Starting phenix.real_space_refine on Fri Jul 3 15:38:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yii_39320/07_2026/8yii_39320.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yii_39320/07_2026/8yii_39320.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yii_39320/07_2026/8yii_39320.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yii_39320/07_2026/8yii_39320.map" model { file = "/net/cci-nas-00/data/ceres_data/8yii_39320/07_2026/8yii_39320.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yii_39320/07_2026/8yii_39320.cif" } resolution = 3.42 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= 0.003 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 106 5.49 5 Mg 5 5.21 5 S 67 5.16 5 C 9083 2.51 5 N 2543 2.21 5 O 3051 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 55 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14855 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 12470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1541, 12470 Classifications: {'peptide': 1541} Link IDs: {'PTRANS': 63, 'TRANS': 1477} Chain breaks: 2 Chain: "B" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 143 Classifications: {'peptide': 16} Link IDs: {'TRANS': 15} Chain: "C" Number of atoms: 2210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 2210 Classifications: {'RNA': 104} Modifications used: {'p5*END': 1, 'rna2p_pyr': 3, 'rna3p_pur': 49, 'rna3p_pyr': 52} Link IDs: {'rna2p': 3, 'rna3p': 100} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 32 Unusual residues: {' MG': 5, 'ADP': 1} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 2.96, per 1000 atoms: 0.20 Number of scatterers: 14855 At special positions: 0 Unit cell: (92.88, 95.04, 177.12, 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 67 16.00 P 106 15.00 Mg 5 11.99 O 3051 8.00 N 2543 7.00 C 9083 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: 1.07 Conformation dependent library (CDL) restraints added in 364.1 milliseconds 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2976 Finding SS restraints... Secondary structure from input PDB file: 71 helices and 11 sheets defined 54.1% alpha, 10.8% beta 40 base pairs and 60 stacking pairs defined. Time for finding SS restraints: 1.71 Creating SS restraints... Processing helix chain 'A' and resid 9 through 22 removed outlier: 3.851A pdb=" N LYS A 21 " --> pdb=" O ASP A 17 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER A 22 " --> pdb=" O HIS A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 45 Processing helix chain 'A' and resid 46 through 49 removed outlier: 3.665A pdb=" N PHE A 49 " --> pdb=" O SER A 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 46 through 49' Processing helix chain 'A' and resid 66 through 81 Processing helix chain 'A' and resid 89 through 97 removed outlier: 6.291A pdb=" N VAL A 94 " --> pdb=" O GLU A 91 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ASP A 95 " --> pdb=" O GLN A 92 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ASP A 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 98 through 109 removed outlier: 4.234A pdb=" N GLU A 105 " --> pdb=" O MET A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 129 through 131 No H-bonds generated for 'chain 'A' and resid 129 through 131' Processing helix chain 'A' and resid 141 through 144 Processing helix chain 'A' and resid 148 through 160 Processing helix chain 'A' and resid 183 through 195 removed outlier: 3.696A pdb=" N LYS A 187 " --> pdb=" O ASN A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 213 removed outlier: 3.650A pdb=" N ASN A 210 " --> pdb=" O LYS A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 252 Processing helix chain 'A' and resid 271 through 292 Processing helix chain 'A' and resid 292 through 313 removed outlier: 3.725A pdb=" N ILE A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 346 removed outlier: 3.878A pdb=" N MET A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 363 Processing helix chain 'A' and resid 364 through 379 Processing helix chain 'A' and resid 394 through 411 removed outlier: 3.674A pdb=" N CYS A 398 " --> pdb=" O ARG A 394 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 445 through 452 Processing helix chain 'A' and resid 462 through 466 removed outlier: 3.886A pdb=" N GLU A 466 " --> pdb=" O VAL A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 495 removed outlier: 3.720A pdb=" N ALA A 495 " --> pdb=" O SER A 491 " (cutoff:3.500A) Processing helix chain 'A' and resid 510 through 535 removed outlier: 3.623A pdb=" N ALA A 529 " --> pdb=" O HIS A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 552 Processing helix chain 'A' and resid 561 through 563 No H-bonds generated for 'chain 'A' and resid 561 through 563' Processing helix chain 'A' and resid 567 through 569 No H-bonds generated for 'chain 'A' and resid 567 through 569' Processing helix chain 'A' and resid 570 through 582 removed outlier: 3.575A pdb=" N THR A 581 " --> pdb=" O ARG A 577 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ILE A 582 " --> pdb=" O TYR A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 606 removed outlier: 3.717A pdb=" N ASP A 603 " --> pdb=" O GLU A 599 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG A 604 " --> pdb=" O ASP A 600 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 612 removed outlier: 3.585A pdb=" N ALA A 610 " --> pdb=" O GLY A 607 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N GLY A 612 " --> pdb=" O SER A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 637 through 656 Processing helix chain 'A' and resid 672 through 677 Processing helix chain 'A' and resid 680 through 687 removed outlier: 3.506A pdb=" N TRP A 683 " --> pdb=" O PHE A 680 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS A 685 " --> pdb=" O