Starting phenix.real_space_refine on Thu Feb 5 01:53:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ehx_48070/02_2026/9ehx_48070.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ehx_48070/02_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ehx_48070/02_2026/9ehx_48070.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ehx_48070/02_2026/9ehx_48070.map" model { file = "/net/cci-nas-00/data/ceres_data/9ehx_48070/02_2026/9ehx_48070.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ehx_48070/02_2026/9ehx_48070.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.013 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-2.0-5952/lib/python3.9/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: 2.55, per 1000 atoms: 0.18 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: 1.22 Conformation dependent library (CDL) restraints added in 388.0 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: 1.49 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: 1.59 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=" CB ASN A1129 " pdb=" CG ASN A1129 " ideal model delta sigma weight residual 1.516 1.570 -0.054 2.50e-02 1.60e+03 4.75e+00 bond pdb=" CA ASP A1570 " pdb=" CB ASP A1570 " ideal model delta sigma weight residual 1.523 1.562 -0.039 1.94e-02 2.66e+03 3.96e+00 bond pdb=" CA ASN A1129 " pdb=" CB ASN A1129 " ideal model delta sigma weight residual 1.529 1.560 -0.031 1.62e-02 3.81e+03 3.70e+00 bond pdb=" N ASN A 599 " pdb=" CA ASN A 599 " ideal model delta sigma weight residual 1.461 1.490 -0.029 1.52e-02 4.33e+03 3.53e+00 bond pdb=" CA ASN A1461 " pdb=" CB ASN A1461 " ideal model delta sigma weight residual 1.531 1.559 -0.028 1.51e-02 4.39e+03 3.36e+00 ... (remaining 14550 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.10: 20045 4.10 - 8.20: 149 8.20 - 12.30: 17 12.30 - 16.40: 5 16.40 - 20.49: 1 Bond angle restraints: 20217 Sorted by residual: angle pdb=" CB MET A1167 " pdb=" CG MET A1167 " pdb=" SD MET A1167 " ideal model delta sigma weight residual 112.70 133.19 -20.49 3.00e+00 1.11e-01 4.67e+01 angle pdb=" CA GLN A1596 " pdb=" CB GLN A1596 " pdb=" CG GLN A1596 " ideal model delta sigma weight residual 114.10 126.48 -12.38 2.00e+00 2.50e-01 3.83e+01 angle pdb=" CB MET A 1 " pdb=" CG MET A 1 " pdb=" SD MET A 1 " ideal model delta sigma weight residual 112.70 128.94 -16.24 3.00e+00 1.11e-01 2.93e+01 angle pdb=" CA GLU A 603 " pdb=" CB GLU A 603 " pdb=" CG GLU A 603 " ideal model delta sigma weight residual 114.10 124.44 -10.34 2.00e+00 2.50e-01 2.67e+01 angle pdb=" N MET A1167 " pdb=" CA MET A1167 " pdb=" CB MET A1167 " ideal model delta sigma weight residual 110.16 117.71 -7.55 1.48e+00 4.57e-01 2.60e+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: 1804 0.063 - 0.127: 380 0.127 - 0.190: 79 0.190 - 0.253: 11 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: 5.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 14.100 Find NCS groups from input model: 0.080 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:7.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 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 0.054 14555 Z= 0.233 Angle : 1.020 20.495 20217 Z= 0.557 Chirality : 0.056 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 covalent geometry : bond 0.00496 (14555) covalent geometry : angle 1.01989 (20217) hydrogen bonds : bond 0.13565 ( 648) hydrogen bonds : angle 6.24140 ( 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 : 0.445 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: 0.4647 time to fit residues: 61.8299 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 : 0.305 ------------------------------------------------------------------------------- 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: 1.9990 chunk 91 optimal weight: 0.4980 chunk 55 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.105025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.085938 restraints weight = 28070.152| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.67 r_work: 0.3090 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14555 Z= 0.145 Angle : 0.576 7.886 20217 Z= 0.313 Chirality : 0.040 0.226 2279 Planarity : 0.003 0.032 2125 Dihedral : 18.115 171.426 3354 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.96 % Allowed : 13.56 % Favored : 84.48 % 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: 0.88 (0.22), residues: 1359 helix: 0.83 (0.20), residues: 636 sheet: 0.49 (0.42), residues: 143 loop : 0.54 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 620 TYR 0.015 0.001 TYR A 656 PHE 0.015 0.001 PHE A 497 TRP 0.018 0.002 TRP A 698 HIS 0.009 0.001 HIS A1579 Details of bonding type rmsd covalent geometry : bond 0.00312 (14555) covalent geometry : angle 0.57599 (20217) hydrogen bonds : bond 0.04315 ( 648) hydrogen bonds : angle 4.72389 ( 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 140 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8615 (p0) cc_final: 0.7949 (t0) REVERT: A 637 LYS cc_start: 0.8873 (mtpt) cc_final: 0.8597 (ttpp) REVERT: A 694 PHE cc_start: 0.8763 (t80) cc_final: 0.8427 (t80) REVERT: A 708 LYS cc_start: 0.8561 (tptp) cc_final: 0.8040 (tptm) REVERT: A 712 ASP cc_start: 0.8133 (m-30) cc_final: 0.7568 (m-30) REVERT: A 739 GLU cc_start: 0.7360 (mt-10) cc_final: 0.6696 (mt-10) REVERT: A 744 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7936 (m110) REVERT: A 761 HIS cc_start: 0.7219 (m-70) cc_final: 0.6994 (m-70) REVERT: A 766 GLU cc_start: 0.8825 (tp30) cc_final: 0.8292 (mt-10) REVERT: A 780 LYS cc_start: 0.9041 (tttp) cc_final: 0.8549 (tmmt) REVERT: A 784 ASP cc_start: 0.8957 (m-30) cc_final: 0.8622 (m-30) REVERT: A 829 LYS cc_start: 0.8593 (mttt) cc_final: 0.8251 (mmpt) REVERT: A 878 TRP cc_start: 0.7775 (t-100) cc_final: 0.7233 (t-100) REVERT: A 942 GLU cc_start: 0.8814 (tp30) cc_final: 0.8493 (tm-30) REVERT: A 1014 LEU cc_start: 0.8419 (OUTLIER) cc_final: 0.7832 (mm) REVERT: A 1033 ILE cc_start: 0.8499 (mm) cc_final: 0.8282 (mt) REVERT: A 1047 ARG cc_start: 0.8090 (mtt180) cc_final: 0.7753 (mtt-85) REVERT: A 1115 ASP cc_start: 0.8228 (m-30) cc_final: 0.7969 (m-30) REVERT: A 1167 MET cc_start: 0.8723 (mpt) cc_final: 0.7362 (mpp) REVERT: A 1268 LYS cc_start: 0.9256 (mtpp) cc_final: 0.8979 (mppt) REVERT: A 1377 ASP cc_start: 0.8648 (t0) cc_final: 0.8269 (t0) REVERT: A 1381 GLN cc_start: 0.9029 (tt0) cc_final: 0.8783 (mt0) REVERT: A 1432 LYS cc_start: 0.8221 (mttt) cc_final: 0.7585 (tttt) REVERT: A 1523 PHE cc_start: 0.7485 (m-80) cc_final: 0.6237 (m-80) REVERT: A 1563 LEU cc_start: 0.8273 (OUTLIER) cc_final: 0.7615 (pp) REVERT: A 1617 MET cc_start: 0.8916 (ptt) cc_final: 0.8657 (mpm) outliers start: 24 outliers final: 5 residues processed: 132 average time/residue: 0.5296 time to fit residues: 77.7797 Evaluate side-chains 105 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 1014 LEU Chi-restraints excluded: chain A residue 1320 ASN Chi-restraints excluded: chain A residue 1433 LEU Chi-restraints excluded: chain A residue 1563 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 0 optimal weight: 3.9990 chunk 2 optimal weight: 0.9990 chunk 74 optimal weight: 0.0370 chunk 114 optimal weight: 3.9990 chunk 116 optimal weight: 0.9990 chunk 53 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 140 optimal weight: 2.9990 chunk 97 optimal weight: 0.0000 overall best weight: 0.6068 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A 60 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.105023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.086061 restraints weight = 28291.867| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.67 r_work: 0.3094 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8384 moved from start: 0.1396 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= 0.125 Angle : 0.524 7.864 20217 Z= 0.285 Chirality : 0.039 0.228 2279 Planarity : 0.003 0.040 2125 Dihedral : 18.091 172.843 3348 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.12 % Allowed : 13.48 % Favored : 84.40 % 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: 1.23 (0.23), residues: 1359 helix: 1.31 (0.21), residues: 631 sheet: 0.65 (0.42), residues: 148 loop : 0.47 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1540 TYR 0.016 0.001 TYR A1354 PHE 0.013 0.001 PHE A 497 TRP 0.016 0.001 TRP A 698 HIS 0.004 0.001 HIS A1579 Details of bonding type rmsd covalent geometry : bond 0.00262 (14555) covalent geometry : angle 0.52365 (20217) hydrogen bonds : bond 0.03793 ( 648) hydrogen bonds : angle 4.36450 ( 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 141 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 115 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8613 (p0) cc_final: 0.7903 (t0) REVERT: A 637 LYS cc_start: 0.8922 (mtpt) cc_final: 0.8714 (ttpp) REVERT: A 694 PHE cc_start: 0.8758 (t80) cc_final: 0.8441 (t80) REVERT: A 708 LYS cc_start: 0.8559 (tptp) cc_final: 0.8118 (tptm) REVERT: A 712 ASP cc_start: 0.8117 (m-30) cc_final: 0.7644 (m-30) REVERT: A 730 ILE cc_start: 0.8493 (tt) cc_final: 0.8033 (pt) REVERT: A 739 GLU cc_start: 0.7298 (mt-10) cc_final: 0.6716 (mt-10) REVERT: A 761 HIS cc_start: 0.7128 (m-70) cc_final: 0.6917 (m-70) REVERT: A 766 GLU cc_start: 0.8856 (tp30) cc_final: 0.8319 (mt-10) REVERT: A 780 LYS cc_start: 0.9024 (tttp) cc_final: 0.8511 (tmmt) REVERT: A 784 ASP cc_start: 0.8951 (m-30) cc_final: 0.8578 (m-30) REVERT: A 795 SER cc_start: 0.8975 (m) cc_final: 0.8650 (t) REVERT: A 798 GLN cc_start: 0.8619 (mt0) cc_final: 0.8328 (mt0) REVERT: A 829 LYS cc_start: 0.8618 (mttt) cc_final: 0.8261 (mmpt) REVERT: A 878 TRP cc_start: 0.7776 (t-100) cc_final: 0.7261 (t-100) REVERT: A 942 GLU cc_start: 0.8815 (tp30) cc_final: 0.8438 (tm-30) REVERT: A 1014 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.7790 (mm) REVERT: A 1047 ARG cc_start: 0.8107 (mtt180) cc_final: 0.7816 (mtt-85) REVERT: A 1115 ASP cc_start: 0.8231 (m-30) cc_final: 0.7986 (m-30) REVERT: A 1116 LYS cc_start: 0.8735 (mmmt) cc_final: 0.8462 (mmmm) REVERT: A 1167 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.7116 (mpp) REVERT: A 1268 LYS cc_start: 0.9267 (mtpp) cc_final: 0.8978 (mppt) REVERT: A 1377 ASP cc_start: 0.8696 (t0) cc_final: 0.8310 (t0) REVERT: A 1381 GLN cc_start: 0.9037 (tt0) cc_final: 0.8829 (mt0) REVERT: A 1432 LYS cc_start: 0.8239 (mttt) cc_final: 0.7600 (tttt) REVERT: A 1523 PHE cc_start: 0.7375 (m-80) cc_final: 0.6173 (m-10) REVERT: A 1563 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7467 (pp) REVERT: A 1594 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8512 (mp) outliers start: 26 outliers final: 10 residues processed: 131 average time/residue: 0.4920 time to fit residues: 71.8234 Evaluate side-chains 115 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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 855 THR Chi-restraints excluded: chain A residue 858 VAL 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 1433 LEU Chi-restraints excluded: chain A residue 1493 VAL Chi-restraints excluded: chain A residue 1508 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 1622 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 0.0770 chunk 54 optimal weight: 1.9990 chunk 123 optimal weight: 0.0000 chunk 76 optimal weight: 5.9990 chunk 135 optimal weight: 6.9990 chunk 61 optimal weight: 0.1980 chunk 11 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 36 optimal weight: 0.0970 chunk 13 optimal weight: 5.9990 overall best weight: 0.4742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3540 r_free = 0.3540 target = 0.105654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.086689 restraints weight = 28322.881| |-----------------------------------------------------------------------------| r_work (start): 0.3230 rms_B_bonded: 2.67 r_work: 0.3105 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.1701 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= 0.111 Angle : 0.504 9.464 20217 Z= 0.273 Chirality : 0.038 0.222 2279 Planarity : 0.003 0.038 2125 Dihedral : 18.005 173.496 3346 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 2.53 % Allowed : 13.48 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.45 (0.23), residues: 1359 helix: 1.58 (0.21), residues: 631 sheet: 0.69 (0.41), residues: 148 loop : 0.50 (0.26), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 732 TYR 0.020 0.001 TYR A1354 PHE 0.012 0.001 PHE A1360 TRP 0.014 0.001 TRP A 698 HIS 0.004 0.001 HIS A 597 Details of bonding type rmsd covalent geometry : bond 0.00234 (14555) covalent geometry : angle 0.50430 (20217) hydrogen bonds : bond 0.03502 ( 648) hydrogen bonds : angle 4.10321 ( 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 149 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 118 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8623 (p0) cc_final: 0.7857 (t0) REVERT: A 452 ASN cc_start: 0.8353 (p0) cc_final: 0.8146 (p0) REVERT: A 637 LYS cc_start: 0.8916 (mtpt) cc_final: 0.8701 (ttpp) REVERT: A 694 PHE cc_start: 0.8746 (t80) cc_final: 0.8440 (t80) REVERT: A 704 ARG cc_start: 0.7694 (mmp80) cc_final: 0.7293 (mmp80) REVERT: A 708 LYS cc_start: 0.8539 (tptp) cc_final: 0.8071 (tptm) REVERT: A 712 ASP cc_start: 0.8108 (m-30) cc_final: 0.7611 (m-30) REVERT: A 730 ILE cc_start: 0.8514 (tt) cc_final: 0.8103 (pt) REVERT: A 761 HIS cc_start: 0.7165 (m-70) cc_final: 0.6950 (m-70) REVERT: A 766 GLU cc_start: 0.8873 (tp30) cc_final: 0.8332 (mt-10) REVERT: A 780 LYS cc_start: 0.9019 (tttp) cc_final: 0.8508 (tmmt) REVERT: A 784 ASP cc_start: 0.8950 (m-30) cc_final: 0.8595 (m-30) REVERT: A 795 SER cc_start: 0.8955 (m) cc_final: 0.8652 (t) REVERT: A 798 GLN cc_start: 0.8568 (mt0) cc_final: 0.8333 (mt0) REVERT: A 829 LYS cc_start: 0.8646 (mttt) cc_final: 0.8321 (mmpt) REVERT: A 878 TRP cc_start: 0.7744 (t-100) cc_final: 0.7233 (t-100) REVERT: A 942 GLU cc_start: 0.8839 (tp30) cc_final: 0.8435 (tm-30) REVERT: A 1047 ARG cc_start: 0.8167 (mtt180) cc_final: 0.7837 (mtt-85) REVERT: A 1115 ASP cc_start: 0.8217 (m-30) cc_final: 0.7992 (m-30) REVERT: A 1116 LYS cc_start: 0.8789 (mmmt) cc_final: 0.8581 (mmmm) REVERT: A 1167 MET cc_start: 0.8665 (OUTLIER) cc_final: 0.7458 (mpt) REVERT: A 1268 LYS cc_start: 0.9259 (mtpp) cc_final: 0.8990 (mppt) REVERT: A 1377 ASP cc_start: 0.8738 (t0) cc_final: 0.8505 (t0) REVERT: A 1432 LYS cc_start: 0.8258 (mttt) cc_final: 0.7639 (tttt) REVERT: A 1486 ASP cc_start: 0.7228 (t0) cc_final: 0.6930 (t0) REVERT: A 1563 LEU cc_start: 0.8088 (OUTLIER) cc_final: 0.7312 (pp) REVERT: A 1594 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8552 (mp) outliers start: 31 outliers final: 12 residues processed: 136 average time/residue: 0.4988 time to fit residues: 76.1063 Evaluate side-chains 123 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 108 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 855 THR 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 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 1622 ILE Chi-restraints excluded: chain A residue 1623 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 21 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 