Starting phenix.real_space_refine on Sat Sep 12 07:29:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ehx_48070/09_2026/9ehx_48070.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ehx_48070/09_2026/9ehx_48070.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 { model { file = "/net/cci-nas-00/data/ceres_data/9ehx_48070/09_2026/9ehx_48070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ehx_48070/09_2026/9ehx_48070.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ehx_48070/09_2026/9ehx_48070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ehx_48070/09_2026/9ehx_48070.map" } 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= 0.013 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 130 5.49 5 Mg 2 5.21 5 S 27 5.16 5 C 8431 2.51 5 N 2446 2.21 5 O 2978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14014 Number of models: 1 Model: "" Number of chains: 6 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: "A" Number of atoms: 11250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1371, 11250 Classifications: {'peptide': 1371} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 36, 'TRANS': 1334} Chain breaks: 5 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: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1967 Classifications: {'RNA': 93} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 8, 'rna3p_pur': 39, 'rna3p_pyr': 42} Link IDs: {'rna2p': 11, 'rna3p': 81} Chain breaks: 1 Chain: "c" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 367 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: 2.96, per 1000 atoms: 0.21 Number of scatterers: 14014 At special positions: 0 Unit cell: (90.8188, 109.149, 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 130 15.00 Mg 2 11.99 O 2978 8.00 N 2446 7.00 C 8431 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: 1.10 Conformation dependent library (CDL) restraints added in 517.0 milliseconds 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2626 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 13 sheets defined 50.5% alpha, 11.7% beta 52 base pairs and 93 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'A' and resid 29 through 33 Processing helix chain 'A' and resid 52 through 82 removed outlier: 3.944A 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: 4.388A 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: 3.992A pdb=" N LEU A 368 " --> pdb=" O GLU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 379 removed outlier: 3.501A pdb=" N HIS A 377 " --> pdb=" O ASP A 374 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS A 379 " --> pdb=" O ILE A 376 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 398 removed outlier: 3.527A pdb=" N HIS A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 431 removed outlier: 3.533A pdb=" N GLN A 426 " --> pdb=" O ASN A 422 " (cutoff:3.500A) removed outlier: 3.850A 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 504 Processing helix chain 'A' and resid 530 through 543 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 removed outlier: 3.694A pdb=" N ILE A 703 " --> pdb=" O LEU A 699 " (cutoff:3.500A) 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 removed outlier: 3.931A pdb=" N LEU A 745 " --> pdb=" O GLU A 741 " (cutoff:3.500A) Processing helix chain 'A' and resid 762 through 773 removed outlier: 4.185A pdb=" N LEU A 770 " --> pdb=" O GLU A 766 " (cutoff:3.500A) Processing helix chain 'A' and resid 779 through 789 removed outlier: 3.670A 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 825 Processing helix chain 'A' and resid 860 through 887 removed outlier: 5.011A pdb=" N GLN A 879 " --> pdb=" O ASP A 875 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ASN A 880 " --> pdb=" O ASP A 876 " (cutoff:3.500A) Processing helix chain 'A' and resid 935 through 945 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 992 through 999 Processing helix chain 'A' and resid 1009 through 1018 Processing helix chain 'A' and resid 1021 through 1034 Processing helix chain 'A' and resid 1048 through 1052 Processing helix chain 'A' and resid 1053 through 1063 removed outlier: 3.994A pdb=" N HIS A1062 " --> pdb=" O LYS A1058 " (cutoff:3.500A) 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 1090 through 1110 removed outlier: 4.651A pdb=" N TYR A1094 " --> pdb=" O GLY A1090 " (cutoff:3.500A) 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 1141 Processing helix chain 'A' and resid 1144 through 1150 removed outlier: 4.032A pdb=" N TYR A1150 " --> pdb=" O ASP A1146 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1177 removed outlier: 3.812A 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 Processing helix chain 'A' and resid 1308 through 1319 removed outlier: 3.575A pdb=" N LEU A1312 " --> pdb=" O THR A1308 " (cutoff:3.500A) Processing helix chain 'A' and resid 1333 through 1346 removed outlier: 3.636A 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 1397 through 1410 removed outlier: 4.191A pdb=" N GLU A1401 " --> pdb=" O PRO A1397 " (cutoff:3.500A) 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 1570 through 1577 Processing helix chain 'A' and resid 1586 through 1595 removed outlier: 4.087A pdb=" N LYS A1595 " --> pdb=" O LEU A1591 " (cutoff:3.500A) 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: 6.363A pdb=" N ILE A 8 " --> pdb=" O ILE A 896 " (cutoff:3.500A) removed outlier: 8.391A pdb=" N GLU A 898 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N ILE A 10 " --> pdb=" O GLU A 898 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A1220 " --> pdb=" O GLY A 38 " (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 513 through 514 Processing sheet with id=AA5, first strand: chain 'A' and resid 597 through 598 Processing sheet with id=AA6, first strand: chain 'A' and resid 630 through 635 removed outlier: 7.609A pdb=" N GLU A 631 " --> pdb=" O THR A 644 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 965 through 969 Processing sheet with id=AA8, first strand: chain 'A' and resid 1441 through 1446 removed outlier: 4.753A pdb=" N PHE A1441 " --> pdb=" O ILE A1373 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ARG A1370 " --> pdb=" O ILE A1244 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N ILE A1244 " --> pdb=" O ARG A1370 " (cutoff:3.500A) removed outlier: 13.834A pdb=" N LYS A1372 " --> pdb=" O ASP A1242 " (cutoff:3.500A) removed outlier: 17.982A pdb=" N ASP A1242 " --> pdb=" O LYS A1372 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLY A1243 " --> pdb=" O ASN A1469 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN A1469 " --> pdb=" O GLY A1243 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE A1467 " --> pdb=" O TYR A1245 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N GLU A1247 " --> pdb=" O TYR A1465 " (cutoff:3.500A) removed outlier: 11.119A pdb=" N TYR A1465 " --> pdb=" O GLU A1247 " (cutoff:3.500A) removed outlier: 18.119A pdb=" N TYR A1249 " --> pdb=" O PHE A1463 " (cutoff:3.500A) removed outlier: 22.749A pdb=" N PHE A1463 " --> pdb=" O TYR A1249 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 1270 through 1273 removed outlier: 4.696A pdb=" N VAL A1261 " --> pdb=" O ILE A1273 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 1276 through 1277 Processing sheet with id=AB2, first strand: chain 'A' and resid 1390 through 1391 Processing sheet with id=AB3, first strand: chain 'A' and resid 1491 through 1496 Processing sheet with id=AB4, first strand: chain 'A' and resid 1530 through 1533 removed outlier: 4.071A pdb=" N ILE A1547 " --> pdb=" O VAL A1533 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR A1546 " --> pdb=" O LYS A1562 " (cutoff:3.500A) 522 hydrogen bonds defined for protein. 