Starting phenix.real_space_refine on Wed Aug 5 11:58:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f6l_50228/08_2026/9f6l_50228.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f6l_50228/08_2026/9f6l_50228.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9f6l_50228/08_2026/9f6l_50228.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f6l_50228/08_2026/9f6l_50228.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9f6l_50228/08_2026/9f6l_50228.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f6l_50228/08_2026/9f6l_50228.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.101 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: 7 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 4 7.16 5 P 26 5.49 5 S 53 5.16 5 C 6066 2.51 5 N 1647 2.21 5 O 1841 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9639 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 9098 Classifications: {'peptide': 1118} Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 1059} Chain breaks: 1 Chain: "P" Number of atoms: 285 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 285 Classifications: {'DNA': 14} Link IDs: {'rna3p': 13} Chain: "T" Number of atoms: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 246 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 10 Unusual residues: {' CA': 2, 'SF4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4834 SG CYS A 651 38.003 19.250 53.220 1.00 99.09 S ATOM 4850 SG CYS A 654 36.437 17.492 47.221 1.00 98.87 S ATOM 4916 SG CYS A 663 42.008 16.185 49.846 1.00 97.49 S ATOM 5640 SG CYS A 747 41.526 21.844 48.347 1.00 94.19 S Time building chain proxies: 1.90, per 1000 atoms: 0.20 Number of scatterers: 9639 At special positions: 0 Unit cell: (103.66, 109.5, 109.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 4 26.01 Ca 2 19.99 S 53 16.00 P 26 15.00 O 1841 8.00 N 1647 7.00 C 6066 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: 0.89 Conformation dependent library (CDL) restraints added in 335.1 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1301 " pdb="FE3 SF4 A1301 " - pdb=" SG CYS A 663 " pdb="FE4 SF4 A1301 " - pdb=" SG CYS A 747 " pdb="FE1 SF4 A1301 " - pdb=" SG CYS A 651 " pdb="FE2 SF4 A1301 " - pdb=" SG CYS A 654 " Number of angles added : 12 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 12 sheets defined 48.6% alpha, 17.2% beta 10 base pairs and 20 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 27 through 48 Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 143 through 147 Processing helix chain 'A' and resid 159 through 181 removed outlier: 3.576A pdb=" N LEU A 163 " --> pdb=" O THR A 159 " (cutoff:3.500A) Proline residue: A 172 - end of helix Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.522A pdb=" N SER A 233 " --> pdb=" O HIS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 367 through 379 removed outlier: 3.573A pdb=" N PHE A 371 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 407 through 414 Processing helix chain 'A' and resid 423 through 432 Processing helix chain 'A' and resid 443 through 451 Processing helix chain 'A' and resid 451 through 473 removed outlier: 3.804A pdb=" N LEU A 455 " --> pdb=" O GLN A 451 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER A 461 " --> pdb=" O THR A 457 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N ASP A 462 " --> pdb=" O TYR A 458 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ALA A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ALA A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N TYR A 468 " --> pdb=" O VAL A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 482 removed outlier: 4.014A pdb=" N PHE A 477 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 483 through 485 No H-bonds generated for 'chain 'A' and resid 483 through 485' Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 496 through 512 removed outlier: 3.842A pdb=" N LEU A 500 " --> pdb=" O GLY A 496 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N CYS A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N GLU A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLN A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 571 removed outlier: 4.157A pdb=" N PHE A 567 " --> pdb=" O ASN A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 584 Processing helix chain 'A' and resid 589 through 593 Processing helix chain 'A' and resid 595 through 613 removed outlier: 3.722A pdb=" N VAL A 599 " --> pdb=" O ASN A 595 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL A 613 " --> pdb=" O SER A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 639 Processing helix chain 'A' and resid 647 through 652 removed outlier: 3.825A pdb=" N CYS A 651 " --> pdb=" O ASP A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 693 Processing helix chain 'A' and resid 706 through 710 removed outlier: 3.802A pdb=" N LEU A 710 " --> pdb=" O PHE A 707 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 731 removed outlier: 4.582A pdb=" N ARG A 728 " --> pdb=" O ALA A 724 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N LYS A 729 " --> pdb=" O ASP A 725 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA A 730 " --> pdb=" O TYR A 726 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 786 Processing helix chain 'A' and resid 787 through 818 removed outlier: 4.222A pdb=" N TYR A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLY A 817 " --> pdb=" O ASN A 813 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 854 removed outlier: 4.168A pdb=" N ILE A 843 " --> pdb=" O GLY A 839 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N GLN A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 905 removed outlier: 3.764A pdb=" N LEU A 897 " --> pdb=" O PRO A 893 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 899 " --> pdb=" O ALA A 895 " (cutoff:3.500A) removed outlier: 4.229A pdb=" N MET A 900 " --> pdb=" O MET A 896 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 901 " --> pdb=" O LEU A 897 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 994 removed outlier: 3.772A pdb=" N LYS A 983 " --> pdb=" O LEU A 979 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU A 991 " --> pdb=" O SER A 987 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N LEU A 994 " --> pdb=" O PHE A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1019 removed outlier: 4.269A pdb=" N LYS A1008 " --> pdb=" O GLY A1004 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N VAL A1009 " --> pdb=" O SER A1005 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ALA A1010 " --> pdb=" O VAL A1006 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N ASP A1015 " --> pdb=" O ASP A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1034 Processing helix chain 'A' and resid 1042 through 1047 removed outlier: 3.558A pdb=" N TYR A1046 " --> pdb=" O LEU A1043 " (cutoff:3.500A) Processing helix chain 'A' and resid 1051 through 1065 removed outlier: 3.676A pdb=" N THR A1056 " --> pdb=" O THR A1052 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ALA A1057 " --> pdb=" O SER A1053 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1069 Processing helix chain 'A' and resid 1097 through 1101 Processing helix chain 'A' and resid 1102 through 1114 removed outlier: 3.507A pdb=" N LYS A1112 " --> pdb=" O HIS A1108 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1128 removed outlier: 4.010A pdb=" N ILE A1127 " --> pdb=" O ASP A1123 " (cutoff:3.500A) Processing helix chain 'A' and resid 1129 through 1145 removed outlier: 3.771A pdb=" N TYR A1133 " --> pdb=" O ASP A1129 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N LYS A1143 " --> pdb=" O SER A1139 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE A1144 " --> pdb=" O ALA A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1152 Processing helix chain 'A' and resid 1164 through 1175 Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 52 removed outlier: 7.126A pdb=" N GLU A 51 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N ALA A 97 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ASN A 65 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N ILE A 87 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 5.565A pdb=" N LEU A 63 " --> pdb=" O ILE A 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 136 removed outlier: 6.681A pdb=" N SER A 156 " --> pdb=" O ALA A 129 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL A 131 " --> pdb=" O ARG A 154 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ARG A 154 " --> pdb=" O VAL A 131 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N THR A 133 " --> pdb=" O TYR A 152 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N TYR A 152 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ARG A 150 " --> pdb=" O PRO A 135 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N ASN A 151 " --> pdb=" O THR A 108 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N THR A 108 " --> pdb=" O ASN A 151 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N TYR A 105 " --> pdb=" O ARG A 222 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 320 through 321 removed outlier: 3.606A pdb=" N PHE A 320 " --> pdb=" O PHE A 332 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLY A 304 " --> pdb=" O CYS A 333 " (cutoff:3.500A) removed outlier: 7.982A pdb=" N PHE A 335 " --> pdb=" O GLY A 304 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N LEU A 306 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N GLU A 337 " --> pdb=" O LEU A 306 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR A 308 " --> pdb=" O GLU A 337 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N MET A 294 " --> pdb=" O ASN A 309 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE A 274 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N THR A 361 " --> pdb=" O MET A 405 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 390 through 391 Processing sheet with id=AA5, first strand: chain 'A' and resid 534 through 539 removed outlier: 6.591A pdb=" N GLU A 674 " --> pdb=" O ASP A 535 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLU A 537 " --> pdb=" O ARG A 672 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ARG A 672 " --> pdb=" O GLU A 537 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N TYR A 539 " --> pdb=" O GLN A 670 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N GLN A 670 " --> pdb=" O TYR A 539 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG A 665 " --> pdb=" O ILE A 746 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET A 667 " --> pdb=" O THR A 744 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 545 through 546 removed outlier: 6.727A pdb=" N VAL A 867 " --> pdb=" O PRO A 856 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU A 858 " --> pdb=" O TRP A 865 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N ILE A 622 " --> pdb=" O PRO A 936 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N HIS A 624 " --> pdb=" O ASP A 934 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 550 through 553 removed outlier: 3.633A pdb=" N GLY A 550 " --> pdb=" O LEU A 942 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 558 through 560 Processing sheet with id=AA9, first strand: chain 'A' and resid 875 through 879 removed outlier: 3.715A pdb=" N VAL A 888 " --> pdb=" O PHE A 878 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 907 through 913 removed outlier: 5.778A pdb=" N