Starting phenix.real_space_refine on Thu Jul 2 19:01:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f6j_50226/07_2026/9f6j_50226.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f6j_50226/07_2026/9f6j_50226.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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9f6j_50226/07_2026/9f6j_50226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f6j_50226/07_2026/9f6j_50226.map" model { file = "/net/cci-nas-00/data/ceres_data/9f6j_50226/07_2026/9f6j_50226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f6j_50226/07_2026/9f6j_50226.cif" } 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= 0.004 sd= 0.096 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 4 7.16 5 P 32 5.49 5 S 53 5.16 5 C 6123 2.51 5 N 1662 2.21 5 O 1877 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9751 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9091 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 9091 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: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 367 Classifications: {'DNA': 18} Link IDs: {'rna3p': 17} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'SF4': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4827 SG CYS A 651 39.716 19.391 53.715 1.00 58.40 S ATOM 4843 SG CYS A 654 37.813 17.520 48.017 1.00 56.47 S ATOM 4909 SG CYS A 663 43.920 16.788 49.787 1.00 48.76 S ATOM 5633 SG CYS A 747 42.860 21.938 48.845 1.00 46.18 S Time building chain proxies: 1.83, per 1000 atoms: 0.19 Number of scatterers: 9751 At special positions: 0 Unit cell: (105.12, 108.04, 110.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 4 26.01 S 53 16.00 P 32 15.00 O 1877 8.00 N 1662 7.00 C 6123 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: 0.77 Conformation dependent library (CDL) restraints added in 223.8 milliseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1301 " pdb="FE3 SF4 A1301 " - pdb=" SG CYS A 663 " pdb="FE2 SF4 A1301 " - pdb=" SG CYS A 654 " pdb="FE1 SF4 A1301 " - pdb=" SG CYS A 651 " pdb="FE4 SF4 A1301 " - pdb=" SG CYS A 747 " 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: 45 helices and 12 sheets defined 49.6% alpha, 16.0% beta 13 base pairs and 27 stacking pairs defined. Time for finding SS restraints: 0.94 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 171 Processing helix chain 'A' and resid 171 through 181 removed outlier: 4.030A pdb=" N LYS A 175 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N LYS A 176 " --> pdb=" O PRO A 172 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN A 177 " --> pdb=" O ALA A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 236 Processing helix chain 'A' and resid 339 through 355 removed outlier: 3.675A pdb=" N GLU A 353 " --> pdb=" O GLU A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 379 removed outlier: 3.538A pdb=" N PHE A 371 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL A 372 " --> pdb=" O ASP A 368 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N HIS A 379 " --> pdb=" O ARG A 375 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 407 through 415 removed outlier: 3.681A pdb=" N SER A 415 " --> pdb=" O VAL A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 422 Processing helix chain 'A' and resid 423 through 433 Processing helix chain 'A' and resid 440 through 442 No H-bonds generated for 'chain 'A' and resid 440 through 442' Processing helix chain 'A' and resid 443 through 451 Processing helix chain 'A' and resid 452 through 473 removed outlier: 3.806A pdb=" N VAL A 460 " --> pdb=" O ALA A 456 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N SER A 461 " --> pdb=" O THR A 457 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ASP A 462 " --> pdb=" O TYR A 458 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N ALA A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N ALA A 465 " --> pdb=" O SER A 461 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR A 466 " --> pdb=" O ASP A 462 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 483 removed outlier: 4.144A pdb=" N PHE A 477 " --> pdb=" O TYR A 473 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N PHE A 479 " --> pdb=" O HIS A 475 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N THR A 483 " --> pdb=" O PHE A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 495 Processing helix chain 'A' and resid 496 through 512 removed outlier: 3.984A pdb=" N VAL A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 565 through 572 Processing helix chain 'A' and resid 573 through 584 removed outlier: 3.891A pdb=" N ALA A 581 " --> pdb=" O THR A 577 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 593 removed outlier: 3.820A pdb=" N VAL A 593 " --> pdb=" O VAL A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 613 removed outlier: 3.537A pdb=" N VAL A 599 " --> pdb=" O ASN A 595 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS A 600 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 3.594A 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: 3.772A pdb=" N CYS A 651 " --> pdb=" O ASP A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 691 removed outlier: 3.557A pdb=" N ARG A 685 " --> pdb=" O SER A 681 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N LEU A 690 " --> pdb=" O ILE A 686 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU A 691 " --> pdb=" O GLN A 687 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 710 No H-bonds generated for 'chain 'A' and resid 708 through 710' Processing helix chain 'A' and resid 711 through 731 removed outlier: 3.843A pdb=" N LYS A 729 " --> pdb=" O ASP A 725 " (cutoff:3.500A) Processing helix chain 'A' and resid 752 through 786 Processing helix chain 