 0.372 1722 Planarity : 0.003 0.031 1442 Dihedral : 19.935 173.296 2856 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 2.07 % Allowed : 14.27 % Favored : 83.66 % 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: 1.33 (0.29), residues: 881 helix: 1.58 (0.26), residues: 414 sheet: 0.13 (0.51), residues: 89 loop : 0.43 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 618 TYR 0.046 0.001 TYR A 480 PHE 0.024 0.002 PHE A 607 TRP 0.010 0.001 TRP A 79 HIS 0.004 0.001 HIS A1579 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.18 (10706) covalent geometry : angle 0.54153 / 0.31 (15055) hydrogen bonds : bond 0.04631 / 3.13 ( 451) hydrogen bonds : angle 4.08792 / 2.93 ( 1161) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 49 time to evaluate : 0.207 Fit side-chains REVERT: A 52 MET cc_start: 0.7889 (OUTLIER) cc_final: 0.6470 (mmt) REVERT: A 618 ARG cc_start: 0.7276 (OUTLIER) cc_final: 0.6687 (ttm170) REVERT: A 629 MET cc_start: 0.8512 (mmt) cc_final: 0.8147 (ttt) REVERT: A 1304 ILE cc_start: 0.9097 (pt) cc_final: 0.8806 (pp) REVERT: A 1540 ARG cc_start: 0.9489 (mmm-85) cc_final: 0.9187 (mmm-85) REVERT: A 1569 ASP cc_start: 0.8808 (t70) cc_final: 0.8499 (t0) REVERT: A 1592 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8189 (mp0) REVERT: A 1617 MET cc_start: 0.9215 (OUTLIER) cc_final: 0.8914 (tmm) outliers start: 17 outliers final: 12 residues processed: 61 average time/residue: 0.4028 time to fit residues: 27.0751 Evaluate side-chains 60 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 618 ARG Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1458 THR Chi-restraints excluded: chain A residue 1471 SER Chi-restraints excluded: chain A residue 1517 VAL Chi-restraints excluded: chain A residue 1577 MET Chi-restraints excluded: chain A residue 1592 GLU Chi-restraints excluded: chain A residue 1617 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 44 optimal weight: 0.0020 chunk 48 optimal weight: 6.9990 chunk 89 optimal weight: 20.0000 chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 overall best weight: 0.7588 ------------------------------------------------------------------------------- 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 = 0.3926 r_free = 0.3926 target = 0.128513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.086930 restraints weight = 18174.715| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.29 r_work: 0.3165 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10706 Z= 0.137 Angle : 0.512 8.559 15055 Z= 0.298 Chirality : 0.040 0.362 1722 Planarity : 0.003 0.030 1442 Dihedral : 19.923 174.119 2856 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.32 % Allowed : 14.63 % Favored : 83.05 % 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: 1.38 (0.29), residues: 881 helix: 1.61 (0.27), residues: 416 sheet: 0.14 (0.51), residues: 89 loop : 0.47 (0.33), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 618 TYR 0.039 0.001 TYR A 480 PHE 0.017 0.001 PHE A 607 TRP 0.010 0.001 TRP A 79 HIS 0.004 0.001 HIS A1579 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 (10706) covalent geometry : angle 0.51168 / 0.30 (15055) hydrogen bonds : bond 0.04271 / 2.88 ( 451) hydrogen bonds : angle 3.97492 / 2.85 ( 1161) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 47 time to evaluate : 0.282 Fit side-chains REVERT: A 52 MET cc_start: 0.7839 (OUTLIER) cc_final: 0.6477 (mmt) REVERT: A 480 TYR cc_start: 0.7103 (m-80) cc_final: 0.6886 (m-80) REVERT: A 629 MET cc_start: 0.8520 (mmt) cc_final: 0.8148 (ttt) REVERT: A 1304 ILE cc_start: 0.9116 (pt) cc_final: 0.8835 (pp) REVERT: A 1540 ARG cc_start: 0.9485 (mmm-85) cc_final: 0.9119 (mmm-85) REVERT: A 1569 ASP cc_start: 0.8752 (t70) cc_final: 0.8440 (t0) REVERT: A 1592 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8041 (mp0) REVERT: A 1617 MET cc_start: 0.9244 (OUTLIER) cc_final: 0.8917 (tmm) outliers start: 19 outliers final: 13 residues processed: 61 average time/residue: 0.4817 time to fit residues: 32.2730 Evaluate side-chains 59 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1458 THR Chi-restraints excluded: chain A residue 1471 SER Chi-restraints excluded: chain A residue 1517 VAL Chi-restraints excluded: chain A residue 1577 MET Chi-restraints excluded: chain A residue 1592 GLU Chi-restraints excluded: chain A residue 1617 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 66 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 12 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 