1494 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 130 hydrogen bonds 244 hydrogen bond angles 0 basepair planarities 52 basepair parallelities 93 stacking parallelities Total time for adding SS restraints: 3.53 Time building geometry restraints manager: 1.51 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: 3468 1.33 - 1.46: 4060 1.46 - 1.58: 6735 1.58 - 1.71: 254 1.71 - 1.83: 38 Bond restraints: 14555 Sorted by residual: bond pdb=" C1' DT D 4 " pdb=" N1 DT D 4 " ideal model delta sigma weight residual 1.468 1.533 -0.065 1.40e-02 5.10e+03 2.14e+01 bond pdb=" C1' DC c 24 " pdb=" N1 DC c 24 " ideal model delta sigma weight residual 1.468 1.525 -0.057 1.40e-02 5.10e+03 1.68e+01 bond pdb=" N1 U B 66 " pdb=" C2 U B 66 " ideal model delta sigma weight residual 1.381 1.411 -0.030 9.00e-03 1.23e+04 1.15e+01 bond pdb=" C3' DC C 8 " pdb=" C2' DC C 8 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.29e+00 bond pdb=" C3' DG D 2 " pdb=" C2' DG D 2 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.96e+00 ... (remaining 14550 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.10: 20039 4.10 - 8.20: 155 8.20 - 12.30: 17 12.30 - 16.40: 5 16.40 - 20.49: 1 Bond angle restraints: 20217 Sorted by residual: angle pdb=" C1' U B 66 " pdb=" N1 U B 66 " pdb=" C2 U B 66 " ideal model delta sigma weight residual 117.70 130.18 -12.48 1.20e+00 6.94e-01 1.08e+02 angle pdb=" N1 U B 66 " pdb=" C2 U B 66 " pdb=" O2 U B 66 " ideal model delta sigma weight residual 122.80 129.86 -7.06 7.00e-01 2.04e+00 1.02e+02 angle pdb=" O2 U B 66 " pdb=" C2 U B 66 " pdb=" N3 U B 66 " ideal model delta sigma weight residual 122.20 115.41 6.79 7.00e-01 2.04e+00 9.42e+01 angle pdb=" O4' DG D 3 " pdb=" C1' DG D 3 " pdb=" N9 DG D 3 " ideal model delta sigma weight residual 108.00 113.87 -5.87 7.00e-01 2.04e+00 7.04e+01 angle pdb=" C1' U B 66 " pdb=" N1 U B 66 " pdb=" C6 U B 66 " ideal model delta sigma weight residual 121.20 111.58 9.62 1.40e+00 5.10e-01 4.72e+01 ... (remaining 20212 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.20: 8424 35.20 - 70.39: 372 70.39 - 105.59: 44 105.59 - 140.79: 1 140.79 - 175.98: 2 Dihedral angle restraints: 8843 sinusoidal: 4789 harmonic: 4054 Sorted by residual: dihedral pdb=" O4' U B 66 " pdb=" C1' U B 66 " pdb=" N1 U B 66 " pdb=" C2 U B 66 " ideal model delta sinusoidal sigma weight residual 232.00 132.98 99.02 1 1.70e+01 3.46e-03 3.84e+01 dihedral pdb=" CA ASN A1461 " pdb=" C ASN A1461 " pdb=" N ASN A1462 " pdb=" CA ASN A1462 " ideal model delta harmonic sigma weight residual 180.00 151.20 28.80 0 5.00e+00 4.00e-02 3.32e+01 dihedral pdb=" CA VAL A 858 " pdb=" C VAL A 858 " pdb=" N ASP A 859 " pdb=" CA ASP A 859 " ideal model delta harmonic sigma weight residual 180.00 -151.32 -28.68 0 5.00e+00 4.00e-02 3.29e+01 ... (remaining 8840 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1690 0.063 - 0.127: 435 0.127 - 0.190: 137 0.190 - 0.253: 12 0.253 - 0.317: 5 Chirality restraints: 2279 Sorted by residual: chirality pdb=" CA ASN A1461 " pdb=" N ASN A1461 " pdb=" C ASN A1461 " pdb=" CB ASN A1461 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.51e+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 -2.43 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CA ASN A 599 " pdb=" N ASN A 599 " pdb=" C ASN A 599 " pdb=" CB ASN A 599 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 2276 not shown) Planarity restraints: 2125 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLU A 603 " 0.019 2.00e-02 2.50e+03 3.93e-02 1.54e+01 pdb=" CD GLU A 603 " -0.068 2.00e-02 2.50e+03 pdb=" OE1 GLU A 603 " 0.025 2.00e-02 2.50e+03 pdb=" OE2 GLU A 603 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 74 " 0.028 2.00e-02 2.50e+03 1.81e-02 9.78e+00 pdb=" N9 G B 74 " -0.041 2.00e-02 2.50e+03 pdb=" C8 G B 74 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G B 74 " -0.012 2.00e-02 2.50e+03 pdb=" C5 G B 74 " 0.003 2.00e-02 2.50e+03 pdb=" C6 G B 74 " -0.001 2.00e-02 2.50e+03 pdb=" O6 G B 74 " 0.019 2.00e-02 2.50e+03 pdb=" N1 G B 74 " -0.012 2.00e-02 2.50e+03 pdb=" C2 G B 74 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B 74 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G B 74 " -0.003 2.00e-02 2.50e+03 pdb=" C4 G B 74 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC C 8 " -0.039 2.00e-02 2.50e+03 1.98e-02 8.79e+00 pdb=" N1 DC C 8 " 0.040 2.00e-02 2.50e+03 pdb=" C2 DC C 8 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DC C 8 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DC C 8 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DC C 8 " -0.006 2.00e-02 2.50e+03 pdb=" N4 DC C 8 " -0.011 2.00e-02 2.50e+03 pdb=" C5 DC C 8 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DC C 8 " 0.013 2.00e-02 2.50e+03 ... (remaining 2122 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.02: 7222 3.02 - 3.49: 14252 3.49 - 3.96: 24934 3.96 - 4.43: 28885 4.43 - 4.90: 42408 Nonbonded interactions: 117701 Sorted by model distance: nonbonded pdb=" O4' C B 18 " pdb=" C6 C B 18 " model vdw 2.545 2.672 nonbonded pdb=" O4' U B 66 " pdb=" C6 U B 66 " model vdw 2.551 2.672 nonbonded pdb=" O THR A 598 " pdb=" OD1 ASN A 599 " model vdw 2.573 3.040 nonbonded pdb=" N1 G B 48 " pdb=" C4 G B 48 " model vdw 2.584 2.672 nonbonded pdb=" N1 G B 62 " pdb=" C4 G B 62 " model vdw 2.585 2.672 ... (remaining 117696 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: 3.810 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.830 Find NCS groups from input model: 0.070 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:7.