'A' and resid 787 through 819 removed outlier: 4.338A pdb=" N TYR A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY A 817 " --> pdb=" O ASN A 813 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N VAL A 819 " --> pdb=" O PHE A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 854 removed outlier: 3.979A pdb=" N CYS A 836 " --> pdb=" O ALA A 832 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY A 839 " --> pdb=" O VAL A 835 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG A 847 " --> pdb=" O ILE A 843 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ILE A 850 " --> pdb=" O ALA A 846 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLN A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ILE A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 906 removed outlier: 3.814A pdb=" N LEU A 897 " --> pdb=" O PRO A 893 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE A 899 " --> pdb=" O ALA A 895 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N MET A 900 " --> pdb=" O MET A 896 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR A 906 " --> pdb=" O LYS A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 971 through 975 Processing helix chain 'A' and resid 979 through 994 removed outlier: 3.619A pdb=" N GLU A 991 " --> pdb=" O SER A 987 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N LEU A 994 " --> pdb=" O PHE A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1020 removed outlier: 4.184A pdb=" N LYS A1008 " --> pdb=" O GLY A1004 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N VAL A1009 " --> pdb=" O SER A1005 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA A1010 " --> pdb=" O VAL A1006 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TYR A1012 " --> pdb=" O LYS A1008 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N TRP A1013 " --> pdb=" O VAL A1009 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL A1016 " --> pdb=" O TYR A1012 " (cutoff:3.500A) Processing helix chain 'A' and resid 1027 through 1034 removed outlier: 3.926A pdb=" N GLU A1031 " --> pdb=" O SER A1027 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1047 Processing helix chain 'A' and resid 1051 through 1065 removed outlier: 3.552A pdb=" N PHE A1063 " --> pdb=" O ARG A1059 " (cutoff:3.500A) Processing helix chain 'A' and resid 1065 through 1070 removed outlier: 4.730A pdb=" N VAL A1069 " --> pdb=" O GLY A1065 " (cutoff:3.500A) Processing helix chain 'A' and resid 1088 through 1091 Processing helix chain 'A' and resid 1097 through 1101 Processing helix chain 'A' and resid 1102 through 1114 Processing helix chain 'A' and resid 1123 through 1128 Processing helix chain 'A' and resid 1129 through 1145 removed outlier: 3.730A pdb=" N TYR A1133 " --> pdb=" O ASP A1129 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER A1139 " --> pdb=" O GLU A1135 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLN A1142 " --> pdb=" O GLY A1138 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LYS A1143 " --> pdb=" O SER A1139 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ILE A1144 " --> pdb=" O ALA A1140 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1151 Processing helix chain 'A' and resid 1164 through 1175 removed outlier: 3.636A pdb=" N ASN A1175 " --> pdb=" O LEU A1171 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 52 removed outlier: 6.839A pdb=" N GLU A 51 " --> pdb=" O LYS A 95 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N ALA A 97 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN A 65 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ILE A 87 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LEU A 63 " --> pdb=" O ILE A 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 130 through 136 removed outlier: 3.720A pdb=" N ASP A 220 " --> pdb=" O ALA A 107 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 337 removed outlier: 4.344A pdb=" N THR A 308 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 4.952A pdb=" N GLU A 337 " --> pdb=" O THR A 308 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N MET A 294 " --> pdb=" O ASN A 309 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ALA A 277 " --> pdb=" O MET A 294 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ILE A 296 " --> pdb=" O ALA A 275 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N ALA A 275 " --> pdb=" O ILE A 296 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N TYR A 298 " --> pdb=" O ALA A 273 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ALA A 273 " --> pdb=" O TYR A 298 " (cutoff:3.500A) removed outlier: 4.767A pdb=" N ILE A 300 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 7.463A pdb=" N VAL A 271 " --> pdb=" O ILE A 300 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N LEU A 272 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 3.537A 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 536 removed outlier: 6.765A pdb=" N GLU A 674 " --> pdb=" O ASP A 535 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR A 745 " --> pdb=" O VAL A 646 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 550 through 553 removed outlier: 3.547A pdb=" N ALA A 939 " --> pdb=" O PHE A 959 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 558 through 561 Processing sheet with id=AA8, first strand: chain 'A' and resid 855 through 859 removed outlier: 3.592A pdb=" N ARG A 855 " --> pdb=" O VAL A 867 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N TRP A 865 " --> pdb=" O LEU A 857 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N LEU A 859 " --> pdb=" O GLY A 863 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N GLY A 863 " --> pdb=" O LEU A 859 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 694 through 695 Processing sheet with id=AB1, first strand: chain 'A' and resid 875 through 879 Processing sheet with id=AB2, first strand: chain 'A' and resid 907 through 913 removed outlier: 5.848A pdb=" N ASP A 908 " --> pdb=" O GLU A 926 " (cutoff:3.500A) removed outlier: 7.228A pdb=" N GLU A 926 " --> pdb=" O ASP A 908 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1078 through 1080 429 hydrogen bonds defined for protein. 