Starting phenix.real_space_refine on Thu Feb 5 01:34:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ehf_48052/02_2026/9ehf_48052.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ehf_48052/02_2026/9ehf_48052.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ehf_48052/02_2026/9ehf_48052.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ehf_48052/02_2026/9ehf_48052.map" model { file = "/net/cci-nas-00/data/ceres_data/9ehf_48052/02_2026/9ehf_48052.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ehf_48052/02_2026/9ehf_48052.cif" } resolution = 2.6 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= 0.009 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 27 5.16 5 C 8402 2.51 5 N 2439 2.21 5 O 2971 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s 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: 13972 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 11185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1363, 11185 Classifications: {'peptide': 1363} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 36, 'TRANS': 1326} Chain breaks: 6 Unresolved non-hydrogen bonds: 64 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'ASN:plan1': 2, 'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 20 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: 242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 242 Classifications: {'DNA': 12} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 11} 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: "c" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 370 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} 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: 4.26, per 1000 atoms: 0.30 Number of scatterers: 13972 At special positions: 0 Unit cell: (88.3192, 110.816, 142.477, 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 27 16.00 P 131 15.00 Mg 2 11.99 O 2971 8.00 N 2439 7.00 C 8402 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.13 Conformation dependent library (CDL) restraints added in 432.4 milliseconds 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2612 Finding SS restraints... Secondary structure from input PDB file: 65 helices and 12 sheets defined 51.4% alpha, 11.4% beta 52 base pairs and 92 stacking pairs defined. Time for finding SS restraints: 1.87 Creating SS restraints... Processing helix chain 'A' and resid 29 through 33 removed outlier: 3.856A pdb=" N LEU A 33 " --> pdb=" O LEU A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 82 removed outlier: 3.840A 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 324 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: 3.887A 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 398 Processing helix chain 'A' and resid 416 through 431 removed outlier: 3.517A pdb=" N GLN A 426 " --> pdb=" O ASN A 422 " (cutoff:3.500A) removed outlier: 3.913A 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 495 Processing helix chain 'A' and resid 496 through 503 Processing helix chain 'A' and resid 520 through 525 removed outlier: 3.728A pdb=" N SER A 525 " --> pdb=" O GLN A 521 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 543 removed outlier: 3.516A pdb=" N LEU A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 566 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 677 Processing helix chain 'A' and resid 679 through 688 Processing helix chain 'A' and resid 691 through 703 Processing helix chain 'A' and resid 705 through 721 Processing helix chain 'A' and resid 723 through 734 Processing helix chain 'A' and resid 739 through 750 Processing helix chain 'A' and resid 762 through 773 Processing helix chain 'A' and resid 779 through 789 removed outlier: 3.807A pdb=" N LYS A 789 " --> pdb=" O ARG A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 804 Processing helix chain 'A' and resid 814 through 824 Processing helix chain 'A' and resid 860 through 887 removed outlier: 5.013A pdb=" N GLN A 879 " --> pdb=" O ASP A 875 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ASN A 880 " --> pdb=" O ASP A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 944 Processing helix chain 'A' and resid 983 through 985 No H-bonds generated for 'chain 'A' and resid 983 through 985' Processing helix chain 'A' and resid 991 through 999 Processing helix chain 'A' and resid 1004 through 1008 Processing helix chain 'A' and resid 1009 through 1018 Processing helix chain 'A' and resid 1021 through 1034 Processing helix chain 'A' and resid 1053 through 1063 Processing helix chain 'A' and resid 1064 through 1066 No H-bonds generated for 'chain 'A' and resid 1064 through 1066' Processing helix chain 'A' and resid 1070 through 1081 Processing helix chain 'A' and resid 1082 through 1087 Processing helix chain 'A' and resid 1091 through 1110 Processing helix chain 'A' and resid 1113 through 1115 No H-bonds generated for 'chain 'A' and resid 1113 through 1115' Processing helix chain 'A' and resid 1127 through 1131 Processing helix chain 'A' and resid 1132 through 1144 Processing helix chain 'A' and resid 1144 through 1150 Processing helix chain 'A' and resid 1159 through 1177 removed outlier: 3.842A pdb=" N LEU A1163 " --> pdb=" O SER A1159 " (cutoff:3.500A) Processing helix chain 'A' and resid 1208 through 1213 Processing helix chain 'A' and resid 1282 through 1292 Processing helix chain 'A' and resid 1293 through 1296 removed outlier: 3.543A 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: 3.740A pdb=" N LEU A1312 " --> pdb=" O THR A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1333 through 1346 removed outlier: 3.746A 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 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 1579 Processing helix chain 'A' and resid 1586 through 1595 Processing helix chain 'A' and resid 1608 through 1624 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 25 Processing sheet with id=AA2, first strand: chain 'A' and resid 24 through 25 removed outlier: 9.640A pdb=" N SER A1220 " --> pdb=" O LYS A 36 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N GLY A 38 " --> pdb=" O SER A1220 " (cutoff:3.500A) removed outlier: 7.904A pdb=" N LYS A1222 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL A 40 " --> pdb=" O LYS A1222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 463 through 465 Processing sheet with id=AA4, first strand: chain 'A' and resid 597 through 598 Processing sheet with id=AA5, first strand: chain 'A' and resid 630 through 635 removed outlier: 7.590A pdb=" N GLU A 631 " --> pdb=" O THR A 644 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 966 through 969 Processing sheet with id=AA7, first strand: chain 'A' and resid 1441 through 1446 removed outlier: 4.690A pdb=" N PHE A1441 " --> pdb=" O ILE A1373 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU A1443 " --> pdb=" O VAL A1371 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG A1370 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 8.841A pdb=" N ILE A1244 " --> pdb=" O ARG A1370 " (cutoff:3.500A) removed outlier: 13.744A pdb=" N LYS A1372 " --> pdb=" O ASP A1242 " (cutoff:3.500A) removed outlier: 17.962A pdb=" N ASP A1242 " --> pdb=" O LYS A1372 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N GLY A1243 " --> pdb=" O ASN A1469 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN A1469 " --> pdb=" O GLY A1243 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ILE A1467 " --> pdb=" O TYR A1245 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLU A1247 " --> pdb=" O TYR A1465 " (cutoff:3.500A) removed outlier: 10.883A pdb=" N TYR A1465 " --> pdb=" O GLU A1247 " (cutoff:3.500A) removed outlier: 18.133A pdb=" N TYR A1249 " --> pdb=" O PHE A1463 " (cutoff:3.500A) removed outlier: 22.719A pdb=" N PHE A1463 " --> pdb=" O TYR A1249 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 1270 through 1273 removed outlier: 4.663A pdb=" N VAL A1261 " --> pdb=" O ILE A1273 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1276 through 1277 Processing sheet with id=AB1, first strand: chain 'A' and resid 1390 through 1391 Processing sheet with id=AB2, first strand: chain 'A' and resid 1491 through 1496 Processing sheet with id=AB3, first strand: chain 'A' and resid 1530 through 1533 removed outlier: 4.078A pdb=" N ILE A1547 " --> pdb=" O VAL A1533 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N THR A1546 " --> pdb=" O LYS A1562 " (cutoff:3.500A) 532 hydrogen bonds defined for protein. 1521 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 131 hydrogen bonds 246 hydrogen bond angles 0 basepair planarities 52 basepair parallelities 92 stacking parallelities Total time for adding SS restraints: 3.51 Time building geometry restraints manager: 1.42 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: 3352 1.33 - 1.46: 3797 1.46 - 1.58: 7068 1.58 - 1.70: 260 1.70 - 1.82: 38 Bond restraints: 14515 Sorted by residual: bond pdb=" C3' DG D 3 " pdb=" O3' DG D 3 " ideal model delta sigma weight residual 1.422 1.488 -0.066 3.00e-02 1.11e+03 4.84e+00 bond pdb=" CB ASP A1570 " pdb=" CG ASP A1570 " ideal model delta sigma weight residual 1.516 1.563 -0.047 2.50e-02 1.60e+03 3.50e+00 bond pdb=" CG1 ILE A 787 " pdb=" CD1 ILE A 787 " ideal model delta sigma weight residual 1.513 1.442 0.071 3.90e-02 6.57e+02 3.29e+00 bond pdb=" CB ASP A1022 " pdb=" CG ASP A1022 " ideal model delta sigma weight residual 1.516 1.561 -0.045 2.50e-02 1.60e+03 3.26e+00 bond pdb=" CB ASN A1217 " pdb=" CG ASN A1217 " ideal model delta sigma weight residual 1.516 1.560 -0.044 2.50e-02 1.60e+03 3.16e+00 ... (remaining 14510 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.29: 19965 3.29 - 6.58: 181 6.58 - 9.88: 21 9.88 - 13.17: 2 13.17 - 16.46: 3 Bond angle restraints: 20172 Sorted by residual: angle pdb=" CB MET A 629 " pdb=" CG MET A 629 " pdb=" SD MET A 629 " ideal model delta sigma weight residual 112.70 129.16 -16.46 3.00e+00 1.11e-01 3.01e+01 angle pdb=" CB MET A 1 " pdb=" CG MET A 1 " pdb=" SD MET A 1 " ideal model delta sigma weight residual 112.70 126.83 -14.13 3.00e+00 1.11e-01 2.22e+01 angle pdb=" CG ARG A1540 " pdb=" CD ARG A1540 " pdb=" NE ARG A1540 " ideal model delta sigma weight residual 112.00 122.18 -10.18 2.20e+00 2.07e-01 2.14e+01 angle pdb=" C3' DG D 3 " pdb=" O3' DG D 3 " pdb=" P DT D 4 " ideal model delta sigma weight residual 120.20 126.66 -6.46 1.50e+00 4.44e-01 1.86e+01 angle pdb=" CB ILE A 730 " pdb=" CG1 ILE A 730 " pdb=" CD1 ILE A 730 " ideal model delta sigma weight residual 113.80 122.61 -8.81 2.10e+00 2.27e-01 1.76e+01 ... (remaining 20167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.64: 8276 32.64 - 65.28: 491 65.28 - 97.92: 51 97.92 - 130.56: 1 130.56 - 163.19: 1 Dihedral angle restraints: 8820 sinusoidal: 4790 harmonic: 4030 Sorted by residual: dihedral pdb=" CA ASN A 453 " pdb=" C ASN A 453 " pdb=" N ASN A 454 " pdb=" CA ASN A 454 " ideal model delta harmonic sigma weight residual -180.00 -152.77 -27.23 0 5.00e+00 4.00e-02 2.97e+01 dihedral pdb=" CA TYR A 449 " pdb=" C TYR A 449 " pdb=" N LEU A 450 " pdb=" CA LEU A 450 " ideal model delta harmonic sigma weight residual -180.00 -152.90 -27.10 0 5.00e+00 4.00e-02 2.94e+01 dihedral pdb=" CA ASP A 957 " pdb=" C ASP A 957 " pdb=" N GLY A 958 " pdb=" CA GLY A 958 " ideal model delta harmonic sigma weight residual -180.00 -153.48 -26.52 0 5.00e+00 4.00e-02 2.81e+01 ... (remaining 8817 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1489 0.044 - 0.087: 564 0.087 - 0.131: 162 0.131 - 0.175: 50 0.175 - 0.219: 12 Chirality restraints: 2277 Sorted by residual: chirality pdb=" C1' A B 86 " pdb=" O4' A B 86 " pdb=" C2' A B 86 " pdb=" N9 A B 86 " both_signs ideal model delta sigma weight residual False 2.44 2.22 0.22 2.00e-01 2.50e+01 1.20e+00 chirality pdb=" C1' C B 34 " pdb=" O4' C B 34 " pdb=" C2' C B 34 " pdb=" N1 C B 34 " both_signs ideal model delta sigma weight residual False 2.47 2.25 0.22 2.00e-01 2.50e+01 1.19e+00 chirality pdb=" C1' A B 51 " pdb=" O4' A B 51 " pdb=" C2' A B 51 " pdb=" N9 A B 51 " both_signs ideal model delta sigma weight residual False 2.46 2.24 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 2274 not shown) Planarity restraints: 2113 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 824 " 0.439 9.50e-02 1.11e+02 1.98e-01 2.96e+01 pdb=" NE ARG A 824 " -0.040 2.00e-02 2.50e+03 pdb=" CZ ARG A 824 " 0.037 2.00e-02 2.50e+03 pdb=" NH1 ARG A 824 " -0.017 2.00e-02 2.50e+03 pdb=" NH2 ARG A 824 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A1006 " -0.316 9.50e-02 1.11e+02 1.43e-01 1.61e+01 pdb=" NE ARG A1006 " 0.030 2.00e-02 2.50e+03 pdb=" CZ ARG A1006 " -0.030 2.00e-02 2.50e+03 pdb=" NH1 ARG A1006 " 0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG A1006 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 310 " -0.313 9.50e-02 1.11e+02 1.41e-01 1.51e+01 pdb=" NE ARG A 310 " 0.029 2.00e-02 2.50e+03 pdb=" CZ ARG A 310 " -0.027 2.00e-02 2.50e+03 pdb=" NH1 ARG A 310 " 0.013 2.00e-02 2.50e+03 pdb=" NH2 ARG A 310 " -0.001 2.00e-02 2.50e+03 ... (remaining 2110 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 7236 3.02 - 3.49: 13869 3.49 - 3.96: 25603 3.96 - 4.43: 29718 4.43 - 4.90: 42960 Nonbonded interactions: 119386 Sorted by model distance: nonbonded pdb=" O4' C B 18 " pdb=" C6 C B 18 " model vdw 2.549 2.672 nonbonded pdb=" O5' DG C 3 " pdb=" O4' DG C 3 " model vdw 2.549 2.432 nonbonded pdb=" N1 G B 11 " pdb=" C4 G B 11 " model vdw 2.584 2.672 nonbonded pdb=" N1 G B 62 " pdb=" C4 G B 62 " model vdw 2.587 2.672 nonbonded pdb=" N1 G B 31 " pdb=" C4 G B 31 " model vdw 2.589 2.672 ... (remaining 119381 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: 11.750 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: 0.020 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 17.130 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 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 0.071 14515 Z= 0.232 Angle : 0.911 16.460 20172 Z= 0.508 Chirality : 0.053 0.219 2277 Planarity : 0.011 0.198 2113 Dihedral : 18.250 163.195 6208 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 1.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 0.49 % Allowed : 12.82 % Favored : 86.69 % 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: -0.08 (0.22), residues: 1349 helix: -0.10 (0.19), residues: 635 sheet: -0.12 (0.38), residues: 161 loop : 0.29 (0.28), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.042 0.004 ARG A 824 TYR 0.026 0.003 TYR A1194 PHE 0.040 0.002 PHE A 783 TRP 0.029 0.003 TRP A1459 HIS 0.007 0.001 HIS A1177 Details of bonding type rmsd covalent geometry : bond 0.00500 (14515) covalent geometry : angle 0.91147 (20172) hydrogen bonds : bond 0.12389 ( 659) hydrogen bonds : angle 5.97710 ( 1767) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 88 time to evaluate : 0.490 Fit side-chains REVERT: A 89 LYS cc_start: 0.7984 (mmpt) cc_final: 0.7615 (mtmm) REVERT: A 418 LYS cc_start: 0.7295 (tppt) cc_final: 0.6728 (mptt) REVERT: A 515 GLU cc_start: 0.8653 (tt0) cc_final: 0.8264 (tm-30) REVERT: A 555 GLU cc_start: 0.8519 (tp30) cc_final: 0.8194 (tp30) REVERT: A 806 GLU cc_start: 0.8457 (tt0) cc_final: 0.7690 (mp0) REVERT: A 898 GLU cc_start: 0.8028 (tt0) cc_final: 0.7593 (pp20) REVERT: A 1006 ARG cc_start: 0.7802 (mtt90) cc_final: 0.7104 (mtm-85) REVERT: A 1068 ASP cc_start: 0.7092 (m-30) cc_final: 0.6645 (t0) REVERT: A 1268 LYS cc_start: 0.8774 (mtmm) cc_final: 0.8484 (mppt) REVERT: A 1358 MET cc_start: 0.8836 (tpt) cc_final: 0.8439 (tpt) outliers start: 6 outliers final: 4 residues processed: 92 average time/residue: 0.6136 time to fit residues: 62.1764 Evaluate side-chains 84 