Starting phenix.real_space_refine on Thu Jan 16 18:31:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f6j_50226/01_2025/9f6j_50226.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f6j_50226/01_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_50226/01_2025/9f6j_50226.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f6j_50226/01_2025/9f6j_50226.map" model { file = "/net/cci-nas-00/data/ceres_data/9f6j_50226/01_2025/9f6j_50226.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f6j_50226/01_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-5571/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: 6.02, per 1000 atoms: 0.62 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: 2.62 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: 3.50 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: 4.62 Time building geometry restraints manager: 3.07 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: 0.910 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: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 30.530 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.960 ------------------------------------------------------------------------------- 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 0.034 10045 Z= 0.165 Angle : 0.641 6.621 13714 Z= 0.391 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 *********************** 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 : 1.075 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: 0.3048 time to fit residues: 76.4122 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 : 1.145 ------------------------------------------------------------------------------- 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 = 0.097763 restraints weight = 19809.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.098228 restraints weight = 13417.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.098583 restraints weight = 10680.844| |-----------------------------------------------------------------------------| r_work (final): 0.3321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 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 10045 Z= 0.190 Angle : 0.603 6.418 13714 Z= 0.331 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 *********************** 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 : 1.052 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: 0.8461 (m-80) REVERT: A 444 MET cc_start: 0.7523 (ptp) cc_final: 0.7225 (ptp) REVERT: A 688 HIS cc_start: 0.8605 (t-170) cc_final: 0.8315 (m170) REVERT: A 779 LEU cc_start: 0.8027 (tt) cc_final: 0.7748 (tt) REVERT: A 1165 ASP cc_start: 0.7297 (p0) cc_final: 0.7075 (m-30) outliers start: 20 outliers final: 11 residues processed: 121 average time/residue: 0.2261 time to fit residues: 38.9240 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 : 1.118 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.7980 chunk 99 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3805 r_free = 0.3805 target = 0.130960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.098114 restraints weight = 20079.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.098608 restraints weight = 13317.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.099001 restraints weight = 11008.333| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.3111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10045 Z= 0.163 Angle : 0.542 6.504 13714 Z= 0.297 Chirality : 0.041 0.179 1480 Planarity : 0.004 0.039 1659 Dihedral : 15.076 83.830 1573 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.42 % Allowed : 9.70 % 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 (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: 0.75 (0.25), residues: 1114 helix: 1.04 (0.24), residues: 458 sheet: 0.27 (0.35), residues: 194 loop : 0.22 (0.30), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 671 HIS 0.003 0.001 HIS A1163 PHE 0.032 0.001 PHE A 971 TYR 0.012 0.001 TYR A1133 ARG 0.003 0.000 ARG A1082 *********************** 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: 24 poor density : 92 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ASP cc_start: 0.7453 (m-30) cc_final: 0.6823 (p0) REVERT: A 138 ASP cc_start: 0.8576 (t0) cc_final: 0.7373 (p0) REVERT: A 244 TYR cc_start: 0.8704 (m-80) cc_final: 0.7687 (m-80) REVERT: A 447 MET cc_start: 0.8129 (mmt) cc_final: 0.7668 (mmp) REVERT: A 473 TYR cc_start: 0.8304 (m-80) cc_final: 0.8038 (m-10) REVERT: A 688 HIS cc_start: 0.8601 (t-170) cc_final: 0.8365 (m170) REVERT: A 783 VAL cc_start: 0.8060 (t) cc_final: 0.7824 (t) outliers start: 24 outliers final: 16 residues processed: 108 average time/residue: 0.2174 time to fit residues: 33.4079 Evaluate side-chains 98 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 LYS 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: 0.0970 chunk 105 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 104 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 10 optimal weight: 0.6980 chunk 36 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.130360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.097814 restraints weight = 19910.