1224 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 31 hydrogen bonds 62 hydrogen bond angles 0 basepair planarities 13 basepair parallelities 27 stacking parallelities Total time for adding SS restraints: 1.83 Time building geometry restraints manager: 1.00 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: 4293 1.43 - 1.64: 5662 1.64 - 1.85: 78 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 10045 Sorted by residual: bond pdb=" C3' DA P 29 " pdb=" C2' DA P 29 " ideal model delta sigma weight residual 1.516 1.555 -0.039 8.00e-03 1.56e+04 2.42e+01 bond pdb=" C3' DG P 28 " pdb=" C2' DG P 28 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.13e+01 bond pdb=" C3' DA P 21 " pdb=" C2' DA P 21 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.40e+00 bond pdb=" C1' DT T 7 " pdb=" N1 DT T 7 " ideal model delta sigma weight residual 1.468 1.510 -0.042 1.40e-02 5.10e+03 9.00e+00 bond pdb=" C3' DA T 13 " pdb=" C2' DA T 13 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.29e+00 ... (remaining 10040 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.33: 12955 1.33 - 2.66: 634 2.66 - 3.99: 103 3.99 - 5.32: 16 5.32 - 6.65: 6 Bond angle restraints: 13714 Sorted by residual: angle pdb=" C4' DA P 29 " pdb=" O4' DA P 29 " pdb=" C1' DA P 29 " ideal model delta sigma weight residual 110.10 105.58 4.52 1.00e+00 1.00e+00 2.04e+01 angle pdb=" N3 DT P 30 " pdb=" C4 DT P 30 " pdb=" O4 DT P 30 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT T 18 " pdb=" C4 DT T 18 " pdb=" O4 DT T 18 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT T 17 " pdb=" C4 DT T 17 " pdb=" O4 DT T 17 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.74e+01 angle pdb=" C4' DG T 15 " pdb=" O4' DG T 15 " pdb=" C1' DG T 15 " ideal model delta sigma weight residual 110.10 105.93 4.17 1.00e+00 1.00e+00 1.74e+01 ... (remaining 13709 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 5358 17.79 - 35.57: 472 35.57 - 53.36: 127 53.36 - 71.15: 44 71.15 - 88.93: 18 Dihedral angle restraints: 6019 sinusoidal: 2720 harmonic: 3299 Sorted by residual: dihedral pdb=" CA GLU A 438 " pdb=" C GLU A 438 " pdb=" N LEU A 439 " pdb=" CA LEU A 439 " ideal model delta harmonic sigma weight residual 180.00 151.87 28.13 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA GLU A 337 " pdb=" C GLU A 337 " pdb=" N PRO A 338 " pdb=" CA PRO A 338 " ideal model delta harmonic sigma weight residual -180.00 -153.57 -26.43 0 5.00e+00 4.00e-02 2.79e+01 dihedral pdb=" CA PRO A1025 " pdb=" C PRO A1025 " pdb=" N ASP A1026 " pdb=" CA ASP A1026 " ideal model delta harmonic sigma weight residual -180.00 -156.14 -23.86 0 5.00e+00 4.00e-02 2.28e+01 ... (remaining 6016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1161 0.048 - 0.097: 243 0.097 - 0.145: 61 0.145 - 0.193: 10 0.193 - 0.241: 5 Chirality restraints: 1480 Sorted by residual: chirality pdb=" C3' DG P 20 " pdb=" C4' DG P 20 " pdb=" O3' DG P 20 " pdb=" C2' DG P 20 " both_signs ideal model delta sigma weight residual False -2.73 -2.49 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" C3' DA P 22 " pdb=" C4' DA P 22 " pdb=" O3' DA P 22 " pdb=" C2' DA P 22 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" C3' DT T 18 " pdb=" C4' DT T 18 " pdb=" O3' DT T 18 " pdb=" C2' DT T 18 " both_signs ideal model delta sigma weight residual False -2.73 -2.53 -0.20 2.00e-01 2.50e+01 9.64e-01 ... (remaining 1477 not shown) Planarity restraints: 1659 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR A 892 " -0.016 2.00e-02 2.50e+03 2.60e-02 1.35e+01 pdb=" CG TYR A 892 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR A 892 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TYR A 892 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR A 892 " 0.038 2.00e-02 2.50e+03 pdb=" CE2 TYR A 892 " 0.019 2.00e-02 2.50e+03 pdb=" CZ TYR A 892 " 0.025 2.00e-02 2.50e+03 pdb=" OH TYR A 892 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 671 " -0.033 2.00e-02 2.50e+03 1.87e-02 8.77e+00 pdb=" CG TRP A 671 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP A 671 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP A 671 " 0.016 2.00e-02 2.50e+03 pdb=" NE1 TRP A 671 " 0.018 2.00e-02 2.50e+03 pdb=" CE2 TRP A 671 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP A 671 " 0.026 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 671 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 671 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 671 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 310 " -0.223 9.50e-02 1.11e+02 1.01e-01 7.78e+00 pdb=" NE ARG A 310 " 0.021 2.00e-02 2.50e+03 pdb=" CZ ARG A 310 " -0.020 2.00e-02 2.50e+03 pdb=" NH1 ARG A 310 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG A 310 " -0.001 2.00e-02 2.50e+03 ... (remaining 1656 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1935 2.78 - 3.31: 9257 3.31 - 3.84: 14978 3.84 - 4.37: 17391 4.37 - 4.90: 29728 Nonbonded interactions: 73289 Sorted by model distance: nonbonded pdb=" OE1 GLU A 396 " pdb=" NH1 ARG A 494 " model vdw 2.253 3.120 nonbonded pdb=" ND2 ASN A 177 " pdb=" O ASP A 216 " model vdw 2.319 3.120 nonbonded pdb=" OG SER A 643 " pdb=" OE2 GLU A 750 " model vdw 2.327 3.040 nonbonded pdb=" OH TYR A 100 " pdb=" OD2 ASP A 235 " model vdw 2.333 3.040 nonbonded pdb=" OD1 ASP A 725 " pdb=" NH2 ARG A 728 " model vdw 2.339 3.120 ... (remaining 73284 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: 0.710 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: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.910 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 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 0.047 10049 Z= 0.247 Angle : 0.922 47.045 13726 Z= 0.459 Chirality : 0.045 0.241 1480 Planarity : 0.009 0.101 1659 Dihedral : 16.082 88.933 3883 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 1.