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 1207 ASP Chi-restraints excluded: chain A residue 1240 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.0010 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 604 GLN A 659 HIS A 670 ASN A 702 HIS A1129 ASN A1148 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.113076 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.089856 restraints weight = 21467.779| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 2.00 r_work: 0.3152 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.0934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14515 Z= 0.174 Angle : 0.568 7.765 20172 Z= 0.309 Chirality : 0.040 0.246 2277 Planarity : 0.004 0.039 2113 Dihedral : 18.368 161.920 3361 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 3.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 1.56 % Allowed : 11.50 % Favored : 86.94 % 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 (0.23), residues: 1349 helix: 1.06 (0.20), residues: 636 sheet: 0.01 (0.40), residues: 154 loop : 0.67 (0.28), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A1078 TYR 0.013 0.001 TYR A 656 PHE 0.020 0.002 PHE A 783 TRP 0.015 0.002 TRP A 698 HIS 0.005 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00388 (14515) covalent geometry : angle 0.56763 (20172) hydrogen bonds : bond 0.04514 ( 659) hydrogen bonds : angle 4.64693 ( 1767) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.493 Fit side-chains REVERT: A 42 GLU cc_start: 0.8257 (OUTLIER) cc_final: 0.7516 (tp30) REVERT: A 407 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8147 (mp10) REVERT: A 418 LYS cc_start: 0.7347 (tppt) cc_final: 0.6882 (ttmm) REVERT: A 515 GLU cc_start: 0.8670 (tt0) cc_final: 0.8243 (tm-30) REVERT: A 708 LYS cc_start: 0.7626 (tttt) cc_final: 0.7035 (tmtm) REVERT: A 898 GLU cc_start: 0.7977 (tt0) cc_final: 0.7268 (pp20) REVERT: A 942 GLU cc_start: 0.8331 (mm-30) cc_final: 0.7817 (mm-30) REVERT: A 1006 ARG cc_start: 0.7862 (mtt90) cc_final: 0.7644 (mtm-85) REVERT: A 1268 LYS cc_start: 0.8811 (mtmm) cc_final: 0.8545 (mppt) REVERT: A 1540 ARG cc_start: 0.8262 (mmm-85) cc_final: 0.7927 (mmm160) outliers start: 19 outliers final: 5 residues processed: 102 average time/residue: 0.6153 time to fit residues: 69.0290 Evaluate side-chains 85 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 78 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 1622 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 81 optimal weight: 3.9990 chunk 90 optimal weight: 4.9990 chunk 63 optimal weight: 0.0980 chunk 72 optimal weight: 4.9990 chunk 74 optimal weight: 4.9990 chunk 95 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 100 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 604 GLN A 848 GLN A 931 ASN A 938 ASN A1082 ASN A1148 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.110292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.086909 restraints weight = 21612.794| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.02 r_work: 0.3101 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14515 Z= 0.212 Angle : 0.569 10.433 20172 Z= 0.308 Chirality : 0.042 0.272 2277 Planarity : 0.004 0.038 2113 Dihedral : 18.318 159.443 3355 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.30 % Allowed : 11.83 % Favored : 85.87 % 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: 1.15 (0.23), residues: 1349 helix: 1.27 (0.20), residues: 634 sheet: -0.21 (0.38), residues: 171 loop : 0.70 (0.28), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A1078 TYR 0.014 0.002 TYR A1265 PHE 0.016 0.002 PHE A 497 TRP 0.014 0.002 TRP A 79 HIS 0.007 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00477 (14515) covalent geometry : angle 0.56902 (20172) hydrogen bonds : bond 0.04674 ( 659) hydrogen bonds : angle 4.50904 ( 1767) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 92 time to evaluate : 0.492 Fit side-chains revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7525 (tp30) REVERT: A 407 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7868 (mp10) REVERT: A 418 LYS cc_start: 0.7349 (tppt) cc_final: 0.6940 (ttmm) REVERT: A 515 GLU cc_start: 0.8687 (tt0) cc_final: 0.8214 (tm-30) REVERT: A 516 TYR cc_start: 0.8517 (m-80) cc_final: 0.8219 (m-80) REVERT: A 708 LYS cc_start: 0.7576 (tttt) cc_final: 0.6976 (tmtm) REVERT: A 771 LEU cc_start: 0.7294 (OUTLIER) cc_final: 0.6819 (mp) REVERT: A 898 GLU cc_start: 0.7960 (tt0) cc_final: 0.7227 (pp20) REVERT: A 938 ASN cc_start: 0.7979 (OUTLIER) cc_final: 0.7647 (m-40) REVERT: A 942 GLU cc_start: 0.8381 (mm-30) cc_final: 0.7835 (mm-30) REVERT: A 1268 LYS cc_start: 0.8837 (mtmm) cc_final: 0.8563 (mppt) REVERT: A 1358 MET cc_start: 0.8874 (tpt) cc_final: 0.8486 (tpt) REVERT: A 1540 ARG cc_start: 0.8301 (mmm-85) cc_final: 0.7965 (mmm160) outliers start: 28 outliers final: 10 residues processed: 114 average time/residue: 0.5491 time to fit residues: 69.3401 Evaluate side-chains 97 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 83 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 823 HIS Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 938 ASN Chi-restraints excluded: chain A residue 1011 ASN Chi-restraints excluded: chain A