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.098278 restraints weight = 13469.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.098838 restraints weight = 10981.956| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10045 Z= 0.159 Angle : 0.525 7.891 13714 Z= 0.284 Chirality : 0.040 0.143 1480 Planarity : 0.004 0.038 1659 Dihedral : 15.054 83.629 1573 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.32 % Allowed : 11.31 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.85 (0.25), residues: 1114 helix: 1.19 (0.24), residues: 458 sheet: 0.22 (0.35), residues: 201 loop : 0.24 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 671 HIS 0.003 0.001 HIS A 242 PHE 0.025 0.001 PHE A 971 TYR 0.010 0.001 TYR A 754 ARG 0.005 0.000 ARG A 446 *********************** 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 111 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 88 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8896 (OUTLIER) cc_final: 0.8031 (tmm-80) REVERT: A 83 ASP cc_start: 0.7348 (m-30) cc_final: 0.6682 (p0) REVERT: A 138 ASP cc_start: 0.8573 (t0) cc_final: 0.7283 (p0) REVERT: A 221 MET cc_start: 0.8613 (ptm) cc_final: 0.8320 (ptt) REVERT: A 244 TYR cc_start: 0.8705 (m-80) cc_final: 0.7819 (m-80) REVERT: A 263 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8496 (mm) REVERT: A 359 MET cc_start: 0.8635 (tpp) cc_final: 0.8056 (mpp) REVERT: A 447 MET cc_start: 0.8231 (mmt) cc_final: 0.7977 (mmt) REVERT: A 473 TYR cc_start: 0.8445 (m-80) cc_final: 0.8050 (m-10) REVERT: A 559 ARG cc_start: 0.7424 (tmm-80) cc_final: 0.6520 (ptt-90) REVERT: A 688 HIS cc_start: 0.8603 (t-170) cc_final: 0.8347 (m170) outliers start: 23 outliers final: 18 residues processed: 105 average time/residue: 0.2381 time to fit residues: 35.2850 Evaluate side-chains 97 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 1.377 ------------------------------------------------------------------------------- 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 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 445 CYS 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 755 VAL 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: 0.8980 chunk 35 optimal weight: 0.0170 chunk 50 optimal weight: 5.9990 chunk 109 optimal weight: 0.5980 chunk 16 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 33 optimal weight: 0.2980 chunk 84 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 overall best weight: 0.5218 ------------------------------------------------------------------------------- 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 = 0.3810 r_free = 0.3810 target = 0.131364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.099042 restraints weight = 19855.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.099165 restraints weight = 13341.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.099599 restraints weight = 11417.315| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 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 : 0.002 0.022 10045 Z= 0.142 Angle : 0.512 7.575 13714 Z= 0.272 Chirality : 0.039 0.133 1480 Planarity : 0.004 0.036 1659 Dihedral : 14.877 83.146 1573 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.22 % Allowed : 12.42 % Favored : 85.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.89 (0.25), residues: 1114 helix: 1.34 (0.24), residues: 458 sheet: 0.20 (0.36), residues: 205 loop : 0.15 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 671 HIS 0.002 0.001 HIS A 242 PHE 0.020 0.001 PHE A 971 TYR 0.009 0.001 TYR A 754 ARG 0.007 0.000 ARG A 446 *********************** 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 108 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 86 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8049 (tmm-80) REVERT: A 83 ASP cc_start: 0.7332 (m-30) cc_final: 0.6709 (p0) REVERT: A 103 TYR cc_start: 0.8454 (p90) cc_final: 0.8179 (p90) REVERT: A 138 ASP cc_start: 0.8555 (t0) cc_final: 0.7274 (p0) REVERT: A 244 TYR cc_start: 0.8656 (m-80) cc_final: 0.7960 (m-80) REVERT: A 263 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8512 (mm) REVERT: A 359 MET cc_start: 0.8630 (tpp) cc_final: 0.8023 (mpp) REVERT: A 383 MET cc_start: 0.5787 (ttp) cc_final: 0.5311 (ttm) REVERT: A 473 TYR cc_start: 0.8455 (m-80) cc_final: 0.8050 (m-10) REVERT: A 528 THR cc_start: 0.6641 (OUTLIER) cc_final: 