chunk 88 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 74 optimal weight: 0.6980 chunk 86 optimal weight: 0.5980 chunk 111 optimal weight: 0.9980 chunk 146 optimal weight: 4.9990 chunk 125 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 106 optimal weight: 0.3980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3526 r_free = 0.3526 target = 0.104832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.085627 restraints weight = 28265.685| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.68 r_work: 0.3084 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 14555 Z= 0.124 Angle : 0.502 9.226 20217 Z= 0.271 Chirality : 0.038 0.225 2279 Planarity : 0.003 0.038 2125 Dihedral : 17.974 173.628 3346 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 2.94 % Allowed : 14.13 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.50 (0.23), residues: 1359 helix: 1.66 (0.21), residues: 637 sheet: 0.65 (0.42), residues: 148 loop : 0.47 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 732 TYR 0.020 0.001 TYR A1354 PHE 0.015 0.001 PHE A1523 TRP 0.012 0.001 TRP A 79 HIS 0.003 0.001 HIS A 597 Details of bonding type rmsd covalent geometry : bond 0.00269 (14555) covalent geometry : angle 0.50238 (20217) hydrogen bonds : bond 0.03565 ( 648) hydrogen bonds : angle 4.06940 ( 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 150 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 114 time to evaluate : 0.512 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8632 (p0) cc_final: 0.8212 (p0) REVERT: A 426 GLN cc_start: 0.8404 (OUTLIER) cc_final: 0.8073 (mp10) REVERT: A 452 ASN cc_start: 0.8438 (p0) cc_final: 0.8159 (p0) REVERT: A 563 LEU cc_start: 0.9097 (mt) cc_final: 0.8793 (tp) REVERT: A 694 PHE cc_start: 0.8751 (t80) cc_final: 0.8421 (t80) REVERT: A 708 LYS cc_start: 0.8540 (tptp) cc_final: 0.8058 (tptm) REVERT: A 712 ASP cc_start: 0.8095 (m-30) cc_final: 0.7639 (m-30) REVERT: A 730 ILE cc_start: 0.8538 (tt) cc_final: 0.8133 (pt) REVERT: A 746 ILE cc_start: 0.8565 (OUTLIER) cc_final: 0.7651 (mt) REVERT: A 750 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.6603 (pm20) REVERT: A 766 GLU cc_start: 0.8887 (tp30) cc_final: 0.8337 (mt-10) REVERT: A 780 LYS cc_start: 0.9022 (tttp) cc_final: 0.8510 (tmmt) REVERT: A 784 ASP cc_start: 0.8953 (m-30) cc_final: 0.8576 (m-30) REVERT: A 795 SER cc_start: 0.8967 (m) cc_final: 0.8669 (t) REVERT: A 798 GLN cc_start: 0.8613 (mt0) cc_final: 0.8342 (mt0) REVERT: A 829 LYS cc_start: 0.8701 (mttt) cc_final: 0.8348 (mmpt) REVERT: A 878 TRP cc_start: 0.7806 (t-100) cc_final: 0.7310 (t-100) REVERT: A 942 GLU cc_start: 0.8862 (tp30) cc_final: 0.8454 (tm-30) REVERT: A 1047 ARG cc_start: 0.8179 (mtt180) cc_final: 0.7853 (mtt-85) REVERT: A 1078 ARG cc_start: 0.6506 (OUTLIER) cc_final: 0.5086 (ttt180) REVERT: A 1133 ILE cc_start: 0.8088 (mp) cc_final: 0.7748 (mm) REVERT: A 1167 MET cc_start: 0.8681 (OUTLIER) cc_final: 0.7506 (mpt) REVERT: A 1268 LYS cc_start: 0.9275 (mtpp) cc_final: 0.9000 (mppt) REVERT: A 1377 ASP cc_start: 0.8764 (t0) cc_final: 0.8508 (t0) REVERT: A 1432 LYS cc_start: 0.8213 (mttt) cc_final: 0.7639 (tttt) REVERT: A 1486 ASP cc_start: 0.7253 (t0) cc_final: 0.6942 (t0) REVERT: A 1563 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7315 (pp) REVERT: A 1594 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8601 (mp) outliers start: 36 outliers final: 15 residues processed: 140 average time/residue: 0.4930 time to fit residues: 76.8335 Evaluate side-chains 126 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.504 ------------------------------------------------------------------------------- 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 606 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 858 VAL 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 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 1533 VAL Chi-restraints excluded: chain A residue 1535 THR 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: 2.9990 chunk 1 optimal weight: 0.0770 chunk 76 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 142 optimal weight: 4.9990 chunk 110 optimal weight: 0.5980 chunk 104 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 129 optimal weight: 6.9990 chunk 40 optimal weight: 0.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A1162 HIS A1490 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.104832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.085789 restraints weight = 28335.824| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.68 r_work: 0.3088 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3088 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14555 Z= 0.122 Angle : 0.510 10.309 20217 Z= 0.271 Chirality : 0.038 0.222 2279 Planarity : 0.003 0.036 2125 Dihedral : 17.966 173.724 3346 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.45 % Allowed : 15.03 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.55 (0.23), residues: 1359 helix: 1.72 (0.21), residues: 638 sheet: 0.62 (0.42), residues: 146 