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 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 0.065 14555 Z= 0.330 Angle : 1.071 20.495 20217 Z= 0.715 Chirality : 0.063 0.317 2279 Planarity : 0.008 0.084 2125 Dihedral : 17.917 175.983 6217 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.65 % Allowed : 15.93 % Favored : 83.42 % Cbeta Deviations : 0.30 % 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: -0.26 (0.21), residues: 1359 helix: -0.40 (0.19), residues: 629 sheet: 0.19 (0.40), residues: 142 loop : 0.25 (0.26), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.003 ARG A 310 TYR 0.039 0.003 TYR A 516 PHE 0.029 0.002 PHE A1523 TRP 0.029 0.003 TRP A 698 HIS 0.016 0.002 HIS A1579 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.33 (14555) covalent geometry : angle 1.07108 / 0.71 (20217) hydrogen bonds : bond 0.13565 / 14.29 ( 648) hydrogen bonds : angle 6.24140 / 6.29 ( 1738) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 113 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8549 (p0) cc_final: 0.7942 (t0) REVERT: A 637 LYS cc_start: 0.8893 (mtpt) cc_final: 0.8597 (ttpp) REVERT: A 708 LYS cc_start: 0.8478 (tptp) cc_final: 0.7915 (tptm) REVERT: A 712 ASP cc_start: 0.8098 (m-30) cc_final: 0.7603 (m-30) REVERT: A 744 ASN cc_start: 0.8211 (OUTLIER) cc_final: 0.7876 (m110) REVERT: A 746 ILE cc_start: 0.8591 (mt) cc_final: 0.8371 (mp) REVERT: A 761 HIS cc_start: 0.7634 (m-70) cc_final: 0.7224 (m90) REVERT: A 766 GLU cc_start: 0.8732 (tp30) cc_final: 0.8323 (mt-10) REVERT: A 780 LYS cc_start: 0.8978 (tttp) cc_final: 0.8508 (tmmt) REVERT: A 784 ASP cc_start: 0.8920 (m-30) cc_final: 0.8607 (m-30) REVERT: A 829 LYS cc_start: 0.8567 (mttt) cc_final: 0.8197 (mmpt) REVERT: A 878 TRP cc_start: 0.7718 (t-100) cc_final: 0.7217 (t-100) REVERT: A 942 GLU cc_start: 0.8802 (tp30) cc_final: 0.8510 (tm-30) REVERT: A 1115 ASP cc_start: 0.8201 (m-30) cc_final: 0.7920 (m-30) REVERT: A 1268 LYS cc_start: 0.9242 (mtpp) cc_final: 0.8949 (mppt) REVERT: A 1384 ASP cc_start: 0.8665 (p0) cc_final: 0.8436 (p0) REVERT: A 1426 ASN cc_start: 0.8840 (t0) cc_final: 0.8516 (t0) REVERT: A 1432 LYS cc_start: 0.8095 (mttt) cc_final: 0.7435 (tmtt) REVERT: A 1521 ASN cc_start: 0.7698 (m-40) cc_final: 0.7077 (t0) REVERT: A 1523 PHE cc_start: 0.7700 (m-80) cc_final: 0.5237 (m-80) REVERT: A 1617 MET cc_start: 0.8916 (ptt) cc_final: 0.8694 (mpm) outliers start: 8 outliers final: 4 residues processed: 119 average time/residue: 0.4844 time to fit residues: 64.8313 Evaluate side-chains 112 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 818 SER Chi-restraints excluded: chain A residue 825 MET Chi-restraints excluded: chain A residue 1514 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.4980 chunk 55 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.105590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.086600 restraints weight = 28039.996| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 2.66 r_work: 0.3102 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14555 Z= 0.146 Angle : 0.593 7.983 20217 Z= 0.338 Chirality : 0.042 0.405 2279 Planarity : 0.003 0.029 2125 Dihedral : 18.171 170.244 3354 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.04 % Allowed : 13.89 % Favored : 84.07 % 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: 0.73 (0.22), residues: 1359 helix: 0.69 (0.20), residues: 637 sheet: 0.46 (0.41), residues: 143 loop : 0.47 (0.26), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A1540 TYR 0.016 0.002 TYR A 656 PHE 0.019 0.001 PHE A1523 TRP 0.017 0.002 TRP A 698 HIS 0.007 0.001 HIS A1579 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.15 (14555) covalent geometry : angle 0.59286 / 0.34 (20217) hydrogen bonds : bond 0.04969 / 4.96 ( 648) hydrogen bonds : angle 4.92155 / 5.00 ( 1738) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 114 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8565 (p0) cc_final: 0.7931 (t0) REVERT: A 637 LYS cc_start: 0.8852 (mtpt) cc_final: 0.8570 (ttpp) REVERT: A 694 PHE cc_start: 0.8767 (t80) cc_final: 0.8472 (t80) REVERT: A 708 LYS cc_start: 0.8573 (tptp) cc_final: 0.8055 (tptm) REVERT: A 712 ASP cc_start: 0.8152 (m-30) cc_final: 0.7614 (m-30) REVERT: A 744 ASN cc_start: 0.8244 (OUTLIER) cc_final: 0.7983 (m110) REVERT: A 766 GLU cc_start: 0.8796 (tp30) cc_final: 0.8280 (mt-10) REVERT: A 780 LYS cc_start: 0.9019 (tttp) cc_final: 0.8528 (tmmt) REVERT: A 784 ASP cc_start: 0.8927 (m-30) cc_final: 0.8592 (m-30) REVERT: A 829 LYS cc_start: 0.8581 (mttt) cc_final: 0.8224 (mmpt) REVERT: A 878 TRP cc_start: 0.7751 (t-100) cc_final: 0.7223 (t-100) REVERT: A 942 GLU cc_start: 0.8802 (tp30) cc_final: 0.8487 (tm-30) REVERT: A 1014 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.7793 (mm) REVERT: A 1021 ASP cc_start: 0.8099 (t0) cc_final: 0.7875 (t0) REVERT: A 1115 ASP cc_start: 0.8225 (m-30) cc_final: 0.7952 (m-30) REVERT: A 1167 MET cc_start: 0.8748 (mpt) cc_final: 0.7531 (mpp) REVERT: A 1268 LYS cc_start: 0.9251 (mtpp) cc_final: 0.8982 (mppt) REVERT: A 1339 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7873 (mt-10) REVERT: A 1432 LYS cc_start: 0.8206 (mttt) cc_final: 0.7568 (tttt) REVERT: A 1521 ASN cc_start: 0.7872 (m-40) cc_final: 0.7397 (t0) REVERT: A 1523 PHE cc_start: 0.7490 (m-80) cc_final: 0.6340 (m-80) REVERT: A 1563 LEU cc_start: 0.8304 (mm) cc_final: 0.7734 (pp) REVERT: A 1594 LEU cc_start: 0.8889 (mt) cc_final: 0.8583 (mp) REVERT: A 1617 MET cc_start: 0.8935 (ptt) cc_final: 0.8671 (mpm) outliers start: 25 outliers final: 8 residues processed: 128 average time/residue: 0.5164 time to fit residues: 73.9063 Evaluate side-chains 107 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 957 ASP Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1320 ASN Chi-restraints excluded: chain A residue 1433 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 0 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 chunk 114 optimal weight: 0.6980 chunk 116 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 95 optimal weight: 6.9990 chunk 100 optimal weight: 0.9980 chunk 140 optimal weight: 7.9990 chunk 97 optimal weight: 0.9980 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN A1338 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.101931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.082788 restraints weight = 28516.696| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.67 r_work: 0.3035 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14555 Z= 0.195 Angle : 0.585 7.947 20217 Z= 0.328 Chirality : 0.043 0.415 2279 Planarity : 0.004 0.048 2125 Dihedral : 18.068 171.875 3348 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.78 % Allowed : 13.64 % Favored : 83.58 % 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: 1.07 (0.23), residues: 1359 helix: 1.14 (0.21), residues: 628 sheet: 0.72 (0.43), residues: 138 loop : 0.40 (0.26), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 704 TYR 