Starting phenix.real_space_refine on Wed Feb 4 11:50:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ehr_48062/02_2026/9ehr_48062.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ehr_48062/02_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_48062/02_2026/9ehr_48062.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ehr_48062/02_2026/9ehr_48062.map" model { file = "/net/cci-nas-00/data/ceres_data/9ehr_48062/02_2026/9ehr_48062.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ehr_48062/02_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/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: 1.78, per 1000 atoms: 0.17 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: 0.58 Conformation dependent library (CDL) restraints added in 248.3 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: 1.11 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: 2.13 Time building geometry restraints manager: 0.77 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=" CA ASP A1569 " pdb=" CB ASP A1569 " ideal model delta sigma weight residual 1.523 1.573 -0.050 1.94e-02 2.66e+03 6.55e+00 bond pdb=" CG1 ILE A1573 " pdb=" CD1 ILE A1573 " ideal model delta sigma weight residual 1.513 1.425 0.088 3.90e-02 6.57e+02 5.15e+00 bond pdb=" CB ASP A1570 " pdb=" CG ASP A1570 " ideal model delta sigma weight residual 1.516 1.570 -0.054 2.50e-02 1.60e+03 4.67e+00 bond pdb=" C3' U B 66 " pdb=" O3' U B 66 " ideal model delta sigma weight residual 1.427 1.456 -0.029 1.50e-02 4.44e+03 3.64e+00 bond pdb=" CG1 ILE A1593 " pdb=" CD1 ILE A1593 " ideal model delta sigma weight residual 1.513 1.439 0.074 3.90e-02 6.57e+02 3.62e+00 ... (remaining 10701 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.43: 14593 2.43 - 4.86: 371 4.86 - 7.29: 65 7.29 - 9.72: 20 9.72 - 12.16: 6 Bond angle restraints: 15055 Sorted by residual: angle pdb=" C3' U B 66 " pdb=" O3' U B 66 " pdb=" P U B 67 " ideal model delta sigma weight residual 120.20 127.99 -7.79 1.50e+00 4.44e-01 2.70e+01 angle pdb=" CA LYS A1520 " pdb=" CB LYS A1520 " pdb=" CG LYS A1520 " ideal model delta sigma weight residual 114.10 123.79 -9.69 2.00e+00 2.50e-01 2.35e+01 angle pdb=" CA ILE A1430 " pdb=" CB ILE A1430 " pdb=" CG1 ILE A1430 " ideal model delta sigma weight residual 110.40 118.47 -8.07 1.70e+00 3.46e-01 2.25e+01 angle pdb=" CA ILE A1593 " pdb=" CB ILE A1593 " pdb=" CG1 ILE A1593 " ideal model delta sigma weight residual 110.40 117.88 -7.48 1.70e+00 3.46e-01 1.94e+01 angle pdb=" CB GLN A 473 " pdb=" CG GLN A 473 " pdb=" CD GLN A 473 " ideal model delta sigma weight residual 112.60 119.94 -7.34 1.70e+00 3.46e-01 1.86e+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: 1318 0.056 - 0.112: 319 0.112 - 0.169: 65 0.169 - 0.225: 12 0.225 - 0.281: 8 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=" 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 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 2.46 2.20 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: 4.280 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.520 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 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:6.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 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= 0.233 Angle : 0.988 12.156 15055 Z= 0.530 Chirality : 0.054 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 covalent geometry : bond 0.00508 (10706) covalent geometry : angle 0.98783 (15055) hydrogen bonds : bond 0.13437 ( 451) hydrogen bonds : angle 5.92010 ( 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 : 0.207 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: 0.5094 time to fit residues: 34.2065 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 : 0.278 ------------------------------------------------------------------------------- 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: 2.9990 chunk 97 optimal weight: 3.9990 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: 6.9990 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3932 r_free = 0.3932 target = 0.128982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.087749 restraints weight = 18238.836| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.30 r_work: 0.3175 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10706 Z= 0.173 Angle : 0.601 7.005 15055 Z= 0.324 