Starting phenix.real_space_refine on Wed Aug 5 12:19:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f6j_50226/08_2026/9f6j_50226.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f6j_50226/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9f6j_50226/08_2026/9f6j_50226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f6j_50226/08_2026/9f6j_50226.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9f6j_50226/08_2026/9f6j_50226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f6j_50226/08_2026/9f6j_50226.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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-2.2rc3-6140/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: 2.00, per 1000 atoms: 0.21 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: 0.76 Conformation dependent library (CDL) restraints added in 277.8 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: 1.00 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: 1.56 Time building geometry restraints manager: 1.02 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: 12952 1.33 - 2.66: 635 2.66 - 3.99: 105 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: 0.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 11.270 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: 0.010 Load rotamer database and sin/cos tables:0.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.280 ------------------------------------------------------------------------------- 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 : 0.923 47.045 13726 Z= 0.461 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 0.66966 / 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 : 0.225 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: 0.8472 (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: 0.5929 (m-10) REVERT: A 416 TYR cc_start: 0.7901 (m-80) cc_final: 0.7688 (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: 0.0957 time to fit residues: 24.5338 Evaluate side-chains 86 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 = 0.130038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.097254 restraints weight = 20041.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.097396 restraints weight = 13261.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.097791 restraints weight = 11448.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.098360 restraints weight = 9709.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.098496 restraints weight = 8803.317| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10049 Z= 0.173 Angle : 0.819 37.420 13726 Z= 0.375 Chirality : 0.045 0.172 1480 Planarity : 0.005 0.046 1659 Dihedral : 15.889 89.784 1573 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 2.12 % Allowed : 8.18 % 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: 0.06 (0.24), residues: 1114 helix: 0.30 (0.23), residues: 457 sheet: 0.00 (0.33), residues: 214 loop : 0.01 (0.31), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 975 TYR 0.020 0.001 TYR A 467 PHE 0.036 0.002 PHE A 119 TRP 0.019 0.001 TRP A 671 HIS 0.014 0.001 HIS A 229 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.17 (10045) covalent geometry : angle 0.67806 / 0.37 (13714) hydrogen bonds : bond 0.05631 / 3.71 ( 460) hydrogen bonds : angle 5.52369 / 3.90 ( 1286) metal coordination : bond 0.00810 / 0.40 ( 4) metal coordination : angle 15.53887 / 11.67 ( 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 129 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.8874 (p90) cc_final: 0.8555 (p90) REVERT: A 138 ASP cc_start: 0.8483 (t0) cc_final: 0.7338 (p0) REVERT: A 157 PHE cc_start: 0.8863 (m-80) cc_final: 0.8466 (m-80) REVERT: A 601 ASP cc_start: 0.8161 (m-30) cc_final: 0.7891 (t0) REVERT: A 688 HIS cc_start: 0.8500 (t-170) cc_final: 0.8246 (m170) REVERT: A 1165 ASP cc_start: 0.7439 (p0) cc_final: 0.7077 (m-30) outliers start: 21 outliers final: 12 residues processed: 120 average time/residue: 0.0799 time to fit residues: 13.7636 Evaluate side-chains 92 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0170 chunk 100 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 95 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 81 optimal weight: 0.4980 chunk 67 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 105 optimal weight: 0.2980 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.130878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.098796 restraints weight = 19875.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.098970 restraints weight = 12866.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.099322 restraints weight = 11343.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.099933 restraints weight = 9537.