0.023 0.002 TYR A 516 PHE 0.016 0.002 PHE A1398 TRP 0.017 0.002 TRP A 698 HIS 0.006 0.001 HIS A1579 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.19 (14555) covalent geometry : angle 0.58517 / 0.33 (20217) hydrogen bonds : bond 0.04760 / 4.71 ( 648) hydrogen bonds : angle 4.60714 / 4.69 ( 1738) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8608 (p0) cc_final: 0.7911 (t0) REVERT: A 452 ASN cc_start: 0.8662 (p0) cc_final: 0.8319 (p0) REVERT: A 637 LYS cc_start: 0.8902 (mtpt) cc_final: 0.8669 (ttpp) REVERT: A 694 PHE cc_start: 0.8838 (t80) cc_final: 0.8479 (t80) REVERT: A 704 ARG cc_start: 0.7597 (mmp80) cc_final: 0.7389 (mmp80) REVERT: A 708 LYS cc_start: 0.8536 (tptp) cc_final: 0.8115 (tptm) REVERT: A 712 ASP cc_start: 0.8129 (m-30) cc_final: 0.7649 (m-30) REVERT: A 730 ILE cc_start: 0.8455 (tt) cc_final: 0.7996 (pt) REVERT: A 744 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7903 (m110) REVERT: A 766 GLU cc_start: 0.8836 (tp30) cc_final: 0.8268 (mt-10) REVERT: A 780 LYS cc_start: 0.9024 (tttp) cc_final: 0.8538 (tmmt) REVERT: A 784 ASP cc_start: 0.8966 (m-30) cc_final: 0.8601 (m-30) REVERT: A 829 LYS cc_start: 0.8639 (mttt) cc_final: 0.8282 (mmpt) REVERT: A 878 TRP cc_start: 0.7950 (t-100) cc_final: 0.7396 (t-100) REVERT: A 942 GLU cc_start: 0.8825 (tp30) cc_final: 0.8473 (tm-30) REVERT: A 1021 ASP cc_start: 0.8123 (t0) cc_final: 0.7908 (t0) REVERT: A 1047 ARG cc_start: 0.8107 (mtt180) cc_final: 0.7739 (mtt-85) REVERT: A 1115 ASP cc_start: 0.8234 (m-30) cc_final: 0.7970 (m-30) REVERT: A 1167 MET cc_start: 0.8705 (OUTLIER) cc_final: 0.7326 (mpp) REVERT: A 1268 LYS cc_start: 0.9290 (mtpp) cc_final: 0.9008 (mppt) REVERT: A 1345 TYR cc_start: 0.8225 (m-80) cc_final: 0.7823 (m-80) REVERT: A 1432 LYS cc_start: 0.8379 (mttt) cc_final: 0.7759 (tttt) REVERT: A 1563 LEU cc_start: 0.8303 (mm) cc_final: 0.7622 (pp) REVERT: A 1594 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8578 (mp) REVERT: A 1617 MET cc_start: 0.8954 (ptt) cc_final: 0.8683 (mpm) outliers start: 34 outliers final: 14 residues processed: 123 average time/residue: 0.4955 time to fit residues: 68.2987 Evaluate side-chains 112 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 957 ASP Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1383 LEU Chi-restraints excluded: chain A residue 1413 THR Chi-restraints excluded: chain A residue 1433 LEU Chi-restraints excluded: chain A residue 1493 VAL Chi-restraints excluded: chain A residue 1594 LEU Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1623 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 1 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 123 optimal weight: 0.0030 chunk 76 optimal weight: 4.9990 chunk 135 optimal weight: 0.2980 chunk 61 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 126 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 overall best weight: 0.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN A 60 HIS A1490 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.103886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.084839 restraints weight = 28421.492| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 2.68 r_work: 0.3071 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14555 Z= 0.120 Angle : 0.512 9.711 20217 Z= 0.293 Chirality : 0.040 0.409 2279 Planarity : 0.003 0.042 2125 Dihedral : 18.077 172.402 3348 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.53 % Allowed : 13.56 % Favored : 83.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.22 (0.23), residues: 1359 helix: 1.38 (0.21), residues: 631 sheet: 0.56 (0.42), residues: 148 loop : 0.40 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 732 TYR 0.014 0.001 TYR A1354 PHE 0.011 0.001 PHE A 497 TRP 0.013 0.001 TRP A 698 HIS 0.004 0.001 HIS A1579 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (14555) covalent geometry : angle 0.51218 / 0.29 (20217) hydrogen bonds : bond 0.04175 / 4.02 ( 648) hydrogen bonds : angle 4.32280 / 4.38 ( 1738) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8614 (p0) cc_final: 0.7857 (t0) REVERT: A 452 ASN cc_start: 0.8560 (p0) cc_final: 0.8201 (p0) REVERT: A 637 LYS cc_start: 0.8923 (mtpt) cc_final: 0.8715 (ttpp) REVERT: A 694 PHE cc_start: 0.8785 (t80) cc_final: 0.8438 (t80) REVERT: A 708 LYS cc_start: 0.8524 (tptp) cc_final: 0.8097 (tptm) REVERT: A 712 ASP cc_start: 0.8111 (m-30) cc_final: 0.7620 (m-30) REVERT: A 730 ILE cc_start: 0.8468 (tt) cc_final: 0.8015 (pt) REVERT: A 750 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.6775 (pm20) REVERT: A 766 GLU cc_start: 0.8853 (tp30) cc_final: 0.8294 (mt-10) REVERT: A 780 LYS cc_start: 0.9013 (tttp) cc_final: 0.8532 (tmmt) REVERT: A 784 ASP cc_start: 0.8948 (m-30) cc_final: 0.8577 (m-30) REVERT: A 795 SER cc_start: 0.8968 (m) cc_final: 0.8649 (t) REVERT: A 829 LYS cc_start: 0.8670 (mttt) cc_final: 0.8333 (mmpt) REVERT: A 878 TRP cc_start: 0.7756 (t-100) cc_final: 0.7248 (t-100) REVERT: A 942 GLU cc_start: 0.8846 (tp30) cc_final: 0.8456 (tm-30) REVERT: A 1047 ARG cc_start: 0.8061 (mtt180) cc_final: 0.7707 (mtt-85) REVERT: A 1115 ASP cc_start: 0.8209 (m-30) cc_final: 0.7960 (m-30) REVERT: A 1116 LYS cc_start: 0.8782 (mmmt) cc_final: 0.8529 (mmmm) REVERT: A 1167 MET cc_start: 0.8673 (OUTLIER) cc_final: 0.7185 (mpp) REVERT: A 1268 LYS cc_start: 0.9268 (mtpp) cc_final: 0.8991 (mppt) REVERT: A 1432 LYS cc_start: 0.8330 (mttt) cc_final: 0.7687 (tttt) REVERT: A 1523 PHE cc_start: 0.7333 (m-80) cc_final: 0.6321 (m-10) REVERT: A 1594 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8506 (mp) outliers start: 31 outliers final: 12 residues processed: 128 average time/residue: 0.4941 time to fit residues: 70.9775 Evaluate side-chains 110 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1320 ASN Chi-restraints excluded: chain A residue 1383 LEU Chi-restraints excluded: chain A residue 1433 LEU Chi-restraints excluded: chain A residue 1533 VAL Chi-restraints excluded: chain A residue 1594 LEU Chi-restraints excluded: chain A residue 1622 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 21 optimal weight: 0.4980 chunk 70 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 0.0040 chunk 86 optimal weight: 0.8980 chunk 111 optimal weight: 0.9990 chunk 146 optimal weight: 10.0000 chunk 125 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN A 761 HIS A1490 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.103768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.084703 restraints weight = 28238.656| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.67 r_work: 0.3072 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14555 Z= 0.123 Angle : 0.510 8.546 20217 Z= 0.290 Chirality : 0.040 0.406 2279 Planarity : 0.003 0.042 2125 Dihedral : 18.021 172.659 3346 