residue 1546 THR Chi-restraints excluded: chain A residue 1622 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 120 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 96 optimal weight: 1.9990 chunk 95 optimal weight: 3.9990 chunk 114 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 145 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 93 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 604 GLN A 670 ASN A 931 ASN A1148 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.110182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.086962 restraints weight = 21786.599| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.01 r_work: 0.3103 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2990 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14515 Z= 0.203 Angle : 0.554 10.469 20172 Z= 0.299 Chirality : 0.041 0.268 2277 Planarity : 0.004 0.037 2113 Dihedral : 18.284 159.210 3355 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 2.38 % Allowed : 12.57 % Favored : 85.05 % 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: 1.17 (0.23), residues: 1349 helix: 1.37 (0.20), residues: 636 sheet: -0.30 (0.38), residues: 164 loop : 0.62 (0.28), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1078 TYR 0.013 0.002 TYR A1265 PHE 0.015 0.002 PHE A1420 TRP 0.013 0.002 TRP A 79 HIS 0.006 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00457 (14515) covalent geometry : angle 0.55427 (20172) hydrogen bonds : bond 0.04442 ( 659) hydrogen bonds : angle 4.43944 ( 1767) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.7525 (tp30) REVERT: A 418 LYS cc_start: 0.7380 (tppt) cc_final: 0.6970 (ttmm) REVERT: A 515 GLU cc_start: 0.8645 (tt0) cc_final: 0.8225 (tm-30) REVERT: A 555 GLU cc_start: 0.8490 (tp30) cc_final: 0.8251 (tp30) REVERT: A 708 LYS cc_start: 0.7576 (tttt) cc_final: 0.6981 (tmtm) REVERT: A 898 GLU cc_start: 0.7962 (tt0) cc_final: 0.7209 (OUTLIER) REVERT: A 942 GLU cc_start: 0.8396 (mm-30) cc_final: 0.7792 (mm-30) REVERT: A 1358 MET cc_start: 0.8861 (tpt) cc_final: 0.8427 (tpt) REVERT: A 1540 ARG cc_start: 0.8332 (mmm-85) cc_final: 0.7909 (mmm160) outliers start: 29 outliers final: 12 residues processed: 108 average time/residue: 0.5540 time to fit residues: 66.1601 Evaluate side-chains 92 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 704 ARG Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 823 HIS Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 1011 ASN Chi-restraints excluded: chain A residue 1622 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 129 optimal weight: 2.9990 chunk 90 optimal weight: 0.0870 chunk 97 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 85 optimal weight: 0.8980 chunk 139 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 491 GLN A 604 GLN A 931 ASN A1148 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.111205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.088092 restraints weight = 21708.698| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.01 r_work: 0.3121 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14515 Z= 0.169 Angle : 0.528 10.582 20172 Z= 0.285 Chirality : 0.039 0.259 2277 Planarity : 0.003 0.037 2113 Dihedral : 18.219 159.928 3355 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 3.20 % Allowed : 11.67 % Favored : 85.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.23), residues: 1349 helix: 1.49 (0.20), residues: 637 sheet: -0.28 (0.38), residues: 164 loop : 0.63 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1078 TYR 0.012 0.001 TYR A1265 PHE 0.015 0.001 PHE A1420 TRP 0.014 0.002 TRP A 79 HIS 0.005 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00376 (14515) covalent geometry : angle 0.52839 (20172) hydrogen bonds : bond 0.04138 ( 659) hydrogen bonds : angle 4.31910 ( 1767) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 90 time to evaluate : 0.467 Fit side-chains revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.7511 (tp30) REVERT: A 407 GLN cc_start: 0.8513 (OUTLIER) cc_final: 0.7897 (mp10) REVERT: A 418 LYS cc_start: 0.7356 (tppt) cc_final: 0.6902 (ttmm) REVERT: A 515 GLU cc_start: 0.8664 (tt0) cc_final: 0.8177 (tm-30) REVERT: A 555 GLU cc_start: 0.8512 (tp30) cc_final: 0.8240 (tp30) REVERT: A 898 GLU cc_start: 0.7938 (tt0) cc_final: 0.7143 (OUTLIER) REVERT: A 900 ASN cc_start: 0.6265 (t0) cc_final: 0.6057 (m110) REVERT: A 942 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7759 (mm-30) REVERT: A 1540 ARG cc_start: 0.8273 (mmm-85) cc_final: 0.7878 (mmm160) outliers start: 39 outliers final: 17 residues processed: 120 average time/residue: 0.5850 time to fit residues: 77.2716 Evaluate side-chains 106 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 617 GLN Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 823 HIS Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 857 ILE Chi-restraints excluded: chain A residue 973 ARG Chi-restraints excluded: chain A residue 1011 ASN Chi-restraints excluded: chain A residue 1546 THR Chi-restraints excluded: chain A residue 1573 ILE Chi-restraints excluded: chain A residue 1622 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 76 optimal weight: 1.9990 chunk 116 optimal weight: 0.6980 chunk 