Starting phenix.real_space_refine on Wed Apr 30 19:13:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f6j_50226/04_2025/9f6j_50226.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f6j_50226/04_2025/9f6j_50226.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f6j_50226/04_2025/9f6j_50226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f6j_50226/04_2025/9f6j_50226.map" model { file = "/net/cci-nas-00/data/ceres_data/9f6j_50226/04_2025/9f6j_50226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f6j_50226/04_2025/9f6j_50226.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 6.35, per 1000 atoms: 0.65 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: 2.83 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 3.92 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: 4.52 Time building geometry restraints manager: 3.34 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 1.525 1.555 -0.030 2.00e-02 2.50e+03 2.30e+00 bond pdb=" C4' DA P 29 " pdb=" O4' DA P 29 " ideal model delta sigma weight residual 1.450 1.421 0.029 2.00e-02 2.50e+03 2.03e+00 bond pdb=" C3' DG P 28 " pdb=" C2' DG P 28 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 8.05e-01 bond pdb=" C2' DA T 21 " pdb=" C1' DA T 21 " ideal model delta sigma weight residual 1.525 1.507 0.018 2.00e-02 2.50e+03 7.75e-01 bond pdb=" O4' DA P 29 " pdb=" C1' DA P 29 " ideal model delta sigma weight residual 1.414 1.397 0.017 2.00e-02 2.50e+03 7.26e-01 ... (remaining 10040 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 13000 1.32 - 2.65: 598 2.65 - 3.97: 106 3.97 - 5.30: 8 5.30 - 6.62: 2 Bond angle restraints: 13714 Sorted by residual: angle pdb=" N GLY A 330 " pdb=" CA GLY A 330 " pdb=" C GLY A 330 " ideal model delta sigma weight residual 112.34 118.96 -6.62 2.04e+00 2.40e-01 1.05e+01 angle pdb=" O3' DA P 21 " pdb=" C3' DA P 21 " pdb=" C2' DA P 21 " ideal model delta sigma weight residual 111.50 116.05 -4.55 1.50e+00 4.44e-01 9.20e+00 angle pdb=" C2' DA P 29 " pdb=" C1' DA P 29 " pdb=" N9 DA P 29 " ideal model delta sigma weight residual 113.50 117.86 -4.36 1.50e+00 4.44e-01 8.47e+00 angle pdb=" N ILE A 312 " pdb=" CA ILE A 312 " pdb=" C ILE A 312 " ideal model delta sigma weight residual 112.12 109.74 2.38 8.40e-01 1.42e+00 8.03e+00 angle pdb=" C4' DA P 29 " pdb=" O4' DA P 29 " pdb=" C1' DA P 29 " ideal model delta sigma weight residual 109.70 105.58 4.12 1.50e+00 4.44e-01 7.53e+00 ... (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 - 0.037: 1025 0.037 - 0.075: 326 0.075 - 0.112: 99 0.112 - 0.150: 26 0.150 - 0.187: 4 Chirality restraints: 1480 Sorted by residual: chirality pdb=" C4' DA P 29 " pdb=" C5' DA P 29 " pdb=" O4' DA P 29 " pdb=" C3' DA P 29 " both_signs ideal model delta sigma weight residual False -2.53 -2.34 -0.19 2.00e-01 2.50e+01 8.75e-01 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 -2.66 -2.49 -0.17 2.00e-01 2.50e+01 7.31e-01 chirality pdb=" CA PHE A 905 " pdb=" N PHE A 905 " pdb=" C PHE A 905 " pdb=" CB PHE A 905 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.99e-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: 1.060 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 32.950 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7799 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= 0.136 Angle : 0.903 47.045 13726 Z= 0.395 Chirality : 0.042 0.187 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.033 0.006 TRP A 671 HIS 0.011 0.002 HIS A 708 PHE 0.028 0.004 PHE A 119 TYR 0.050 0.005 TYR A 892 ARG 0.022 0.003 ARG A 310 Details of bonding type rmsd hydrogen bonds : bond 0.14756 ( 460) hydrogen bonds : angle 7.19942 ( 1286) metal coordination : bond 0.03407 ( 4) metal coordination : angle 21.50317 ( 12) covalent geometry : bond 0.00264 (10045) covalent geometry : angle 0.64143 (13714) *********************** 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 : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.8885 (p90) cc_final: 0.8471 (p90) REVERT: A 157 PHE cc_start: 0.8835 (m-80) cc_final: 0.8392 (m-10) REVERT: A 397 TYR cc_start: 0.7417 (m-80) cc_final: 0.5931 (m-10) REVERT: A 416 TYR cc_start: 0.7901 (m-80) cc_final: 0.7687 (m-10) REVERT: A 601 ASP cc_start: 0.7940 (m-30) cc_final: 0.7714 (t0) REVERT: A 688 HIS cc_start: 0.8493 (t-170) cc_final: 0.8241 (m170) REVERT: A 791 VAL cc_start: 0.8192 (t) cc_final: 0.7712 (p) REVERT: A 818 TYR cc_start: 0.8572 (t80) cc_final: 0.7131 (t80) REVERT: A 857 LEU cc_start: 0.9259 (mt) cc_final: 0.8912 (mt) outliers start: 0 outliers final: 0 residues processed: 194 average time/residue: 0.2996 time to fit residues: 75.7817 Evaluate side-chains 85 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.9990 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 45 optimal weight: 0.3980 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 65 optimal weight: 0.1980 chunk 102 optimal weight: 3.