0.6370 (p) REVERT: A 559 ARG cc_start: 0.7469 (tmm-80) cc_final: 0.6566 (ptt-90) REVERT: A 562 MET cc_start: 0.8713 (mmm) cc_final: 0.8426 (mmm) REVERT: A 688 HIS cc_start: 0.8686 (t-170) cc_final: 0.8338 (m170) outliers start: 22 outliers final: 15 residues processed: 103 average time/residue: 0.2717 time to fit residues: 39.8254 Evaluate side-chains 93 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 75 time to evaluate : 1.547 ------------------------------------------------------------------------------- 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 300 ILE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 444 MET 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 755 VAL 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 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: 2.9990 chunk 90 optimal weight: 0.2980 chunk 89 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 111 optimal weight: 6.9990 chunk 68 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- 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 = 0.3797 r_free = 0.3797 target = 0.130316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.097783 restraints weight = 19913.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.097916 restraints weight = 13554.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.098356 restraints weight = 11455.740| |-----------------------------------------------------------------------------| r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.3990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10045 Z= 0.164 Angle : 0.514 6.995 13714 Z= 0.276 Chirality : 0.039 0.133 1480 Planarity : 0.004 0.038 1659 Dihedral : 14.832 79.994 1573 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 2.22 % Allowed : 13.33 % 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 (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: 1.35 (0.24), residues: 460 sheet: 0.21 (0.36), residues: 205 loop : 0.11 (0.30), residues: 449 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 0.023 0.001 PHE A 119 TYR 0.010 0.001 TYR A 754 ARG 0.008 0.000 ARG A 446 *********************** 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 103 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 81 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8089 (tmm-80) REVERT: A 83 ASP cc_start: 0.7383 (m-30) cc_final: 0.6695 (p0) REVERT: A 103 TYR cc_start: 0.8481 (p90) cc_final: 0.8224 (p90) REVERT: A 138 ASP cc_start: 0.8499 (t0) cc_final: 0.7323 (p0) REVERT: A 244 TYR cc_start: 0.8705 (m-80) cc_final: 0.8055 (m-80) REVERT: A 263 LEU cc_start: 0.8915 (OUTLIER) cc_final: 0.8541 (mm) REVERT: A 359 MET cc_start: 0.8778 (tpp) cc_final: 0.8214 (mpp) REVERT: A 528 THR cc_start: 0.6698 (OUTLIER) cc_final: 0.6423 (p) REVERT: A 559 ARG cc_start: 0.7484 (tmm-80) cc_final: 0.6614 (ptt-90) REVERT: A 562 MET cc_start: 0.8577 (mmm) cc_final: 0.8286 (mmm) REVERT: A 688 HIS cc_start: 0.8731 (t-170) cc_final: 0.8422 (m170) REVERT: A 1068 MET cc_start: 0.6668 (mmm) cc_final: 0.6316 (mmm) outliers start: 22 outliers final: 16 residues processed: 99 average time/residue: 0.2329 time to fit residues: 33.0793 Evaluate side-chains 91 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 72 time to evaluate : 1.082 ------------------------------------------------------------------------------- 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 360 VAL Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 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: 5.9990 chunk 76 optimal weight: 0.9980 chunk 105 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 83 optimal weight: 0.0980 chunk 99 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3804 r_free = 0.3804 target = 0.130778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.098293 restraints weight = 20193.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.098272 restraints weight = 13624.441| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.098780 restraints weight = 11592.239| |-----------------------------------------------------------------------------| r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10045 Z= 0.155 Angle : 0.516 7.893 13714 Z= 0.273 Chirality : 0.039 0.133 1480 Planarity : 0.004 0.037 1659 Dihedral : 14.788 78.812 1573 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.53 % Allowed : 13.23 % 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 (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: 0.87 (0.25), residues: 1114 helix: 1.35 (0.24), residues: 467 sheet: 0.21 (0.36), residues: 205 loop : 0.06 (0.30), residues: 442 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 0.016 0.001 PHE A 971 TYR 0.012 0.001 TYR A1133 ARG 0.008 0.000 ARG A 446 *********************** 