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.100061 restraints weight = 8577.836| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.2656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 10049 Z= 0.127 Angle : 0.658 26.879 13726 Z= 0.324 Chirality : 0.044 0.398 1480 Planarity : 0.004 0.039 1659 Dihedral : 15.691 88.617 1573 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.22 % Allowed : 9.90 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.25), residues: 1114 helix: 0.68 (0.24), residues: 456 sheet: -0.10 (0.34), residues: 207 loop : 0.23 (0.31), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A1082 TYR 0.017 0.001 TYR A1133 PHE 0.037 0.002 PHE A 971 TRP 0.015 0.001 TRP A 671 HIS 0.003 0.001 HIS A 422 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.13 (10045) covalent geometry : angle 0.58310 / 0.32 (13714) hydrogen bonds : bond 0.04753 / 3.12 ( 460) hydrogen bonds : angle 4.92378 / 3.48 ( 1286) metal coordination : bond 0.00348 / 0.17 ( 4) metal coordination : angle 10.34388 / 8.04 ( 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 116 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7630 (m-30) cc_final: 0.7381 (m-30) REVERT: A 103 TYR cc_start: 0.8838 (p90) cc_final: 0.8611 (p90) REVERT: A 138 ASP cc_start: 0.8564 (t0) cc_final: 0.7390 (p0) REVERT: A 157 PHE cc_start: 0.8881 (m-80) cc_final: 0.8418 (m-80) REVERT: A 559 ARG cc_start: 0.7806 (tmm-80) cc_final: 0.6734 (ptt-90) REVERT: A 623 TYR cc_start: 0.8383 (m-10) cc_final: 0.8144 (m-10) REVERT: A 688 HIS cc_start: 0.8526 (t-170) cc_final: 0.8244 (m170) REVERT: A 1165 ASP cc_start: 0.7387 (p0) cc_final: 0.7021 (m-30) outliers start: 22 outliers final: 15 residues processed: 107 average time/residue: 0.0771 time to fit residues: 12.3604 Evaluate side-chains 92 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 445 CYS 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 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: 0.5980 chunk 41 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 960 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.129427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.096715 restraints weight = 20326.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.097036 restraints weight = 13982.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.097336 restraints weight = 11529.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.097970 restraints weight = 9892.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.098138 restraints weight = 8988.048| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10049 Z= 0.129 Angle : 0.616 24.304 13726 Z= 0.308 Chirality : 0.042 0.143 1480 Planarity : 0.004 0.038 1659 Dihedral : 15.523 86.323 1573 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.42 % Allowed : 10.81 % Favored : 86.77 % 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: 0.56 (0.25), residues: 1114 helix: 0.90 (0.24), residues: 458 sheet: -0.11 (0.35), residues: 207 loop : 0.27 (0.31), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 446 TYR 0.018 0.001 TYR A 244 PHE 0.030 0.002 PHE A 119 TRP 0.012 0.001 TRP A 671 HIS 0.003 0.001 HIS A1168 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (10045) covalent geometry : angle 0.55164 / 0.31 (13714) hydrogen bonds : bond 0.04504 / 2.96 ( 460) hydrogen bonds : angle 4.68342 / 3.34 ( 1286) metal coordination : bond 0.00641 / 0.32 ( 4) metal coordination : angle 9.31176 / 7.26 ( 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 105 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 81 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.8821 (p90) cc_final: 0.8572 (p90) REVERT: A 138 ASP cc_start: 0.8595 (t0) cc_final: 0.7319 (p0) REVERT: A 157 PHE cc_start: 0.8838 (m-80) cc_final: 0.8546 (m-80) REVERT: A 447 MET cc_start: 0.8121 (mmt) cc_final: 0.7798 (mmt) REVERT: A 559 ARG cc_start: 0.7845 (tmm-80) cc_final: 0.6883 (ptt-90) REVERT: A 688 HIS cc_start: 0.8607 (t-170) cc_final: 0.8327 (m170) REVERT: A 1165 ASP cc_start: 0.7547 (p0) cc_final: 0.7182 (m-30) outliers start: 24 outliers final: 18 residues processed: 96 average time/residue: 0.0782 time to fit residues: 10.8749 Evaluate side-chains 95 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 72 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 354 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 506 MET 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 40 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 32 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 11 optimal weight: 0.0010 chunk 83 optimal weight: 0.0170 chunk 53 optimal weight: 5.9990 chunk 109 optimal weight: 0.0970 chunk 108 optimal weight: 1.9990 overall best weight: 0.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 708 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.130326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.097864 restraints weight = 20130.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.098231 restraints weight = 13635.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.098549 restraints weight = 11320.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.099243 restraints weight = 9631.