137 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 127 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 78 optimal weight: 0.0470 chunk 5 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 GLN A 604 GLN A 848 GLN A 931 ASN A1148 GLN A1287 ASN A1515 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.111452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.088554 restraints weight = 21501.099| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 1.99 r_work: 0.3132 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14515 Z= 0.155 Angle : 0.523 11.375 20172 Z= 0.281 Chirality : 0.039 0.255 2277 Planarity : 0.003 0.037 2113 Dihedral : 18.173 160.713 3355 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.47 % Allowed : 13.15 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.23), residues: 1349 helix: 1.59 (0.20), residues: 637 sheet: -0.29 (0.38), residues: 164 loop : 0.64 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1078 TYR 0.011 0.001 TYR A1265 PHE 0.015 0.001 PHE A1420 TRP 0.013 0.001 TRP A 79 HIS 0.005 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00345 (14515) covalent geometry : angle 0.52253 (20172) hydrogen bonds : bond 0.03995 ( 659) hydrogen bonds : angle 4.24915 ( 1767) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 93 time to evaluate : 0.432 Fit side-chains revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7492 (tp30) REVERT: A 407 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7817 (mp10) REVERT: A 418 LYS cc_start: 0.7349 (tppt) cc_final: 0.6900 (ttmm) REVERT: A 491 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7528 (mp-120) REVERT: A 515 GLU cc_start: 0.8688 (tt0) cc_final: 0.8211 (tm-30) REVERT: A 555 GLU cc_start: 0.8505 (tp30) cc_final: 0.8222 (tp30) REVERT: A 898 GLU cc_start: 0.7919 (tt0) cc_final: 0.7180 (OUTLIER) REVERT: A 900 ASN cc_start: 0.6247 (OUTLIER) cc_final: 0.6040 (m110) REVERT: A 942 GLU cc_start: 0.8361 (mm-30) cc_final: 0.7762 (mm-30) REVERT: A 1358 MET cc_start: 0.8848 (tpt) cc_final: 0.8478 (tpt) REVERT: A 1540 ARG cc_start: 0.8296 (mmm-85) cc_final: 0.7918 (mmm160) outliers start: 30 outliers final: 15 residues processed: 116 average time/residue: 0.5043 time to fit residues: 64.6670 Evaluate side-chains 105 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 491 GLN Chi-restraints excluded: chain A residue 617 GLN Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 823 HIS Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 973 ARG Chi-restraints excluded: chain A residue 1573 ILE Chi-restraints excluded: chain A residue 1622 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 42 optimal weight: 0.7980 chunk 125 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 64 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 chunk 135 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 341 HIS A 604 GLN A 931 ASN A1148 GLN A1515 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.111483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.088497 restraints weight = 21454.087| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.99 r_work: 0.3128 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14515 Z= 0.162 Angle : 0.529 11.824 20172 Z= 0.284 Chirality : 0.039 0.255 2277 Planarity : 0.003 0.037 2113 Dihedral : 18.154 160.901 3355 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.55 % Allowed : 13.56 % Favored : 83.89 % 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 (0.23), residues: 1349 helix: 1.60 (0.20), residues: 638 sheet: -0.33 (0.38), residues: 164 loop : 0.63 (0.28), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1078 TYR 0.012 0.001 TYR A1160 PHE 0.014 0.001 PHE A1420 TRP 0.012 0.001 TRP A 79 HIS 0.005 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00363 (14515) covalent geometry : angle 0.52928 (20172) hydrogen bonds : bond 0.04034 ( 659) hydrogen bonds : angle 4.24766 ( 1767) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 88 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7486 (tp30) REVERT: A 407 GLN cc_start: 0.8471 (OUTLIER) cc_final: 0.7828 (mp10) REVERT: A 418 LYS cc_start: 0.7348 (tppt) cc_final: 0.6899 (ttmm) REVERT: A 515 GLU cc_start: 0.8727 (tt0) cc_final: 0.8218 (tm-30) REVERT: A 555 GLU cc_start: 0.8526 (tp30) cc_final: 0.8234 (tp30) REVERT: A 898 GLU cc_start: 0.7932 (tt0) cc_final: 0.7174 (OUTLIER) REVERT: A 900 ASN cc_start: 0.6275 (t0) cc_final: 0.6054 (m110) REVERT: A 942 GLU cc_start: 0.8356 (mm-30) cc_final: 0.7758 (mm-30) REVERT: A 1358 MET cc_start: 0.8843 (tpt) cc_final: 0.8442 (tpt) REVERT: A 1540 ARG cc_start: 0.8300 (mmm-85) cc_final: 0.7915 (mmm160) outliers start: 31 outliers final: 17 residues processed: 111 average time/residue: 0.5238 time to fit residues: 64.4136 Evaluate side-chains 102 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 84 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 617 GLN Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 772 PHE Chi-restraints excluded: chain A residue 823 HIS Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 973 ARG Chi-restraints excluded: chain A residue 1427 VAL Chi-restraints excluded: chain A residue 1573 ILE Chi-restraints excluded: chain A residue 1622 