Chirality : 0.041 0.243 1722 Planarity : 0.004 0.045 1442 Dihedral : 19.977 168.479 2860 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.07 % Allowed : 12.68 % Favored : 85.24 % 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: 0.85 (0.28), residues: 881 helix: 0.90 (0.26), residues: 413 sheet: 0.41 (0.52), residues: 89 loop : 0.42 (0.31), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 618 TYR 0.040 0.002 TYR A 480 PHE 0.014 0.002 PHE A1420 TRP 0.011 0.002 TRP A 87 HIS 0.005 0.001 HIS A1579 Details of bonding type rmsd covalent geometry : bond 0.00376 (10706) covalent geometry : angle 0.60056 (15055) hydrogen bonds : bond 0.04451 ( 451) hydrogen bonds : angle 4.39077 ( 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: 17 poor density : 59 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 618 ARG cc_start: 0.7678 (tmm-80) cc_final: 0.7410 (ttm-80) REVERT: A 629 MET cc_start: 0.8477 (mmt) cc_final: 0.8110 (ttt) REVERT: A 808 LYS cc_start: 0.8260 (mtmm) cc_final: 0.7632 (mmmt) REVERT: A 1257 GLU cc_start: 0.8592 (mp0) cc_final: 0.8375 (mm-30) REVERT: A 1304 ILE cc_start: 0.8949 (pt) cc_final: 0.8643 (pp) REVERT: A 1540 ARG cc_start: 0.9439 (mmm-85) cc_final: 0.9133 (mmm-85) REVERT: A 1592 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: A 1617 MET cc_start: 0.8986 (OUTLIER) cc_final: 0.8701 (tmm) outliers start: 17 outliers final: 7 residues processed: 73 average time/residue: 0.4275 time to fit residues: 33.9763 Evaluate side-chains 59 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL 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 1240 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: 10.0000 chunk 31 optimal weight: 7.9990 chunk 2 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 61 optimal weight: 0.3980 chunk 49 optimal weight: 3.9990 overall best weight: 1.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 476 ASN A1490 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.126342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.085130 restraints weight = 18330.918| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 2.29 r_work: 0.3126 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1559 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= 0.203 Angle : 0.580 7.032 15055 Z= 0.312 Chirality : 0.041 0.269 1722 Planarity : 0.003 0.031 1442 Dihedral : 19.988 172.881 2856 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.20 % Allowed : 12.56 % Favored : 85.24 % 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: 1.13 (0.28), residues: 881 helix: 1.26 (0.26), residues: 413 sheet: 0.31 (0.51), residues: 89 loop : 0.47 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 102 TYR 0.037 0.002 TYR A 480 PHE 0.017 0.002 PHE A1420 TRP 0.012 0.002 TRP A 477 HIS 0.006 0.001 HIS A1579 Details of bonding type rmsd covalent geometry : bond 0.00447 (10706) covalent geometry : angle 0.58041 (15055) hydrogen bonds : bond 0.04381 ( 451) hydrogen bonds : angle 4.19700 ( 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 72 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 54 time to evaluate : 0.311 Fit side-chains REVERT: A 629 MET cc_start: 0.8513 (mmt) cc_final: 0.8119 (ttt) REVERT: A 808 LYS cc_start: 0.8334 (mtmm) cc_final: 0.7605 (mmmt) REVERT: A 1540 ARG cc_start: 0.9478 (mmm-85) cc_final: 0.9078 (mmm-85) REVERT: A 1569 ASP cc_start: 0.8706 (t70) cc_final: 0.8441 (t0) REVERT: A 1592 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.7663 (mp0) REVERT: A 1617 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8878 (tmm) outliers start: 18 outliers final: 10 residues processed: 70 average time/residue: 0.4299 time to fit residues: 32.6934 Evaluate side-chains 59 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.311 ------------------------------------------------------------------------------- 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 1458 THR Chi-restraints excluded: chain A residue 1471 SER 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: 3.9990 chunk 90 optimal weight: 3.9990 chunk 77 optimal weight: 0.2980 chunk 9 optimal weight: 0.0170 chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 93 optimal weight: 2.9990 chunk 100 optimal weight: 7.9990 chunk 42 optimal weight: 0.7980 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 466 