Starting phenix.real_space_refine on Fri May 16 20:50:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yii_39320/05_2025/8yii_39320.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yii_39320/05_2025/8yii_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_39320/05_2025/8yii_39320.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yii_39320/05_2025/8yii_39320.map" model { file = "/net/cci-nas-00/data/ceres_data/8yii_39320/05_2025/8yii_39320.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yii_39320/05_2025/8yii_39320.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 8.51, per 1000 atoms: 0.57 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: 3.60 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 5.99 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: 8.45 Time building geometry restraints manager: 4.23 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=" N PRO A 872 " pdb=" CA PRO A 872 " ideal model delta sigma weight residual 1.472 1.454 0.018 1.17e-02 7.31e+03 2.25e+00 bond pdb=" CA TYR A1037 " pdb=" C TYR A1037 " ideal model delta sigma weight residual 1.522 1.541 -0.019 1.38e-02 5.25e+03 1.85e+00 bond pdb=" C LYS A1667 " pdb=" O LYS A1667 " ideal model delta sigma weight residual 1.242 1.226 0.016 1.16e-02 7.43e+03 1.84e+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=" 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=" CA TYR A 918 " pdb=" CB TYR A 918 " pdb=" CG TYR A 918 " ideal model delta sigma weight residual 113.90 121.08 -7.18 1.80e+00 3.09e-01 1.59e+01 angle pdb=" CB MET A 922 " pdb=" CG MET A 922 " pdb=" SD MET A 922 " ideal model delta sigma weight residual 112.70 101.46 11.24 3.00e+00 1.11e-01 1.40e+01 angle pdb=" N VAL A1206 " pdb=" CA VAL A1206 " pdb=" C VAL A1206 " ideal model delta sigma weight residual 112.29 109.17 3.12 9.40e-01 1.13e+00 1.10e+01 angle pdb=" N PRO A 872 " pdb=" CD PRO A 872 " pdb=" CG PRO A 872 " ideal model delta sigma weight residual 103.20 98.47 4.73 1.50e+00 4.44e-01 9.94e+00 ... (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: 1.940 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: 0.440 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 41.200 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.050 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 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= 0.146 Angle : 0.640 11.318 21312 Z= 0.352 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.016 0.001 TRP A1634 HIS 0.003 0.001 HIS A 576 PHE 0.022 0.001 PHE A 589 TYR 0.027 0.001 TYR A1037 ARG 0.006 0.000 ARG A1658 Details of bonding type rmsd hydrogen bonds : bond 0.15258 ( 702) hydrogen bonds : angle 6.47148 ( 1925) covalent geometry : bond 0.00300 (15379) covalent geometry : angle 0.63957 (21312) *********************** 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 : 2.131 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: 0.2836 time to fit residues: 62.0631 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 : 1.607 ------------------------------------------------------------------------------- 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 139 optimal weight: 0.9990 chunk 125 optimal weight: 3.9990 chunk 69 optimal weight: 10.0000 chunk 42 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 66 optimal weight: 0.0010 chunk 129 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 78 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 149 optimal weight: 9.9990 overall best weight: 0.7992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 148 HIS A 287 GLN ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 841 GLN ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1250 ASN A1704 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.115261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.080651 restraints weight = 31257.258| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.85 r_work: 0.3116 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.0884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15379 Z= 0.124 Angle : 0.566 8.606 21312 Z= 0.292 Chirality : 0.039 0.226 2477 Planarity : 0.004 0.042 2337 Dihedral : 17.173 163.222 3358 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.00 % Favored : 95.93 % Rotamer: Outliers : 2.36 % Allowed : 16.14 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.21), residues: 1549 helix: 0.84 (0.19), residues: 751 sheet: -0.38 (0.37), residues: 179 loop : -0.69 (0.25), residues: 619 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 814 HIS 0.003 0.001 HIS A 934 PHE 0.017 0.001 PHE A1473 TYR 0.019 0.001 TYR A1232 ARG 0.003 0.000 ARG A 900 Details of bonding type rmsd hydrogen bonds : bond 0.04388 ( 702) hydrogen bonds : angle 4.85778 ( 1925) covalent geometry : bond 0.00262 (15379) covalent geometry : angle 0.56563 (21312) *********************** 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 164 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 131 time to evaluate : 1.