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 HIS A 394 GLN A 422 HIS A 852 GLN A 960 ASN A1036 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.131053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.097749 restraints weight = 19810.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.098213 restraints weight = 13428.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.098571 restraints weight = 10693.851| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10049 Z= 0.141 Angle : 0.667 25.033 13726 Z= 0.332 Chirality : 0.042 0.148 1480 Planarity : 0.005 0.042 1659 Dihedral : 15.522 88.723 1573 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 2.02 % Allowed : 7.98 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.25), residues: 1114 helix: 0.60 (0.23), residues: 459 sheet: 0.12 (0.34), residues: 207 loop : 0.11 (0.31), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 671 HIS 0.013 0.001 HIS A 229 PHE 0.027 0.002 PHE A 119 TYR 0.012 0.001 TYR A 467 ARG 0.004 0.000 ARG A 446 Details of bonding type rmsd hydrogen bonds : bond 0.04828 ( 460) hydrogen bonds : angle 5.05708 ( 1286) metal coordination : bond 0.00548 ( 4) metal coordination : angle 9.62829 ( 12) covalent geometry : bond 0.00300 (10045) covalent geometry : angle 0.60312 (13714) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 1.110 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 138 ASP cc_start: 0.8498 (t0) cc_final: 0.7336 (p0) REVERT: A 157 PHE cc_start: 0.8862 (m-80) cc_final: 0.8460 (m-80) REVERT: A 444 MET cc_start: 0.7523 (ptp) cc_final: 0.7226 (ptp) REVERT: A 688 HIS cc_start: 0.8605 (t-170) cc_final: 0.8315 (m170) REVERT: A 779 LEU cc_start: 0.8028 (tt) cc_final: 0.7748 (tt) REVERT: A 1165 ASP cc_start: 0.7298 (p0) cc_final: 0.7076 (m-30) outliers start: 20 outliers final: 11 residues processed: 121 average time/residue: 0.2417 time to fit residues: 41.9935 Evaluate side-chains 92 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 1.170 ------------------------------------------------------------------------------- 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 445 CYS 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 1151 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 3 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 25 optimal weight: 0.4980 chunk 9 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 99 optimal weight: 1.9990 chunk 100 optimal weight: 1.9990 chunk 86 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 580 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.130647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.097697 restraints weight = 20106.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.098091 restraints weight = 13445.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.098492 restraints weight = 11159.047| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 10049 Z= 0.123 Angle : 0.594 21.001 13726 Z= 0.299 Chirality : 0.041 0.217 1480 Planarity : 0.004 0.039 1659 Dihedral : 15.096 83.962 1573 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.42 % Allowed : 9.60 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.25), residues: 1114 helix: 1.01 (0.24), residues: 459 sheet: 0.26 (0.35), residues: 194 loop : 0.22 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 671 HIS 0.003 0.001 HIS A1163 PHE 0.033 0.002 PHE A 971 TYR 0.012 0.001 TYR A 244 ARG 0.003 0.000 ARG A1082 Details of bonding type rmsd hydrogen bonds : bond 0.04273 ( 460) hydrogen bonds : angle 4.62175 ( 1286) metal coordination : bond 0.00491 ( 4) metal coordination : angle 8.13920 ( 12) covalent geometry : bond 0.00264 (10045) covalent geometry : angle 0.54352 (13714) *********************** 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 114 