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % 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: -1.09 (0.23), residues: 1114 helix: -0.85 (0.21), residues: 453 sheet: -0.15 (0.32), residues: 202 loop : -0.63 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.022 0.003 ARG A 310 TYR 0.050 0.005 TYR A 892 PHE 0.028 0.004 PHE A 119 TRP 0.033 0.006 TRP A 671 HIS 0.011 0.002 HIS A 708 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.25 (10045) covalent geometry : angle 0.66807 / 0.46 (13714) hydrogen bonds : bond 0.14756 / 8.95 ( 460) hydrogen bonds : angle 7.19942 / 5.14 ( 1286) metal coordination : bond 0.03407 / 1.71 ( 4) metal coordination : angle 21.50317 / 15.67 ( 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 194 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.233 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.8885 (p90) cc_final: 0.8471 (p90) REVERT: A 157 PHE cc_start: 0.8835 (m-80) cc_final: 0.8392 (m-10) REVERT: A 397 TYR cc_start: 0.7417 (m-80) cc_final: 0.5931 (m-10) REVERT: A 416 TYR cc_start: 0.7901 (m-80) cc_final: 0.7687 (m-10) REVERT: A 601 ASP cc_start: 0.7940 (m-30) cc_final: 0.7714 (t0) REVERT: A 688 HIS cc_start: 0.8493 (t-170) cc_final: 0.8241 (m170) REVERT: A 791 VAL cc_start: 0.8192 (t) cc_final: 0.7712 (p) REVERT: A 818 TYR cc_start: 0.8571 (t80) cc_final: 0.7131 (t80) REVERT: A 857 LEU cc_start: 0.9260 (mt) cc_final: 0.8912 (mt) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.1062 time to fit residues: 27.0064 Evaluate side-chains 85 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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: 1.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.0570 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 0.1980 chunk 62 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 1.9990 overall best weight: 1.2504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 229 HIS A 394 GLN A 422 HIS A 580 HIS A 852 GLN A1067 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.130052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.097265 restraints weight = 19941.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.097311 restraints weight = 13286.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.097729 restraints weight = 11484.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.098292 restraints weight = 9764.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.098438 restraints weight = 8854.723| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10049 Z= 0.170 Angle : 0.812 37.176 13726 Z= 0.373 Chirality : 0.045 0.172 1480 Planarity : 0.005 0.046 1659 Dihedral : 15.928 89.802 1573 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.22 % Allowed : 8.08 % Favored : 89.70 % 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: 0.08 (0.25), residues: 1114 helix: 0.31 (0.23), residues: 457 sheet: 0.00 (0.33), residues: 214 loop : 0.03 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 559 TYR 0.022 0.002 TYR A 467 PHE 0.037 0.002 PHE A 119 TRP 0.019 0.001 TRP A 671 HIS 0.015 0.002 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.17 (10045) covalent geometry : angle 0.67266 / 0.37 (13714) hydrogen bonds : bond 0.05571 / 3.67 ( 460) hydrogen bonds : angle 5.48539 / 3.87 ( 1286) metal coordination : bond 0.00766 / 0.38 ( 4) metal coordination : angle 15.36780 / 11.56 ( 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 130 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 108 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.8878 (p90) cc_final: 0.8552 (p90) REVERT: A 138 ASP cc_start: 0.8485 (t0) cc_final: 0.7341 (p0) REVERT: A 157 PHE cc_start: 0.8865 (m-80) cc_final: 0.8471 (m-80) REVERT: A 601 ASP cc_start: 0.8153 (m-30) cc_final: 0.7890 (t0) REVERT: A 688 HIS cc_start: 0.8501 (t-170) cc_final: 0.8245 (m170) REVERT: A 1165 ASP cc_start: 0.7430 (p0) cc_final: 0.7070 (m-30) outliers start: 22 outliers final: 13 residues processed: 121 average time/residue: 0.0725 time to fit residues: 12.4155 Evaluate side-chains 92 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 454 THR Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1145 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 89 optimal weight: 0.0970 chunk 100 optimal weight: 0.9990 chunk 59 optimal weight: 7.9990 chunk 99 optimal weight: 0.5980 chunk 95 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 78 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.130420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.097572 restraints weight = 19906.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.098022 restraints weight = 13380.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.098420 restraints weight = 10532.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.099026 restraints weight = 9467.