HIS A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 741 through 749 removed outlier: 3.718A pdb=" N GLN A 749 " --> pdb=" O TYR A 745 " (cutoff:3.500A) Processing helix chain 'A' and resid 792 through 810 removed outlier: 3.586A pdb=" N LEU A 796 " --> pdb=" O ASN A 792 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE A 807 " --> pdb=" O HIS A 803 " (cutoff:3.500A) Processing helix chain 'A' and resid 845 through 852 Processing helix chain 'A' and resid 862 through 869 Processing helix chain 'A' and resid 873 through 877 removed outlier: 4.218A pdb=" N PHE A 877 " --> pdb=" O PRO A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 916 through 926 Processing helix chain 'A' and resid 954 through 958 removed outlier: 3.648A pdb=" N GLY A 957 " --> pdb=" O HIS A 954 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LYS A 958 " --> pdb=" O ASN A 955 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 954 through 958' Processing helix chain 'A' and resid 960 through 964 removed outlier: 3.645A pdb=" N LYS A 964 " --> pdb=" O ALA A 961 " (cutoff:3.500A) Processing helix chain 'A' and resid 972 through 974 No H-bonds generated for 'chain 'A' and resid 972 through 974' Processing helix chain 'A' and resid 983 through 991 removed outlier: 4.115A pdb=" N PHE A 991 " --> pdb=" O LEU A 987 " (cutoff:3.500A) Processing helix chain 'A' and resid 991 through 1016 Processing helix chain 'A' and resid 1020 through 1024 removed outlier: 3.585A pdb=" N ASN A1024 " --> pdb=" O LEU A1021 " (cutoff:3.500A) Processing helix chain 'A' and resid 1174 through 1182 Processing helix chain 'A' and resid 1190 through 1199 Processing helix chain 'A' and resid 1200 through 1204 Processing helix chain 'A' and resid 1209 through 1232 removed outlier: 3.978A pdb=" N ILE A1214 " --> pdb=" O GLU A1210 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU A1215 " --> pdb=" O ARG A1211 " (cutoff:3.500A) Processing helix chain 'A' and resid 1236 through 1248 removed outlier: 3.826A pdb=" N LYS A1246 " --> pdb=" O GLU A1242 " (cutoff:3.500A) Processing helix chain 'A' and resid 1249 through 1260 Processing helix chain 'A' and resid 1261 through 1266 removed outlier: 4.090A pdb=" N LYS A1264 " --> pdb=" O ASP A1261 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LEU A1266 " --> pdb=" O PRO A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1272 through 1277 Processing helix chain 'A' and resid 1285 through 1295 Processing helix chain 'A' and resid 1303 through 1309 Processing helix chain 'A' and resid 1313 through 1319 Processing helix chain 'A' and resid 1324 through 1339 removed outlier: 4.102A pdb=" N GLY A1334 " --> pdb=" O ARG A1330 " (cutoff:3.500A) Processing helix chain 'A' and resid 1363 through 1382 Processing helix chain 'A' and resid 1383 through 1393 Processing helix chain 'A' and resid 1422 through 1430 removed outlier: 3.563A pdb=" N ILE A1426 " --> pdb=" O ASN A1422 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASP A1427 " --> pdb=" O THR A1423 " (cutoff:3.500A) removed outlier: 4.700A pdb=" N GLY A1428 " --> pdb=" O THR A1424 " (cutoff:3.500A) Processing helix chain 'A' and resid 1432 through 1441 removed outlier: 3.611A pdb=" N LEU A1436 " --> pdb=" O ASN A1432 " (cutoff:3.500A) Processing helix chain 'A' and resid 1446 through 1455 removed outlier: 4.280A pdb=" N LEU A1450 " --> pdb=" O ASP A1446 " (cutoff:3.500A) Processing helix chain 'A' and resid 1461 through 1466 Processing helix chain 'A' and resid 1467 through 1491 removed outlier: 4.625A pdb=" N LEU A1471 " --> pdb=" O SER A1467 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N PHE A1473 " --> pdb=" O GLN A1469 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ILE A1474 " --> pdb=" O GLU A1470 " (cutoff:3.500A) Processing helix chain 'A' and resid 1495 through 1507 Processing helix chain 'A' and resid 1508 through 1519 Processing helix chain 'A' and resid 1520 through 1525 removed outlier: 3.762A pdb=" N PHE A1523 " --> pdb=" O ARG A1520 " (cutoff:3.500A) Processing helix chain 'A' and resid 1529 through 1547 removed outlier: 3.902A pdb=" N ILE A1535 " --> pdb=" O LYS A1531 " (cutoff:3.500A) Processing helix chain 'A' and resid 1610 through 1628 removed outlier: 3.573A pdb=" N ASP A1614 " --> pdb=" O LYS A1610 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N CYS A1627 " --> pdb=" O VAL A1623 " (cutoff:3.500A) Processing helix chain 'A' and resid 1629 through 1651 Proline residue: A1643 - end of helix Processing helix chain 'A' and resid 1655 through 1663 Processing helix chain 'A' and resid 1701 through 1719 Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 27 removed outlier: 6.275A pdb=" N SER A 134 " --> pdb=" O ARG A 167 " (cutoff:3.500A) removed outlier: 8.304A pdb=" N VAL A 169 " --> pdb=" O SER A 134 " (cutoff:3.500A) removed outlier: 6.338A pdb=" N VAL A 136 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N LEU A 171 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE A 138 " --> pdb=" O LEU A 171 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N ARG A 59 " --> pdb=" O VAL A 135 " (cutoff:3.500A) removed outlier: 8.404A pdb=" N ILE A 137 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N LEU A 61 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 7.488A pdb=" N ASP A 139 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET A 63 " --> pdb=" O ASP A 139 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ALA A 60 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N GLY A 114 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N PHE A 62 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N GLY A 86 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N THR A 115 " --> pdb=" O GLY A 86 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N TYR A 88 " --> pdb=" O THR A 115 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 421 through 424 removed outlier: 6.060A pdb=" N VAL A 476 " --> pdb=" O VAL A 503 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N PHE A 505 " --> pdb=" O VAL A 476 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE A 478 " --> pdb=" O PHE A 505 " (cutoff:3.500A) removed outlier: 9.104A pdb=" N ALA A 507 " --> pdb=" O ILE A 478 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 260 through 261 removed outlier: 4.455A pdb=" N ARG A 260 " --> pdb=" O ARG A 269 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 558 through 559 removed outlier: 3.586A pdb=" N PHE A 558 " --> pdb=" O LEU A 566 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 593 through 596 removed outlier: 3.684A pdb=" N ILE A 630 " --> pdb=" O ILE A 618 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 702 through 706 Processing sheet with id=AA7, first strand: chain 'A' and resid 768 through 772 Processing sheet with id=AA8, first strand: chain 'A' and resid 768 through 772 removed outlier: 4.674A pdb=" N TYR A 754 " --> pdb=" O ILE A 729 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N GLN A 841 " --> pdb=" O GLY A 837 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 819 through 820 Processing sheet with id=AB1, first strand: chain 'A' and resid 970 through 971 removed outlier: 3.520A pdb=" N ILE A 940 " --> pdb=" O LEU A 971 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ARG A 943 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N VAL A 895 " --> pdb=" O ARG A 943 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N LYS A 880 " --> pdb=" O VAL A 895 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE A 881 " --> pdb=" O PHE A 979 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1680 through 1688 removed outlier: 3.529A pdb=" N VAL A1695 " --> pdb=" O CYS A1684 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N PHE A1686 " --> pdb=" O ILE A1693 " (cutoff:3.500A) 610 hydrogen bonds defined for protein. 1737 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 102 hydrogen bonds 188 hydrogen bond angles 0 basepair planarities 40 basepair parallelities 60 stacking parallelities Total time for adding SS restraints: 3.68 Time building geometry restraints manager: 1.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4334 1.34 - 1.46: 2997 1.46 - 1.57: 7731 1.57 - 1.69: 212 1.69 - 1.81: 105 Bond restraints: 15379 Sorted by residual: bond pdb=" P G C 1 " pdb=" OP3 G C 1 " ideal model delta sigma weight residual 1.480 1.605 -0.125 2.00e-02 2.50e+03 3.88e+01 bond pdb=" CB PRO A 872 " pdb=" CG PRO A 872 " ideal model delta sigma weight residual 1.492 1.641 -0.149 5.00e-02 4.00e+02 8.84e+00 bond pdb=" C4 C C 54 " pdb=" C5 C C 54 " ideal model delta sigma weight residual 1.425 1.411 0.014 8.00e-03 1.56e+04 3.11e+00 bond pdb=" C5 C C 54 " pdb=" C6 C C 54 " ideal model delta sigma weight residual 1.339 1.325 0.014 8.00e-03 1.56e+04 3.09e+00 bond pdb=" C8 G C 90 " pdb=" N7 G C 90 " ideal model delta sigma weight residual 1.305 1.296 0.009 6.00e-03 2.78e+04 2.39e+00 ... (remaining 15374 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.26: 21021 2.26 - 4.53: 243 4.53 - 6.79: 43 6.79 - 9.05: 3 9.05 - 11.32: 2 Bond angle restraints: 21312 Sorted by residual: angle pdb=" C5 G C 90 " pdb=" C6 G C 90 " pdb=" O6 G C 90 " ideal model delta sigma weight residual 128.60 122.43 6.17 6.00e-01 2.78e+00 1.06e+02 angle pdb=" O6 G C 90 " pdb=" C6 G C 90 " pdb=" N1 G C 90 " ideal model delta sigma weight residual 119.90 125.93 -6.03 6.00e-01 2.78e+00 1.01e+02 angle pdb=" N4 C C 14 " pdb=" C4 C C 14 " pdb=" C5 C C 14 " ideal model delta sigma weight residual 120.20 125.98 -5.78 7.00e-01 2.04e+00 6.81e+01 angle pdb=" CA PRO A 872 " pdb=" N PRO A 872 " pdb=" CD PRO A 872 " ideal model delta sigma weight residual 112.00 100.68 11.32 1.40e+00 5.10e-01 6.54e+01 angle pdb=" N3 C C 14 " pdb=" C4 C C 14 " pdb=" N4 C C 14 " ideal model delta sigma weight residual 118.00 112.38 5.62 7.00e-01 2.04e+00 6.45e+01 ... (remaining 21307 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.80: 8891 32.80 - 65.59: 516 65.59 - 98.39: 64 98.39 - 131.18: 2 131.18 - 163.98: 1 Dihedral angle restraints: 9474 sinusoidal: 4886 harmonic: 4588 Sorted by residual: dihedral pdb=" O4' U C 103 " pdb=" C1' U C 103 " pdb=" N1 U C 103 " pdb=" C2 U C 103 " ideal model delta sinusoidal sigma weight residual -128.00 35.98 -163.98 1 1.70e+01 3.46e-03 6.51e+01 dihedral pdb=" C5' ADP A1801 " pdb=" O5' ADP A1801 " pdb=" PA ADP A1801 " pdb=" O2A ADP A1801 " ideal model delta sinusoidal sigma weight residual -60.00 -160.78 100.78 1 2.00e+01 2.50e-03 2.85e+01 dihedral pdb=" O1B ADP A1801 " pdb=" O3A ADP A1801 " pdb=" PB ADP A1801 " pdb=" PA ADP A1801 " ideal model delta sinusoidal sigma weight residual -60.00 -157.35 97.34 1 2.00e+01 2.50e-03 2.71e+01 ... (remaining 9471 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1878 0.038 - 0.076: 441 0.076 - 0.114: 132 0.114 - 0.151: 22 0.151 - 0.189: 4 Chirality restraints: 2477 Sorted by residual: chirality pdb=" CA PRO A 872 " pdb=" N PRO A 872 " pdb=" C PRO A 872 " pdb=" CB PRO A 872 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.95e-01 chirality pdb=" C3' G C 97 " pdb=" C4' G C 97 " pdb=" O3' G C 97 " pdb=" C2' G C 97 " both_signs ideal model delta sigma weight residual False -2.48 -2.29 -0.18 2.00e-01 2.50e+01 8.45e-01 chirality pdb=" CB ILE A1301 " pdb=" CA ILE A1301 " pdb=" CG1 ILE A1301 " pdb=" CG2 ILE A1301 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.21e-01 ... (remaining 2474 not shown) Planarity restraints: 2337 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 871 " 0.075 5.00e-02 4.00e+02 1.05e-01 1.77e+01 pdb=" N PRO A 872 " -0.182 5.00e-02 4.00e+02 pdb=" CA PRO A 872 " 