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7462 (m-30) cc_final: 0.6777 (p0) REVERT: A 138 ASP cc_start: 0.8588 (t0) cc_final: 0.7377 (p0) REVERT: A 244 TYR cc_start: 0.8725 (m-80) cc_final: 0.7669 (m-80) REVERT: A 447 MET cc_start: 0.8104 (mmt) cc_final: 0.7642 (mmp) REVERT: A 473 TYR cc_start: 0.8322 (m-80) cc_final: 0.8051 (m-10) REVERT: A 688 HIS cc_start: 0.8628 (t-170) cc_final: 0.8373 (m170) REVERT: A 1165 ASP cc_start: 0.7592 (p0) cc_final: 0.7223 (m-30) outliers start: 24 outliers final: 17 residues processed: 107 average time/residue: 0.2421 time to fit residues: 37.1158 Evaluate side-chains 100 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 6.9990 chunk 100 optimal weight: 0.4980 chunk 35 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.126884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.094104 restraints weight = 20006.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.094349 restraints weight = 13921.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.094656 restraints weight = 11408.798| |-----------------------------------------------------------------------------| r_work (final): 0.3254 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.3496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10049 Z= 0.155 Angle : 0.632 24.584 13726 Z= 0.308 Chirality : 0.042 0.145 1480 Planarity : 0.005 0.042 1659 Dihedral : 15.207 82.823 1573 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.63 % Allowed : 11.21 % Favored : 86.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1114 helix: 0.96 (0.24), residues: 461 sheet: 0.08 (0.35), residues: 201 loop : 0.14 (0.31), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 671 HIS 0.004 0.001 HIS A1168 PHE 0.031 0.002 PHE A 971 TYR 0.015 0.001 TYR A 754 ARG 0.005 0.000 ARG A 955 Details of bonding type rmsd hydrogen bonds : bond 0.04896 ( 460) hydrogen bonds : angle 4.58695 ( 1286) metal coordination : bond 0.01027 ( 4) metal coordination : angle 9.54692 ( 12) covalent geometry : bond 0.00355 (10045) covalent geometry : angle 0.56528 (13714) *********************** 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 112 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 1.326 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8058 (tmm-80) REVERT: A 83 ASP cc_start: 0.7567 (m-30) cc_final: 0.6580 (p0) REVERT: A 138 ASP cc_start: 0.8617 (t0) cc_final: 0.7464 (p0) REVERT: A 221 MET cc_start: 0.8663 (ptm) cc_final: 0.8243 (ptp) REVERT: A 263 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8682 (mm) REVERT: A 293 ILE cc_start: 0.7972 (mt) cc_final: 0.7626 (tp) REVERT: A 359 MET cc_start: 0.8698 (tpp) cc_final: 0.8081 (mpp) REVERT: A 447 MET cc_start: 0.8167 (mmt) cc_final: 0.7871 (mmt) REVERT: A 473 TYR cc_start: 0.8587 (m-80) cc_final: 0.8309 (m-10) REVERT: A 559 ARG cc_start: 0.7578 (tmm-80) cc_final: 0.6485 (ptt-90) REVERT: A 688 HIS cc_start: 0.8674 (t-170) cc_final: 0.8370 (m170) REVERT: A 1165 ASP cc_start: 0.7644 (p0) cc_final: 0.7303 (m-30) outliers start: 26 outliers final: 19 residues processed: 105 average time/residue: 0.2955 time to fit residues: 44.5601 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 : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 72 LEU Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 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 54 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 50 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 33 optimal weight: 0.0170 chunk 84 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.5824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.126268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.093780 restraints weight = 19997.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.093920 restraints weight = 14039.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.094312 restraints weight = 11766.143| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 10049 Z= 0.161 Angle : 0.629 22.932 13726 Z= 0.307 Chirality : 0.042 0.268 1480 Planarity : 0.005 0.043 1659 Dihedral : 15.184 82.623 1573 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.73 % Allowed : 12.73 % Favored : 84.