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.37 % Allowed : 14.30 % Favored : 83.33 % 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: 1359 helix: 1.54 (0.21), residues: 631 sheet: 0.59 (0.41), residues: 148 loop : 0.40 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 732 TYR 0.026 0.001 TYR A1354 PHE 0.011 0.001 PHE A 682 TRP 0.012 0.001 TRP A 698 HIS 0.004 0.001 HIS A 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (14555) covalent geometry : angle 0.51009 / 0.29 (20217) hydrogen bonds : bond 0.04107 / 3.93 ( 648) hydrogen bonds : angle 4.24500 / 4.36 ( 1738) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.592 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8613 (p0) cc_final: 0.7835 (t0) REVERT: A 452 ASN cc_start: 0.8526 (p0) cc_final: 0.8178 (p0) REVERT: A 637 LYS cc_start: 0.8924 (mtpt) cc_final: 0.8701 (ttpp) REVERT: A 694 PHE cc_start: 0.8770 (t80) cc_final: 0.8465 (t80) REVERT: A 708 LYS cc_start: 0.8519 (tptp) cc_final: 0.8057 (tptm) REVERT: A 712 ASP cc_start: 0.8097 (m-30) cc_final: 0.7579 (m-30) REVERT: A 730 ILE cc_start: 0.8484 (tt) cc_final: 0.8061 (pt) REVERT: A 744 ASN cc_start: 0.8148 (OUTLIER) cc_final: 0.7877 (m110) REVERT: A 750 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.6748 (pm20) REVERT: A 766 GLU cc_start: 0.8875 (tp30) cc_final: 0.8320 (mt-10) REVERT: A 780 LYS cc_start: 0.9019 (tttp) cc_final: 0.8521 (tmmt) REVERT: A 784 ASP cc_start: 0.8960 (m-30) cc_final: 0.8577 (m-30) REVERT: A 795 SER cc_start: 0.8981 (m) cc_final: 0.8656 (t) REVERT: A 829 LYS cc_start: 0.8659 (mttt) cc_final: 0.8327 (mmpt) REVERT: A 878 TRP cc_start: 0.7819 (t-100) cc_final: 0.7303 (t-100) REVERT: A 942 GLU cc_start: 0.8852 (tp30) cc_final: 0.8462 (tm-30) REVERT: A 1033 ILE cc_start: 0.8368 (mm) cc_final: 0.8099 (mt) REVERT: A 1047 ARG cc_start: 0.8093 (mtt180) cc_final: 0.7734 (mtt-85) REVERT: A 1078 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.4990 (ttt180) REVERT: A 1115 ASP cc_start: 0.8216 (m-30) cc_final: 0.7981 (m-30) REVERT: A 1116 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8589 (mmmm) REVERT: A 1167 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.7497 (mpt) REVERT: A 1268 LYS cc_start: 0.9269 (mtpp) cc_final: 0.9000 (mppt) REVERT: A 1432 LYS cc_start: 0.8357 (mttt) cc_final: 0.7740 (tttt) REVERT: A 1563 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7829 (mm) REVERT: A 1594 LEU cc_start: 0.8916 (OUTLIER) cc_final: 0.8586 (mp) outliers start: 29 outliers final: 15 residues processed: 123 average time/residue: 0.5021 time to fit residues: 69.5789 Evaluate side-chains 119 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1078 ARG Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1320 ASN Chi-restraints excluded: chain A residue 1383 LEU Chi-restraints excluded: chain A residue 1433 LEU Chi-restraints excluded: chain A residue 1533 VAL Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain A residue 1573 ILE Chi-restraints excluded: chain A residue 1594 LEU Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1623 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 41 optimal weight: 1.9990 chunk 1 optimal weight: 0.2980 chunk 76 optimal weight: 6.9990 chunk 39 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 142 optimal weight: 9.9990 chunk 110 optimal weight: 0.9980 chunk 104 optimal weight: 0.9980 chunk 122 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN A 761 HIS A1490 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.103539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.084643 restraints weight = 28322.503| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.65 r_work: 0.3073 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14555 Z= 0.134 Angle : 0.518 10.923 20217 Z= 0.289 Chirality : 0.040 0.403 2279 Planarity : 0.003 0.039 2125 Dihedral : 17.968 172.647 3346 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 3.02 % Allowed : 13.97 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1359 helix: 1.55 (0.21), residues: 637 sheet: 0.53 (0.41), residues: 148 loop : 0.33 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 732 TYR 0.020 0.001 TYR A 516 PHE 0.019 0.001 PHE A1576 TRP 0.011 0.001 TRP A 79 HIS 0.003 0.001 HIS A 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.13 (14555) covalent geometry : angle 0.51769 / 0.29 (20217) hydrogen bonds : bond 0.04070 / 3.86 ( 648) hydrogen bonds : angle 4.16243 / 4.25 ( 1738) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 107 time to evaluate : 0.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8618 (p0) cc_final: 0.8192 (p0) REVERT: A 426 GLN cc_start: 0.8417 (OUTLIER) cc_final: 0.8078 (mp10) REVERT: A 452 ASN cc_start: 0.8576 (p0) cc_final: 0.8235 (p0) REVERT: A 637 LYS cc_start: 0.8918 (mtpt) cc_final: 0.8686 (ttpp) REVERT: A 694 PHE cc_start: 0.8781 (t80) cc_final: 0.8437 (t80) REVERT: A 708 LYS cc_start: 0.8519 (tptp) cc_final: 0.8042 (tptm) REVERT: A 712 ASP cc_start: 0.8118 (m-30) cc_final: 0.7668 (m-30) REVERT: A 730 ILE cc_start: 0.8510 (tt) cc_final: 0.8090 (pt) REVERT: A 744 ASN cc_start: 0.8101 (OUTLIER) cc_final: 0.7809 (m110) REVERT: A 746 ILE cc_start: 0.8642 (OUTLIER) cc_final: 0.7811 (mt) REVERT: A 750 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.6898 (pm20) REVERT: A 766 GLU cc_start: 0.8882 (tp30) cc_final: 0.8349 (mt-10) REVERT: A 780 LYS cc_start: 0.9010 (tttp) cc_final: 0.8503 (tmmt) REVERT: A 784 ASP cc_start: 0.8956 (m-30) cc_final: 0.8582 (m-30) REVERT: A 795 SER cc_start: 0.8988 (OUTLIER) cc_final: 0.8665 (t) REVERT: A 829 LYS cc_start: 0.8675 (mttt) cc_final: 0.8341 (mmpt) REVERT: A 878 TRP cc_start: 0.7865 (t-100) cc_final: 0.7349 (t-100) REVERT: A 942 GLU cc_start: 0.8874 (tp30) cc_final: 0.8472 (tm-30) REVERT: A 1033 ILE cc_start: 0.8428 (OUTLIER) cc_final: 0.8200 (mt) REVERT: A 1047 ARG cc_start: 0.8128 (mtt180) cc_final: 0.7762 (mtt-85) REVERT: A 1078 ARG cc_start: 0.6538 (OUTLIER) cc_final: 0.4987 (ttt180) REVERT: A 1115 ASP cc_start: 0.8220 (m-30) cc_final: 0.7988 (m-30) REVERT: A 1133 ILE cc_start: 0.8067 (mp) cc_final: 0.7753 (mm) REVERT: A 1167 MET cc_start: 0.8683 (OUTLIER) cc_final: 0.7529 (mpt) REVERT: A 1214 ILE cc_start: 0.8025 (OUTLIER) cc_final: 0.7433 (mp) REVERT: A 1268 LYS cc_start: 0.9300 (mtpp) cc_final: 0.9019 (mppt) REVERT: A 1432 LYS cc_start: 0.8379 (mttt) cc_final: 0.7759 (tttt) REVERT: A 1486 ASP cc_start: 0.7220 (t0) cc_final: 0.6928 (t0) REVERT: A 1563 LEU cc_start: 0.8107 (OUTLIER) cc_final: 0.7862 (mm) REVERT: A 1594 LEU cc_start: 0.8917 (OUTLIER) cc_final: 0.8576 (mp) outliers start: 37 outliers final: 17 residues processed: 130 average time/residue: 0.4948 time to fit residues: 72.4534 Evaluate side-chains 127 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 