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.099378 restraints weight = 8661.950| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10049 Z= 0.113 Angle : 0.580 20.398 13726 Z= 0.295 Chirality : 0.041 0.167 1480 Planarity : 0.004 0.037 1659 Dihedral : 15.438 85.825 1573 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.83 % Allowed : 11.21 % 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: 0.70 (0.25), residues: 1114 helix: 1.09 (0.25), residues: 458 sheet: 0.03 (0.35), residues: 204 loop : 0.20 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 114 TYR 0.017 0.001 TYR A1133 PHE 0.024 0.001 PHE A 119 TRP 0.012 0.001 TRP A 671 HIS 0.002 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (10045) covalent geometry : angle 0.53131 / 0.29 (13714) hydrogen bonds : bond 0.04143 / 2.73 ( 460) hydrogen bonds : angle 4.48159 / 3.19 ( 1286) metal coordination : bond 0.00384 / 0.19 ( 4) metal coordination : angle 7.89202 / 6.12 ( 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 111 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 83 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8827 (OUTLIER) cc_final: 0.7955 (tmm-80) REVERT: A 138 ASP cc_start: 0.8575 (t0) cc_final: 0.7274 (p0) REVERT: A 244 TYR cc_start: 0.8621 (m-80) cc_final: 0.8164 (m-80) REVERT: A 263 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8453 (mm) REVERT: A 528 THR cc_start: 0.6533 (OUTLIER) cc_final: 0.6211 (p) REVERT: A 559 ARG cc_start: 0.7516 (tmm-80) cc_final: 0.6662 (ptt-90) REVERT: A 623 TYR cc_start: 0.8293 (m-10) cc_final: 0.8069 (m-10) REVERT: A 688 HIS cc_start: 0.8625 (t-170) cc_final: 0.8355 (m170) REVERT: A 1119 LEU cc_start: 0.5082 (mm) cc_final: 0.4660 (mm) REVERT: A 1165 ASP cc_start: 0.7542 (p0) cc_final: 0.7201 (m-30) outliers start: 28 outliers final: 19 residues processed: 101 average time/residue: 0.0776 time to fit residues: 11.4215 Evaluate side-chains 97 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG 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 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 378 VAL 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 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: 1.9990 chunk 109 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 24 optimal weight: 0.2980 chunk 66 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 overall best weight: 2.2588 ------------------------------------------------------------------------------- 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 = 0.3727 r_free = 0.3727 target = 0.125267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.092273 restraints weight = 20464.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.092446 restraints weight = 14842.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.092762 restraints weight = 11872.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.093396 restraints weight = 10202.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.093580 restraints weight = 9249.308| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10049 Z= 0.215 Angle : 0.704 27.503 13726 Z= 0.345 Chirality : 0.044 0.174 1480 Planarity : 0.005 0.044 1659 Dihedral : 15.552 83.657 1573 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.93 % Allowed : 12.63 % Favored : 84.44 % 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: 0.34 (0.25), residues: 1114 helix: 0.81 (0.24), residues: 462 sheet: -0.17 (0.36), residues: 205 loop : -0.03 (0.31), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 114 TYR 0.016 0.002 TYR A 397 PHE 0.026 0.002 PHE A 971 TRP 0.012 0.002 TRP A 62 HIS 0.007 0.002 HIS A1163 Details of bonding type rmsd/Z covalent geometry : bond 0.00497 / 0.21 (10045) covalent geometry : angle 0.62432 / 0.34 (13714) hydrogen bonds : bond 0.05523 / 3.66 ( 460) hydrogen bonds : angle 4.80079 / 3.40 ( 1286) metal coordination : bond 0.01740 / 0.87 ( 4) metal coordination : angle 11.04053 / 8.40 ( 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: 29 poor density : 83 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8952 (OUTLIER) cc_final: 0.8045 (tmm-80) REVERT: A 138 ASP cc_start: 0.8681 (t0) cc_final: 0.7493 (p0) REVERT: A 263 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8689 (mm) REVERT: A 367 PHE cc_start: 0.8184 (t80) cc_final: 0.7965 (t80) REVERT: A 473 TYR cc_start: 0.8668 (m-80) cc_final: 0.8178 (m-10) REVERT: A 559 ARG cc_start: 0.7618 (tmm-80) cc_final: 0.6739 (ptt-90) REVERT: A 688 HIS cc_start: 0.8671 (t-170) cc_final: 0.8358 (m170) REVERT: A 779 LEU cc_start: 0.8610 (tp) cc_final: 0.8328 (tt) REVERT: A 843 ILE cc_start: 0.9323 (OUTLIER) cc_final: 0.9050 (tp) REVERT: A 1119 LEU cc_start: 0.5256 (mm) cc_final: 0.4892 (mm) REVERT: A 1165 ASP cc_start: 0.7607 (p0) cc_final: 0.7235 (m-30) outliers start: 29 outliers final: 18 residues processed: 104 average time/residue: 0.0749 time to fit residues: 11.3003 Evaluate side-chains 97 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 76 time to evaluate : 0.238 ------------------------------------------------------------------------------- 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 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 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 755 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 850 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 22 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 60 optimal weight: 0.0370 chunk 18 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 overall best weight: 0.7058 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.127785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.095561 restraints weight = 20188.