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.099098 restraints weight = 8592.005| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10049 Z= 0.129 Angle : 0.663 27.384 13726 Z= 0.326 Chirality : 0.044 0.363 1480 Planarity : 0.004 0.041 1659 Dihedral : 15.681 88.304 1573 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.22 % Allowed : 9.80 % Favored : 87.98 % 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: 0.40 (0.25), residues: 1114 helix: 0.68 (0.24), residues: 458 sheet: -0.14 (0.34), residues: 207 loop : 0.24 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 446 TYR 0.016 0.001 TYR A1133 PHE 0.036 0.002 PHE A 971 TRP 0.014 0.001 TRP A 671 HIS 0.004 0.001 HIS A 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 (10045) covalent geometry : angle 0.58517 / 0.33 (13714) hydrogen bonds : bond 0.04801 / 3.15 ( 460) hydrogen bonds : angle 4.92535 / 3.48 ( 1286) metal coordination : bond 0.00411 / 0.20 ( 4) metal coordination : angle 10.56005 / 8.20 ( 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 112 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 90 time to evaluate : 0.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.8840 (p90) cc_final: 0.8607 (p90) REVERT: A 138 ASP cc_start: 0.8579 (t0) cc_final: 0.7397 (p0) REVERT: A 157 PHE cc_start: 0.8908 (m-80) cc_final: 0.8427 (m-80) REVERT: A 559 ARG cc_start: 0.7815 (tmm-80) cc_final: 0.6738 (ptt-90) REVERT: A 688 HIS cc_start: 0.8501 (t-170) cc_final: 0.8285 (m170) REVERT: A 1033 ILE cc_start: 0.8469 (tt) cc_final: 0.8238 (tt) REVERT: A 1165 ASP cc_start: 0.7400 (p0) cc_final: 0.7028 (m-30) outliers start: 22 outliers final: 16 residues processed: 103 average time/residue: 0.0811 time to fit residues: 12.2898 Evaluate side-chains 93 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 111 optimal weight: 20.0000 chunk 94 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 70 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 43 optimal weight: 0.5980 chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 5.9990 chunk 75 optimal weight: 0.9990 chunk 58 optimal weight: 0.0670 chunk 46 optimal weight: 0.1980 overall best weight: 0.4518 ------------------------------------------------------------------------------- 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 = 0.3802 r_free = 0.3802 target = 0.130942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.098495 restraints weight = 20077.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.098796 restraints weight = 13274.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.099197 restraints weight = 11320.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.099777 restraints weight = 9530.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.099940 restraints weight = 8631.563| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.3014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 10049 Z= 0.114 Angle : 0.589 21.478 13726 Z= 0.301 Chirality : 0.041 0.143 1480 Planarity : 0.004 0.040 1659 Dihedral : 15.452 86.352 1573 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.32 % Allowed : 11.01 % Favored : 86.67 % 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: 0.60 (0.25), residues: 1114 helix: 0.93 (0.24), residues: 459 sheet: -0.10 (0.34), residues: 207 loop : 0.28 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 446 TYR 0.020 0.001 TYR A 244 PHE 0.030 0.001 PHE A 971 TRP 0.013 0.001 TRP A 671 HIS 0.002 0.001 HIS A 475 Details of bonding type rmsd/Z covalent geometry : bond 0.00218 / 0.11 (10045) covalent geometry : angle 0.53544 / 0.30 (13714) hydrogen bonds : bond 0.04185 / 2.75 ( 460) hydrogen bonds : angle 4.59739 / 3.29 ( 1286) metal coordination : bond 0.00291 / 0.15 ( 4) metal coordination : angle 8.29496 / 6.44 ( 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 110 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7489 (m-30) cc_final: 0.6493 (p0) REVERT: A 138 ASP cc_start: 0.8546 (t0) cc_final: 0.7255 (p0) REVERT: A 157 PHE cc_start: 0.8872 (m-80) cc_final: 0.8509 (m-80) REVERT: A 244 TYR cc_start: 0.8677 (m-80) cc_final: 0.8162 (m-80) REVERT: A 559 ARG cc_start: 0.7807 (tmm-80) cc_final: 0.6866 (ptt-90) REVERT: A 623 TYR cc_start: 0.8315 (m-10) cc_final: 0.8063 (m-10) REVERT: A 688 HIS cc_start: 0.8601 (t-170) cc_final: 0.8326 (m170) REVERT: A 1165 ASP cc_start: 0.7495 (p0) cc_final: 0.7131 (m-30) outliers start: 23 outliers final: 17 residues processed: 100 average time/residue: 0.0848 time to fit residues: 12.1437 Evaluate side-chains 93 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 296 ILE Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 40 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 chunk 11 optimal weight: 0.0970 chunk 83 optimal weight: 0.0670 chunk 53 optimal weight: 3.9990 chunk 109 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 overall best weight: 1.0320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 708 HIS A 960 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.129232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.096961 restraints weight = 20213.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.097355 restraints weight = 13813.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.097930 restraints weight = 11401.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.098505 restraints weight = 9371.