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 504 LEU cc_start: 0.8396 (pp) cc_final: 0.8194 (tt) REVERT: A 744 MET cc_start: 0.8804 (tpp) cc_final: 0.8500 (mmt) REVERT: A 847 GLU cc_start: 0.8521 (mp0) cc_final: 0.8227 (tp30) REVERT: A 873 ARG cc_start: 0.7739 (mmt-90) cc_final: 0.7532 (mmp80) REVERT: A 918 TYR cc_start: 0.7575 (t80) cc_final: 0.7296 (t80) REVERT: A 934 HIS cc_start: 0.7255 (t-90) cc_final: 0.6634 (t-90) REVERT: A 1681 MET cc_start: 0.5804 (ppp) cc_final: 0.5379 (tmm) outliers start: 33 outliers final: 15 residues processed: 154 average time/residue: 0.2586 time to fit residues: 60.8392 Evaluate side-chains 130 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 1.510 ------------------------------------------------------------------------------- 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 996 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 1494 MET Chi-restraints excluded: chain A residue 1674 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 45 optimal weight: 8.9990 chunk 99 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 57 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 137 optimal weight: 1.9990 chunk 164 optimal weight: 10.0000 chunk 160 optimal weight: 10.0000 chunk 161 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 92 GLN A 407 ASN A 562 ASN A 570 ASN A 800 HIS ** A 801 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1019 HIS A1250 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.108748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.074908 restraints weight = 31986.787| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.99 r_work: 0.2958 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 15379 Z= 0.371 Angle : 0.785 8.953 21312 Z= 0.404 Chirality : 0.048 0.268 2477 Planarity : 0.005 0.045 2337 Dihedral : 17.156 151.231 3358 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.42 % Favored : 94.51 % Rotamer: Outliers : 4.36 % Allowed : 16.86 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.21), residues: 1549 helix: 0.04 (0.18), residues: 760 sheet: -0.68 (0.37), residues: 183 loop : -0.86 (0.25), residues: 606 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 97 HIS 0.008 0.002 HIS A1185 PHE 0.026 0.003 PHE A1473 TYR 0.040 0.003 TYR A1468 ARG 0.008 0.001 ARG A 866 Details of bonding type rmsd hydrogen bonds : bond 0.05788 ( 702) hydrogen bonds : angle 5.22324 ( 1925) covalent geometry : bond 0.00824 (15379) covalent geometry : angle 0.78532 (21312) *********************** 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 177 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 116 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 140 GLU cc_start: 0.8050 (mp0) cc_final: 0.7582 (mp0) REVERT: A 550 HIS cc_start: 0.8419 (OUTLIER) cc_final: 0.8181 (t-90) REVERT: A 671 ARG cc_start: 0.6843 (tpp80) cc_final: 0.6486 (ttt-90) REVERT: A 847 GLU cc_start: 0.8533 (mp0) cc_final: 0.8260 (tp30) REVERT: A 934 HIS cc_start: 0.7550 (t-90) cc_final: 0.6880 (t-90) REVERT: A 935 LYS cc_start: 0.7491 (OUTLIER) cc_final: 0.7068 (ttpp) REVERT: A 1037 TYR cc_start: 0.6639 (t80) cc_final: 0.6382 (t80) REVERT: A 1417 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7255 (mpp) REVERT: A 1681 MET cc_start: 0.5841 (ppp) cc_final: 0.5507 (tmm) outliers start: 61 outliers final: 37 residues processed: 160 average time/residue: 0.2462 time to fit residues: 60.5087 Evaluate side-chains 151 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 111 time to evaluate : 1.448 ------------------------------------------------------------------------------- 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 63 MET Chi-restraints excluded: chain A residue 69 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 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 550 HIS 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 809 ASP Chi-restraints excluded: chain A residue 882 VAL Chi-restraints excluded: chain A residue 935 LYS Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 999 MET 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 1284 LEU Chi-restraints excluded: chain A residue 1405 THR Chi-restraints excluded: chain A residue 1417 MET Chi-restraints excluded: chain A residue 1422 ASN Chi-restraints excluded: chain A residue 1468 TYR Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1620 ILE Chi-restraints excluded: chain A residue 1674 ILE Chi-restraints excluded: chain A residue 1717 