loop : 0.48 (0.26), residues: 575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1540 TYR 0.019 0.001 TYR A1354 PHE 0.021 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 covalent geometry : bond 0.00264 (14555) covalent geometry : angle 0.51028 (20217) hydrogen bonds : bond 0.03502 ( 648) hydrogen bonds : angle 3.99878 ( 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 141 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 111 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8643 (p0) cc_final: 0.8258 (p0) REVERT: A 426 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.8086 (mp10) REVERT: A 452 ASN cc_start: 0.8425 (p0) cc_final: 0.8144 (p0) REVERT: A 694 PHE cc_start: 0.8762 (t80) cc_final: 0.8451 (t80) REVERT: A 704 ARG cc_start: 0.7697 (mmp80) cc_final: 0.7329 (mmp80) REVERT: A 708 LYS cc_start: 0.8543 (tptp) cc_final: 0.8022 (tptm) REVERT: A 712 ASP cc_start: 0.8116 (m-30) cc_final: 0.7641 (m-30) REVERT: A 730 ILE cc_start: 0.8547 (tt) cc_final: 0.8125 (pt) REVERT: A 746 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.7762 (mt) REVERT: A 750 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.6696 (pm20) REVERT: A 766 GLU cc_start: 0.8882 (tp30) cc_final: 0.8329 (mt-10) REVERT: A 780 LYS cc_start: 0.9005 (tttp) cc_final: 0.8483 (tmmt) REVERT: A 784 ASP cc_start: 0.8948 (m-30) cc_final: 0.8563 (m-30) REVERT: A 795 SER cc_start: 0.8946 (m) cc_final: 0.8656 (t) REVERT: A 798 GLN cc_start: 0.8612 (mt0) cc_final: 0.8356 (mt0) REVERT: A 829 LYS cc_start: 0.8709 (mttt) cc_final: 0.8346 (mmpt) REVERT: A 878 TRP cc_start: 0.7795 (t-100) cc_final: 0.7305 (t-100) REVERT: A 942 GLU cc_start: 0.8872 (tp30) cc_final: 0.8464 (tm-30) REVERT: A 1047 ARG cc_start: 0.8188 (mtt180) cc_final: 0.7859 (mtt-85) REVERT: A 1078 ARG cc_start: 0.6493 (OUTLIER) cc_final: 0.5058 (ttt180) REVERT: A 1133 ILE cc_start: 0.8120 (mp) cc_final: 0.7798 (mm) REVERT: A 1167 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.7578 (mpt) REVERT: A 1214 ILE cc_start: 0.7932 (OUTLIER) cc_final: 0.7327 (mp) REVERT: A 1268 LYS cc_start: 0.9316 (mtpp) cc_final: 0.9016 (mppt) REVERT: A 1377 ASP cc_start: 0.8791 (t0) cc_final: 0.8526 (t0) REVERT: A 1432 LYS cc_start: 0.8269 (mttt) cc_final: 0.7696 (tttt) REVERT: A 1439 LYS cc_start: 0.8703 (mttm) cc_final: 0.8318 (mttm) REVERT: A 1486 ASP cc_start: 0.7227 (t0) cc_final: 0.6913 (t0) REVERT: A 1563 LEU cc_start: 0.8090 (OUTLIER) cc_final: 0.7252 (pp) REVERT: A 1594 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8564 (mp) outliers start: 30 outliers final: 15 residues processed: 133 average time/residue: 0.5305 time to fit residues: 78.8732 Evaluate side-chains 125 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 102 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 606 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 858 VAL 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 1413 THR Chi-restraints excluded: chain A residue 1433 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 1622 ILE 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: 5.9990 chunk 85 optimal weight: 0.4980 chunk 95 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 121 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A1490 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.104245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.085253 restraints weight = 28374.124| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.66 r_work: 0.3080 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14555 Z= 0.126 Angle : 0.512 10.838 20217 Z= 0.272 Chirality : 0.038 0.221 2279 Planarity : 0.003 0.038 2125 Dihedral : 17.954 173.701 3346 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.53 % Allowed : 15.36 % Favored : 82.11 % 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: 1.51 (0.23), residues: 1359 helix: 1.67 (0.21), residues: 644 sheet: 0.58 (0.42), residues: 146 loop : 0.48 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A1540 TYR 0.021 0.001 TYR A 516 PHE 0.015 0.001 PHE A1576 TRP 0.011 0.001 TRP A 79 HIS 0.003 0.001 HIS A1162 Details of bonding type rmsd covalent geometry : bond 0.00274 (14555) covalent geometry : angle 0.51173 (20217) hydrogen bonds : bond 0.03539 ( 648) hydrogen bonds : angle 3.96334 ( 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 135 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8621 (p0) cc_final: 0.8233 (p0) REVERT: A 426 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.8053 (mp10) REVERT: A 452 ASN cc_start: 0.8452 (p0) cc_final: 0.8168 (p0) REVERT: A 563 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8572 (tp) REVERT: A 694 PHE cc_start: 0.8760 (t80) cc_final: 0.8451 (t80) REVERT: A 708 LYS cc_start: 0.8587 (tptp) cc_final: 0.8088 (tptm) REVERT: A 712 ASP cc_start: 0.8122 (m-30) cc_final: 0.7657 (m-30) REVERT: A 730 ILE cc_start: 0.8558 (tt) cc_final: 0.8139 (pt) REVERT: A 746 ILE cc_start: 0.8584 (OUTLIER) cc_final: 0.7764 (mt) REVERT: A 750 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.6632 (pm20) REVERT: A 766 GLU cc_start: 0.8880 (tp30) cc_final: 0.8327 (mt-10) REVERT: A 780 LYS cc_start: 0.9010 (tttp) cc_final: 0.8487 (tmmt) REVERT: A 784 ASP cc_start: 0.8955 (m-30) cc_final: 0.8563 (m-30) REVERT: A 795 SER cc_start: 0.8958 (m) cc_final: 0.8671 (t) REVERT: A 798 GLN cc_start: 0.8628 (mt0) cc_final: 0.8375 (mt0) REVERT: A 829 LYS cc_start: 0.8752 (mttt) cc_final: 0.8384 (mmpt) REVERT: A 878 TRP cc_start: 0.7847 (t-100) cc_final: 0.7348 (t-100) REVERT: A 942 GLU cc_start: 0.8871 (tp30) cc_final: 0.8473 (tm-30) REVERT: A 1047 ARG cc_start: 0.8212 (mtt180) cc_final: 0.7877 (mtt-85) REVERT: A 1167 MET cc_start: 0.8680 (OUTLIER) cc_final: 0.7242 (mpp) REVERT: A 1214 ILE cc_start: 0.7960 (OUTLIER) cc_final: 0.7336 (mp) REVERT: A 1268 LYS cc_start: 0.9309 (mtpp) cc_final: 0.9017 (mppt) REVERT: A 1377 ASP cc_start: 0.8803 (t0) cc_final: 0.8533 (t0) REVERT: A 1432 LYS cc_start: 0.8272 (mttt) cc_final: 0.7730 (tttt) REVERT: A 1486 ASP cc_start: 0.7269 (t0) cc_final: 0.6931 (t0) REVERT: A 1563 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7270 (pp) REVERT: A 1594 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8533 (mp) outliers start: 31 outliers final: 15 residues processed: 128 average time/residue: 0.4921 time to fit residues: 70.9447 Evaluate side-chains 122 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 99 time to evaluate : 0.453 ------------------------------------------------------------------------------- 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 606 THR Chi-restraints excluded: chain A residue 746 ILE Chi-restraints excluded: chain A residue 750 GLU Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 1014 LEU 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 1622 ILE 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: 6.9990 chunk 60 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 139 optimal weight: 4.9990 chunk 140 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 62 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A1157 GLN A1490 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.102271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.083308 restraints weight = 28329.348| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.59 r_work: 0.3051 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14555 Z= 0.164 Angle : 0.545 11.495 20217 Z= 0.287 Chirality : 0.039 0.222 2279 Planarity : 0.003 0.036 2125 Dihedral : 17.955 173.027 3346 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.70 % Allowed : 15.52 % Favored : 81.78 % 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: 0.45 (0.41), residues: 146 loop : 0.39 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A1540 TYR 0.021 0.001 TYR A1354 PHE 0.016 0.001 PHE A1576 TRP 0.011 0.001 TRP A 79 HIS 0.003 0.001 HIS A 60 Details of bonding type rmsd covalent geometry : bond 0.00364 (14555) covalent geometry : angle 0.54458 (20217) hydrogen bonds : bond 0.03788 ( 648) hydrogen bonds : angle 4.01748 ( 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 133 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 100 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8628 (p0) cc_final: 0.8229 (p0) REVERT: A 426 GLN cc_start: 0.8379 (OUTLIER) cc_final: 0.8080 (mp10) REVERT: A 452 ASN cc_start: 0.8578 (p0) cc_final: 0.8251 (p0) REVERT: A 563 LEU cc_start: 0.9090 (tp) cc_final: 0.8714 (tp) REVERT: A 694 PHE cc_start: 0.8799 (t80) cc_final: 0.8484 (t80) REVERT: A 704 ARG cc_start: 0.7738 (mmp80) cc_final: 0.7431 (mmp80) REVERT: A 708 LYS cc_start: 0.8540 (tptp) cc_final: 0.8077 (tptm) REVERT: A 712 ASP cc_start: 0.8103 (m-30) cc_final: 0.7628 (m-30) REVERT: A 730 ILE cc_start: 0.8543 (tt) cc_final: 0.8114 (pt) REVERT: A 744 ASN cc_start: 0.8076 (OUTLIER) cc_final: 0.7822 (m110) REVERT: A 746 ILE cc_start: 0.8611 (OUTLIER) cc_final: 0.7777 (mt) REVERT: A 750 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.6683 (pm20) REVERT: A 766 GLU cc_start: 0.8889 (tp30) cc_final: 0.8331 (mt-10) REVERT: A 780 LYS cc_start: 0.9013 (tttp) cc_final: 0.8522 (tmmt) REVERT: A 784 ASP cc_start: 0.8980 (m-30) cc_final: 0.8615 (m-30) REVERT: A 795 SER cc_start: 0.8981 (m) cc_final: 0.8693 (t) REVERT: A 829 LYS cc_start: 0.8819 (mttt) cc_final: 0.8433 (mmpt) REVERT: A 878 TRP cc_start: 0.7918 (t-100) cc_final: 0.7387 (t-100) REVERT: A 942 GLU cc_start: 0.8877 (tp30) cc_final: 0.8486 (tm-30) REVERT: A 1047 ARG cc_start: 0.8222 (mtt180) cc_final: 0.7894 (mtt-85) REVERT: A 1167 MET cc_start: 0.8685 (OUTLIER) cc_final: 0.7437 (mpt) REVERT: A 1214 ILE cc_start: 0.8009 (OUTLIER) cc_final: 0.7301 (mp) REVERT: A 1268 LYS cc_start: 0.9313 (mtpp) cc_final: 0.9027 (mppt) REVERT: A 1377 ASP cc_start: 0.8838 (t0) cc_final: 0.8555 (t0) REVERT: A 1432 LYS cc_start: 0.8287 (mttt) cc_final: 0.7743 (tttt) REVERT: A 1486 ASP cc_start: 0.7290 (t0) cc_final: 0.6948 (t0) REVERT: A 1563 LEU cc_start: 0.8168 (OUTLIER) cc_final: 0.7920 (mm) REVERT: A 1594 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8526 (mp) outliers start: 33 outliers