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 68 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 25 optimal weight: 0.0000 chunk 92 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 125 optimal weight: 0.0070 chunk 15 optimal weight: 0.5980 chunk 59 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 overall best weight: 0.5206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 491 GLN A 604 GLN A 931 ASN A1148 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.112689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.089795 restraints weight = 21453.681| |-----------------------------------------------------------------------------| r_work (start): 0.3292 rms_B_bonded: 1.99 r_work: 0.3152 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14515 Z= 0.133 Angle : 0.511 12.721 20172 Z= 0.274 Chirality : 0.038 0.244 2277 Planarity : 0.003 0.037 2113 Dihedral : 18.113 162.130 3355 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 2.14 % Allowed : 14.05 % Favored : 83.81 % 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 (0.23), residues: 1349 helix: 1.70 (0.20), residues: 638 sheet: -0.29 (0.39), residues: 163 loop : 0.67 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1078 TYR 0.013 0.001 TYR A1160 PHE 0.015 0.001 PHE A1420 TRP 0.013 0.001 TRP A 79 HIS 0.004 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00294 (14515) covalent geometry : angle 0.51079 (20172) hydrogen bonds : bond 0.03770 ( 659) hydrogen bonds : angle 4.14668 ( 1767) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.8256 (OUTLIER) cc_final: 0.7442 (tp30) REVERT: A 407 GLN cc_start: 0.8463 (OUTLIER) cc_final: 0.7829 (mp10) REVERT: A 418 LYS cc_start: 0.7365 (tppt) cc_final: 0.6942 (ttmm) REVERT: A 555 GLU cc_start: 0.8560 (tp30) cc_final: 0.8280 (tp30) REVERT: A 898 GLU cc_start: 0.7849 (tt0) cc_final: 0.7211 (OUTLIER) REVERT: A 942 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7741 (mm-30) REVERT: A 1268 LYS cc_start: 0.8861 (mtmm) cc_final: 0.8564 (mppt) REVERT: A 1358 MET cc_start: 0.8828 (tpt) cc_final: 0.8418 (tpt) REVERT: A 1439 LYS cc_start: 0.8617 (mttt) cc_final: 0.8386 (mmtp) REVERT: A 1540 ARG cc_start: 0.8321 (mmm-85) cc_final: 0.7942 (mmm160) outliers start: 26 outliers final: 14 residues processed: 113 average time/residue: 0.5095 time to fit residues: 63.3193 Evaluate side-chains 103 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 407 GLN Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 823 HIS Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 973 ARG Chi-restraints excluded: chain A residue 1427 VAL Chi-restraints excluded: chain A residue 1573 ILE Chi-restraints excluded: chain A residue 1622 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 142 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 115 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 117 optimal weight: 0.5980 chunk 132 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 491 GLN A 604 GLN A 931 ASN A 938 ASN A1148 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.110728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.087544 restraints weight = 21594.045| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.01 r_work: 0.3111 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14515 Z= 0.195 Angle : 0.548 13.158 20172 Z= 0.294 Chirality : 0.040 0.260 2277 Planarity : 0.003 0.038 2113 Dihedral : 18.135 161.109 3355 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 2.14 % Allowed : 14.30 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.31 (0.23), residues: 1349 helix: 1.60 (0.20), residues: 637 sheet: -0.36 (0.38), residues: 164 loop : 0.56 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A1078 TYR 0.013 0.001 TYR A1160 PHE 0.013 0.001 PHE A1420 TRP 0.012 0.002 TRP A 79 HIS 0.006 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00438 (14515) covalent geometry : angle 0.54849 (20172) hydrogen bonds : bond 0.04202 ( 659) hydrogen bonds : angle 4.24551 ( 1767) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.464 Fit side-chains REVERT: A 42 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.7512 (tp30) REVERT: A 418 LYS cc_start: 0.7364 (tppt) cc_final: 0.6860 (ttmm) REVERT: A 491 GLN cc_start: 0.8482 (OUTLIER) cc_final: 0.7605 (mp-120) REVERT: A 515 GLU cc_start: 0.8671 (mp0) cc_final: 0.8310 (tm-30) REVERT: A 555 GLU cc_start: 0.8528 (tp30) cc_final: 0.8224 (tp30) REVERT: A 708 LYS cc_start: 0.7582 (tttt) cc_final: 0.6978 (tmtm) REVERT: A 898 GLU cc_start: 0.7942 (tt0) cc_final: 0.7115 (OUTLIER) REVERT: A 900 ASN cc_start: 0.6295 (OUTLIER) cc_final: 0.5797 (m110) REVERT: A 938 ASN cc_start: 0.7740 (OUTLIER) cc_final: 0.7376 (m-40) REVERT: A 942 GLU cc_start: 0.8354 (mm-30) cc_final: 0.7735 (mm-30) REVERT: A 1358 MET cc_start: 0.8846 (tpt) cc_final: 0.8425 (tpt) REVERT: A 1540 ARG cc_start: 0.8375 (mmm-85) cc_final: 0.7993 (mmm160) REVERT: A 1624 ASN cc_start: 0.7331 (t0) cc_final: 0.7088 (p0) outliers start: 26 outliers final: 14 residues processed: 106 average time/residue: 0.5396 time to fit residues: 63.3404 Evaluate side-chains 98 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 491 GLN Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 