426 GLN Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1005 LEU Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1078 ARG Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1214 ILE Chi-restraints excluded: chain A residue 1215 THR Chi-restraints excluded: chain A residue 1320 ASN Chi-restraints excluded: chain A residue 1383 LEU Chi-restraints excluded: chain A residue 1433 LEU Chi-restraints excluded: chain A residue 1533 VAL Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain A residue 1594 LEU Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1615 LEU Chi-restraints excluded: chain A residue 1623 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 142 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 95 optimal weight: 0.4980 chunk 100 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 121 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 39 optimal weight: 0.1980 chunk 22 optimal weight: 4.9990 chunk 88 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN A 761 HIS A1162 HIS A1490 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.104146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.085306 restraints weight = 28301.906| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 2.66 r_work: 0.3081 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14555 Z= 0.119 Angle : 0.507 11.287 20217 Z= 0.284 Chirality : 0.039 0.393 2279 Planarity : 0.003 0.040 2125 Dihedral : 17.958 172.854 3346 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.78 % Allowed : 14.22 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.23), residues: 1359 helix: 1.62 (0.21), residues: 637 sheet: 0.55 (0.42), residues: 148 loop : 0.35 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A1540 TYR 0.016 0.001 TYR A1354 PHE 0.017 0.001 PHE A1576 TRP 0.011 0.001 TRP A 79 HIS 0.003 0.001 HIS A 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (14555) covalent geometry : angle 0.50731 / 0.28 (20217) hydrogen bonds : bond 0.03931 / 3.70 ( 648) hydrogen bonds : angle 4.08072 / 4.15 ( 1738) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 109 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 PHE cc_start: 0.7887 (t80) cc_final: 0.7589 (t80) REVERT: A 34 ASP cc_start: 0.8614 (p0) cc_final: 0.8184 (p0) REVERT: A 426 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8085 (mp10) REVERT: A 452 ASN cc_start: 0.8494 (p0) cc_final: 0.8192 (p0) REVERT: A 563 LEU cc_start: 0.9073 (OUTLIER) cc_final: 0.8473 (tp) REVERT: A 694 PHE cc_start: 0.8754 (t80) cc_final: 0.8403 (t80) REVERT: A 708 LYS cc_start: 0.8481 (tptp) cc_final: 0.7984 (tptm) REVERT: A 712 ASP cc_start: 0.8107 (m-30) cc_final: 0.7644 (m-30) REVERT: A 730 ILE cc_start: 0.8535 (tt) cc_final: 0.8127 (pt) REVERT: A 744 ASN cc_start: 0.8098 (OUTLIER) cc_final: 0.7796 (m110) REVERT: A 746 ILE cc_start: 0.8633 (OUTLIER) cc_final: 0.8316 (mt) REVERT: A 766 GLU cc_start: 0.8888 (tp30) cc_final: 0.8352 (mt-10) REVERT: A 780 LYS cc_start: 0.9007 (tttp) cc_final: 0.8535 (tmmt) REVERT: A 784 ASP cc_start: 0.8956 (m-30) cc_final: 0.8626 (m-30) REVERT: A 795 SER cc_start: 0.8964 (m) cc_final: 0.8649 (t) REVERT: A 829 LYS cc_start: 0.8722 (mttt) cc_final: 0.8363 (mmpt) REVERT: A 878 TRP cc_start: 0.7851 (t-100) cc_final: 0.7350 (t-100) REVERT: A 942 GLU cc_start: 0.8888 (tp30) cc_final: 0.8487 (tm-30) REVERT: A 1026 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7866 (tp30) REVERT: A 1033 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.8193 (mt) REVERT: A 1047 ARG cc_start: 0.8126 (mtt180) cc_final: 0.7752 (mtt-85) REVERT: A 1078 ARG cc_start: 0.6588 (OUTLIER) cc_final: 0.5049 (ttt180) REVERT: A 1115 ASP cc_start: 0.8216 (m-30) cc_final: 0.7991 (m-30) REVERT: A 1133 ILE cc_start: 0.8087 (mp) cc_final: 0.7784 (mm) REVERT: A 1167 MET cc_start: 0.8653 (OUTLIER) cc_final: 0.7494 (mpt) REVERT: A 1214 ILE cc_start: 0.8000 (OUTLIER) cc_final: 0.7380 (mp) REVERT: A 1268 LYS cc_start: 0.9301 (mtpp) cc_final: 0.9017 (mppt) REVERT: A 1432 LYS cc_start: 0.8363 (mttt) cc_final: 0.7770 (tttt) REVERT: A 1486 ASP cc_start: 0.7233 (t0) cc_final: 0.6932 (t0) REVERT: A 1594 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8580 (mp) outliers start: 34 outliers final: 17 residues processed: 132 average time/residue: 0.4834 time to fit residues: 72.1283 Evaluate side-chains 131 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 104 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 426 GLN Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1026 GLU Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1078 ARG Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1214 ILE Chi-restraints excluded: chain A residue 1320 ASN Chi-restraints excluded: chain A residue 1383 LEU Chi-restraints excluded: chain A residue 1433 LEU Chi-restraints excluded: chain A residue 1533 VAL Chi-restraints excluded: chain A residue 1535 THR Chi-restraints excluded: chain A residue 1573 ILE Chi-restraints excluded: chain A residue 1594 LEU Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1623 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 76 optimal weight: 4.9990 chunk 60 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 chunk 140 optimal weight: 8.9990 chunk 73 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 62 optimal weight: 0.3980 chunk 91 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN A1490 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.102795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.083982 restraints weight = 28230.413| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.60 r_work: 0.3058 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14555 Z= 0.144 Angle : 0.526 11.104 20217 Z= 0.291 Chirality : 0.040 0.392 2279 Planarity : 0.003 0.039 2125 Dihedral : 17.925 172.392 3346 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.94 % Allowed : 14.71 % Favored : 82.35 % 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: 1359 helix: 1.59 (0.21), residues: 643 sheet: 0.57 (0.42), residues: 146 loop : 0.32 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 732 TYR 0.019 0.001 TYR A1354 PHE 0.017 0.001 PHE A1576 TRP 0.011 0.001 TRP A 79 HIS 0.003 0.001 HIS A 597 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (14555) covalent geometry : angle 0.52608 / 0.29 (20217) hydrogen bonds : bond 0.04083 / 3.84 ( 648) hydrogen bonds : angle 4.08473 / 4.15 ( 1738) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 104 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 PHE cc_start: 0.7985 (t80) cc_final: 0.7719 (t80) REVERT: A 34 ASP cc_start: 0.8636 (p0) cc_final: 0.8233 (p0) REVERT: A 426 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8068 (mp10) REVERT: A 452 ASN cc_start: 0.8566 (p0) cc_final: 