ASP A 908 " --> pdb=" O GLU A 926 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N GLU A 926 " --> pdb=" O ASP A 908 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 1037 through 1038 removed outlier: 3.704A pdb=" N ARG A1037 " --> pdb=" O CYS A1076 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS A1076 " --> pdb=" O ARG A1037 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 1078 through 1080 435 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 23 hydrogen bonds 46 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 20 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.43: 4234 1.43 - 1.64: 5594 1.64 - 1.85: 78 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 9918 Sorted by residual: bond pdb=" C1' DC T 11 " pdb=" N1 DC T 11 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.29e+01 bond pdb=" C3' DA T 13 " pdb=" C2' DA T 13 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DC P 25 " pdb=" C2' DC P 25 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.12e+01 bond pdb=" C1' DC T 12 " pdb=" N1 DC T 12 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.03e+01 bond pdb=" C3' DC P 31 " pdb=" C2' DC P 31 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.21e+00 ... (remaining 9913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 12198 1.01 - 2.02: 994 2.02 - 3.02: 239 3.02 - 4.03: 68 4.03 - 5.04: 17 Bond angle restraints: 13516 Sorted by residual: angle pdb=" O4' DG T 15 " pdb=" C1' DG T 15 " pdb=" N9 DG T 15 " ideal model delta sigma weight residual 108.00 111.05 -3.05 7.00e-01 2.04e+00 1.90e+01 angle pdb=" O4' DT T 18 " pdb=" C1' DT T 18 " pdb=" N1 DT T 18 " ideal model delta sigma weight residual 108.00 110.99 -2.99 7.00e-01 2.04e+00 1.82e+01 angle pdb=" N3 DT P 26 " pdb=" C4 DT P 26 " pdb=" O4 DT P 26 " ideal model delta sigma weight residual 119.90 122.43 -2.53 6.00e-01 2.78e+00 1.78e+01 angle pdb=" O4' DC T 19 " pdb=" C1' DC T 19 " pdb=" N1 DC T 19 " ideal model delta sigma weight residual 108.00 110.94 -2.94 7.00e-01 2.04e+00 1.77e+01 angle pdb=" O4' DA P 22 " pdb=" C1' DA P 22 " pdb=" C2' DA P 22 " ideal model delta sigma weight residual 105.90 102.56 3.34 8.00e-01 1.56e+00 1.74e+01 ... (remaining 13511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 5289 17.94 - 35.88: 458 35.88 - 53.82: 161 53.82 - 71.76: 33 71.76 - 89.70: 19 Dihedral angle restraints: 5960 sinusoidal: 2661 harmonic: 3299 Sorted by residual: dihedral pdb=" CA PHE A 905 " pdb=" C PHE A 905 " pdb=" N THR A 906 " pdb=" CA THR A 906 " ideal model delta harmonic sigma weight residual -180.00 -150.30 -29.70 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" CA ARG A 52 " pdb=" C ARG A 52 " pdb=" N LEU A 53 " pdb=" CA LEU A 53 " ideal model delta harmonic sigma weight residual 180.00 151.30 28.70 0 5.00e+00 4.00e-02 3.29e+01 dihedral pdb=" CA VAL A1069 " pdb=" C VAL A1069 " pdb=" N LYS A1070 " pdb=" CA LYS A1070 " ideal model delta harmonic sigma weight residual -180.00 -152.41 -27.59 0 5.00e+00 4.00e-02 3.04e+01 ... (remaining 5957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1192 0.053 - 0.107: 214 0.107 - 0.160: 46 0.160 - 0.213: 3 0.213 - 0.267: 1 Chirality restraints: 1456 Sorted by residual: chirality pdb=" C4' DA T 13 " pdb=" C5' DA T 13 " pdb=" O4' DA T 13 " pdb=" C3' DA T 13 " both_signs ideal model delta sigma weight residual False -2.53 -2.27 -0.27 2.00e-01 2.50e+01 1.78e+00 chirality pdb=" C3' DC T 11 " pdb=" C4' DC T 11 " pdb=" O3' DC T 11 " pdb=" C2' DC T 11 " both_signs ideal model delta sigma weight residual False -2.73 -2.55 -0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" CA ARG A 749 " pdb=" N ARG A 749 " pdb=" C ARG A 749 " pdb=" CB ARG A 749 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.45e-01 ... (remaining 1453 not shown) Planarity restraints: 1655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A1138 " -0.018 2.00e-02 2.50e+03 3.50e-02 1.23e+01 pdb=" C GLY A1138 " 0.061 2.00e-02 2.50e+03 pdb=" O GLY A1138 " -0.023 2.00e-02 2.50e+03 pdb=" N SER A1139 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT P 26 " 0.022 2.00e-02 2.50e+03 2.11e-02 1.11e+01 pdb=" N1 DT P 26 " -0.055 2.00e-02 2.50e+03 pdb=" C2 DT P 26 " 0.030 2.00e-02 2.50e+03 pdb=" O2 DT P 26 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DT P 26 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DT P 26 " -0.000 2.00e-02 2.50e+03 pdb=" O4 DT P 26 " -0.000 2.00e-02 2.50e+03 pdb=" C5 DT P 26 " 0.002 2.00e-02 2.50e+03 pdb=" C7 DT P 26 " 0.006 2.00e-02 2.50e+03 pdb=" C6 DT P 26 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 476 " -0.016 2.00e-02 2.50e+03 3.25e-02 1.06e+01 pdb=" C PRO A 476 " 0.056 2.00e-02 2.50e+03 pdb=" O PRO A 476 " -0.021 2.00e-02 2.50e+03 pdb=" N PHE A 477 " -0.019 2.00e-02 2.50e+03 ... (remaining 1652 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 217 2.69 - 3.24: 9703 3.24 - 3.80: 14215 3.80 - 4.35: 18138 4.35 - 4.90: 30515 Nonbonded interactions: 72788 Sorted by model distance: nonbonded pdb=" OP1 DC P 31 " pdb="CA CA A1303 " model vdw 2.141 2.510 nonbonded pdb=" OP1 DC P 31 " pdb="CA CA A1302 " model vdw 2.151 2.510 nonbonded pdb=" O5' DC P 31 " pdb="CA CA A1303 " model vdw 2.202 2.510 nonbonded pdb=" OE2 GLU A 223 " pdb=" NH2 ARG A 231 " model vdw 2.225 3.120 nonbonded pdb=" OG1 THR A 528 " pdb=" OD1 ASP A 530 " model vdw 2.257 3.040 ... (remaining 72783 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.840 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 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 0.058 9922 Z= 0.247 Angle : 0.838 26.651 13528 Z= 0.466 Chirality : 0.044 0.267 1456 Planarity : 0.009 0.084 1655 Dihedral : 16.408 89.702 3824 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 1.