742 ILE Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 823 HIS Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 938 ASN Chi-restraints excluded: chain A residue 973 ARG Chi-restraints excluded: chain A residue 1427 VAL Chi-restraints excluded: chain A residue 1573 ILE Chi-restraints excluded: chain A residue 1622 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 144 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 25 optimal weight: 0.0570 chunk 5 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 110 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 604 GLN ** A 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 931 ASN A 938 ASN ** A1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1148 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.110905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.087814 restraints weight = 21554.698| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.00 r_work: 0.3113 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.234 14515 Z= 0.225 Angle : 0.934 59.188 20172 Z= 0.560 Chirality : 0.039 0.258 2277 Planarity : 0.003 0.038 2113 Dihedral : 18.137 161.100 3355 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.23 % Allowed : 15.28 % Favored : 83.48 % Cbeta Deviations : 0.15 % 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: 1.28 (0.23), residues: 1349 helix: 1.56 (0.20), residues: 637 sheet: -0.36 (0.38), residues: 164 loop : 0.56 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1078 TYR 0.013 0.001 TYR A1160 PHE 0.013 0.001 PHE A1420 TRP 0.012 0.001 TRP A 79 HIS 0.006 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00486 (14515) covalent geometry : angle 0.93393 (20172) hydrogen bonds : bond 0.04226 ( 659) hydrogen bonds : angle 4.24746 ( 1767) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2698 Ramachandran restraints generated. 1349 Oldfield, 0 Emsley, 1349 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.465 Fit side-chains REVERT: A 42 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7507 (tp30) REVERT: A 418 LYS cc_start: 0.7356 (tppt) cc_final: 0.6853 (ttmm) REVERT: A 515 GLU cc_start: 0.8671 (mp0) cc_final: 0.8329 (tm-30) REVERT: A 516 TYR cc_start: 0.8583 (m-80) cc_final: 0.8226 (m-80) REVERT: A 555 GLU cc_start: 0.8523 (tp30) cc_final: 0.8219 (tp30) REVERT: A 708 LYS cc_start: 0.7577 (tttt) cc_final: 0.6973 (tmtm) REVERT: A 898 GLU cc_start: 0.7945 (tt0) cc_final: 0.7112 (OUTLIER) REVERT: A 900 ASN cc_start: 0.6285 (OUTLIER) cc_final: 0.5789 (m110) REVERT: A 942 GLU cc_start: 0.8318 (mm-30) cc_final: 0.7689 (mm-30) REVERT: A 1358 MET cc_start: 0.8846 (tpt) cc_final: 0.8422 (tpt) REVERT: A 1540 ARG cc_start: 0.8372 (mmm-85) cc_final: 0.7986 (mmm160) REVERT: A 1624 ASN cc_start: 0.7329 (t0) cc_final: 0.7087 (p0) outliers start: 15 outliers final: 13 residues processed: 93 average time/residue: 0.5621 time to fit residues: 57.6892 Evaluate side-chains 96 residues out of total 1234 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLU Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 361 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 603 GLU Chi-restraints excluded: chain A residue 769 VAL Chi-restraints excluded: chain A residue 823 HIS Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 900 ASN Chi-restraints excluded: chain A residue 973 ARG Chi-restraints excluded: chain A residue 1427 VAL Chi-restraints excluded: chain A residue 1622 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 147 random chunks: chunk 45 optimal weight: 1.9990 chunk 137 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 90 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 chunk 123 optimal weight: 0.3980 chunk 101 optimal weight: 1.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 604 GLN ** A 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 931 ASN ** A 938 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1081 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1148 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.110905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.087814 restraints weight = 21497.324| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.00 r_work: 0.3113 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2995 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.234 14515 Z= 0.225 Angle : 0.934 59.188 20172 Z= 0.560 Chirality : 0.039 0.258 2277 Planarity : 0.003 0.038 2113 Dihedral : 18.137 161.100 3355 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.23 % Allowed : 15.28 % Favored : 83.48 % Cbeta Deviations : 0.15 % 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: 1.28 (0.23), residues: 1349 helix: 1.56 (0.20), residues: 637 sheet: -0.36 (0.38), residues: 164 loop : 0.56 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A1078 TYR 0.013 0.001 TYR A1160 PHE 0.013 0.001 PHE A1420 TRP 0.012 0.001 TRP A 79 HIS 0.006 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00486 (14515) covalent geometry : angle 0.93393 (20172) hydrogen bonds : bond 0.04226 ( 659) hydrogen bonds : angle 4.24746 ( 1767) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4495.51 seconds wall clock time: 77 minutes 37.16 seconds (4657.16 seconds total)