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 476 ASN A 478 GLN 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 = 0.129366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.089269 restraints weight = 18410.596| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 2.25 r_work: 0.3180 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3052 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1744 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= 0.127 Angle : 0.528 7.197 15055 Z= 0.286 Chirality : 0.038 0.249 1722 Planarity : 0.003 0.030 1442 Dihedral : 19.909 174.332 2856 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.20 % Allowed : 14.39 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.37 (0.29), residues: 881 helix: 1.51 (0.26), residues: 415 sheet: 0.33 (0.51), residues: 89 loop : 0.53 (0.33), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 618 TYR 0.040 0.001 TYR A 480 PHE 0.022 0.001 PHE A 540 TRP 0.008 0.001 TRP A 79 HIS 0.004 0.001 HIS A1579 Details of bonding type rmsd covalent geometry : bond 0.00272 (10706) covalent geometry : angle 0.52814 (15055) hydrogen bonds : bond 0.03605 ( 451) hydrogen bonds : angle 3.93598 ( 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 73 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 55 time to evaluate : 0.257 Fit side-chains REVERT: A 478 GLN cc_start: 0.9073 (OUTLIER) cc_final: 0.8866 (mp10) REVERT: A 543 ASP cc_start: 0.8347 (m-30) cc_final: 0.8121 (m-30) REVERT: A 629 MET cc_start: 0.8531 (mmt) cc_final: 0.8169 (ttt) REVERT: A 1304 ILE cc_start: 0.9080 (pt) cc_final: 0.8780 (pp) REVERT: A 1540 ARG cc_start: 0.9479 (mmm-85) cc_final: 0.9126 (mmm-85) REVERT: A 1569 ASP cc_start: 0.8694 (t70) cc_final: 0.8433 (t0) REVERT: A 1592 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7875 (mp0) REVERT: A 1617 MET cc_start: 0.9238 (OUTLIER) cc_final: 0.8937 (tmm) outliers start: 18 outliers final: 12 residues processed: 69 average time/residue: 0.4869 time to fit residues: 36.5360 Evaluate side-chains 60 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASN 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 478 GLN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 22 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 32 optimal weight: 9.9990 chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 89 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 466 ASN A 478 GLN A 810 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.127368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.086148 restraints weight = 18222.427| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.28 r_work: 0.3146 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 10706 Z= 0.165 Angle : 0.539 7.469 15055 Z= 0.291 Chirality : 0.039 0.257 1722 Planarity : 0.003 0.030 1442 Dihedral : 19.889 174.867 2856 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.44 % Allowed : 14.39 % Favored : 83.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.47 (0.29), residues: 881 helix: 1.65 (0.27), residues: 414 sheet: 0.23 (0.51), residues: 89 loop : 0.56 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 662 TYR 0.036 0.001 TYR A 480 PHE 0.018 0.002 PHE A 540 TRP 0.010 0.001 TRP A 79 HIS 0.003 0.001 HIS A1579 Details of bonding type rmsd covalent geometry : bond 0.00363 (10706) covalent geometry : angle 0.53905 (15055) hydrogen bonds : bond 0.03909 ( 451) hydrogen bonds : angle 3.96115 ( 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 65 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 45 time to evaluate : 0.205 Fit side-chains REVERT: A 52 MET cc_start: 0.8010 (OUTLIER) cc_final: 0.6603 (mmt) REVERT: A 543 ASP cc_start: 0.8417 (m-30) cc_final: 0.8185 (m-30) REVERT: A 629 MET cc_start: 0.8636 (mmt) cc_final: 0.8122 (ttt) REVERT: A 1540 ARG cc_start: 0.9424 (mmm-85) cc_final: 0.9089 (mmm-85) REVERT: A 1569 ASP cc_start: 0.8681 (t70) cc_final: 0.8391 (t0) REVERT: A 1592 GLU cc_start: 0.8589 (OUTLIER) cc_final: 0.8052 (mp0) REVERT: A 1617 MET cc_start: 0.9257 (OUTLIER) cc_final: 0.8963 (tmm) outliers start: 20 outliers final: 10 residues processed: 61 average time/residue: 0.4418 time to fit residues: 29.5065 Evaluate side-chains 54 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 41 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 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: 