0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 872 " 0.057 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET A 768 " 0.029 5.00e-02 4.00e+02 4.38e-02 3.07e+00 pdb=" N PRO A 769 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 769 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 769 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 148 " 0.028 5.00e-02 4.00e+02 4.18e-02 2.79e+00 pdb=" N PRO A 149 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 149 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 149 " 0.023 5.00e-02 4.00e+02 ... (remaining 2334 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 124 2.53 - 3.13: 11496 3.13 - 3.72: 25914 3.72 - 4.31: 34468 4.31 - 4.90: 54169 Nonbonded interactions: 126171 Sorted by model distance: nonbonded pdb=" OP1 G C 23 " pdb="MG MG A1803 " model vdw 1.943 2.170 nonbonded pdb=" OE1 GLU A1213 " pdb="MG MG A1805 " model vdw 1.988 2.170 nonbonded pdb=" OP1 U C 84 " pdb="MG MG A1802 " model vdw 2.011 2.170 nonbonded pdb=" OE1 GLU A1210 " pdb="MG MG A1805 " model vdw 2.030 2.170 nonbonded pdb=" OE2 GLU A1617 " pdb="MG MG A1803 " model vdw 2.044 2.170 ... (remaining 126166 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: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.500 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 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 : 0.003 0.149 15379 Z= 0.160 Angle : 0.640 11.318 21312 Z= 0.423 Chirality : 0.037 0.189 2477 Planarity : 0.004 0.105 2337 Dihedral : 18.822 163.978 6498 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.39 % Favored : 95.55 % Rotamer: Outliers : 0.50 % Allowed : 16.64 % Favored : 82.86 % 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: -0.01 (0.22), residues: 1549 helix: 0.72 (0.19), residues: 746 sheet: -0.37 (0.38), residues: 187 loop : -0.67 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1658 TYR 0.027 0.001 TYR A1037 PHE 0.022 0.001 PHE A 589 TRP 0.016 0.001 TRP A1634 HIS 0.003 0.001 HIS A 576 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.16 (15379) covalent geometry : angle 0.63959 / 0.42 (21312) hydrogen bonds : bond 0.15258 / 10.30 ( 702) hydrogen bonds : angle 6.47148 / 4.73 ( 1925) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 142 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 THR cc_start: 0.6991 (p) cc_final: 0.6494 (t) REVERT: A 847 GLU cc_start: 0.8330 (mp0) cc_final: 0.8117 (tp30) REVERT: A 1246 LYS cc_start: 0.8566 (mppt) cc_final: 0.8265 (mmmt) REVERT: A 1389 MET cc_start: 0.7996 (tpp) cc_final: 0.7719 (mmm) outliers start: 7 outliers final: 2 residues processed: 147 average time/residue: 0.1061 time to fit residues: 23.7072 Evaluate side-chains 127 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 125 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 1674 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.0070 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 0.0010 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 9.9990 overall best weight: 0.4604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 148 HIS A 287 GLN A 801 GLN A 841 GLN ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1250 ASN A1704 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.115932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.081288 restraints weight = 31275.724| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.87 r_work: 0.3130 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 15379 Z= 0.120 Angle : 0.553 9.213 21312 Z= 0.296 Chirality : 0.039 0.243 2477 Planarity : 0.004 0.044 2337 Dihedral : 17.262 166.847 3358 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.13 % Favored : 95.80 % Rotamer: Outliers : 2.21 % Allowed : 15.79 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.05 (0.21), residues: 1549 helix: 0.80 (0.19), residues: 752 sheet: -0.41 (0.37), residues: 177 loop : -0.68 (0.25), residues: 620 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1448 TYR 0.018 0.001 TYR A1232 PHE 0.016 0.001 PHE A1473 TRP 0.016 0.002 TRP A 814 HIS 0.003 0.001 HIS A 576 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (15379) covalent geometry : angle 0.55254 / 0.30 (21312) hydrogen bonds : bond 0.05028 / 3.44 ( 702) hydrogen bonds : angle 5.02343 / 3.63 ( 1925) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 132 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 LEU cc_start: 0.8331 (pp) cc_final: 0.8121 (tt) REVERT: A 847 GLU cc_start: 0.8493 (mp0) cc_final: 0.8241 (tp30) REVERT: A 934 HIS cc_start: 0.7275 (t-90) cc_final: 0.6825 (t-90) REVERT: A 1246 LYS cc_start: 0.8585 (mppt) cc_final: 0.8313 (mmmt) REVERT: A 1489 GLU cc_start: 0.8537 (tm-30) cc_final: 0.8333 (tm-30) REVERT: A 1681 MET cc_start: 0.5686 (ppp) cc_final: 0.5292 (tmm) REVERT: A 1704 GLN cc_start: 0.8419 (tp40) cc_final: 0.8178 (tp-100) outliers start: 31 outliers final: 15 residues processed: 154 average time/residue: 0.1013 time to fit residues: 24.2695 Evaluate side-chains 131 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 158 THR Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1035 ILE Chi-restraints excluded: chain A residue 1171 VAL Chi-restraints excluded: chain A residue 1202 SER Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1688 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 39 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 99 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 125 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 101 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 562 ASN ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.114223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.083274 restraints weight = 31524.179| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.66 r_work: 0.3080 