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.095763 restraints weight = 13692.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.096151 restraints weight = 11631.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.096725 restraints weight = 9759.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.096880 restraints weight = 8844.563| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.3613 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= 0.125 Angle : 0.617 21.748 13726 Z= 0.308 Chirality : 0.042 0.364 1480 Planarity : 0.004 0.039 1659 Dihedral : 15.536 84.072 1573 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.32 % Allowed : 13.43 % Favored : 84.24 % 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: 0.54 (0.26), residues: 1114 helix: 1.09 (0.25), residues: 459 sheet: -0.08 (0.36), residues: 205 loop : -0.02 (0.31), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 114 TYR 0.012 0.001 TYR A 224 PHE 0.024 0.001 PHE A 971 TRP 0.010 0.001 TRP A 671 HIS 0.004 0.001 HIS A1108 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (10045) covalent geometry : angle 0.56573 / 0.31 (13714) hydrogen bonds : bond 0.04446 / 2.93 ( 460) hydrogen bonds : angle 4.54860 / 3.23 ( 1286) metal coordination : bond 0.00466 / 0.23 ( 4) metal coordination : angle 8.38773 / 6.50 ( 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 108 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.7974 (tmm-80) REVERT: A 138 ASP cc_start: 0.8597 (t0) cc_final: 0.7461 (p0) REVERT: A 215 LEU cc_start: 0.7939 (tt) cc_final: 0.7729 (tp) REVERT: A 221 MET cc_start: 0.8350 (ppp) cc_final: 0.7920 (ppp) REVERT: A 244 TYR cc_start: 0.8793 (m-80) cc_final: 0.8066 (m-80) REVERT: A 263 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8549 (mm) REVERT: A 359 MET cc_start: 0.8857 (tpp) cc_final: 0.8380 (mpp) REVERT: A 367 PHE cc_start: 0.8188 (t80) cc_final: 0.7980 (t80) REVERT: A 447 MET cc_start: 0.8110 (mmt) cc_final: 0.7820 (mmt) REVERT: A 473 TYR cc_start: 0.8641 (m-80) cc_final: 0.8156 (m-10) REVERT: A 528 THR cc_start: 0.6649 (OUTLIER) cc_final: 0.6347 (p) REVERT: A 559 ARG cc_start: 0.7528 (tmm-80) cc_final: 0.6669 (ptt-90) REVERT: A 688 HIS cc_start: 0.8665 (t-170) cc_final: 0.8359 (m170) REVERT: A 779 LEU cc_start: 0.8515 (tp) cc_final: 0.8233 (tt) REVERT: A 1017 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8405 (tp) REVERT: A 1119 LEU cc_start: 0.5045 (mm) cc_final: 0.4745 (mm) REVERT: A 1165 ASP cc_start: 0.7577 (p0) cc_final: 0.7263 (m-30) outliers start: 23 outliers final: 15 residues processed: 100 average time/residue: 0.0882 time to fit residues: 12.6373 Evaluate side-chains 97 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 78 time to evaluate : 0.232 ------------------------------------------------------------------------------- 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 360 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 378 VAL 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 850 ILE Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1017 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 45 optimal weight: 0.9990 chunk 109 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 35 optimal weight: 0.1980 chunk 23 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 72 optimal weight: 9.9990 chunk 111 optimal weight: 20.0000 chunk 42 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 58 optimal weight: 0.0670 overall best weight: 1.0524 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.127125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.095126 restraints weight = 20152.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.095285 restraints weight = 13720.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.095558 restraints weight = 11643.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.096261 restraints weight = 9873.