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1114 helix: 1.08 (0.24), residues: 456 sheet: -0.06 (0.35), residues: 205 loop : -0.00 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 671 HIS 0.004 0.001 HIS A1163 PHE 0.026 0.002 PHE A 971 TYR 0.011 0.001 TYR A 754 ARG 0.007 0.000 ARG A 446 Details of bonding type rmsd hydrogen bonds : bond 0.04814 ( 460) hydrogen bonds : angle 4.58682 ( 1286) metal coordination : bond 0.01036 ( 4) metal coordination : angle 9.03748 ( 12) covalent geometry : bond 0.00372 (10045) covalent geometry : angle 0.56985 (13714) *********************** 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 110 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8989 (OUTLIER) cc_final: 0.8554 (tmm-80) REVERT: A 83 ASP cc_start: 0.7665 (m-30) cc_final: 0.6576 (p0) REVERT: A 138 ASP cc_start: 0.8733 (t0) cc_final: 0.7762 (p0) REVERT: A 221 MET cc_start: 0.8664 (ptm) cc_final: 0.8205 (ptp) REVERT: A 244 TYR cc_start: 0.8786 (m-80) cc_final: 0.7945 (m-80) REVERT: A 263 LEU cc_start: 0.8978 (OUTLIER) cc_final: 0.8717 (mm) REVERT: A 359 MET cc_start: 0.8688 (tpp) cc_final: 0.8157 (mpp) REVERT: A 447 MET cc_start: 0.8187 (mmt) cc_final: 0.7948 (mmt) REVERT: A 528 THR cc_start: 0.6482 (OUTLIER) cc_final: 0.6172 (p) REVERT: A 559 ARG cc_start: 0.7653 (tmm-80) cc_final: 0.6813 (ptt-90) REVERT: A 688 HIS cc_start: 0.8751 (t-170) cc_final: 0.8408 (m170) outliers start: 27 outliers final: 20 residues processed: 106 average time/residue: 0.2277 time to fit residues: 34.5517 Evaluate side-chains 92 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 69 time to evaluate : 1.056 ------------------------------------------------------------------------------- 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 131 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 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 29 optimal weight: 0.1980 chunk 90 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 96 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 111 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.128240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.096346 restraints weight = 20085.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.096233 restraints weight = 13259.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.096726 restraints weight = 11833.493| |-----------------------------------------------------------------------------| r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.4062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10049 Z= 0.119 Angle : 0.571 16.402 13726 Z= 0.288 Chirality : 0.040 0.144 1480 Planarity : 0.004 0.040 1659 Dihedral : 15.074 81.331 1573 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.32 % Allowed : 13.54 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.25), residues: 1114 helix: 1.21 (0.24), residues: 461 sheet: 0.13 (0.37), residues: 195 loop : -0.07 (0.30), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 671 HIS 0.003 0.001 HIS A 242 PHE 0.026 0.001 PHE A 971 TYR 0.011 0.001 TYR A1133 ARG 0.007 0.000 ARG A 446 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 460) hydrogen bonds : angle 4.33102 ( 1286) metal coordination : bond 0.00452 ( 4) metal coordination : angle 6.67852 ( 12) covalent geometry : bond 0.00261 (10045) covalent geometry : angle 0.53651 (13714) *********************** 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 102 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 79 time to evaluate : 1.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8552 (tmm-80) REVERT: A 83 ASP cc_start: 0.7566 (m-30) cc_final: 0.6509 (p0) REVERT: A 138 ASP cc_start: 0.8667 (t0) cc_final: 0.7686 (p0) REVERT: A 244 TYR cc_start: 0.8686 (m-80) cc_final: 0.7801 (m-80) REVERT: A 263 LEU cc_start: 0.8946 (OUTLIER) cc_final: 0.8659 (mm) REVERT: A 359 MET cc_start: 0.8807 (tpp) cc_final: 0.8273 (mpp) REVERT: A 383 MET cc_start: 0.5536 (ttp) cc_final: 0.5255 (ttm) REVERT: A 528 THR cc_start: 0.6716 (OUTLIER) cc_final: 0.6435 (p) REVERT: A 559 ARG cc_start: 0.7573 (tmm-80) cc_final: 0.6723 (ptt-90) REVERT: A 688 HIS cc_start: 0.8622 (t-170) cc_final: 0.8391 (m170) REVERT: A 1068 MET cc_start: 0.6807 (mmm) cc_final: 0.6515 (mmm) outliers start: 23 outliers final: 19 residues processed: 98 average time/residue: 0.2397 time to fit residues: 33.2918 Evaluate side-chains 92 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 70 time to evaluate : 1.