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 92 optimal weight: 8.9990 chunk 157 optimal weight: 2.9990 chunk 117 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 105 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 89 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 801 GLN ** 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 = 0.3821 r_free = 0.3821 target = 0.112784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.077935 restraints weight = 31218.018| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.84 r_work: 0.3064 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15379 Z= 0.129 Angle : 0.579 8.046 21312 Z= 0.296 Chirality : 0.039 0.235 2477 Planarity : 0.004 0.043 2337 Dihedral : 17.139 155.700 3358 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.94 % Favored : 96.00 % Rotamer: Outliers : 2.86 % Allowed : 18.57 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.21), residues: 1549 helix: 0.58 (0.19), residues: 752 sheet: -0.57 (0.36), residues: 192 loop : -0.76 (0.25), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A1634 HIS 0.003 0.001 HIS A1663 PHE 0.018 0.001 PHE A1473 TYR 0.019 0.001 TYR A1232 ARG 0.003 0.000 ARG A1211 Details of bonding type rmsd hydrogen bonds : bond 0.04166 ( 702) hydrogen bonds : angle 4.71677 ( 1925) covalent geometry : bond 0.00278 (15379) covalent geometry : angle 0.57879 (21312) *********************** 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 169 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 129 time to evaluate : 1.529 Fit side-chains revert: symmetry clash REVERT: A 233 THR cc_start: 0.7016 (p) cc_final: 0.6497 (t) REVERT: A 338 VAL cc_start: 0.8712 (m) cc_final: 0.8506 (m) REVERT: A 458 MET cc_start: 0.8477 (tpp) cc_final: 0.7921 (tpt) REVERT: A 504 LEU cc_start: 0.8418 (pp) cc_final: 0.8138 (tt) REVERT: A 551 PHE cc_start: 0.8307 (m-10) cc_final: 0.7897 (m-10) REVERT: A 847 GLU cc_start: 0.8529 (mp0) cc_final: 0.8248 (tp30) REVERT: A 934 HIS cc_start: 0.7480 (t-90) cc_final: 0.7145 (t-90) REVERT: A 1037 TYR cc_start: 0.6614 (t80) cc_final: 0.5878 (t80) REVERT: A 1681 MET cc_start: 0.5825 (ppp) cc_final: 0.5300 (tmm) REVERT: A 1682 VAL cc_start: 0.8562 (t) cc_final: 0.8338 (t) outliers start: 40 outliers final: 19 residues processed: 155 average time/residue: 0.2633 time to fit residues: 63.3772 Evaluate side-chains 133 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 322 MET Chi-restraints excluded: chain A residue 332 LYS Chi-restraints excluded: chain A residue 344 MET 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 668 LEU Chi-restraints excluded: chain A residue 672 VAL 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 1171 VAL Chi-restraints excluded: chain A residue 1212 LEU Chi-restraints excluded: chain A residue 1302 ILE 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 126 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 95 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 86 optimal weight: 20.0000 chunk 123 optimal weight: 0.4980 chunk 105 optimal weight: 3.9990 chunk 146 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3816 r_free = 0.3816 target = 0.112386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.077326 restraints weight = 31802.385| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.86 r_work: 0.3055 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15379 Z= 0.155 Angle : 0.577 7.652 21312 Z= 0.297 Chirality : 0.039 0.240 2477 Planarity : 0.004 0.042 2337 Dihedral : 17.033 155.750 3358 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 4.58 % Favored : 95.35 % Rotamer: Outliers : 3.43 % Allowed : 18.79 % Favored : 77.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.21), residues: 1549 helix: 0.64 (0.19), residues: 747 sheet: -0.67 (0.36), residues: 191 loop : -0.73 (0.25), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1634 HIS 0.003 0.001 HIS A 576 PHE 0.019 0.001 PHE A1473 TYR 0.020 0.001 TYR A1232 ARG 0.003 0.000 ARG A1658 Details of bonding type rmsd hydrogen bonds : bond 0.04197 ( 702) hydrogen bonds : angle 4.65729 ( 1925) covalent geometry : bond 0.00342 (15379) covalent geometry : angle 0.57674 (21312) *********************** 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 171 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 123 time to evaluate : 1.