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.02 (0.23), residues: 1114 helix: -0.95 (0.20), residues: 452 sheet: 0.49 (0.37), residues: 181 loop : -0.70 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.003 ARG A 167 TYR 0.028 0.005 TYR A 726 PHE 0.023 0.004 PHE A 367 TRP 0.031 0.007 TRP A 865 HIS 0.007 0.002 HIS A 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.25 ( 9918) covalent geometry : angle 0.67449 / 0.46 (13516) hydrogen bonds : bond 0.16312 / 11.08 ( 458) hydrogen bonds : angle 7.54394 / 5.18 ( 1288) metal coordination : bond 0.03458 / 1.73 ( 4) metal coordination : angle 16.71321 / 9.68 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8145 (m-30) cc_final: 0.7335 (p0) REVERT: A 119 PHE cc_start: 0.8582 (t80) cc_final: 0.8381 (t80) REVERT: A 447 MET cc_start: 0.9296 (mpp) cc_final: 0.8456 (mpp) REVERT: A 818 TYR cc_start: 0.8472 (t80) cc_final: 0.8004 (t80) REVERT: A 878 PHE cc_start: 0.7505 (m-80) cc_final: 0.6673 (m-10) REVERT: A 896 MET cc_start: 0.8941 (tmm) cc_final: 0.8626 (tmm) REVERT: A 952 LEU cc_start: 0.9080 (mt) cc_final: 0.8746 (mp) REVERT: A 974 LYS cc_start: 0.7017 (mmtt) cc_final: 0.6770 (tptt) REVERT: A 1087 SER cc_start: 0.8774 (m) cc_final: 0.8543 (p) REVERT: A 1135 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8168 (tm-30) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1215 time to fit residues: 25.7144 Evaluate side-chains 77 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 108 optimal weight: 0.0970 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 7.9990 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 GLN A 342 HIS A 511 HIS A 772 HIS A1163 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.111091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.083636 restraints weight = 22814.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.085996 restraints weight = 13389.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.087529 restraints weight = 9454.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.088650 restraints weight = 7605.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.089190 restraints weight = 6534.945| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9922 Z= 0.154 Angle : 0.716 17.510 13528 Z= 0.357 Chirality : 0.045 0.182 1456 Planarity : 0.005 0.052 1655 Dihedral : 16.023 83.749 1509 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.51 % Allowed : 9.17 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.30 (0.25), residues: 1114 helix: 0.65 (0.23), residues: 465 sheet: 0.60 (0.38), residues: 188 loop : -0.32 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 616 TYR 0.013 0.002 TYR A 397 PHE 0.019 0.002 PHE A 596 TRP 0.013 0.002 TRP A 671 HIS 0.007 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 ( 9918) covalent geometry : angle 0.65845 / 0.36 (13516) hydrogen bonds : bond 0.05732 / 3.83 ( 458) hydrogen bonds : angle 5.48777 / 3.78 ( 1288) metal coordination : bond 0.00541 / 0.27 ( 4) metal coordination : angle 9.49189 / 5.60 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8136 (m-30) cc_final: 0.7480 (p0) REVERT: A 119 PHE cc_start: 0.8534 (t80) cc_final: 0.8316 (t80) REVERT: A 285 PHE cc_start: 0.7608 (OUTLIER) cc_final: 0.6702 (t80) REVERT: A 383 MET cc_start: 0.8773 (tpp) cc_final: 0.8300 (ttm) REVERT: A 405 MET cc_start: 0.9255 (tpp) cc_final: 0.8949 (mmm) REVERT: A 447 MET cc_start: 0.9401 (mpp) cc_final: 0.8432 (mpp) REVERT: A 561 ARG cc_start: 0.8008 (mtm-85) cc_final: 0.7745 (mtt-85) REVERT: A 630 MET cc_start: 0.8454 (ttp) cc_final: 0.8191 (ttp) REVERT: A 896 MET cc_start: 0.9023 (tmm) cc_final: 0.8651 (tmm) REVERT: A 952 LEU cc_start: 0.9150 (mt) cc_final: 0.8918 (mp) REVERT: A 953 LYS cc_start: 0.8614 (mppt) cc_final: 0.8399 (mppt) REVERT: A 1024 MET cc_start: 0.7805 (ttm) cc_final: 0.7299 (ttm) REVERT: A 1039 MET cc_start: 0.8422 (OUTLIER) cc_final: 0.7938 (tpt) REVERT: A 1087 SER cc_start: 0.8789 (m) cc_final: 0.8584 (p) REVERT: A 1135 GLU cc_start: 0.8218 (tm-30) cc_final: 0.8018 (tm-30) REVERT: A 1147 ILE cc_start: 0.8541 (mt) cc_final: 0.8206 (mt) outliers start: 15 outliers final: 9 residues processed: 97 average time/residue: 0.1093 time to fit residues: 14.8082 Evaluate side-chains 81 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 170 ILE Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 688 HIS Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 37 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 29 optimal weight: 0.0970 chunk 82 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 108 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.109549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.082416 restraints weight = 23010.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.084562 restraints weight = 14306.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.086031 restraints weight = 10405.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.087025 restraints weight = 8439.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.087481 restraints weight = 7362.225| |-----------------------------------------------------------------------------| r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9922 Z= 0.142 Angle : 0.619 13.043 13528 Z= 0.322 Chirality : 0.044 0.212 1456 Planarity : 0.005 0.036 1655 Dihedral : 15.806 81.528 1509 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.61 % Allowed : 10.28 % Favored : 88.