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.096400 restraints weight = 8879.560| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.3705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10049 Z= 0.132 Angle : 0.608 20.579 13726 Z= 0.304 Chirality : 0.042 0.210 1480 Planarity : 0.004 0.040 1659 Dihedral : 15.523 83.108 1573 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.12 % Allowed : 14.34 % 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: 0.55 (0.25), residues: 1114 helix: 1.09 (0.25), residues: 459 sheet: -0.03 (0.35), residues: 205 loop : -0.05 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 114 TYR 0.011 0.001 TYR A1133 PHE 0.021 0.001 PHE A 971 TRP 0.012 0.001 TRP A 671 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.13 (10045) covalent geometry : angle 0.55954 / 0.30 (13714) hydrogen bonds : bond 0.04486 / 2.95 ( 460) hydrogen bonds : angle 4.49527 / 3.17 ( 1286) metal coordination : bond 0.00687 / 0.34 ( 4) metal coordination : angle 8.04507 / 6.18 ( 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 101 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.225 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.7984 (tmm-80) REVERT: A 138 ASP cc_start: 0.8613 (t0) cc_final: 0.7475 (p0) REVERT: A 221 MET cc_start: 0.8246 (ppp) cc_final: 0.7741 (ppp) REVERT: A 244 TYR cc_start: 0.8840 (m-80) cc_final: 0.8079 (m-80) REVERT: A 263 LEU cc_start: 0.8880 (OUTLIER) cc_final: 0.8598 (mm) REVERT: A 359 MET cc_start: 0.8881 (tpp) cc_final: 0.8373 (mpp) REVERT: A 367 PHE cc_start: 0.8195 (t80) cc_final: 0.7976 (t80) REVERT: A 473 TYR cc_start: 0.8668 (m-80) cc_final: 0.8177 (m-10) REVERT: A 528 THR cc_start: 0.6600 (OUTLIER) cc_final: 0.6296 (p) REVERT: A 559 ARG cc_start: 0.7589 (tmm-80) cc_final: 0.6722 (ptt-90) REVERT: A 688 HIS cc_start: 0.8677 (t-170) cc_final: 0.8366 (m170) REVERT: A 779 LEU cc_start: 0.8535 (tp) cc_final: 0.8263 (tt) REVERT: A 1119 LEU cc_start: 0.5048 (mm) cc_final: 0.4763 (mm) REVERT: A 1165 ASP cc_start: 0.7455 (p0) cc_final: 0.7250 (m-30) outliers start: 21 outliers final: 18 residues processed: 97 average time/residue: 0.0790 time to fit residues: 11.1820 Evaluate side-chains 96 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 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 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 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 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 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: 5.9990 chunk 65 optimal weight: 8.9990 chunk 26 optimal weight: 0.3980 chunk 47 optimal weight: 3.9990 chunk 5 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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 = 0.3715 r_free = 0.3715 target = 0.124086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3246 r_free = 0.3246 target = 0.092597 restraints weight = 20181.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.092569 restraints weight = 13865.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.093168 restraints weight = 11959.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.093679 restraints weight = 9627.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.093836 restraints weight = 8870.919| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.3828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 10049 Z= 0.222 Angle : 0.718 27.230 13726 Z= 0.345 Chirality : 0.045 0.235 1480 Planarity : 0.005 0.044 1659 Dihedral : 15.657 81.104 1573 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 2.42 % Allowed : 14.34 % Favored : 83.23 % 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: 0.25 (0.25), residues: 1114 helix: 0.86 (0.24), residues: 456 sheet: -0.22 (0.35), residues: 205 loop : -0.22 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 494 TYR 0.012 0.002 TYR A 397 PHE 0.022 0.002 PHE A 971 TRP 0.012 0.002 TRP A 62 HIS 0.008 0.002 HIS A1108 Details of bonding type rmsd/Z covalent geometry : bond 0.00517 / 0.22 (10045) covalent geometry : angle 0.63780 / 0.34 (13714) hydrogen bonds : bond 0.05542 / 3.64 ( 460) hydrogen bonds : angle 4.81985 / 3.41 ( 1286) metal coordination : bond 0.01650 / 0.83 ( 4) metal coordination : angle 11.16159 / 8.39 ( 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 99 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 75 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8075 (tmm-80) REVERT: A 138 ASP cc_start: 0.8736 (t0) cc_final: 0.7721 (p0) REVERT: A 221 MET cc_start: 0.8338 (ppp) cc_final: 0.7922 (ppp) REVERT: A 263 LEU cc_start: 0.8970 (OUTLIER) cc_final: 0.8744 (mm) REVERT: A 367 PHE cc_start: 0.8174 (t80) cc_final: 0.7973 (t80) REVERT: A 473 TYR cc_start: 0.8790 (m-80) cc_final: 0.8313 (m-10) REVERT: A 528 THR cc_start: 0.6610 (OUTLIER) cc_final: 0.6299 (p) REVERT: A 559 ARG cc_start: 0.7892 (tmm-80) cc_final: 0.7050 (ptt-90) REVERT: A 688 HIS cc_start: 0.8687 (t-170) cc_final: 0.8360 (m170) REVERT: A 1119 LEU cc_start: 0.5110 (mm) cc_final: 0.4833 (mm) outliers start: 24 outliers final: 18 residues processed: 94 average time/residue: 0.0785 time to fit residues: 10.7383 Evaluate side-chains 90 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.219 ------------------------------------------------------------------------------- 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 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 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 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 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: 2.9990 chunk 82 optimal weight: 0.0970 chunk 78 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 69 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 75 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 overall best weight: 0.7778 ------------------------------------------------------------------------------- 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 = 0.3749 r_free = 0.3749 target = 0.126698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.095381 restraints weight = 19861.