2.9990 chunk 40 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 99 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 4 optimal weight: 1.9990 chunk 54 optimal weight: 0.0770 overall best weight: 0.6938 ------------------------------------------------------------------------------- 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 = 0.3921 r_free = 0.3921 target = 0.128170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.087041 restraints weight = 18342.720| |-----------------------------------------------------------------------------| r_work (start): 0.3312 rms_B_bonded: 2.28 r_work: 0.3166 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10706 Z= 0.138 Angle : 0.528 7.895 15055 Z= 0.285 Chirality : 0.038 0.249 1722 Planarity : 0.003 0.029 1442 Dihedral : 19.873 175.345 2856 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.44 % Allowed : 14.51 % 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: 1.48 (0.29), residues: 881 helix: 1.68 (0.27), residues: 412 sheet: 0.21 (0.51), residues: 89 loop : 0.55 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 662 TYR 0.043 0.001 TYR A 480 PHE 0.016 0.001 PHE A1420 TRP 0.009 0.001 TRP A 79 HIS 0.003 0.001 HIS A1579 Details of bonding type rmsd covalent geometry : bond 0.00300 (10706) covalent geometry : angle 0.52769 (15055) hydrogen bonds : bond 0.03673 ( 451) hydrogen bonds : angle 3.85269 ( 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 67 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 47 time to evaluate : 0.307 Fit side-chains REVERT: A 52 MET cc_start: 0.7892 (OUTLIER) cc_final: 0.6659 (mmt) REVERT: A 490 ILE cc_start: 0.8597 (mp) cc_final: 0.8392 (mt) REVERT: A 629 MET cc_start: 0.8569 (mmt) cc_final: 0.8091 (ttt) REVERT: A 1297 ASP cc_start: 0.8869 (t70) cc_final: 0.8607 (t70) REVERT: A 1540 ARG cc_start: 0.9404 (mmm-85) cc_final: 0.9070 (mmm-85) REVERT: A 1592 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.7985 (mp0) REVERT: A 1617 MET cc_start: 0.9256 (OUTLIER) cc_final: 0.8954 (tmm) outliers start: 20 outliers final: 13 residues processed: 62 average time/residue: 0.4443 time to fit residues: 30.1742 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 : 0.272 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.9980 chunk 25 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 48 optimal weight: 8.9990 chunk 89 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 chunk 95 optimal weight: 4.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 ASN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.124855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.083103 restraints weight = 18208.006| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.30 r_work: 0.3094 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10706 Z= 0.246 Angle : 0.594 8.540 15055 Z= 0.320 Chirality : 0.041 0.266 1722 Planarity : 0.004 0.032 1442 Dihedral : 19.954 174.707 2856 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.68 % Allowed : 15.12 % 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: 1.39 (0.29), residues: 881 helix: 1.64 (0.27), residues: 405 sheet: 0.00 (0.49), residues: 97 loop : 0.54 (0.33), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 662 TYR 0.016 0.002 TYR A1329 PHE 0.016 0.002 PHE A1420 TRP 0.011 0.002 TRP A 79 HIS 0.004 0.001 HIS A1579 Details of bonding type rmsd covalent geometry : bond 0.00547 (10706) covalent geometry : angle 0.59358 (15055) hydrogen bonds : bond 0.04571 ( 451) hydrogen bonds : angle 4.09276 ( 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 69 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 47 time to evaluate : 0.329 Fit side-chains REVERT: A 629 MET cc_start: 0.8634 (mmt) cc_final: 0.8142 (ttt) REVERT: A 1297 ASP cc_start: 0.8925 (t70) cc_final: 0.8665 (t70) REVERT: A 1569 ASP cc_start: 0.8691 (t70) cc_final: 0.8392 (t0) REVERT: A 1592 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8162 (mp0) REVERT: A 1613 GLU cc_start: 0.8964 (OUTLIER) cc_final: 0.8582 (pp20) REVERT: A 1617 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8936 (tmm) outliers start: 22 outliers final: 14 residues processed: 66 average time/residue: 0.4079 time to fit residues: 29.6667 Evaluate side-chains 57 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 40 time to evaluate : 0.253 ------------------------------------------------------------------------------- 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 404 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 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 1613 GLU Chi-restraints excluded: chain A residue 1617 MET Chi-restraints excluded: chain A residue 1622 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 66 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 30 optimal weight: 7.9990 chunk 83 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 33 optimal weight: 0.0060 chunk 43 optimal weight: 0.