chunk 33 optimal weight: 0.3980 chunk 43 optimal weight: 0.0070 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 466 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.128914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.089035 restraints weight = 18198.451| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.23 r_work: 0.3193 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3063 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8709 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10706 Z= 0.121 Angle : 0.503 8.878 15055 Z= 0.294 Chirality : 0.039 0.355 1722 Planarity : 0.003 0.030 1442 Dihedral : 19.883 174.797 2856 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 2.56 % Allowed : 15.00 % Favored : 82.44 % 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: 1.45 (0.29), residues: 881 helix: 1.66 (0.27), residues: 414 sheet: 0.14 (0.51), residues: 89 loop : 0.53 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 102 TYR 0.035 0.001 TYR A 480 PHE 0.020 0.001 PHE A 607 TRP 0.009 0.001 TRP A 79 HIS 0.003 0.001 HIS A1579 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.12 (10706) covalent geometry : angle 0.50283 / 0.29 (15055) hydrogen bonds : bond 0.04080 / 2.75 ( 451) hydrogen bonds : angle 3.90121 / 2.80 ( 1161) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 49 time to evaluate : 0.281 Fit side-chains REVERT: A 52 MET cc_start: 0.7841 (OUTLIER) cc_final: 0.6584 (mmt) REVERT: A 629 MET cc_start: 0.8570 (mmt) cc_final: 0.8188 (ttt) REVERT: A 1304 ILE cc_start: 0.9129 (pt) cc_final: 0.8877 (pp) REVERT: A 1540 ARG cc_start: 0.9440 (mmm-85) cc_final: 0.9105 (mmm-85) REVERT: A 1569 ASP cc_start: 0.8716 (t70) cc_final: 0.8406 (t0) REVERT: A 1592 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8014 (mp0) REVERT: A 1617 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.8941 (tmm) outliers start: 21 outliers final: 13 residues processed: 65 average time/residue: 0.4467 time to fit residues: 31.9767 Evaluate side-chains 60 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1458 THR Chi-restraints excluded: chain A residue 1471 SER Chi-restraints excluded: chain A residue 1517 VAL Chi-restraints excluded: chain A residue 1577 MET Chi-restraints excluded: chain A residue 1592 GLU Chi-restraints excluded: chain A residue 1617 MET Chi-restraints excluded: chain A residue 1622 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 48 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 22 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 82 optimal weight: 0.4980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 466 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.127662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.086403 restraints weight = 18231.671| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.28 r_work: 0.3154 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3023 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10706 Z= 0.165 Angle : 0.534 9.229 15055 Z= 0.308 Chirality : 0.041 0.357 1722 Planarity : 0.003 0.050 1442 Dihedral : 19.868 174.849 2856 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.83 % Allowed : 15.98 % Favored : 82.20 % 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: 1.40 (0.29), residues: 881 helix: 1.64 (0.27), residues: 414 sheet: 0.06 (0.51), residues: 89 loop : 0.50 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 662 TYR 0.013 0.001 TYR A 480 PHE 0.030 0.002 PHE A 607 TRP 0.010 0.001 TRP A 79 HIS 0.003 0.001 HIS A1579 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.16 (10706) covalent geometry : angle 0.53424 / 0.31 (15055) hydrogen bonds : bond 0.04480 / 3.04 ( 451) hydrogen bonds : angle 3.98189 / 2.86 ( 1161) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.368 Fit side-chains REVERT: A 52 MET cc_start: 0.7835 (OUTLIER) cc_final: 0.6610 (mmt) REVERT: A 618 ARG cc_start: 0.7039 (tpp80) cc_final: 0.6784 (ttm170) REVERT: A 629 MET cc_start: 0.8599 (mmt) cc_final: 0.8092 (ttt) REVERT: A 1540 ARG cc_start: 0.9427 (mmm-85) cc_final: 0.9085 (mmm-85) REVERT: A 1569 ASP cc_start: 0.8720 (t70) cc_final: 0.8414 (t0) REVERT: A 1592 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.7986 (mp0) REVERT: A 1617 MET cc_start: 0.9265 (OUTLIER) cc_final: 0.8947 (tmm) outliers start: 15 outliers final: 12 residues processed: 56 average time/residue: 0.4847 time to fit residues: 29.8997 Evaluate side-chains 57 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1458 THR Chi-restraints