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.098623 restraints weight = 8569.846| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10049 Z= 0.131 Angle : 0.590 22.092 13726 Z= 0.299 Chirality : 0.041 0.148 1480 Planarity : 0.004 0.042 1659 Dihedral : 15.398 85.193 1573 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 3.03 % Allowed : 11.01 % Favored : 85.96 % 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: 0.71 (0.26), residues: 1114 helix: 1.12 (0.25), residues: 458 sheet: 0.02 (0.36), residues: 203 loop : 0.18 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 446 TYR 0.015 0.001 TYR A 103 PHE 0.027 0.001 PHE A 971 TRP 0.011 0.001 TRP A 671 HIS 0.003 0.001 HIS A1163 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.13 (10045) covalent geometry : angle 0.53352 / 0.30 (13714) hydrogen bonds : bond 0.04375 / 2.89 ( 460) hydrogen bonds : angle 4.55015 / 3.24 ( 1286) metal coordination : bond 0.00773 / 0.39 ( 4) metal coordination : angle 8.51103 / 6.62 ( 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 109 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8847 (OUTLIER) cc_final: 0.7992 (tmm-80) REVERT: A 83 ASP cc_start: 0.7539 (m-30) cc_final: 0.6454 (p0) REVERT: A 138 ASP cc_start: 0.8594 (t0) cc_final: 0.7290 (p0) REVERT: A 157 PHE cc_start: 0.8852 (m-80) cc_final: 0.8644 (m-80) REVERT: A 221 MET cc_start: 0.8524 (ptm) cc_final: 0.8288 (ptm) REVERT: A 263 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8482 (mm) REVERT: A 473 TYR cc_start: 0.8466 (m-80) cc_final: 0.7936 (m-10) REVERT: A 528 THR cc_start: 0.6582 (OUTLIER) cc_final: 0.6263 (p) REVERT: A 559 ARG cc_start: 0.7575 (tmm-80) cc_final: 0.6717 (ptt-90) REVERT: A 688 HIS cc_start: 0.8595 (t-170) cc_final: 0.8345 (m170) REVERT: A 1165 ASP cc_start: 0.7553 (p0) cc_final: 0.7194 (m-30) outliers start: 30 outliers final: 22 residues processed: 101 average time/residue: 0.0909 time to fit residues: 13.0572 Evaluate side-chains 98 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 73 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 853 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 91 optimal weight: 3.9990 chunk 88 optimal weight: 0.8980 chunk 109 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 14 optimal weight: 0.4980 chunk 101 optimal weight: 5.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- 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 = 0.3752 r_free = 0.3752 target = 0.127074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.094894 restraints weight = 20143.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.095370 restraints weight = 13765.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.095884 restraints weight = 11481.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.096386 restraints weight = 9416.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.096534 restraints weight = 8648.635| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.3439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10049 Z= 0.169 Angle : 0.638 24.533 13726 Z= 0.319 Chirality : 0.043 0.161 1480 Planarity : 0.005 0.065 1659 Dihedral : 15.454 84.044 1573 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 3.13 % Allowed : 11.52 % Favored : 85.35 % 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: 0.58 (0.26), residues: 1114 helix: 1.01 (0.24), residues: 461 sheet: -0.04 (0.36), residues: 207 loop : 0.11 (0.31), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 446 TYR 0.020 0.001 TYR A 397 PHE 0.031 0.002 PHE A 971 TRP 0.010 0.001 TRP A 671 HIS 0.005 0.001 HIS A1163 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (10045) covalent geometry : angle 0.57228 / 0.32 (13714) hydrogen bonds : bond 0.04878 / 3.21 ( 460) hydrogen bonds : angle 4.63862 / 3.30 ( 1286) metal coordination : bond 0.01214 / 0.61 ( 4) metal coordination : angle 9.53939 / 7.38 ( 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 112 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 81 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8023 (tmm-80) REVERT: A 83 ASP cc_start: 0.7695 (m-30) cc_final: 0.6636 (p0) REVERT: A 138 ASP cc_start: 0.8616 (t0) cc_final: 0.7450 (p0) REVERT: A 221 MET cc_start: 0.8584 (ptm) cc_final: 0.8265 (ptm) REVERT: A 244 TYR cc_start: 0.8781 (m-80) cc_final: 0.8179 (m-80) REVERT: A 263 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8558 (mm) REVERT: A 473 TYR cc_start: 0.8608 (m-80) cc_final: 0.8087 (m-10) REVERT: A 528 THR cc_start: 0.6723 (OUTLIER) cc_final: 0.6420 (p) REVERT: A 559 ARG cc_start: 0.7557 (tmm-80) cc_final: 0.6690 (ptt-90) REVERT: A 688 HIS cc_start: 0.8613 (t-170) cc_final: 0.8344 (m170) REVERT: A 1165 ASP cc_start: 0.7540 (p0) cc_final: 0.7178 (m-30) outliers start: 31 outliers final: 23 residues processed: 104 average time/residue: 0.0785 time to fit residues: 11.6871 Evaluate side-chains 101 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 75 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 293 ILE Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 22 optimal weight: 1.9990 chunk 87 optimal weight: 0.5980 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 69 optimal weight: 0.0570 chunk 17 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.8900 ------------------------------------------------------------------------------- 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 = 0.3764 r_free = 0.3764 target = 0.127964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.095723 restraints weight = 19968.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.095970 restraints weight = 13298.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.096341 restraints weight = 11477.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.096975 restraints weight = 9564.