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15379 Z= 0.141 Angle : 0.552 7.971 21312 Z= 0.293 Chirality : 0.039 0.227 2477 Planarity : 0.004 0.045 2337 Dihedral : 17.118 166.793 3358 Min Nonbonded Distance : 1.866 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.58 % Favored : 95.35 % Rotamer: Outliers : 2.00 % Allowed : 18.14 % Favored : 79.86 % 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: 0.01 (0.21), residues: 1549 helix: 0.83 (0.19), residues: 745 sheet: -0.59 (0.36), residues: 185 loop : -0.71 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 900 TYR 0.019 0.001 TYR A1232 PHE 0.019 0.001 PHE A1473 TRP 0.011 0.001 TRP A1634 HIS 0.003 0.001 HIS A1663 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (15379) covalent geometry : angle 0.55226 / 0.29 (21312) hydrogen bonds : bond 0.04575 / 3.13 ( 702) hydrogen bonds : angle 4.75837 / 3.42 ( 1925) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 123 time to evaluate : 0.551 Fit side-chains revert: symmetry clash REVERT: A 504 LEU cc_start: 0.8425 (pp) cc_final: 0.8220 (tt) REVERT: A 847 GLU cc_start: 0.8499 (mp0) cc_final: 0.8257 (tp30) REVERT: A 918 TYR cc_start: 0.7585 (t80) cc_final: 0.7318 (t80) REVERT: A 934 HIS cc_start: 0.7364 (t-90) cc_final: 0.7109 (t-90) REVERT: A 1489 GLU cc_start: 0.8556 (tm-30) cc_final: 0.8342 (tm-30) REVERT: A 1674 ILE cc_start: 0.6404 (OUTLIER) cc_final: 0.5520 (mm) REVERT: A 1681 MET cc_start: 0.5854 (ppp) cc_final: 0.5414 (tmm) outliers start: 28 outliers final: 16 residues processed: 143 average time/residue: 0.1187 time to fit residues: 26.0569 Evaluate side-chains 128 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 111 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1035 ILE Chi-restraints excluded: chain A residue 1171 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1688 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 59 optimal weight: 3.9990 chunk 34 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 4.9990 chunk 151 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 143 optimal weight: 0.0570 chunk 91 optimal weight: 8.9990 chunk 108 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 overall best weight: 0.9302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 562 ASN A 800 HIS ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1656 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.114735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.080132 restraints weight = 31492.687| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.85 r_work: 0.3101 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15379 Z= 0.120 Angle : 0.530 7.604 21312 Z= 0.279 Chirality : 0.038 0.265 2477 Planarity : 0.004 0.047 2337 Dihedral : 17.102 168.113 3358 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.07 % Favored : 95.87 % Rotamer: Outliers : 2.36 % Allowed : 18.36 % Favored : 79.29 % 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: 0.07 (0.21), residues: 1549 helix: 0.90 (0.19), residues: 748 sheet: -0.61 (0.36), residues: 185 loop : -0.72 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 873 TYR 0.016 0.001 TYR A1232 PHE 0.017 0.001 PHE A1473 TRP 0.012 0.001 TRP A1634 HIS 0.003 0.001 HIS A 576 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (15379) covalent geometry : angle 0.52997 / 0.28 (21312) hydrogen bonds : bond 0.04252 / 2.90 ( 702) hydrogen bonds : angle 4.64191 / 3.33 ( 1925) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.586 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 847 GLU cc_start: 0.8477 (mp0) cc_final: 0.8243 (tp30) REVERT: A 934 HIS cc_start: 0.7353 (t-90) cc_final: 0.7008 (t-90) REVERT: A 1037 TYR cc_start: 0.6626 (t80) cc_final: 0.6241 (t80) REVERT: A 1489 GLU cc_start: 0.8527 (tm-30) cc_final: 0.8315 (tm-30) REVERT: A 1674 ILE cc_start: 0.6432 (OUTLIER) cc_final: 0.5583 (mm) REVERT: A 1681 MET cc_start: 0.6004 (ppp) cc_final: 0.5540 (tmm) outliers start: 33 outliers final: 15 residues processed: 143 average time/residue: 0.1059 time to fit residues: 23.4228 Evaluate side-chains 128 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 675 ILE Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1035 ILE Chi-restraints excluded: chain A residue 1171 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1674 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 68 optimal weight: 5.9990 chunk 152 optimal weight: 1.9990 chunk 154 optimal weight: 9.9990 chunk 161 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 48 optimal weight: 0.1980 chunk 143 optimal weight: 0.2980 chunk 65 optimal weight: 6.9990 chunk 163 optimal weight: 10.0000 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 562 ASN ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1704 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.112435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.081130 restraints weight = 31795.142| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.81 r_work: 0.3033 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15379 Z= 0.190 Angle : 0.587 7.609 21312 Z= 0.309 Chirality : 0.041 0.239 2477 Planarity : 0.004 0.047 2337 Dihedral : 17.028 165.851 3358 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 3.36 % Allowed : 17.36 % Favored : 79.29 % 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: -0.10 (0.21), residues: 1549 helix: 0.70 (0.19), residues: 754 sheet: -0.68 (0.36), residues: 192 loop : -0.72 (0.26), residues: 603 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A1658 TYR 0.020 0.002 TYR A1468 PHE 0.021 0.002 PHE A1481 TRP 0.012 0.002 TRP A1634 HIS 0.005 0.001 HIS A1385 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.19 (15379) covalent geometry : angle 0.58711 / 0.31 (21312) hydrogen bonds : bond 0.04681 / 3.16 ( 702) hydrogen bonds : angle 4.69975 / 3.37 ( 