final: 19 residues processed: 127 average time/residue: 0.4825 time to fit residues: 69.1287 Evaluate side-chains 125 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 98 time to evaluate : 0.494 ------------------------------------------------------------------------------- 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 606 THR 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 855 THR Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 1014 LEU 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 1471 SER 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 1573 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 148 random chunks: chunk 46 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 117 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 139 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 ASN A1338 HIS A1490 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.100944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.081925 restraints weight = 28527.763| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.66 r_work: 0.3022 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14555 Z= 0.185 Angle : 0.561 11.849 20217 Z= 0.296 Chirality : 0.040 0.222 2279 Planarity : 0.003 0.041 2125 Dihedral : 17.981 172.731 3346 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 2.53 % Allowed : 16.09 % Favored : 81.37 % 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: 1.29 (0.22), residues: 1359 helix: 1.58 (0.21), residues: 644 sheet: 0.27 (0.41), residues: 146 loop : 0.31 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 633 TYR 0.023 0.002 TYR A 516 PHE 0.015 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 covalent geometry : bond 0.00413 (14555) covalent geometry : angle 0.56141 (20217) hydrogen bonds : bond 0.03947 ( 648) hydrogen bonds : angle 4.07155 ( 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 131 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 100 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.8660 (p0) cc_final: 0.8250 (p0) REVERT: A 426 GLN cc_start: 0.8397 (OUTLIER) cc_final: 0.8085 (mp10) REVERT: A 452 ASN cc_start: 0.8691 (p0) cc_final: 0.8334 (p0) REVERT: A 563 LEU cc_start: 0.9087 (tp) cc_final: 0.8722 (tp) REVERT: A 694 PHE cc_start: 0.8802 (t80) cc_final: 0.8479 (t80) REVERT: A 708 LYS cc_start: 0.8552 (tptp) cc_final: 0.8057 (tptm) REVERT: A 712 ASP cc_start: 0.8122 (m-30) cc_final: 0.7630 (m-30) REVERT: A 730 ILE cc_start: 0.8528 (tt) cc_final: 0.8088 (pt) REVERT: A 744 ASN cc_start: 0.8057 (OUTLIER) cc_final: 0.7804 (m110) REVERT: A 746 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.7914 (mt) REVERT: A 750 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.6737 (pm20) REVERT: A 766 GLU cc_start: 0.8899 (tp30) cc_final: 0.8330 (mt-10) REVERT: A 780 LYS cc_start: 0.9003 (tttp) cc_final: 0.8524 (tmmt) REVERT: A 784 ASP cc_start: 0.8967 (m-30) cc_final: 0.8618 (m-30) REVERT: A 829 LYS cc_start: 0.8832 (mttt) cc_final: 0.8450 (mmpt) REVERT: A 878 TRP cc_start: 0.8004 (t-100) cc_final: 0.7429 (t-100) REVERT: A 942 GLU cc_start: 0.8895 (tp30) cc_final: 0.8499 (tm-30) REVERT: A 1047 ARG cc_start: 0.8226 (mtt180) cc_final: 0.7889 (mtt-85) REVERT: A 1167 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.7414 (mpt) REVERT: A 1214 ILE cc_start: 0.7980 (OUTLIER) cc_final: 0.7241 (mp) REVERT: A 1268 LYS cc_start: 0.9334 (mtpp) cc_final: 0.9050 (mppt) REVERT: A 1377 ASP cc_start: 0.8851 (t0) cc_final: 0.8567 (t0) REVERT: A 1432 LYS cc_start: 0.8321 (mttt) cc_final: 0.7769 (tttt) REVERT: A 1486 ASP cc_start: 0.7282 (t0) cc_final: 0.6933 (t0) REVERT: A 1563 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7953 (mm) REVERT: A 1594 LEU cc_start: 0.8868 (OUTLIER) cc_final: 0.8520 (mp) outliers start: 31 outliers final: 16 residues processed: 126 average time/residue: 0.4732 time to fit residues: 67.4693 Evaluate side-chains 117 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.520 ------------------------------------------------------------------------------- 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 606 THR 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 858 VAL 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 1214 ILE Chi-restraints excluded: chain A residue 1320 ASN Chi-restraints excluded: chain A residue 1383 LEU Chi-restraints excluded: chain A residue 1471 SER 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 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: 0.8980 chunk 88 optimal weight: 1.9990 chunk 124 optimal weight: 0.0040 chunk 68 optimal weight: 0.7980 chunk 146 optimal weight: 4.9990 chunk 109 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 74 optimal weight: 0.0570 chunk 57 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 overall best weight: 0.5310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3503 r_free = 0.3503 target = 0.103331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.084343 restraints weight = 28345.005| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 2.67 r_work: 0.3063 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14555 Z= 0.117 Angle : 0.524 12.102 20217 Z= 0.278 Chirality : 0.038 0.215 2279 Planarity : 0.003 0.053 2125 Dihedral : 17.975 173.543 3346 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.12 % Allowed : 16.67 % Favored : 81.