0.8261 (p0) REVERT: A 563 LEU cc_start: 0.9076 (tp) cc_final: 0.8540 (tp) REVERT: A 694 PHE cc_start: 0.8785 (t80) cc_final: 0.8452 (t80) REVERT: A 704 ARG cc_start: 0.7674 (mmp80) cc_final: 0.7320 (mmp80) REVERT: A 708 LYS cc_start: 0.8510 (tptp) cc_final: 0.8034 (tptm) REVERT: A 712 ASP cc_start: 0.8092 (m-30) cc_final: 0.7622 (m-30) REVERT: A 730 ILE cc_start: 0.8534 (tt) cc_final: 0.8121 (pt) REVERT: A 744 ASN cc_start: 0.8091 (OUTLIER) cc_final: 0.7790 (m110) REVERT: A 746 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8343 (mt) REVERT: A 766 GLU cc_start: 0.8869 (tp30) cc_final: 0.8316 (mt-10) REVERT: A 780 LYS cc_start: 0.9011 (tttp) cc_final: 0.8520 (tmmt) REVERT: A 784 ASP cc_start: 0.8963 (m-30) cc_final: 0.8618 (m-30) REVERT: A 795 SER cc_start: 0.9005 (OUTLIER) cc_final: 0.8689 (t) REVERT: A 829 LYS cc_start: 0.8745 (mttt) cc_final: 0.8384 (mmpt) REVERT: A 878 TRP cc_start: 0.7918 (t-100) cc_final: 0.7405 (t-100) REVERT: A 942 GLU cc_start: 0.8900 (tp30) cc_final: 0.8506 (tm-30) REVERT: A 1026 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7860 (tp30) REVERT: A 1033 ILE cc_start: 0.8398 (OUTLIER) cc_final: 0.8196 (mt) REVERT: A 1047 ARG cc_start: 0.8175 (mtt180) cc_final: 0.7784 (mtt-85) REVERT: A 1078 ARG cc_start: 0.6605 (OUTLIER) cc_final: 0.5084 (ttt180) REVERT: A 1115 ASP cc_start: 0.8224 (m-30) cc_final: 0.7998 (m-30) REVERT: A 1133 ILE cc_start: 0.8107 (mp) cc_final: 0.7822 (mm) REVERT: A 1167 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.7535 (mpt) REVERT: A 1214 ILE cc_start: 0.8024 (OUTLIER) cc_final: 0.7306 (mp) REVERT: A 1268 LYS cc_start: 0.9326 (mtpp) cc_final: 0.9031 (mppt) REVERT: A 1432 LYS cc_start: 0.8368 (mttt) cc_final: 0.7780 (tttt) REVERT: A 1486 ASP cc_start: 0.7273 (t0) cc_final: 0.6955 (t0) REVERT: A 1563 LEU cc_start: 0.8064 (OUTLIER) cc_final: 0.7245 (pp) REVERT: A 1594 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8517 (mp) outliers start: 36 outliers final: 16 residues processed: 130 average time/residue: 0.4889 time to fit residues: 71.6197 Evaluate side-chains 129 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 102 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 426 GLN Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1026 GLU Chi-restraints excluded: chain A residue 1033 ILE Chi-restraints excluded: chain A residue 1078 ARG Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1214 ILE Chi-restraints excluded: chain A residue 1320 ASN Chi-restraints excluded: chain A residue 1383 LEU Chi-restraints excluded: chain A residue 1433 LEU Chi-restraints excluded: chain A residue 1533 VAL Chi-restraints excluded: chain A residue 1535 THR Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain A residue 1594 LEU Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1623 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 0.6980 chunk 117 optimal weight: 3.9990 chunk 134 optimal weight: 0.7980 chunk 2 optimal weight: 2.9990 chunk 144 optimal weight: 10.0000 chunk 61 optimal weight: 0.0770 chunk 22 optimal weight: 0.8980 chunk 139 optimal weight: 8.9990 chunk 131 optimal weight: 3.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN A1490 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.103837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.084967 restraints weight = 28271.116| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 2.65 r_work: 0.3076 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14555 Z= 0.117 Angle : 0.511 10.714 20217 Z= 0.284 Chirality : 0.039 0.381 2279 Planarity : 0.003 0.041 2125 Dihedral : 17.945 172.585 3346 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.53 % Allowed : 15.52 % Favored : 81.94 % 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: 1.41 (0.23), residues: 1359 helix: 1.63 (0.21), residues: 644 sheet: 0.64 (0.42), residues: 145 loop : 0.34 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A1540 TYR 0.015 0.001 TYR A1354 PHE 0.015 0.001 PHE A1576 TRP 0.012 0.001 TRP A 79 HIS 0.003 0.001 HIS A 702 Details of bonding type rmsd/Z covalent geometry : bond 0.00235 / 0.12 (14555) covalent geometry : angle 0.51077 / 0.28 (20217) hydrogen bonds : bond 0.03917 / 3.67 ( 648) hydrogen bonds : angle 4.02560 / 4.07 ( 1738) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 PHE cc_start: 0.7913 (t80) cc_final: 0.7617 (t80) REVERT: A 34 ASP cc_start: 0.8619 (p0) cc_final: 0.8207 (p0) REVERT: A 452 ASN cc_start: 0.8520 (p0) cc_final: 0.8245 (p0) REVERT: A 563 LEU cc_start: 0.9074 (tp) cc_final: 0.8524 (tp) REVERT: A 694 PHE cc_start: 0.8774 (t80) cc_final: 0.8437 (t80) REVERT: A 708 LYS cc_start: 0.8470 (tptp) cc_final: 0.7975 (tptm) REVERT: A 712 ASP cc_start: 0.8134 (m-30) cc_final: 0.7659 (m-30) REVERT: A 730 ILE cc_start: 0.8538 (tt) cc_final: 0.8127 (pt) REVERT: A 746 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.7750 (mt) REVERT: A 750 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.6565 (pm20) REVERT: A 766 GLU cc_start: 0.8875 (tp30) cc_final: 0.8324 (mt-10) REVERT: A 780 LYS cc_start: 0.8999 (tttp) cc_final: 0.8510 (tmmt) REVERT: A 784 ASP cc_start: 0.8958 (m-30) cc_final: 0.8610 (m-30) REVERT: A 795 SER cc_start: 0.8958 (OUTLIER) cc_final: 0.8650 (t) REVERT: A 829 LYS cc_start: 0.8737 (mttt) cc_final: 0.8373 (mmpt) REVERT: A 878 TRP cc_start: 0.7869 (t-100) cc_final: 0.7369 (t-100) REVERT: A 942 GLU cc_start: 0.8876 (tp30) cc_final: 0.8484 (tm-30) REVERT: A 1047 ARG cc_start: 0.8149 (mtt180) cc_final: 0.7774 (mtt-85) REVERT: A 1078 ARG cc_start: 0.6581 (OUTLIER) cc_final: 0.5056 (ttt180) REVERT: A 1115 ASP cc_start: 0.8215 (m-30) cc_final: 0.7990 (m-30) REVERT: A 1167 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.7581 (mpt) REVERT: A 1214 ILE cc_start: 0.8004 (OUTLIER) cc_final: 0.7274 (mp) REVERT: A 1268 LYS cc_start: 0.9312 (mtpp) cc_final: 0.9023 (mppt) REVERT: A 1432 LYS cc_start: 0.8355 (mttt) cc_final: 0.7779 (tttt) REVERT: A 1439 LYS cc_start: 0.8753 (mttm) cc_final: 0.8377 (mttm) REVERT: A 1486 ASP cc_start: 0.7244 (t0) cc_final: 0.6932 (t0) REVERT: A 1563 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7218 (pp) REVERT: A 1594 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8523 (mp) outliers start: 31 outliers final: 19 residues processed: 129 average time/residue: 0.4529 time to fit residues: 66.3786 Evaluate side-chains 130 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 426 GLN Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1078 ARG Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1214 ILE Chi-restraints excluded: chain A residue 1320 ASN Chi-restraints excluded: chain A residue 1383 LEU Chi-restraints excluded: chain A residue 1433 LEU Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain A residue 