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.097102 restraints weight = 8647.361| |-----------------------------------------------------------------------------| r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10049 Z= 0.127 Angle : 0.595 21.363 13726 Z= 0.301 Chirality : 0.042 0.347 1480 Planarity : 0.004 0.046 1659 Dihedral : 15.455 83.822 1573 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.83 % Allowed : 12.42 % Favored : 84.75 % 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: 0.64 (0.26), residues: 1114 helix: 1.11 (0.25), residues: 459 sheet: 0.02 (0.36), residues: 205 loop : 0.07 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 114 TYR 0.012 0.001 TYR A 754 PHE 0.014 0.001 PHE A 367 TRP 0.010 0.001 TRP A 671 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 (10045) covalent geometry : angle 0.54361 / 0.30 (13714) hydrogen bonds : bond 0.04462 / 2.94 ( 460) hydrogen bonds : angle 4.51301 / 3.22 ( 1286) metal coordination : bond 0.00576 / 0.29 ( 4) metal coordination : angle 8.23350 / 6.39 ( 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 110 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8901 (OUTLIER) cc_final: 0.7995 (tmm-80) REVERT: A 83 ASP cc_start: 0.7618 (m-30) cc_final: 0.6486 (p0) REVERT: A 138 ASP cc_start: 0.8588 (t0) cc_final: 0.7442 (p0) REVERT: A 244 TYR cc_start: 0.8741 (m-80) cc_final: 0.8057 (m-80) REVERT: A 263 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8534 (mm) REVERT: A 473 TYR cc_start: 0.8612 (m-80) cc_final: 0.8044 (m-10) REVERT: A 528 THR cc_start: 0.6654 (OUTLIER) cc_final: 0.6344 (p) REVERT: A 559 ARG cc_start: 0.7570 (tmm-80) cc_final: 0.6678 (ptt-90) REVERT: A 688 HIS cc_start: 0.8664 (t-170) cc_final: 0.8362 (m170) outliers start: 28 outliers final: 21 residues processed: 103 average time/residue: 0.0877 time to fit residues: 12.8164 Evaluate side-chains 98 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 45 optimal weight: 0.7980 chunk 109 optimal weight: 0.5980 chunk 50 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 103 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 98 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1036 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.125908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.094225 restraints weight = 20262.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.094250 restraints weight = 13871.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.094909 restraints weight = 11915.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.095397 restraints weight = 9639.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.095544 restraints weight = 8942.393| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10049 Z= 0.170 Angle : 0.644 23.502 13726 Z= 0.320 Chirality : 0.043 0.178 1480 Planarity : 0.005 0.045 1659 Dihedral : 15.508 82.273 1573 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.93 % Allowed : 12.93 % Favored : 84.14 % 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: 0.51 (0.26), residues: 1114 helix: 1.02 (0.24), residues: 461 sheet: -0.03 (0.36), residues: 205 loop : -0.05 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 114 TYR 0.014 0.001 TYR A 397 PHE 0.019 0.002 PHE A 104 TRP 0.011 0.001 TRP A 671 HIS 0.005 0.001 HIS A1163 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (10045) covalent geometry : angle 0.58342 / 0.32 (13714) hydrogen bonds : bond 0.04882 / 3.22 ( 460) hydrogen bonds : angle 4.60205 / 3.27 ( 1286) metal coordination : bond 0.01184 / 0.59 ( 4) metal coordination : angle 9.26628 / 7.10 ( 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 103 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8038 (tmm-80) REVERT: A 83 ASP cc_start: 0.7710 (m-30) cc_final: 0.6588 (p0) REVERT: A 138 ASP cc_start: 0.8655 (t0) cc_final: 0.7531 (p0) REVERT: A 215 LEU cc_start: 0.7876 (tt) cc_final: 0.7676 (tp) REVERT: A 244 TYR cc_start: 0.8854 (m-80) cc_final: 0.8036 (m-80) REVERT: A 263 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8669 (mm) REVERT: A 447 MET cc_start: 0.8133 (mmt) cc_final: 0.7807 (mmt) REVERT: A 473 TYR cc_start: 0.8697 (m-80) cc_final: 0.8205 (m-10) REVERT: A 528 THR cc_start: 0.6679 (OUTLIER) cc_final: 0.6376 (p) REVERT: A 559 ARG cc_start: 0.7620 (tmm-80) cc_final: 0.6767 (ptt-90) REVERT: A 688 HIS cc_start: 0.8654 (t-170) cc_final: 0.8356 (m170) outliers start: 29 outliers final: 24 residues processed: 97 average time/residue: 0.0899 time to fit residues: 12.4160 Evaluate side-chains 97 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 70 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1016 VAL Chi-restraints excluded: chain A residue 1017 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 39 optimal weight: 0.9990 chunk 65 optimal weight: 9.9990 chunk 26 optimal weight: 0.0010 chunk 47 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 80 optimal weight: 0.6980 chunk 25 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 27 optimal weight: 8.9990 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.0990 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.126901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.094920 restraints weight = 20146.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.094946 restraints weight = 13542.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.095389 restraints weight = 11789.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.095939 restraints weight = 9749.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.096109 restraints weight = 8873.743| |-----------------------------------------------------------------------------| r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10049 Z= 0.132 Angle : 0.608 21.047 13726 Z= 0.306 Chirality : 0.041 0.163 1480 Planarity : 0.004 0.047 1659 Dihedral : 15.529 81.871 1573 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.83 % Allowed : 13.23 % Favored : 83.94 % 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: 0.61 (0.25), residues: 1114 helix: 1.11 (0.25), residues: 458 sheet: 0.11 (0.36), residues: 199 loop : -0.05 (0.30), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 114 TYR 0.011 0.001 TYR A 754 PHE 0.016 0.001 PHE A 157 TRP 0.011 0.001 TRP A 671 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.13 (10045) covalent geometry : angle 0.55746 / 0.31 (13714) hydrogen bonds : bond 0.04539 / 2.99 ( 460) hydrogen bonds : angle 4.45015 / 3.13 ( 1286) metal