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.25), residues: 1114 helix: 1.23 (0.24), residues: 465 sheet: 0.56 (0.38), residues: 203 loop : -0.38 (0.29), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 579 TYR 0.013 0.001 TYR A 910 PHE 0.017 0.002 PHE A 596 TRP 0.013 0.001 TRP A 671 HIS 0.004 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 9918) covalent geometry : angle 0.59254 / 0.32 (13516) hydrogen bonds : bond 0.04885 / 3.28 ( 458) hydrogen bonds : angle 5.08202 / 3.49 ( 1288) metal coordination : bond 0.00489 / 0.25 ( 4) metal coordination : angle 5.99356 / 3.66 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7957 (m-30) cc_final: 0.7509 (p0) REVERT: A 119 PHE cc_start: 0.8576 (t80) cc_final: 0.8347 (t80) REVERT: A 285 PHE cc_start: 0.7626 (OUTLIER) cc_final: 0.6705 (t80) REVERT: A 383 MET cc_start: 0.8741 (tpp) cc_final: 0.8394 (ttm) REVERT: A 405 MET cc_start: 0.9292 (tpp) cc_final: 0.9029 (mmm) REVERT: A 447 MET cc_start: 0.9218 (mpp) cc_final: 0.8568 (mpp) REVERT: A 471 MET cc_start: 0.8298 (tpp) cc_final: 0.7417 (mtp) REVERT: A 561 ARG cc_start: 0.7865 (mtm-85) cc_final: 0.7661 (mtt90) REVERT: A 630 MET cc_start: 0.8296 (ttp) cc_final: 0.8065 (ttp) REVERT: A 645 MET cc_start: 0.8633 (mpt) cc_final: 0.8146 (mpp) REVERT: A 688 HIS cc_start: 0.8833 (OUTLIER) cc_final: 0.8617 (t-90) REVERT: A 896 MET cc_start: 0.9001 (tmm) cc_final: 0.8628 (tmm) REVERT: A 1024 MET cc_start: 0.7837 (ttm) cc_final: 0.7398 (ttm) REVERT: A 1039 MET cc_start: 0.7831 (OUTLIER) cc_final: 0.7420 (tpt) REVERT: A 1107 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8327 (mmtm) outliers start: 16 outliers final: 8 residues processed: 91 average time/residue: 0.1118 time to fit residues: 14.2597 Evaluate side-chains 79 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 67 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 688 HIS Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1039 MET Chi-restraints excluded: chain A residue 1107 LYS Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 48 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 83 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 92 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.110652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.083268 restraints weight = 23042.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.085602 restraints weight = 13687.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.087167 restraints weight = 9716.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.088230 restraints weight = 7784.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.088827 restraints weight = 6731.021| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9922 Z= 0.115 Angle : 0.572 13.839 13528 Z= 0.296 Chirality : 0.042 0.206 1456 Planarity : 0.004 0.042 1655 Dihedral : 15.608 79.679 1509 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 1.81 % Allowed : 10.89 % Favored : 87.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.25), residues: 1114 helix: 1.53 (0.24), residues: 466 sheet: 0.65 (0.38), residues: 203 loop : -0.33 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 114 TYR 0.014 0.001 TYR A 397 PHE 0.018 0.001 PHE A 707 TRP 0.011 0.001 TRP A 865 HIS 0.002 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 ( 9918) covalent geometry : angle 0.55668 / 0.30 (13516) hydrogen bonds : bond 0.04337 / 2.90 ( 458) hydrogen bonds : angle 4.76492 / 3.28 ( 1288) metal coordination : bond 0.00281 / 0.14 ( 4) metal coordination : angle 4.45339 / 2.83 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7827 (m-30) cc_final: 0.7537 (p0) REVERT: A 119 PHE cc_start: 0.8525 (t80) cc_final: 0.8319 (t80) REVERT: A 285 PHE cc_start: 0.7546 (OUTLIER) cc_final: 0.6678 (t80) REVERT: A 471 MET cc_start: 0.8591 (tpp) cc_final: 0.8126 (tpp) REVERT: A 630 MET cc_start: 0.8348 (ttp) cc_final: 0.8139 (ttp) REVERT: A 645 MET cc_start: 0.8641 (mpt) cc_final: 0.8187 (mpp) REVERT: A 688 HIS cc_start: 0.8885 (OUTLIER) cc_final: 0.8682 (t-90) REVERT: A 896 MET cc_start: 0.9036 (tmm) cc_final: 0.8710 (tmm) REVERT: A 1024 MET cc_start: 0.7824 (ttm) cc_final: 0.7378 (ttm) REVERT: A 1039 MET cc_start: 0.7719 (tpt) cc_final: 0.7062 (tpt) REVERT: A 1107 LYS cc_start: 0.8607 (OUTLIER) cc_final: 0.8324 (mmtm) outliers start: 18 outliers final: 10 residues processed: 94 average time/residue: 0.0949 time to fit residues: 12.9578 Evaluate side-chains 81 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 68 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 688 HIS Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1107 LYS Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 41 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 44 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.107541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.080140 restraints weight = 23015.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.082422 restraints weight = 13608.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.083920 restraints weight = 9622.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.084974 restraints weight = 7714.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.085572 restraints weight = 6671.265| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9922 Z= 0.183 Angle : 0.614 14.667 13528 Z= 0.321 Chirality : 0.043 0.138 1456 Planarity : 0.005 0.054 1655 Dihedral : 15.595 81.049 1509 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.02 % Allowed : 12.30 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.26), residues: 1114 helix: 1.64 (0.24), residues: 467 sheet: 0.56 (0.38), residues: 209 loop : -0.44 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 114 TYR 0.020 0.002 TYR A 910 PHE 0.018 0.002 PHE A 596 TRP 0.015 0.002 TRP A 369 HIS 0.004 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.18 ( 9918) covalent geometry : angle 0.60310 / 0.32 (13516) hydrogen bonds : bond 0.05001 / 3.38 ( 458) hydrogen bonds : angle 4.83089 / 3.31 ( 1288) metal coordination : bond 