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1016 VAL 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 1 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 105 optimal weight: 0.3980 chunk 16 optimal weight: 0.8980 chunk 5 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.129017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.097849 restraints weight = 20171.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.097421 restraints weight = 13406.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.098271 restraints weight = 12281.822| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4255 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= 0.117 Angle : 0.556 16.518 13726 Z= 0.279 Chirality : 0.040 0.140 1480 Planarity : 0.004 0.041 1659 Dihedral : 14.988 78.684 1573 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.83 % Allowed : 13.33 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.25), residues: 1114 helix: 1.30 (0.24), residues: 463 sheet: 0.10 (0.37), residues: 195 loop : -0.13 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 671 HIS 0.003 0.001 HIS A 242 PHE 0.031 0.001 PHE A 971 TYR 0.011 0.001 TYR A 754 ARG 0.008 0.000 ARG A 446 Details of bonding type rmsd hydrogen bonds : bond 0.03972 ( 460) hydrogen bonds : angle 4.22792 ( 1286) metal coordination : bond 0.00469 ( 4) metal coordination : angle 6.68429 ( 12) covalent geometry : bond 0.00258 (10045) covalent geometry : angle 0.51960 (13714) *********************** 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 105 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 77 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8069 (tmm-80) REVERT: A 83 ASP cc_start: 0.7555 (m-30) cc_final: 0.6546 (p0) REVERT: A 138 ASP cc_start: 0.8637 (t0) cc_final: 0.7665 (p0) REVERT: A 221 MET cc_start: 0.8461 (ptm) cc_final: 0.8117 (ptp) REVERT: A 244 TYR cc_start: 0.8703 (m-80) cc_final: 0.7826 (m-80) REVERT: A 263 LEU cc_start: 0.8966 (OUTLIER) cc_final: 0.8676 (mm) REVERT: A 294 MET cc_start: 0.5094 (mmm) cc_final: 0.4809 (tpp) REVERT: A 359 MET cc_start: 0.8795 (tpp) cc_final: 0.8275 (mpp) REVERT: A 528 THR cc_start: 0.6821 (OUTLIER) cc_final: 0.6552 (p) REVERT: A 559 ARG cc_start: 0.7565 (tmm-80) cc_final: 0.6713 (ptt-90) REVERT: A 688 HIS cc_start: 0.8551 (t-170) cc_final: 0.8350 (m170) outliers start: 28 outliers final: 20 residues processed: 98 average time/residue: 0.2494 time to fit residues: 34.9781 Evaluate side-chains 93 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 1.190 ------------------------------------------------------------------------------- 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 131 VAL Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1119 LEU 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 6 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 58 optimal weight: 0.0030 chunk 21 optimal weight: 0.3980 chunk 8 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 71 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 111 optimal weight: 7.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.129000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.097581 restraints weight = 20179.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.097853 restraints weight = 13441.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.098486 restraints weight = 11318.940| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.4387 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= 0.119 Angle : 0.564 16.187 13726 Z= 0.282 Chirality : 0.040 0.138 1480 Planarity : 0.004 0.042 1659 Dihedral : 14.968 77.236 1573 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.93 % Allowed : 13.13 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.25), residues: 1114 helix: 1.37 (0.24), residues: 461 sheet: 0.15 (0.37), residues: 195 loop : -0.11 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 671 HIS 0.002 0.001 HIS A 242 PHE 0.029 0.001 PHE A 971 TYR 0.010 0.001 TYR A 754 ARG 0.008 0.000 ARG A 446 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 460) hydrogen bonds : angle 4.20753 ( 1286) metal coordination : bond 0.00475 ( 4) metal coordination : angle 6.57172 ( 12) covalent geometry : bond 0.00265 (10045) covalent geometry : angle 0.52989 (13714) *********************** 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 106 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 