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.095466 restraints weight = 13076.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.096064 restraints weight = 11357.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.096658 restraints weight = 9017.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.096796 restraints weight = 8214.328| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10049 Z= 0.123 Angle : 0.620 20.413 13726 Z= 0.311 Chirality : 0.042 0.225 1480 Planarity : 0.004 0.039 1659 Dihedral : 15.634 81.476 1573 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.92 % Allowed : 15.05 % Favored : 83.03 % 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: 0.47 (0.25), residues: 1114 helix: 1.08 (0.24), residues: 455 sheet: 0.01 (0.35), residues: 199 loop : -0.20 (0.30), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 114 TYR 0.014 0.001 TYR A 244 PHE 0.021 0.001 PHE A 971 TRP 0.012 0.001 TRP A 671 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.12 (10045) covalent geometry : angle 0.57142 / 0.31 (13714) hydrogen bonds : bond 0.04613 / 3.02 ( 460) hydrogen bonds : angle 4.56768 / 3.22 ( 1286) metal coordination : bond 0.00433 / 0.22 ( 4) metal coordination : angle 8.12178 / 6.17 ( 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 94 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 75 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8006 (tmm-80) REVERT: A 138 ASP cc_start: 0.8675 (t0) cc_final: 0.7671 (p0) REVERT: A 221 MET cc_start: 0.8288 (ppp) cc_final: 0.7834 (ppp) REVERT: A 244 TYR cc_start: 0.8657 (m-80) cc_final: 0.8099 (m-80) REVERT: A 263 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8660 (mm) REVERT: A 359 MET cc_start: 0.8888 (tpp) cc_final: 0.8348 (mpp) REVERT: A 367 PHE cc_start: 0.8177 (t80) cc_final: 0.7944 (t80) REVERT: A 528 THR cc_start: 0.6601 (OUTLIER) cc_final: 0.6287 (p) REVERT: A 559 ARG cc_start: 0.7591 (tmm-80) cc_final: 0.6724 (ptt-90) REVERT: A 688 HIS cc_start: 0.8736 (t-170) cc_final: 0.8410 (m170) REVERT: A 1068 MET cc_start: 0.7490 (mmm) cc_final: 0.6911 (mmm) REVERT: A 1119 LEU cc_start: 0.5104 (mm) cc_final: 0.4859 (mm) outliers start: 19 outliers final: 15 residues processed: 89 average time/residue: 0.0685 time to fit residues: 8.9362 Evaluate side-chains 87 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 300 ILE 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 771 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 94 optimal weight: 0.6980 chunk 99 optimal weight: 8.9990 chunk 41 optimal weight: 0.6980 chunk 112 optimal weight: 20.0000 chunk 93 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 100 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 71 optimal weight: 4.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3755 r_free = 0.3755 target = 0.127139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.096011 restraints weight = 19878.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.096449 restraints weight = 13106.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.096953 restraints weight = 10866.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.097579 restraints weight = 8796.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.097720 restraints weight = 8007.787| |-----------------------------------------------------------------------------| r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.4023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10049 Z= 0.124 Angle : 0.624 18.497 13726 Z= 0.314 Chirality : 0.042 0.225 1480 Planarity : 0.004 0.039 1659 Dihedral : 15.608 80.540 1573 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.82 % Allowed : 15.25 % Favored : 82.93 % 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: 0.45 (0.25), residues: 1114 helix: 1.07 (0.24), residues: 456 sheet: -0.07 (0.35), residues: 205 loop : -0.17 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 821 TYR 0.014 0.001 TYR A 397 PHE 0.019 0.001 PHE A 971 TRP 0.012 0.001 TRP A 671 HIS 0.003 0.001 HIS A 242 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.12 (10045) covalent geometry : angle 0.58405 / 0.31 (13714) hydrogen bonds : bond 0.04470 / 2.93 ( 460) hydrogen bonds : angle 4.49197 / 3.16 ( 1286) metal coordination : bond 0.00486 / 0.24 ( 4) metal coordination : angle 7.43764 / 5.61 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1119.95 seconds wall clock time: 20 minutes 1.67 seconds (1201.67 seconds total)