0.01391 / 0.71 ( 4) metal coordination : angle 3.89808 / 2.40 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7948 (m-30) cc_final: 0.7553 (p0) REVERT: A 119 PHE cc_start: 0.8680 (t80) cc_final: 0.8385 (t80) REVERT: A 285 PHE cc_start: 0.7445 (OUTLIER) cc_final: 0.6699 (t80) REVERT: A 383 MET cc_start: 0.8899 (ttm) cc_final: 0.8661 (ttm) REVERT: A 447 MET cc_start: 0.9308 (OUTLIER) cc_final: 0.8548 (mtp) REVERT: A 471 MET cc_start: 0.8812 (tpp) cc_final: 0.8276 (tpp) REVERT: A 645 MET cc_start: 0.8660 (mpt) cc_final: 0.8301 (mpp) REVERT: A 896 MET cc_start: 0.9104 (tmm) cc_final: 0.8771 (tmm) REVERT: A 1039 MET cc_start: 0.7832 (tpt) cc_final: 0.7176 (tpt) REVERT: A 1107 LYS cc_start: 0.8632 (OUTLIER) cc_final: 0.8340 (mmtm) outliers start: 20 outliers final: 12 residues processed: 87 average time/residue: 0.0731 time to fit residues: 9.2570 Evaluate side-chains 81 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 66 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 514 ILE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 989 VAL Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1107 LYS Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 100 optimal weight: 0.6980 chunk 112 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 93 optimal weight: 1.9990 chunk 103 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 980 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.109229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.082780 restraints weight = 22847.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.085165 restraints weight = 14039.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.086180 restraints weight = 9379.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.086627 restraints weight = 7618.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.086917 restraints weight = 7322.695| |-----------------------------------------------------------------------------| r_work (final): 0.3198 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9922 Z= 0.129 Angle : 0.558 14.067 13528 Z= 0.292 Chirality : 0.041 0.137 1456 Planarity : 0.004 0.045 1655 Dihedral : 15.564 81.318 1509 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 1.51 % Allowed : 13.71 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.05 (0.26), residues: 1114 helix: 1.82 (0.24), residues: 467 sheet: 0.62 (0.38), residues: 203 loop : -0.45 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 114 TYR 0.014 0.001 TYR A 910 PHE 0.014 0.001 PHE A 596 TRP 0.013 0.001 TRP A 369 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.13 ( 9918) covalent geometry : angle 0.54916 / 0.29 (13516) hydrogen bonds : bond 0.04432 / 2.97 ( 458) hydrogen bonds : angle 4.61865 / 3.17 ( 1288) metal coordination : bond 0.00472 / 0.24 ( 4) metal coordination : angle 3.34746 / 2.05 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 74 time to evaluate : 0.233 Fit side-chains revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7889 (m-30) cc_final: 0.7558 (p0) REVERT: A 119 PHE cc_start: 0.8594 (t80) cc_final: 0.8334 (t80) REVERT: A 285 PHE cc_start: 0.7405 (OUTLIER) cc_final: 0.6692 (t80) REVERT: A 447 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8372 (mtp) REVERT: A 460 VAL cc_start: 0.9157 (t) cc_final: 0.8856 (p) REVERT: A 471 MET cc_start: 0.8808 (tpp) cc_final: 0.8184 (tpp) REVERT: A 645 MET cc_start: 0.8657 (mpt) cc_final: 0.8309 (mpp) REVERT: A 896 MET cc_start: 0.9084 (tmm) cc_final: 0.8769 (tmm) REVERT: A 1039 MET cc_start: 0.7634 (tpt) cc_final: 0.6984 (tpt) REVERT: A 1107 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8252 (mmtm) outliers start: 15 outliers final: 9 residues processed: 86 average time/residue: 0.0770 time to fit residues: 9.3905 Evaluate side-chains 81 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1107 LYS Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 48 optimal weight: 7.9990 chunk 90 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 980 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.109316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.082911 restraints weight = 22742.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.085213 restraints weight = 14112.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.086201 restraints weight = 9487.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.086742 restraints weight = 7737.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.086881 restraints weight = 7144.025| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9922 Z= 0.135 Angle : 0.558 14.032 13528 Z= 0.292 Chirality : 0.041 0.135 1456 Planarity : 0.004 0.046 1655 Dihedral : 15.484 81.393 1509 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.22 % Allowed : 12.90 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.26), residues: 1114 helix: 1.91 (0.24), residues: 468 sheet: 0.52 (0.37), residues: 210 loop : -0.46 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A1077 TYR 0.015 0.001 TYR A 910 PHE 0.013 0.002 PHE A 596 TRP 0.013 0.001 TRP A 369 HIS 0.004 0.001 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 9918) covalent geometry : angle 0.54907 / 0.29 (13516) hydrogen bonds : bond 0.04361 / 2.92 ( 458) hydrogen bonds : angle 4.54526 / 3.11 ( 1288) metal coordination : bond 0.00625 / 0.32 ( 4) metal coordination : angle 3.38649 / 2.03 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 83 ASP cc_start: 0.8007 (m-30) cc_final: 0.7681 (p0) REVERT: A 119 PHE cc_start: 0.8602 (t80) cc_final: 0.8381 (t80) REVERT: A 285 PHE cc_start: 0.7372 (OUTLIER) cc_final: 0.6676 (t80) REVERT: A 294 MET cc_start: 0.8139 (mtp) cc_final: 0.7696 (mpp) REVERT: A 447 MET cc_start: 0.9192 (OUTLIER) cc_final: 0.8344 (mtp) REVERT: A 471 MET cc_start: 0.8820 (tpp) cc_final: 0.8157 (tpp) REVERT: A 645 MET cc_start: 0.8738 (mpt) cc_final: 0.8409 (mpp) REVERT: A 896 MET cc_start: 0.9079 (tmm) cc_final: 0.8761 (tmm) REVERT: A 1107 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8255 (mmtm) outliers start: 22 outliers final: 12 residues processed: 92 average time/residue: 0.0888 time to fit residues: 11.8668 Evaluate side-chains 85 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 70 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 610 LEU Chi-restraints excluded: chain A residue 688 HIS Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1107 LYS Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 20 optimal weight: 5.9990 chunk 90 optimal weight: 0.0570 chunk 106 optimal weight: 2.9990 chunk 8 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 10 optimal weight: 0.2980 chunk 5 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 108 optimal weight: 0.7980 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 980 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.111039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.084503 restraints weight = 22646.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.086930 restraints weight = 13914.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.087919 restraints weight = 9247.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.088294 restraints weight = 7791.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.088546 restraints weight = 7210.389| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 9922 Z= 0.107 Angle : 0.544 11.205 13528 Z= 0.284 Chirality : 0.041 0.167 1456 Planarity : 0.004 0.046 1655 Dihedral : 15.359 80.486 1509 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.31 % Allowed : 14.42 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.26), residues: 1114 helix: 2.06 (0.24), residues: 467 sheet: 0.58 (0.37), residues: 212 loop : -0.44 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A1077 TYR 0.011 0.001 TYR A 827 PHE 0.011 0.001 PHE A 596 TRP 0.013 0.001 TRP A 369 HIS 0.002 0.001 HIS A 144 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 ( 9918) covalent geometry : angle 0.53672 / 0.28 (13516) hydrogen bonds : bond 0.03790 / 2.51 ( 458) hydrogen bonds : angle 4.32866 / 2.96 ( 1288) metal coordination : bond 0.00266 / 0.13 ( 4) metal coordination : angle 3.06404 / 1.88 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7928 (m-30) cc_final: 0.7664 (p0) REVERT: A 285 PHE cc_start: 0.7469 (OUTLIER) cc_final: 0.6930 (t80) REVERT: A 294 MET cc_start: 0.8124 (mtp) cc_final: 0.7688 (mpp) REVERT: A 299 MET cc_start: 0.8446 (tpp) cc_final: 0.8020 (tpp) REVERT: A 447 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8369 (mtt) REVERT: A 471 MET cc_start: 0.8889 (tpp) cc_final: 0.8249 (tpp) REVERT: A 645 MET cc_start: 0.8827 (mpt) cc_final: 0.8524 (mpp) REVERT: A 896 MET cc_start: 0.9056 (tmm) cc_final: 0.8745 (tmm) REVERT: A 940 MET cc_start: 0.8216 (ttp) cc_final: 0.7861 (ttp) REVERT: A 1107 LYS cc_start: 0.8534 (OUTLIER) cc_final: 0.8245 (mmtm) outliers start: 13 outliers final: 9 residues processed: 91 average time/residue: 0.0760 time to fit residues: 10.4739 Evaluate side-chains 83 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 71 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 276 ILE Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 815 PHE Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1107 LYS Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 78 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 64 optimal weight: 0.0060 chunk 83 optimal weight: 0.6980 chunk 106 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 10 optimal weight: 0.9980 chunk 98 optimal weight: 3.9990 chunk 101 optimal weight: 7.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 980 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.111011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.083666 restraints weight = 22638.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.085925 restraints weight = 13818.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.087419 restraints weight = 9986.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.088419 restraints weight = 8100.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.088905 restraints weight = 7075.242| |-----------------------------------------------------------------------------| r_work (final): 0.3243 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9922 Z= 0.108 Angle : 0.550 13.082 13528 Z= 0.285 Chirality : 0.041 0.193 1456 Planarity : 0.004 0.045 1655 Dihedral : 15.255 80.164 1509 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.21 % Allowed : 14.92 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.26), residues: 1114 helix: 2.14 (0.24), residues: 467 sheet: 0.55 (0.37), residues: 212 loop : -0.42 (0.30), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1136 TYR 0.011 0.001 TYR A 754 PHE 0.034 0.001 PHE A 119 TRP 0.011 0.001 TRP A 369 HIS 0.002 0.000 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00224 / 0.11 ( 9918) covalent geometry : angle 0.54221 / 0.29 (13516) hydrogen bonds : bond 0.03795 / 2.54 ( 458) hydrogen bonds : angle 4.28963 / 2.93 ( 1288) metal coordination : bond 0.00268 / 0.13 ( 4) metal coordination : angle 3.14695 / 1.93 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 221 MET cc_start: 0.9043 (ptt) cc_final: 0.8309 (ppp) REVERT: A 285 PHE cc_start: 0.7453 (OUTLIER) cc_final: 0.6942 (t80) REVERT: A 294 MET cc_start: 0.8037 (mtp) cc_final: 0.7709 (mpp) REVERT: A 447 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8310 (mtt) REVERT: A 464 VAL cc_start: 0.9154 (OUTLIER) cc_final: 0.8952 (p) REVERT: A 471 MET cc_start: 0.8828 (tpp) cc_final: 0.8244 (tpp) REVERT: A 645 MET cc_start: 0.8832 (mpt) cc_final: 0.8531 (mpp) REVERT: A 896 MET cc_start: 0.9015 (tmm) cc_final: 0.8719 (tmm) REVERT: A 940 MET cc_start: 0.8325 (ttp) cc_final: 0.7994 (ttp) REVERT: A 1107 LYS cc_start: 0.8642 (OUTLIER) cc_final: 0.8329 (mmtm) outliers start: 12 outliers final: 7 residues processed: 87 average time/residue: 0.0760 time to fit residues: 10.0308 Evaluate side-chains 86 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1107 LYS Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 5 optimal weight: 0.8980 chunk 88 optimal weight: 0.0000 chunk 40 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 63 optimal weight: 8.9990 chunk 31 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 80 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 56 optimal weight: 0.9980 overall best weight: 0.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 379 HIS A 980 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.111281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.083786 restraints weight = 22545.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.086041 restraints weight = 13670.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.087572 restraints weight = 9861.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.088578 restraints weight = 7957.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.089169 restraints weight = 6930.005| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9922 Z= 0.109 Angle : 0.544 11.981 13528 Z= 0.281 Chirality : 0.041 0.181 1456 Planarity : 0.004 0.045 1655 Dihedral : 15.139 79.906 1509 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.31 % Allowed : 14.72 % Favored : 83.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.26), residues: 1114 helix: 2.20 (0.24), residues: 466 sheet: 0.45 (0.36), residues: 216 loop : -0.43 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 37 TYR 0.010 0.001 TYR A 298 PHE 0.024 0.001 PHE A 119 TRP 0.010 0.001 TRP A 369 HIS 0.002 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00229 / 0.11 ( 9918) covalent geometry : angle 0.53661 / 0.28 (13516) hydrogen bonds : bond 0.03663 / 2.44 ( 458) hydrogen bonds : angle 4.23901 / 2.90 ( 1288) metal coordination : bond 0.00298 / 0.15 ( 4) metal coordination : angle 3.12666 / 1.90 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.283 Fit side-chains revert: symmetry clash REVERT: A 221 MET cc_start: 0.9046 (ptt) cc_final: 0.8288 (ppp) REVERT: A 285 PHE cc_start: 0.7418 (OUTLIER) cc_final: 0.6944 (t80) REVERT: A 294 MET cc_start: 0.8064 (mtp) cc_final: 0.7692 (mpp) REVERT: A 447 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8327 (mtt) REVERT: A 464 VAL cc_start: 0.9169 (OUTLIER) cc_final: 0.8968 (p) REVERT: A 471 MET cc_start: 0.8876 (tpp) cc_final: 0.8279 (tpp) REVERT: A 645 MET cc_start: 0.8810 (mpt) cc_final: 0.8500 (mpp) REVERT: A 896 MET cc_start: 0.9005 (tmm) cc_final: 0.8650 (tmm) REVERT: A 940 MET cc_start: 0.8377 (ttp) cc_final: 0.8054 (ttp) REVERT: A 1039 MET cc_start: 0.7685 (tpt) cc_final: 0.7252 (tpt) REVERT: A 1107 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.8329 (mmtm) outliers start: 13 outliers final: 8 residues processed: 86 average time/residue: 0.0770 time to fit residues: 10.0047 Evaluate side-chains 88 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 106 ILE Chi-restraints excluded: chain A residue 240 VAL Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 447 MET Chi-restraints excluded: chain A residue 460 VAL Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 979 LEU Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1107 LYS Chi-restraints excluded: chain A residue 1155 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 23 optimal weight: 0.0970 chunk 32 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 5.9990 chunk 15 optimal weight: 0.0870 chunk 72 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 chunk 61 optimal weight: 9.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.9760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 980 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.114565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.086372 restraints weight = 23258.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.088816 restraints weight = 13552.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.090448 restraints weight = 9566.544| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.091403 restraints weight = 7673.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.092162 restraints weight = 6734.514| |-----------------------------------------------------------------------------| r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9922 Z= 0.117 Angle : 0.559 13.420 13528 Z= 0.287 Chirality : 0.041 0.191 1456 Planarity : 0.004 0.045 1655 Dihedral : 15.037 79.881 1509 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.21 % Allowed : 15.12 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.28 (0.26), residues: 1114 helix: 2.22 (0.24), residues: 467 sheet: 0.33 (0.36), residues: 218 loop : -0.37 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 37 TYR 0.012 0.001 TYR A 910 PHE 0.013 0.001 PHE A1122 TRP 0.011 0.001 TRP A 671 HIS 0.002 0.001 HIS A 404 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.12 ( 9918) covalent geometry : angle 0.55067 / 0.29 (13516) hydrogen bonds : bond 0.03727 / 2.48 ( 458) hydrogen bonds : angle 4.22578 / 2.89 ( 1288) metal coordination : bond 0.00462 / 0.23 ( 4) metal coordination : angle 3.21692 / 1.91 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1373.22 seconds wall clock time: 24 minutes 26.17 seconds (1466.17 seconds total)