77 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8093 (tmm-80) REVERT: A 83 ASP cc_start: 0.7548 (m-30) cc_final: 0.6538 (p0) REVERT: A 138 ASP cc_start: 0.8653 (t0) cc_final: 0.7671 (p0) REVERT: A 221 MET cc_start: 0.8422 (ptm) cc_final: 0.8060 (ptp) REVERT: A 244 TYR cc_start: 0.8691 (m-80) cc_final: 0.7788 (m-80) REVERT: A 263 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8682 (mm) REVERT: A 359 MET cc_start: 0.8789 (tpp) cc_final: 0.8274 (mpp) REVERT: A 528 THR cc_start: 0.6836 (OUTLIER) cc_final: 0.6569 (p) REVERT: A 559 ARG cc_start: 0.7554 (tmm-80) cc_final: 0.6737 (ptt-90) REVERT: A 688 HIS cc_start: 0.8576 (t-170) cc_final: 0.8368 (m170) REVERT: A 993 PHE cc_start: 0.8432 (OUTLIER) cc_final: 0.7172 (t80) REVERT: A 1068 MET cc_start: 0.6663 (mmp) cc_final: 0.6099 (mmm) outliers start: 29 outliers final: 19 residues processed: 97 average time/residue: 0.2319 time to fit residues: 32.7493 Evaluate side-chains 96 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 1.078 ------------------------------------------------------------------------------- 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 131 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 109 optimal weight: 0.0370 chunk 62 optimal weight: 9.9990 chunk 11 optimal weight: 0.0870 chunk 46 optimal weight: 0.0070 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.131127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.099260 restraints weight = 20429.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.099139 restraints weight = 13713.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.099742 restraints weight = 11860.306| |-----------------------------------------------------------------------------| r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10049 Z= 0.105 Angle : 0.542 12.618 13726 Z= 0.273 Chirality : 0.039 0.199 1480 Planarity : 0.004 0.056 1659 Dihedral : 14.856 75.516 1573 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 1.92 % Allowed : 13.74 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.25), residues: 1114 helix: 1.52 (0.25), residues: 459 sheet: 0.20 (0.37), residues: 195 loop : -0.10 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 671 HIS 0.004 0.001 HIS A1108 PHE 0.009 0.001 PHE A 332 TYR 0.009 0.001 TYR A 468 ARG 0.008 0.000 ARG A 446 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 460) hydrogen bonds : angle 4.05992 ( 1286) metal coordination : bond 0.00199 ( 4) metal coordination : angle 5.69376 ( 12) covalent geometry : bond 0.00225 (10045) covalent geometry : angle 0.51518 (13714) *********************** 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 110 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8105 (tmm-80) REVERT: A 83 ASP cc_start: 0.7415 (m-30) cc_final: 0.6479 (p0) REVERT: A 103 TYR cc_start: 0.8499 (p90) cc_final: 0.8276 (p90) REVERT: A 138 ASP cc_start: 0.8572 (t0) cc_final: 0.7534 (p0) REVERT: A 244 TYR cc_start: 0.8629 (m-80) cc_final: 0.7842 (m-80) REVERT: A 247 ARG cc_start: 0.7137 (tpt-90) cc_final: 0.6912 (ttm-80) REVERT: A 263 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8627 (mm) REVERT: A 359 MET cc_start: 0.8784 (tpp) cc_final: 0.8216 (mpp) REVERT: A 528 THR cc_start: 0.6767 (OUTLIER) cc_final: 0.6495 (p) REVERT: A 559 ARG cc_start: 0.7488 (tmm-80) cc_final: 0.6683 (ptt-90) REVERT: A 623 TYR cc_start: 0.8289 (m-10) cc_final: 0.8067 (m-10) REVERT: A 688 HIS cc_start: 0.8628 (t-170) cc_final: 0.8380 (m170) REVERT: A 993 PHE cc_start: 0.8315 (OUTLIER) cc_final: 0.7194 (t80) REVERT: A 1068 MET cc_start: 0.6441 (mmp) cc_final: 0.6146 (mmm) outliers start: 19 outliers final: 12 residues processed: 103 average time/residue: 0.2265 time to fit residues: 34.0920 Evaluate side-chains 93 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 131 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1052 THR 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 2 optimal weight: 2.9990 chunk 34 optimal weight: 0.0170 chunk 46 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 56 optimal weight: 0.6980 chunk 88 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 58 optimal weight: 3.9990 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.130665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.098996 restraints weight = 19988.