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.39 (0.23), residues: 1359 helix: 1.68 (0.21), residues: 644 sheet: 0.31 (0.40), residues: 146 loop : 0.34 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 633 TYR 0.018 0.001 TYR A 765 PHE 0.013 0.001 PHE A1576 TRP 0.011 0.001 TRP A 79 HIS 0.004 0.001 HIS A 597 Details of bonding type rmsd covalent geometry : bond 0.00252 (14555) covalent geometry : angle 0.52405 (20217) hydrogen bonds : bond 0.03514 ( 648) hydrogen bonds : angle 3.93838 ( 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 128 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 102 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 20 PHE cc_start: 0.7949 (t80) cc_final: 0.7698 (t80) REVERT: A 34 ASP cc_start: 0.8634 (p0) cc_final: 0.8238 (p0) REVERT: A 426 GLN cc_start: 0.8361 (OUTLIER) cc_final: 0.8055 (mp10) REVERT: A 452 ASN cc_start: 0.8482 (p0) cc_final: 0.8236 (p0) REVERT: A 563 LEU cc_start: 0.9095 (tp) cc_final: 0.8737 (tp) REVERT: A 694 PHE cc_start: 0.8772 (t80) cc_final: 0.8475 (t80) REVERT: A 704 ARG cc_start: 0.7779 (mmp80) cc_final: 0.7499 (mmp80) REVERT: A 708 LYS cc_start: 0.8536 (tptp) cc_final: 0.8055 (tptm) REVERT: A 712 ASP cc_start: 0.8125 (m-30) cc_final: 0.7638 (m-30) REVERT: A 730 ILE cc_start: 0.8490 (tt) cc_final: 0.8076 (pt) REVERT: A 744 ASN cc_start: 0.8026 (OUTLIER) cc_final: 0.7780 (m110) REVERT: A 766 GLU cc_start: 0.8922 (tp30) cc_final: 0.8382 (mt-10) REVERT: A 780 LYS cc_start: 0.8988 (tttp) cc_final: 0.8498 (tmmt) REVERT: A 784 ASP cc_start: 0.8968 (m-30) cc_final: 0.8600 (m-30) REVERT: A 795 SER cc_start: 0.8965 (m) cc_final: 0.8647 (t) REVERT: A 829 LYS cc_start: 0.8842 (mttt) cc_final: 0.8458 (mmpt) REVERT: A 878 TRP cc_start: 0.7844 (t-100) cc_final: 0.7325 (t-100) REVERT: A 942 GLU cc_start: 0.8879 (tp30) cc_final: 0.8480 (tm-30) REVERT: A 1047 ARG cc_start: 0.8215 (mtt180) cc_final: 0.7873 (mtt-85) REVERT: A 1167 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.7432 (mpt) REVERT: A 1214 ILE cc_start: 0.7941 (OUTLIER) cc_final: 0.7236 (mp) REVERT: A 1268 LYS cc_start: 0.9311 (mtpp) cc_final: 0.9057 (mppt) REVERT: A 1377 ASP cc_start: 0.8811 (t0) cc_final: 0.8503 (t0) REVERT: A 1432 LYS cc_start: 0.8241 (mttt) cc_final: 0.7683 (tttt) REVERT: A 1486 ASP cc_start: 0.7252 (t0) cc_final: 0.6925 (t0) REVERT: A 1563 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7971 (mm) REVERT: A 1594 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8471 (mp) outliers start: 26 outliers final: 13 residues processed: 121 average time/residue: 0.4841 time to fit residues: 66.2244 Evaluate side-chains 116 residues out of total 1241 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.432 ------------------------------------------------------------------------------- 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 606 THR Chi-restraints excluded: chain A residue 744 ASN Chi-restraints excluded: chain A residue 858 VAL Chi-restraints excluded: chain A residue 1014 LEU 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 1508 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 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: 2.9990 chunk 31 optimal weight: 0.6980 chunk 128 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 123 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 106 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 125 optimal weight: 1.9990 chunk 103 optimal weight: 0.1980 chunk 87 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1057 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.103058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.084082 restraints weight = 28208.151| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.66 r_work: 0.3055 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.2501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 14555 Z= 0.128 Angle : 0.524 12.136 20217 Z= 0.278 Chirality : 0.038 0.217 2279 Planarity : 0.003 0.053 2125 Dihedral : 17.953 172.950 3346 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.04 % Allowed : 16.67 % Favored : 81.29 % 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: 1.69 (0.21), residues: 644 sheet: 0.33 (0.41), residues: 146 loop : 0.35 (0.26), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 633 TYR 0.020 0.001 TYR A 516 PHE 0.010 0.001 PHE A1398 TRP 0.011 0.001 TRP A 79 HIS 0.003 0.001 HIS A 597 Details of bonding type rmsd covalent geometry : bond 0.00281 (14555) covalent geometry : angle 0.52378 (20217) hydrogen bonds : bond 0.03579 ( 648) hydrogen bonds : angle 3.90641 ( 1738) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3396.93 seconds wall clock time: 59 minutes 20.13 seconds (3560.13 seconds total)