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 458 MET cc_start: 0.8463 (tpp) cc_final: 0.7896 (tpt) REVERT: A 504 LEU cc_start: 0.8378 (pp) cc_final: 0.8102 (tt) REVERT: A 934 HIS cc_start: 0.7536 (t-90) cc_final: 0.7154 (t-90) REVERT: A 1037 TYR cc_start: 0.6692 (t80) cc_final: 0.6004 (t80) REVERT: A 1389 MET cc_start: 0.7909 (mmm) cc_final: 0.7308 (tpp) REVERT: A 1417 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.6936 (mpp) REVERT: A 1604 THR cc_start: 0.4546 (OUTLIER) cc_final: 0.4243 (m) REVERT: A 1681 MET cc_start: 0.5953 (ppp) cc_final: 0.5589 (tmm) outliers start: 48 outliers final: 32 residues processed: 158 average time/residue: 0.2505 time to fit residues: 61.1426 Evaluate side-chains 149 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 1.533 ------------------------------------------------------------------------------- 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 130 LEU Chi-restraints excluded: chain A residue 158 THR 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 304 ILE 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 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 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 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 1360 THR 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 132 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 51 optimal weight: 6.9990 chunk 23 optimal weight: 4.9990 chunk 12 optimal weight: 0.2980 chunk 96 optimal weight: 5.9990 chunk 142 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 112 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1656 HIS A1704 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.113115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.078234 restraints weight = 31650.309| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 2.85 r_work: 0.3074 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.1924 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= 0.134 Angle : 0.564 8.637 21312 Z= 0.289 Chirality : 0.039 0.235 2477 Planarity : 0.004 0.043 2337 Dihedral : 17.024 156.536 3358 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 3.21 % Allowed : 19.57 % Favored : 77.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.21), residues: 1549 helix: 0.74 (0.19), residues: 746 sheet: -0.65 (0.36), residues: 191 loop : -0.70 (0.26), residues: 612 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1634 HIS 0.003 0.001 HIS A1286 PHE 0.018 0.001 PHE A1473 TYR 0.019 0.001 TYR A1232 ARG 0.004 0.000 ARG A 671 Details of bonding type rmsd hydrogen bonds : bond 0.03978 ( 702) hydrogen bonds : angle 4.56502 ( 1925) covalent geometry : bond 0.00292 (15379) covalent geometry : angle 0.56389 (21312) *********************** 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 168 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 123 time to evaluate : 1.549 Fit side-chains revert: symmetry clash REVERT: A 338 VAL cc_start: 0.8696 (m) cc_final: 0.8480 (m) REVERT: A 504 LEU cc_start: 0.8389 (pp) cc_final: 0.8177 (tt) REVERT: A 934 HIS cc_start: 0.7434 (t-90) cc_final: 0.7054 (t-90) REVERT: A 939 MET cc_start: 0.5402 (tpp) cc_final: 0.4825 (tpp) REVERT: A 1037 TYR cc_start: 0.6646 (t80) cc_final: 0.6040 (t80) REVERT: A 1389 MET cc_start: 0.8052 (mmm) cc_final: 0.7526 (tpp) REVERT: A 1417 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.6921 (mpp) REVERT: A 1604 THR cc_start: 0.4666 (OUTLIER) cc_final: 0.4393 (m) REVERT: A 1647 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8231 (tm-30) REVERT: A 1681 MET cc_start: 0.6006 (ppp) cc_final: 0.5613 (tmm) REVERT: A 1704 GLN cc_start: 0.8541 (tp40) cc_final: 0.8299 (tp-100) outliers start: 45 outliers final: 32 residues processed: 156 average time/residue: 0.3040 time to fit residues: 72.3612 Evaluate side-chains 149 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 1.629 ------------------------------------------------------------------------------- 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 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 322 MET Chi-restraints excluded: chain A residue 332 LYS 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 664 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 672 VAL 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 971 LEU Chi-restraints excluded: chain A residue 1021 LEU 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 1284 LEU Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1360 THR 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 1647 GLU Chi-restraints excluded: chain A residue 1674 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 30 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 7.9990 chunk 137 optimal weight: 0.9980 chunk 161 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 75 optimal weight: 4.9990 chunk 159 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 139 optimal weight: 3.