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 ASN ** A 539 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.127375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.085847 restraints weight = 18039.108| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 2.27 r_work: 0.3150 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2231 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= 0.137 Angle : 0.546 8.882 15055 Z= 0.294 Chirality : 0.038 0.245 1722 Planarity : 0.003 0.031 1442 Dihedral : 19.918 175.312 2856 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.07 % Allowed : 15.61 % Favored : 82.32 % 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: 1.43 (0.29), residues: 881 helix: 1.66 (0.26), residues: 412 sheet: 0.14 (0.51), residues: 89 loop : 0.51 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 662 TYR 0.013 0.001 TYR A1329 PHE 0.017 0.001 PHE A1420 TRP 0.010 0.001 TRP A 477 HIS 0.002 0.001 HIS A1579 Details of bonding type rmsd covalent geometry : bond 0.00298 (10706) covalent geometry : angle 0.54565 (15055) hydrogen bonds : bond 0.03706 ( 451) hydrogen bonds : angle 3.90455 ( 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 61 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 44 time to evaluate : 0.290 Fit side-chains REVERT: A 52 MET cc_start: 0.7906 (OUTLIER) cc_final: 0.6676 (mmt) REVERT: A 629 MET cc_start: 0.8626 (mmt) cc_final: 0.8099 (ttt) REVERT: A 665 ARG cc_start: 0.8461 (tmm-80) cc_final: 0.8124 (ttt180) REVERT: A 1297 ASP cc_start: 0.8881 (t70) cc_final: 0.8641 (t70) REVERT: A 1592 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: A 1617 MET cc_start: 0.9248 (OUTLIER) cc_final: 0.8942 (tmm) outliers start: 17 outliers final: 13 residues processed: 57 average time/residue: 0.4612 time to fit residues: 28.7654 Evaluate side-chains 57 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 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 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 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: 4.9990 chunk 32 optimal weight: 7.9990 chunk 11 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 53 optimal weight: 3.9990 chunk 37 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 22 optimal weight: 0.0870 chunk 26 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 82 optimal weight: 0.0670 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3935 r_free = 0.3935 target = 0.127896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.087070 restraints weight = 18252.018| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 2.25 r_work: 0.3148 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10706 Z= 0.147 Angle : 0.542 9.225 15055 Z= 0.293 Chirality : 0.038 0.245 1722 Planarity : 0.003 0.030 1442 Dihedral : 19.864 175.064 2856 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 1.95 % Allowed : 15.85 % 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: 1.47 (0.29), residues: 881 helix: 1.68 (0.26), residues: 412 sheet: 0.21 (0.52), residues: 89 loop : 0.52 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 662 TYR 0.035 0.001 TYR A 480 PHE 0.017 0.001 PHE A1420 TRP 0.010 0.001 TRP A 79 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00322 (10706) covalent geometry : angle 0.54152 (15055) hydrogen bonds : bond 0.03800 ( 451) hydrogen bonds : angle 3.86952 ( 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 60 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 44 time to evaluate : 0.302 Fit side-chains REVERT: A 629 MET cc_start: 0.8630 (mmt) cc_final: 0.8120 (ttt) REVERT: A 665 ARG cc_start: 0.8468 (tmm-80) cc_final: 0.8121 (ttt180) REVERT: A 1297 ASP cc_start: 0.8881 (t70) cc_final: 0.8638 (t70) REVERT: A 1540 ARG cc_start: 0.9373 (mmm-85) cc_final: 