1925) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 118 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 847 GLU cc_start: 0.8512 (mp0) cc_final: 0.8265 (tp30) REVERT: A 934 HIS cc_start: 0.7460 (t-90) cc_final: 0.7064 (t-90) REVERT: A 939 MET cc_start: 0.5278 (tpp) cc_final: 0.4895 (tpp) REVERT: A 1037 TYR cc_start: 0.6633 (t80) cc_final: 0.6073 (t80) REVERT: A 1179 LYS cc_start: 0.7985 (OUTLIER) cc_final: 0.7780 (ptpt) REVERT: A 1389 MET cc_start: 0.7905 (mmm) cc_final: 0.7543 (tpp) REVERT: A 1681 MET cc_start: 0.6112 (ppp) cc_final: 0.5575 (tmm) outliers start: 47 outliers final: 30 residues processed: 150 average time/residue: 0.1067 time to fit residues: 24.9840 Evaluate side-chains 143 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 112 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 41 VAL Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 442 TRP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 675 ILE Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1035 ILE Chi-restraints excluded: chain A residue 1171 VAL Chi-restraints excluded: chain A residue 1179 LYS Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1688 CYS Chi-restraints excluded: chain A residue 1717 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 14 optimal weight: 6.9990 chunk 34 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 122 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 150 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 94 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 109 ASN A 313 GLN ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1704 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.112132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.077107 restraints weight = 31450.553| |-----------------------------------------------------------------------------| r_work (start): 0.3195 rms_B_bonded: 2.84 r_work: 0.3047 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15379 Z= 0.188 Angle : 0.593 8.360 21312 Z= 0.310 Chirality : 0.041 0.237 2477 Planarity : 0.004 0.045 2337 Dihedral : 17.058 165.269 3358 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.14 % Allowed : 18.93 % Favored : 77.93 % 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: -0.12 (0.21), residues: 1549 helix: 0.68 (0.19), residues: 745 sheet: -0.62 (0.36), residues: 192 loop : -0.72 (0.25), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 866 TYR 0.020 0.002 TYR A1468 PHE 0.019 0.002 PHE A1473 TRP 0.012 0.002 TRP A1634 HIS 0.004 0.001 HIS A1385 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.19 (15379) covalent geometry : angle 0.59335 / 0.31 (21312) hydrogen bonds : bond 0.04524 / 3.07 ( 702) hydrogen bonds : angle 4.68745 / 3.37 ( 1925) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 117 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 908 MET cc_start: 0.5774 (mpp) cc_final: 0.5050 (mmp) REVERT: A 934 HIS cc_start: 0.7478 (t-90) cc_final: 0.7106 (t-90) REVERT: A 939 MET cc_start: 0.5311 (tpp) cc_final: 0.4932 (tpp) REVERT: A 1037 TYR cc_start: 0.6640 (t80) cc_final: 0.6084 (t80) REVERT: A 1389 MET cc_start: 0.7988 (mmm) cc_final: 0.7644 (tpp) REVERT: A 1604 THR cc_start: 0.4643 (OUTLIER) cc_final: 0.4348 (m) REVERT: A 1681 MET cc_start: 0.6132 (ppp) cc_final: 0.5764 (tmm) REVERT: A 1704 GLN cc_start: 0.8444 (tp40) cc_final: 0.8196 (tp-100) outliers start: 44 outliers final: 31 residues processed: 149 average time/residue: 0.0944 time to fit residues: 22.3761 Evaluate side-chains 142 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 110 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 26 VAL Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 442 TRP Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 675 ILE Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 914 ASP Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1035 ILE Chi-restraints excluded: chain A residue 1171 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1225 THR Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1717 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 22 optimal weight: 9.9990 chunk 17 optimal weight: 0.3980 chunk 56 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.113884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.079119 restraints weight = 31070.401| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.84 r_work: 0.3084 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15379 Z= 0.119 Angle : 0.547 9.752 21312 Z= 0.286 Chirality : 0.038 0.231 2477 Planarity : 0.003 0.046 2337 Dihedral : 17.088 168.193 3358 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.64 % Allowed : 19.86 % Favored : 77.50 % 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: 0.02 (0.21), residues: 1549 helix: 0.84 (0.19), residues: 741 sheet: -0.61 (0.36), residues: 186 loop : -0.70 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1549 TYR 0.021 0.001 TYR A 918 PHE 0.017 0.001 PHE A1473 TRP 0.014 0.001 TRP A1634 HIS 0.003 0.001 HIS A 576 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 (15379) covalent geometry : angle 0.54730 / 0.29 (21312) hydrogen bonds : bond 0.04088 / 2.77 ( 702) hydrogen bonds : angle 4.53746 / 3.27 ( 1925) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 0.517 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 504 LEU cc_start: 0.8432 (tt) cc_final: 0.8191 (mt) REVERT: A 852 PHE cc_start: 0.7168 (m-80) cc_final: 0.6903 (m-80) REVERT: A 900 ARG cc_start: 0.7418 (mtt90) cc_final: 0.6417 (mpt90) REVERT: A 934 HIS cc_start: 0.7533 (t-90) cc_final: 0.7112 (t-90) REVERT: A 939 MET cc_start: 0.5344 (tpp) cc_final: 0.4991 (tpp) REVERT: A 1037 TYR cc_start: 0.6578 (t80) cc_final: 0.6067 (t80) REVERT: A 1389 MET cc_start: 0.8037 (mmm) cc_final: 0.7520 (tpp) REVERT: A 1417 MET cc_start: 0.6452 (OUTLIER) cc_final: 0.6096 (mpp) REVERT: A 1489 GLU cc_start: 0.8506 (tm-30) cc_final: 0.8296 (tm-30) REVERT: A 1604 THR cc_start: 0.4676 (OUTLIER) cc_final: 0.4363 (m) REVERT: A 1681 MET cc_start: 0.6043 (ppp) cc_final: 0.5644 (tmm) REVERT: A 1682 VAL cc_start: 0.8540 (t) cc_final: 0.8333 (t) outliers start: 37 outliers final: 25 residues processed: 146 average time/residue: 0.0973 time to fit residues: 22.3876 Evaluate side-chains 143 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 116 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 675 ILE Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1035 ILE Chi-restraints excluded: chain A residue 1171 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1284 LEU Chi-restraints excluded: chain A residue 1417 MET Chi-restraints excluded: chain A residue 1462 ASN Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1675 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 69 optimal weight: 10.0000 chunk 28 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 164 optimal weight: 20.0000 chunk 74 optimal weight: 5.9990 chunk 42 optimal weight: 0.0980 chunk 144 optimal weight: 0.9980 chunk 101 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 151 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 562 ASN ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1704 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.113964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.079022 restraints weight = 31448.921| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.87 r_work: 0.3085 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15379 Z= 0.125 Angle : 0.569 16.390 21312 Z= 0.292 Chirality : 0.038 0.231 2477 Planarity : 0.003 0.045 2337 Dihedral : 17.061 169.169 3358 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.57 % Allowed : 19.79 % Favored : 77.64 % 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: 0.06 (0.21), residues: 1549 helix: 0.88 (0.19), residues: 741 sheet: -0.60 (0.36), residues: 186 loop : -0.67 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A1549 TYR 0.031 0.001 TYR A 918 PHE 0.016 0.001 PHE A1473 TRP 0.014 0.001 TRP A1634 HIS 0.003 0.001 HIS A 576 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (15379) covalent geometry : angle 0.56872 / 0.29 (21312) hydrogen bonds : bond 0.04054 / 2.75 ( 702) hydrogen bonds : angle 4.50095 / 3.24 ( 1925) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 117 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 900 ARG cc_start: 0.7370 (mtt90) cc_final: 0.6362 (mpt90) REVERT: A 934 HIS cc_start: 0.7529 (t-90) cc_final: 0.7078 (t-90) REVERT: A 939 MET cc_start: 0.5252 (tpp) cc_final: 0.4927 (tpp) REVERT: A 1037 TYR cc_start: 0.6571 (t80) cc_final: 0.6139 (t80) REVERT: A 1389 MET cc_start: 0.8043 (mmm) cc_final: 0.7517 (tpp) REVERT: A 1604 THR cc_start: 0.4751 (OUTLIER) cc_final: 0.4504 (m) REVERT: A 1681 MET cc_start: 0.6079 (ppp) cc_final: 0.5625 (ppp) REVERT: A 1682 VAL cc_start: 0.8587 (t) cc_final: 0.8324 (t) REVERT: A 1704 GLN cc_start: 0.8334 (tp40) cc_final: 0.8119 (tp-100) outliers start: 36 outliers final: 28 residues processed: 140 average time/residue: 0.1039 time to fit residues: 22.9113 Evaluate side-chains 141 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 112 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 506 THR Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 675 ILE Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1035 ILE Chi-restraints excluded: chain A residue 1171 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1462 ASN Chi-restraints excluded: chain A residue 1494 MET Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1675 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 46 optimal weight: 0.0030 chunk 52 optimal weight: 6.9990 chunk 22 optimal weight: 10.0000 chunk 158 optimal weight: 10.0000 chunk 104 optimal weight: 0.0770 chunk 159 optimal weight: 10.0000 chunk 136 optimal weight: 0.9980 chunk 14 optimal weight: 0.2980 chunk 93 optimal weight: 8.9990 chunk 71 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 overall best weight: 0.8750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.114508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.079952 restraints weight = 31476.118| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.79 r_work: 0.3105 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8008 moved from start: 0.1832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15379 Z= 0.116 Angle : 0.564 17.671 21312 Z= 0.288 Chirality : 0.038 0.229 2477 Planarity : 0.004 0.046 2337 Dihedral : 17.053 170.535 3358 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 2.64 % Allowed : 20.07 % Favored : 77.29 % 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: 0.04 (0.21), residues: 1549 helix: 0.87 (0.19), residues: 742 sheet: -0.58 (0.36), residues: 186 loop : -0.70 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1549 TYR 0.025 0.001 TYR A 11 PHE 0.016 0.001 PHE A1473 TRP 0.014 0.001 TRP A1634 HIS 0.003 0.001 HIS A 576 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (15379) covalent geometry : angle 0.56433 / 0.29 (21312) hydrogen bonds : bond 0.03954 / 2.68 ( 702) hydrogen bonds : angle 4.42206 / 3.17 ( 1925) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 123 time to evaluate : 0.519 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 VAL cc_start: 0.8691 (m) cc_final: 0.8474 (m) REVERT: A 900 ARG cc_start: 0.7352 (mtt90) cc_final: 0.6353 (mpt90) REVERT: A 934 HIS cc_start: 0.7520 (t-90) cc_final: 0.7058 (t-90) REVERT: A 939 MET cc_start: 0.5263 (tpp) cc_final: 0.4946 (tpp) REVERT: A 1037 TYR cc_start: 0.6604 (t80) cc_final: 0.6147 (t80) REVERT: A 1389 MET cc_start: 0.7937 (mmm) cc_final: 0.7494 (tpp) REVERT: A 1489 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8291 (tm-30) REVERT: A 1602 MET cc_start: 0.5271 (tmm) cc_final: 0.5021 (tmm) REVERT: A 1604 THR cc_start: 0.4607 (OUTLIER) cc_final: 0.4360 (m) REVERT: A 1681 MET cc_start: 0.6023 (ppp) cc_final: 0.5612 (ppp) REVERT: A 1682 VAL cc_start: 0.8589 (t) cc_final: 0.8324 (t) outliers start: 37 outliers final: 28 residues processed: 149 average time/residue: 0.1085 time to fit residues: 24.9310 Evaluate side-chains 144 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 115 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 675 ILE Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1035 ILE Chi-restraints excluded: chain A residue 1171 VAL Chi-restraints excluded: chain A residue 1176 ILE Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1462 ASN Chi-restraints excluded: chain A residue 1494 MET Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1675 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 45 optimal weight: 8.9990 chunk 60 optimal weight: 5.9990 chunk 153 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 74 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 122 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 110 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 800 HIS ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1704 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.113828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.078687 restraints weight = 31391.132| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.87 r_work: 0.3079 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15379 Z= 0.148 Angle : 0.584 17.093 21312 Z= 0.299 Chirality : 0.039 0.234 2477 Planarity : 0.004 0.046 2337 Dihedral : 17.018 169.680 3358 Min Nonbonded Distance : 1.867 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.57 % Allowed : 20.00 % Favored : 77.43 % 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: 0.04 (0.21), residues: 1549 helix: 0.86 (0.19), residues: 741 sheet: -0.56 (0.36), residues: 192 loop : -0.70 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1658 TYR 0.024 0.002 TYR A 11 PHE 0.018 0.001 PHE A 959 TRP 0.012 0.001 TRP A1634 HIS 0.003 0.001 HIS A 576 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (15379) covalent geometry : angle 0.58369 / 0.30 (21312) hydrogen bonds : bond 0.04114 / 2.79 ( 702) hydrogen bonds : angle 4.45963 / 3.19 ( 1925) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3098 Ramachandran restraints generated. 1549 Oldfield, 0 Emsley, 1549 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 0.543 Fit side-chains revert: symmetry clash REVERT: A 900 ARG cc_start: 0.7355 (mtt90) cc_final: 0.6371 (mpt90) REVERT: A 908 MET cc_start: 0.5600 (mpp) cc_final: 0.4570 (mmp) REVERT: A 918 TYR cc_start: 0.7610 (t80) cc_final: 0.7398 (t80) REVERT: A 934 HIS cc_start: 0.7534 (t-90) cc_final: 0.7131 (t-90) REVERT: A 939 MET cc_start: 0.5239 (tpp) cc_final: 0.4873 (tpp) REVERT: A 1037 TYR cc_start: 0.6687 (t80) cc_final: 0.6307 (t80) REVERT: A 1602 MET cc_start: 0.5274 (tmm) cc_final: 0.5014 (tmm) REVERT: A 1604 THR cc_start: 0.4506 (OUTLIER) cc_final: 0.4244 (m) REVERT: A 1674 ILE cc_start: 0.6541 (OUTLIER) cc_final: 0.5837 (pt) REVERT: A 1681 MET cc_start: 0.6080 (ppp) cc_final: 0.5681 (tmm) outliers start: 36 outliers final: 29 residues processed: 143 average time/residue: 0.1068 time to fit residues: 23.8758 Evaluate side-chains 145 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 114 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 15 LEU Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 181 ILE Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain A residue 418 VAL Chi-restraints excluded: chain A residue 463 VAL Chi-restraints excluded: chain A residue 466 GLU Chi-restraints excluded: chain A residue 515 ILE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 675 ILE Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 1035 ILE Chi-restraints excluded: chain A residue 1171 VAL Chi-restraints excluded: chain A residue 1176 ILE Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1214 ILE Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1462 ASN Chi-restraints excluded: chain A residue 1494 MET Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1675 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 35 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 126 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 160 optimal weight: 20.0000 chunk 86 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 115 optimal weight: 0.0670 chunk 84 optimal weight: 0.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1704 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.114412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.079656 restraints weight = 31232.302| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 2.80 r_work: 0.3102 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15379 Z= 0.123 Angle : 0.576 17.274 21312 Z= 0.293 Chirality : 0.038 0.231 2477 Planarity : 0.004 0.048 2337 Dihedral : 17.043 170.471 3358 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.64 % Allowed : 20.00 % Favored : 77.36 % 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: 0.07 (0.21), residues: 1549 helix: 0.87 (0.19), residues: 742 sheet: -0.58 (0.37), residues: 176 loop : -0.67 (0.25), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A1549 TYR 0.029 0.001 TYR A 918 PHE 0.017 0.001 PHE A1473 TRP 0.013 0.001 TRP A1634 HIS 0.003 0.001 HIS A 576 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (15379) covalent geometry : angle 0.57593 / 0.29 (21312) hydrogen bonds : bond 0.03961 / 2.69 ( 702) hydrogen bonds : angle 4.41523 / 3.15 ( 1925) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3003.45 seconds wall clock time: 52 minutes 31.50 seconds (3151.50 seconds total)