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 313 GLN ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3800 r_free = 0.3800 target = 0.111335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.081255 restraints weight = 32114.445| |-----------------------------------------------------------------------------| r_work (start): 0.3283 rms_B_bonded: 2.42 r_work: 0.3038 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.2108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15379 Z= 0.186 Angle : 0.606 9.288 21312 Z= 0.308 Chirality : 0.040 0.242 2477 Planarity : 0.004 0.044 2337 Dihedral : 16.995 154.393 3358 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 4.07 % Allowed : 19.29 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.21), residues: 1549 helix: 0.66 (0.19), residues: 746 sheet: -0.69 (0.36), residues: 192 loop : -0.77 (0.26), residues: 611 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1634 HIS 0.004 0.001 HIS A1185 PHE 0.019 0.002 PHE A1473 TYR 0.020 0.002 TYR A1232 ARG 0.004 0.000 ARG A 671 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 702) hydrogen bonds : angle 4.65092 ( 1925) covalent geometry : bond 0.00413 (15379) covalent geometry : angle 0.60562 (21312) *********************** 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 173 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 116 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 908 MET cc_start: 0.5457 (mpp) cc_final: 0.4937 (mmp) REVERT: A 934 HIS cc_start: 0.7617 (t-90) cc_final: 0.7227 (t-90) REVERT: A 1037 TYR cc_start: 0.6743 (t80) cc_final: 0.6277 (t80) REVERT: A 1417 MET cc_start: 0.7512 (OUTLIER) cc_final: 0.7147 (mpp) REVERT: A 1604 THR cc_start: 0.4666 (OUTLIER) cc_final: 0.4390 (m) REVERT: A 1647 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8330 (tm-30) REVERT: A 1681 MET cc_start: 0.5980 (ppp) cc_final: 0.5517 (ppp) outliers start: 57 outliers final: 44 residues processed: 159 average time/residue: 0.2417 time to fit residues: 59.1289 Evaluate side-chains 159 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 112 time to evaluate : 1.450 ------------------------------------------------------------------------------- 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 26 VAL Chi-restraints excluded: chain A residue 79 ARG Chi-restraints excluded: chain A residue 128 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 210 ASN Chi-restraints excluded: chain A residue 216 THR Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 265 LEU Chi-restraints excluded: chain A residue 304 ILE 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 515 ILE Chi-restraints excluded: chain A residue 567 LEU Chi-restraints excluded: chain A residue 608 VAL Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 668 LEU Chi-restraints excluded: chain A residue 672 VAL Chi-restraints excluded: chain A residue 711 LEU Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 853 ARG Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 971 LEU Chi-restraints excluded: chain A residue 996 LEU Chi-restraints excluded: chain A residue 1021 LEU 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 1284 LEU Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1360 THR Chi-restraints excluded: chain A residue 1417 MET Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1647 GLU Chi-restraints excluded: chain A residue 1674 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 128 optimal weight: 3.9990 chunk 58 optimal weight: 0.0970 chunk 32 optimal weight: 0.9990 chunk 105 optimal weight: 0.4980 chunk 146 optimal weight: 0.8980 chunk 153 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 chunk 16 optimal weight: 0.0170 chunk 113 optimal weight: 0.0030 chunk 63 optimal weight: 2.9990 overall best weight: 0.3026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 934 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A1191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1250 ASN A1519 HIS A1704 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.114873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.084743 restraints weight = 31676.106| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.43 r_work: 0.3130 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 15379 Z= 0.103 Angle : 0.557 10.092 21312 Z= 0.281 Chirality : 0.038 0.221 2477 Planarity : 0.003 0.042 2337 Dihedral : 17.026 159.225 3358 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.36 % Allowed : 21.36 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.21), residues: 1549 helix: 0.86 (0.19), residues: 748 sheet: -0.54 (0.36), residues: 179 loop : -0.81 (0.25), residues: 622 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A1634 HIS 0.003 0.001 HIS A 576 PHE 0.018 0.001 PHE A1473 TYR 0.016 0.001 TYR A1232 ARG 0.005 0.000 ARG A 671 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 702) hydrogen bonds : angle 4.45378 ( 1925) covalent geometry : bond 0.00214 (15379) covalent geometry : angle 0.55727 (21312) *********************** 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 159 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 1.475 Fit side-chains revert: symmetry clash REVERT: A 338 VAL cc_start: 0.8623 (m) cc_final: 0.8405 (m) REVERT: A 853 ARG cc_start: 0.7824 (OUTLIER) cc_final: 0.7573 (ptp-110) REVERT: A 900 ARG cc_start: 0.7386 (mtt90) cc_final: 0.6491 (mpt90) REVERT: A 908 MET cc_start: 0.5469 (mpp) cc_final: 0.4904 (mmp) REVERT: A 934 HIS cc_start: 0.7552 (t-90) cc_final: 0.7112 (t-90) REVERT: A 1037 TYR cc_start: 0.6684 (t80) cc_final: 0.6247 (t80) REVERT: A 1544 GLU cc_start: 0.8532 (tp30) cc_final: 0.7806 (mt-10) REVERT: A 1602 MET cc_start: 0.5126 (tmm) cc_final: 0.4924 (tmm) REVERT: A 1604 THR cc_start: 0.4659 (OUTLIER) cc_final: 0.4419 (m) REVERT: A 1674 ILE cc_start: 0.6515 (OUTLIER) cc_final: 0.5765 (pt) REVERT: A 1681 MET cc_start: 0.6049 (ppp) cc_final: 0.5512 (ppp) outliers start: 33 outliers final: 18 residues processed: 152 average time/residue: 0.2582 time to fit residues: 60.1557 Evaluate side-chains 137 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 116 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 304 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 608 VAL Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 853 ARG Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1171 VAL Chi-restraints excluded: chain A residue 1176 ILE Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1462 ASN Chi-restraints excluded: chain A residue 1604 THR Chi-restraints excluded: chain A residue 1674 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 36 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 69 optimal weight: 0.0470 chunk 136 optimal weight: 0.4980 chunk 22 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 15 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3846 r_free = 0.3846 target = 0.114503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.084208 restraints weight = 31904.807| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.50 r_work: 0.3110 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15379 Z= 0.112 Angle : 0.565 10.607 21312 Z= 0.285 Chirality : 0.038 0.229 2477 Planarity : 0.003 0.043 2337 Dihedral : 16.966 160.418 3358 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.29 % Allowed : 21.14 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.21), residues: 1549 helix: 0.90 (0.19), residues: 748 sheet: -0.63 (0.36), residues: 185 loop : -0.78 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A1634 HIS 0.004 0.001 HIS A 576 PHE 0.016 0.001 PHE A1473 TYR 0.018 0.001 TYR A1232 ARG 0.004 0.000 ARG A 671 Details of bonding type rmsd hydrogen bonds : bond 0.03719 ( 702) hydrogen bonds : angle 4.47750 ( 1925) covalent geometry : bond 0.00241 (15379) covalent geometry : angle 0.56467 (21312) *********************** 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 156 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 1.504 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 VAL cc_start: 0.8636 (m) cc_final: 0.8417 (m) REVERT: A 536 VAL cc_start: 0.6445 (p) cc_final: 0.6168 (m) REVERT: A 853 ARG cc_start: 0.7774 (OUTLIER) cc_final: 0.7516 (ptp-110) REVERT: A 908 MET cc_start: 0.5465 (mpp) cc_final: 0.4856 (mmp) REVERT: A 934 HIS cc_start: 0.7530 (t-90) cc_final: 0.7083 (t-90) REVERT: A 1037 TYR cc_start: 0.6706 (t80) cc_final: 0.6347 (t80) REVERT: A 1544 GLU cc_start: 0.8534 (tp30) cc_final: 0.7831 (mt-10) REVERT: A 1602 MET cc_start: 0.5147 (tmm) cc_final: 0.4946 (tmm) REVERT: A 1604 THR cc_start: 0.4282 (OUTLIER) cc_final: 0.4079 (m) REVERT: A 1674 ILE cc_start: 0.6497 (OUTLIER) cc_final: 0.5723 (pt) REVERT: A 1681 MET cc_start: 0.5988 (ppp) cc_final: 0.5445 (ppp) outliers start: 32 outliers final: 21 residues processed: 150 average time/residue: 0.2412 time to fit residues: 55.9110 Evaluate side-chains 140 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 116 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 235 THR Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 322 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 608 VAL Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 853 ARG Chi-restraints excluded: chain A residue 942 VAL Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1171 VAL Chi-restraints excluded: chain A residue 1176 ILE Chi-restraints excluded: chain A residue 1254 LEU Chi-restraints excluded: chain A residue 1302 ILE Chi-restraints excluded: chain A residue 1430 LEU 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 1704 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 75 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 96 optimal weight: 7.9990 