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.099689 restraints weight = 13155.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.100033 restraints weight = 10430.197| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7913 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 10049 Z= 0.111 Angle : 0.557 14.794 13726 Z= 0.280 Chirality : 0.039 0.208 1480 Planarity : 0.004 0.053 1659 Dihedral : 14.824 73.163 1573 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.82 % Allowed : 14.44 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.25), residues: 1114 helix: 1.58 (0.25), residues: 458 sheet: 0.20 (0.37), residues: 195 loop : -0.17 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A1113 HIS 0.003 0.001 HIS A 242 PHE 0.024 0.001 PHE A 971 TYR 0.011 0.001 TYR A 397 ARG 0.010 0.000 ARG A 446 Details of bonding type rmsd hydrogen bonds : bond 0.03587 ( 460) hydrogen bonds : angle 4.02138 ( 1286) metal coordination : bond 0.00369 ( 4) metal coordination : angle 6.10466 ( 12) covalent geometry : bond 0.00246 (10045) covalent geometry : angle 0.52704 (13714) ********************** 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 98 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 80 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8599 (tmm-80) REVERT: A 83 ASP cc_start: 0.7455 (m-30) cc_final: 0.6509 (p0) REVERT: A 103 TYR cc_start: 0.8516 (p90) cc_final: 0.8285 (p90) REVERT: A 138 ASP cc_start: 0.8609 (t0) cc_final: 0.7708 (p0) REVERT: A 244 TYR cc_start: 0.8681 (m-80) cc_final: 0.7868 (m-80) REVERT: A 247 ARG cc_start: 0.7167 (tpt-90) cc_final: 0.6935 (ttm-80) REVERT: A 263 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8674 (mm) REVERT: A 294 MET cc_start: 0.4415 (mmm) cc_final: 0.4166 (mmm) REVERT: A 359 MET cc_start: 0.8785 (tpp) cc_final: 0.8243 (mpp) REVERT: A 528 THR cc_start: 0.6571 (OUTLIER) cc_final: 0.6335 (p) REVERT: A 559 ARG cc_start: 0.7499 (tmm-80) cc_final: 0.6694 (ptt-90) REVERT: A 623 TYR cc_start: 0.8300 (m-10) cc_final: 0.8088 (m-10) REVERT: A 993 PHE cc_start: 0.8381 (OUTLIER) cc_final: 0.7166 (t80) REVERT: A 1068 MET cc_start: 0.6298 (mmp) cc_final: 0.5862 (mmm) outliers start: 18 outliers final: 13 residues processed: 91 average time/residue: 0.2658 time to fit residues: 34.4677 Evaluate side-chains 91 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 1.196 ------------------------------------------------------------------------------- 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 131 VAL Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 293 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 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 993 PHE Chi-restraints excluded: chain A residue 1052 THR 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 56 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 52 optimal weight: 0.0010 chunk 87 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 78 optimal weight: 1.9990 chunk 105 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.130308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.098056 restraints weight = 20080.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.098156 restraints weight = 13317.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.098530 restraints weight = 11291.493| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.4838 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= 0.114 Angle : 0.565 14.989 13726 Z= 0.282 Chirality : 0.040 0.203 1480 Planarity : 0.004 0.052 1659 Dihedral : 14.826 71.592 1573 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.92 % Allowed : 14.34 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.25), residues: 1114 helix: 1.63 (0.25), residues: 456 sheet: 0.18 (0.37), residues: 195 loop : -0.21 (0.29), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A1113 HIS 0.004 0.001 HIS A 688 PHE 0.011 0.001 PHE A 371 TYR 0.009 0.001 TYR A 754 ARG 0.010 0.000 ARG A 446 Details of bonding type rmsd hydrogen bonds : bond 0.03628 ( 460) hydrogen bonds : angle 4.03268 ( 1286) metal coordination : bond 0.00392 ( 4) metal coordination : angle 6.17112 ( 12) covalent geometry : bond 0.00252 (10045) covalent geometry : angle 0.53466 (13714) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3053.01 seconds wall clock time: 55 minutes 36.26 seconds (3336.26 seconds total)