0.9097 (mmm-85) REVERT: A 1592 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8006 (mp0) REVERT: A 1617 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8947 (tmm) outliers start: 16 outliers final: 14 residues processed: 57 average time/residue: 0.4420 time to fit residues: 27.6669 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 : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASN 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 1239 MET 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 Chi-restraints excluded: chain A residue 1622 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 82 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 50 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 45 optimal weight: 0.0870 chunk 36 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 = 0.3947 r_free = 0.3947 target = 0.128679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.088240 restraints weight = 17982.773| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.23 r_work: 0.3166 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2331 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= 0.139 Angle : 0.544 9.374 15055 Z= 0.293 Chirality : 0.038 0.239 1722 Planarity : 0.003 0.031 1442 Dihedral : 19.843 175.060 2856 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.71 % Allowed : 16.22 % 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: 1.50 (0.29), residues: 881 helix: 1.72 (0.26), residues: 412 sheet: 0.25 (0.52), residues: 89 loop : 0.52 (0.33), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 662 TYR 0.015 0.001 TYR A 480 PHE 0.016 0.001 PHE A1420 TRP 0.010 0.001 TRP A 79 HIS 0.002 0.001 HIS A 639 Details of bonding type rmsd covalent geometry : bond 0.00305 (10706) covalent geometry : angle 0.54390 (15055) hydrogen bonds : bond 0.03659 ( 451) hydrogen bonds : angle 3.82815 ( 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 58 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 44 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: A 490 ILE cc_start: 0.8594 (mp) cc_final: 0.8382 (mt) REVERT: A 629 MET cc_start: 0.8629 (mmt) cc_final: 0.8129 (ttt) REVERT: A 665 ARG cc_start: 0.8466 (tmm-80) cc_final: 0.8113 (ttt180) REVERT: A 1540 ARG cc_start: 0.9381 (mmm-85) cc_final: 0.8996 (mmm-85) REVERT: A 1592 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7947 (mp0) REVERT: A 1617 MET cc_start: 0.9257 (OUTLIER) cc_final: 0.8964 (tmm) outliers start: 14 outliers final: 14 residues processed: 55 average time/residue: 0.4077 time to fit residues: 24.5375 Evaluate side-chains 57 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 41 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ASN 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 1239 MET 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 Chi-restraints excluded: chain A residue 1622 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 100 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 8.9990 chunk 57 optimal weight: 0.3980 chunk 85 optimal weight: 0.8980 chunk 81 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 74 optimal weight: 0.0370 chunk 54 optimal weight: 2.9990 overall best weight: 0.8660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3932 r_free = 0.3932 target = 0.127742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.086819 restraints weight = 18290.629| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.28 r_work: 0.3146 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10706 Z= 0.159 Angle : 0.545 9.401 15055 Z= 0.295 Chirality : 0.038 0.241 1722 Planarity : 0.003 0.030 1442 Dihedral : 19.833 174.719 2856 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 1.95 % Allowed : 16.10 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.56 (0.29), residues: 881 helix: 1.79 (0.26), residues: 406 sheet: 0.25 (0.52), residues: 89 loop : 0.55 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 662 TYR 0.013 0.001 TYR A1329 PHE 0.016 0.001 PHE A 469 TRP 0.010 0.001 TRP A 79 HIS 0.002 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00350 (10706) covalent geometry : angle 0.54498 (15055) hydrogen bonds : bond 0.03830 ( 451) hydrogen bonds : angle 3.87594 ( 1161) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3058.43 seconds wall clock time: 52 minutes 51.13 seconds (3171.13 seconds total)