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 151 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 101 optimal weight: 0.7980 chunk 139 optimal weight: 1.9990 chunk 118 optimal weight: 0.0870 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3849 r_free = 0.3849 target = 0.114813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.084244 restraints weight = 31841.791| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.51 r_work: 0.3117 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15379 Z= 0.115 Angle : 0.570 11.159 21312 Z= 0.286 Chirality : 0.038 0.228 2477 Planarity : 0.003 0.043 2337 Dihedral : 16.960 161.363 3358 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.07 % Allowed : 21.64 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.21), residues: 1549 helix: 0.89 (0.19), residues: 748 sheet: -0.64 (0.36), residues: 185 loop : -0.76 (0.25), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1634 HIS 0.004 0.001 HIS A 576 PHE 0.016 0.001 PHE A1473 TYR 0.017 0.001 TYR A1232 ARG 0.005 0.000 ARG A 671 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 702) hydrogen bonds : angle 4.43864 ( 1925) covalent geometry : bond 0.00251 (15379) covalent geometry : angle 0.56988 (21312) ********************** 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 146 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 117 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 338 VAL cc_start: 0.8628 (m) cc_final: 0.8413 (m) REVERT: A 458 MET cc_start: 0.8419 (tpp) cc_final: 0.8057 (tpt) REVERT: A 536 VAL cc_start: 0.6749 (p) cc_final: 0.6467 (m) REVERT: A 853 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7495 (ptp-110) REVERT: A 900 ARG cc_start: 0.7479 (mtt90) cc_final: 0.6553 (mpt90) REVERT: A 908 MET cc_start: 0.5367 (mpp) cc_final: 0.4771 (mmp) REVERT: A 934 HIS cc_start: 0.7524 (t-90) cc_final: 0.7096 (t-90) REVERT: A 1037 TYR cc_start: 0.6682 (t80) cc_final: 0.6279 (t80) REVERT: A 1544 GLU cc_start: 0.8541 (tp30) cc_final: 0.7843 (mt-10) REVERT: A 1602 MET cc_start: 0.5156 (tmm) cc_final: 0.4953 (tmm) REVERT: A 1604 THR cc_start: 0.4422 (OUTLIER) cc_final: 0.4187 (m) REVERT: A 1674 ILE cc_start: 0.6418 (OUTLIER) cc_final: 0.5778 (pt) REVERT: A 1681 MET cc_start: 0.6042 (ppp) cc_final: 0.5596 (tmm) outliers start: 29 outliers final: 20 residues processed: 140 average time/residue: 0.2491 time to fit residues: 53.9422 Evaluate side-chains 137 residues out of total 1400 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LEU Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 304 ILE Chi-restraints excluded: chain A residue 322 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 608 VAL Chi-restraints excluded: chain A residue 664 VAL Chi-restraints excluded: chain A residue 748 LEU Chi-restraints excluded: chain A residue 757 LEU Chi-restraints excluded: chain A residue 853 ARG Chi-restraints excluded: chain A residue 1021 LEU Chi-restraints excluded: chain A residue 1171 VAL Chi-restraints excluded: chain A residue 1176 ILE 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 1430 LEU 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 1704 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 165 random chunks: chunk 114 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 150 optimal weight: 6.9990 chunk 70 optimal weight: 0.0470 chunk 105 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 137 optimal weight: 0.5980 chunk 159 optimal weight: 10.0000 chunk 103 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.0680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3842 r_free = 0.3842 target = 0.114192 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.083642 restraints weight = 31930.471| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.55 r_work: 0.3098 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15379 Z= 0.130 Angle : 0.575 11.223 21312 Z= 0.289 Chirality : 0.039 0.231 2477 Planarity : 0.004 0.043 2337 Dihedral : 16.943 161.370 3358 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.14 % Allowed : 21.29 % Favored : 76.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.21), residues: 1549 helix: 0.87 (0.19), residues: 753 sheet: -0.63 (0.37), residues: 175 loop : -0.68 (0.25), residues: 621 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A1634 HIS 0.003 0.001 HIS A 576 PHE 0.026 0.001 PHE A 502 TYR 0.017 0.001 TYR A1232 ARG 0.004 0.000 ARG A 671 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 702) hydrogen bonds : angle 4.43563 ( 1925) covalent geometry : bond 0.00288 (15379) covalent geometry : angle 0.57529 (21312) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6580.94 seconds wall clock time: 115 minutes 26.63 seconds (6926.63 seconds total)