1514 LEU Chi-restraints excluded: chain A residue 1533 VAL Chi-restraints excluded: chain A residue 1535 THR Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain A residue 1594 LEU Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1623 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 70 optimal weight: 0.7980 chunk 88 optimal weight: 1.9990 chunk 124 optimal weight: 0.4980 chunk 68 optimal weight: 0.9980 chunk 146 optimal weight: 10.0000 chunk 109 optimal weight: 2.9990 chunk 25 optimal weight: 0.0070 chunk 3 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN A1490 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.104190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.085474 restraints weight = 28417.357| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.61 r_work: 0.3087 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 14555 Z= 0.116 Angle : 0.507 10.351 20217 Z= 0.282 Chirality : 0.039 0.373 2279 Planarity : 0.003 0.045 2125 Dihedral : 17.935 172.348 3346 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.53 % Allowed : 15.52 % Favored : 81.94 % 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: 1.44 (0.23), residues: 1359 helix: 1.65 (0.21), residues: 644 sheet: 0.68 (0.42), residues: 145 loop : 0.36 (0.26), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1540 TYR 0.014 0.001 TYR A1354 PHE 0.015 0.001 PHE A1576 TRP 0.012 0.001 TRP A 79 HIS 0.003 0.001 HIS A1162 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (14555) covalent geometry : angle 0.50670 / 0.28 (20217) hydrogen bonds : bond 0.03871 / 3.62 ( 648) hydrogen bonds : angle 3.97415 / 4.02 ( 1738) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2718 Ramachandran restraints generated. 1359 Oldfield, 0 Emsley, 1359 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 109 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 PHE cc_start: 0.7860 (t80) cc_final: 0.7602 (t80) REVERT: A 34 ASP cc_start: 0.8605 (p0) cc_final: 0.8221 (p0) REVERT: A 452 ASN cc_start: 0.8479 (p0) cc_final: 0.8218 (p0) REVERT: A 563 LEU cc_start: 0.9085 (tp) cc_final: 0.8545 (tp) REVERT: A 694 PHE cc_start: 0.8760 (t80) cc_final: 0.8429 (t80) REVERT: A 704 ARG cc_start: 0.7674 (mmp80) cc_final: 0.7390 (mmp80) REVERT: A 708 LYS cc_start: 0.8469 (tptp) cc_final: 0.7973 (tptm) REVERT: A 712 ASP cc_start: 0.8124 (m-30) cc_final: 0.7640 (m-30) REVERT: A 730 ILE cc_start: 0.8540 (tt) cc_final: 0.8135 (pt) REVERT: A 746 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8334 (mt) REVERT: A 766 GLU cc_start: 0.8872 (tp30) cc_final: 0.8322 (mt-10) REVERT: A 780 LYS cc_start: 0.8998 (tttp) cc_final: 0.8514 (tmmt) REVERT: A 784 ASP cc_start: 0.8951 (m-30) cc_final: 0.8603 (m-30) REVERT: A 795 SER cc_start: 0.8958 (OUTLIER) cc_final: 0.8648 (t) REVERT: A 829 LYS cc_start: 0.8772 (mttt) cc_final: 0.8385 (mmpt) REVERT: A 878 TRP cc_start: 0.7851 (t-100) cc_final: 0.7363 (t-100) REVERT: A 942 GLU cc_start: 0.8867 (tp30) cc_final: 0.8477 (tm-30) REVERT: A 1026 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7814 (tp30) REVERT: A 1047 ARG cc_start: 0.8156 (mtt180) cc_final: 0.7758 (mtt-85) REVERT: A 1115 ASP cc_start: 0.8198 (m-30) cc_final: 0.7973 (m-30) REVERT: A 1167 MET cc_start: 0.8694 (OUTLIER) cc_final: 0.7219 (mpp) REVERT: A 1214 ILE cc_start: 0.8002 (OUTLIER) cc_final: 0.7236 (mp) REVERT: A 1268 LYS cc_start: 0.9297 (mtpp) cc_final: 0.9039 (mppt) REVERT: A 1432 LYS cc_start: 0.8349 (mttt) cc_final: 0.7782 (tttt) REVERT: A 1439 LYS cc_start: 0.8723 (mttm) cc_final: 0.8370 (mttm) REVERT: A 1486 ASP cc_start: 0.7226 (t0) cc_final: 0.6913 (t0) REVERT: A 1560 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.7987 (ttp80) REVERT: A 1563 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7201 (pp) REVERT: A 1594 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8524 (mp) outliers start: 31 outliers final: 20 residues processed: 128 average time/residue: 0.5149 time to fit residues: 73.8179 Evaluate side-chains 130 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 102 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 324 ASP Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 426 GLN Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 795 SER Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 899 SER Chi-restraints excluded: chain A residue 967 LEU Chi-restraints excluded: chain A residue 1014 LEU Chi-restraints excluded: chain A residue 1026 GLU Chi-restraints excluded: chain A residue 1167 MET Chi-restraints excluded: chain A residue 1214 ILE Chi-restraints excluded: chain A residue 1320 ASN Chi-restraints excluded: chain A residue 1383 LEU Chi-restraints excluded: chain A residue 1433 LEU Chi-restraints excluded: chain A residue 1508 LEU Chi-restraints excluded: chain A residue 1533 VAL Chi-restraints excluded: chain A residue 1535 THR Chi-restraints excluded: chain A residue 1542 ILE Chi-restraints excluded: chain A residue 1560 ARG Chi-restraints excluded: chain A residue 1563 LEU Chi-restraints excluded: chain A residue 1594 LEU Chi-restraints excluded: chain A residue 1598 THR Chi-restraints excluded: chain A residue 1622 ILE Chi-restraints excluded: chain A residue 1623 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 70 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 123 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 106 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 125 optimal weight: 0.2980 chunk 103 optimal weight: 0.0270 chunk 87 optimal weight: 2.9990 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 53 ASN A1490 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.104431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.085656 restraints weight = 28197.460| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 2.64 r_work: 0.3090 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14555 Z= 0.113 Angle : 0.507 12.246 20217 Z= 0.282 Chirality : 0.039 0.368 2279 Planarity : 0.003 0.064 2125 Dihedral : 17.931 172.112 3346 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.53 % Allowed : 15.52 % Favored : 81.94 % 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: 1.46 (0.23), residues: 1359 helix: 1.66 (0.21), residues: 645 sheet: 0.70 (0.41), residues: 145 loop : 0.36 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG A 633 TYR 0.015 0.001 TYR A1354 PHE 0.014 0.001 PHE A1576 TRP 0.012 0.001 TRP A 79 HIS 0.005 0.001 HIS A1162 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (14555) covalent geometry : angle 0.50710 / 0.28 (20217) hydrogen bonds : bond 0.03824 / 3.58 ( 648) hydrogen bonds : angle 3.97323 / 4.01 ( 1738) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3310.35 seconds wall clock time: 57 minutes 46.69 seconds (3466.69 seconds total)