coordination : bond 0.00639 / 0.32 ( 4) metal coordination : angle 8.26659 / 6.34 ( 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 104 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 76 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8000 (tmm-80) REVERT: A 138 ASP cc_start: 0.8683 (t0) cc_final: 0.7626 (p0) REVERT: A 244 TYR cc_start: 0.8787 (m-80) cc_final: 0.8023 (m-80) REVERT: A 263 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8652 (mm) REVERT: A 359 MET cc_start: 0.8863 (tpp) cc_final: 0.8376 (mpp) REVERT: A 473 TYR cc_start: 0.8699 (m-80) cc_final: 0.8206 (m-10) REVERT: A 528 THR cc_start: 0.6522 (OUTLIER) cc_final: 0.6206 (p) REVERT: A 559 ARG cc_start: 0.7595 (tmm-80) cc_final: 0.6741 (ptt-90) REVERT: A 688 HIS cc_start: 0.8695 (t-170) cc_final: 0.8370 (m170) outliers start: 28 outliers final: 21 residues processed: 97 average time/residue: 0.0889 time to fit residues: 12.6504 Evaluate side-chains 91 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 67 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 378 VAL Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 103 optimal weight: 0.0370 chunk 82 optimal weight: 0.0070 chunk 78 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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 = 0.3769 r_free = 0.3769 target = 0.128317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.096799 restraints weight = 20006.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.097013 restraints weight = 13026.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.097692 restraints weight = 11498.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.098114 restraints weight = 9223.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.098313 restraints weight = 8491.409| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10049 Z= 0.117 Angle : 0.592 16.961 13726 Z= 0.304 Chirality : 0.042 0.225 1480 Planarity : 0.004 0.046 1659 Dihedral : 15.487 81.164 1573 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.32 % Allowed : 13.84 % Favored : 83.84 % 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: 0.68 (0.25), residues: 1114 helix: 1.19 (0.25), residues: 458 sheet: 0.09 (0.36), residues: 198 loop : -0.01 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 114 TYR 0.010 0.001 TYR A 244 PHE 0.013 0.001 PHE A 367 TRP 0.013 0.001 TRP A 671 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.12 (10045) covalent geometry : angle 0.55704 / 0.30 (13714) hydrogen bonds : bond 0.04204 / 2.76 ( 460) hydrogen bonds : angle 4.43737 / 3.13 ( 1286) metal coordination : bond 0.00306 / 0.15 ( 4) metal coordination : angle 6.84506 / 5.16 ( 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 102 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8020 (tmm-80) REVERT: A 83 ASP cc_start: 0.7630 (m-30) cc_final: 0.6471 (p0) REVERT: A 138 ASP cc_start: 0.8655 (t0) cc_final: 0.7577 (p0) REVERT: A 244 TYR cc_start: 0.8719 (m-80) cc_final: 0.8006 (m-80) REVERT: A 263 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8626 (mm) REVERT: A 359 MET cc_start: 0.8867 (tpp) cc_final: 0.8333 (mpp) REVERT: A 383 MET cc_start: 0.5904 (ttp) cc_final: 0.5497 (ttm) REVERT: A 528 THR cc_start: 0.6658 (OUTLIER) cc_final: 0.6360 (p) REVERT: A 559 ARG cc_start: 0.7550 (tmm-80) cc_final: 0.6698 (ptt-90) REVERT: A 562 MET cc_start: 0.8736 (tpp) cc_final: 0.8523 (mmm) REVERT: A 623 TYR cc_start: 0.8340 (m-10) cc_final: 0.8108 (m-10) REVERT: A 688 HIS cc_start: 0.8643 (t-170) cc_final: 0.8349 (m170) REVERT: A 1068 MET cc_start: 0.7388 (mmm) cc_final: 0.6614 (mmm) outliers start: 23 outliers final: 17 residues processed: 98 average time/residue: 0.1063 time to fit residues: 14.7024 Evaluate side-chains 90 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1054 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 94 optimal weight: 0.8980 chunk 99 optimal weight: 0.8980 chunk 41 optimal weight: 2.9990 chunk 112 optimal weight: 20.0000 chunk 93 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 100 optimal weight: 0.8980 chunk 15 optimal weight: 5.9990 chunk 40 optimal weight: 5.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3760 r_free = 0.3760 target = 0.127715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.096367 restraints weight = 19924.866| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.096622 restraints weight = 12779.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.097063 restraints weight = 11147.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.097632 restraints weight = 9083.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.097811 restraints weight = 8243.459| |-----------------------------------------------------------------------------| r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10049 Z= 0.127 Angle : 0.601 17.624 13726 Z= 0.307 Chirality : 0.042 0.198 1480 Planarity : 0.004 0.045 1659 Dihedral : 15.486 80.214 1573 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.22 % Allowed : 14.24 % Favored : 83.54 % 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: 0.60 (0.25), residues: 1114 helix: 1.19 (0.24), residues: 456 sheet: 0.09 (0.36), residues: 198 loop : -0.14 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 114 TYR 0.014 0.001 TYR A 100 PHE 0.048 0.002 PHE A 119 TRP 0.013 0.001 TRP A 671 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (10045) covalent geometry : angle 0.56332 / 0.31 (13714) hydrogen bonds : bond 0.04295 / 2.83 ( 460) hydrogen bonds : angle 4.40123 / 3.10 ( 1286) metal coordination : bond 0.00580 / 0.29 ( 4) metal coordination : angle 7.07862 / 5.35 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1251.04 seconds wall clock time: 22 minutes 20.65 seconds (1340.65 seconds total)