excluded: chain A residue 1471 SER Chi-restraints excluded: chain A residue 1517 VAL Chi-restraints excluded: chain A residue 1577 MET Chi-restraints excluded: chain A residue 1592 GLU Chi-restraints excluded: chain A residue 1617 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 82 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 45 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 466 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.128241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.087165 restraints weight = 17965.969| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.25 r_work: 0.3170 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10706 Z= 0.139 Angle : 0.521 9.534 15055 Z= 0.302 Chirality : 0.040 0.352 1722 Planarity : 0.003 0.039 1442 Dihedral : 19.868 174.989 2856 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.83 % Allowed : 16.10 % Favored : 82.07 % 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: 1.44 (0.29), residues: 881 helix: 1.67 (0.27), residues: 414 sheet: 0.05 (0.51), residues: 89 loop : 0.53 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 662 TYR 0.039 0.001 TYR A 480 PHE 0.026 0.001 PHE A 607 TRP 0.009 0.001 TRP A 79 HIS 0.004 0.001 HIS A1579 Details of bonding type rmsd/Z covalent geometry : bond 0.00280 / 0.14 (10706) covalent geometry : angle 0.52072 / 0.30 (15055) hydrogen bonds : bond 0.04228 / 2.86 ( 451) hydrogen bonds : angle 3.92026 / 2.81 ( 1161) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1762 Ramachandran restraints generated. 881 Oldfield, 0 Emsley, 881 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 47 time to evaluate : 0.299 Fit side-chains REVERT: A 52 MET cc_start: 0.7809 (OUTLIER) cc_final: 0.6589 (mmt) REVERT: A 500 ASP cc_start: 0.8807 (m-30) cc_final: 0.8583 (m-30) REVERT: A 618 ARG cc_start: 0.6957 (tpp80) cc_final: 0.6637 (ttm170) REVERT: A 629 MET cc_start: 0.8575 (mmt) cc_final: 0.8086 (ttt) REVERT: A 664 LYS cc_start: 0.7274 (mmpt) cc_final: 0.7066 (mmmt) REVERT: A 1540 ARG cc_start: 0.9417 (mmm-85) cc_final: 0.9091 (mmm-85) REVERT: A 1569 ASP cc_start: 0.8719 (t70) cc_final: 0.8410 (t0) REVERT: A 1592 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8019 (mp0) REVERT: A 1617 MET cc_start: 0.9272 (OUTLIER) cc_final: 0.8953 (tmm) outliers start: 15 outliers final: 12 residues processed: 59 average time/residue: 0.4259 time to fit residues: 27.8776 Evaluate side-chains 61 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 MET Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 85 LEU Chi-restraints excluded: chain A residue 107 ILE Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 644 THR Chi-restraints excluded: chain A residue 1240 THR Chi-restraints excluded: chain A residue 1458 THR Chi-restraints excluded: chain A residue 1471 SER Chi-restraints excluded: chain A residue 1517 VAL Chi-restraints excluded: chain A residue 1577 MET Chi-restraints excluded: chain A residue 1592 GLU Chi-restraints excluded: chain A residue 1617 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 100 optimal weight: 20.0000 chunk 20 optimal weight: 0.5980 chunk 0 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 81 optimal weight: 0.0970 chunk 94 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 74 optimal weight: 0.0980 chunk 54 optimal weight: 2.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.129932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.089711 restraints weight = 18320.972| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 2.25 r_work: 0.3206 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 10706 Z= 0.119 Angle : 0.506 9.524 15055 Z= 0.294 Chirality : 0.039 0.348 1722 Planarity : 0.003 0.041 1442 Dihedral : 19.841 175.333 2856 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.83 % Allowed : 16.46 % Favored : 81.71 % 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: 1.46 (0.29), residues: 881 helix: 1.71 (0.26), residues: 412 sheet: 0.08 (0.51), residues: 89 loop : 0.52 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 662 TYR 0.017 0.001 TYR A 480 PHE 0.026 0.001 PHE A 607 TRP 0.009 0.001 TRP A 79 HIS 0.003 0.001 HIS A1579 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.12 (10706) covalent geometry : angle 0.50552 / 0.29 (15055) hydrogen bonds : bond 0.04069 / 2.76 ( 451) hydrogen bonds : angle 3.85904 / 2.76 ( 1161) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3286.72 seconds wall clock time: 56 minutes 48.70 seconds (3408.70 seconds total)