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 109 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 84 time to evaluate : 1.099 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8564 (tmm-80) REVERT: A 83 ASP cc_start: 0.7426 (m-30) cc_final: 0.6878 (p0) REVERT: A 103 TYR cc_start: 0.8478 (p90) cc_final: 0.8209 (p90) REVERT: A 138 ASP cc_start: 0.8500 (t0) cc_final: 0.7355 (p0) REVERT: A 221 MET cc_start: 0.8550 (ptm) cc_final: 0.8233 (ptm) REVERT: A 244 TYR cc_start: 0.8693 (m-80) cc_final: 0.8134 (m-80) REVERT: A 263 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8610 (mm) REVERT: A 359 MET cc_start: 0.8763 (tpp) cc_final: 0.8179 (mpp) REVERT: A 383 MET cc_start: 0.5929 (ttp) cc_final: 0.5477 (ttm) REVERT: A 528 THR cc_start: 0.6681 (OUTLIER) cc_final: 0.6405 (p) REVERT: A 559 ARG cc_start: 0.7430 (tmm-80) cc_final: 0.6640 (ptt-90) REVERT: A 688 HIS cc_start: 0.8653 (t-170) cc_final: 0.8405 (m170) REVERT: A 993 PHE cc_start: 0.8396 (OUTLIER) cc_final: 0.7326 (t80) outliers start: 25 outliers final: 17 residues processed: 103 average time/residue: 0.2352 time to fit residues: 34.9544 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 : 1.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 215 LEU 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 444 MET 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 755 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 993 PHE 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 6 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 0.0470 chunk 58 optimal weight: 6.9990 chunk 21 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 90 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 111 optimal weight: 8.9990 overall best weight: 0.6678 ------------------------------------------------------------------------------- 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 = 0.130280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.097473 restraints weight = 20263.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.097777 restraints weight = 13788.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.098103 restraints weight = 11217.115| |-----------------------------------------------------------------------------| r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.4369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10045 Z= 0.151 Angle : 0.506 7.390 13714 Z= 0.269 Chirality : 0.039 0.131 1480 Planarity : 0.004 0.054 1659 Dihedral : 14.747 76.539 1573 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 2.32 % Allowed : 13.33 % 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: 0.93 (0.25), residues: 1114 helix: 1.47 (0.24), residues: 461 sheet: 0.23 (0.37), residues: 205 loop : 0.03 (0.29), residues: 448 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 0.024 0.001 PHE A 971 TYR 0.009 0.001 TYR A 754 ARG 0.009 0.000 ARG A 446 *********************** 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 105 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 82 time to evaluate : 1.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8632 (tmm-80) REVERT: A 83 ASP cc_start: 0.7420 (m-30) cc_final: 0.6693 (p0) REVERT: A 103 TYR cc_start: 0.8515 (p90) cc_final: 0.8290 (p90) REVERT: A 138 ASP cc_start: 0.8612 (t0) cc_final: 0.7565 (p0) REVERT: A 221 MET cc_start: 0.8436 (ptm) cc_final: 0.8111 (ptp) REVERT: A 244 TYR cc_start: 0.8699 (m-80) cc_final: 0.8134 (m-80) REVERT: A 263 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8589 (mm) REVERT: A 293 ILE cc_start: 0.7823 (mt) cc_final: 0.7580 (mp) REVERT: A 359 MET cc_start: 0.8761 (tpp) cc_final: 0.8219 (mpp) REVERT: A 383 MET cc_start: 0.5498 (ttp) cc_final: 0.5169 (ttm) REVERT: A 528 THR cc_start: 0.6405 (OUTLIER) cc_final: 0.6157 (p) REVERT: A 559 ARG cc_start: 0.7483 (tmm-80) cc_final: 0.6679 (ptt-90) REVERT: A 688 HIS cc_start: 0.8659 (t-170) cc_final: 0.8414 (m170) outliers start: 23 outliers final: 17 residues processed: 99 average time/residue: 0.2333 time to fit residues: 33.1287 Evaluate side-chains 96 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 1.075 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 218 ILE 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 528 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1145 ILE 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: 2.9990 chunk 62 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 46 optimal weight: 0.0770 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 106 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 105 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 overall best weight: 0.6540 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.138056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.105584 restraints weight = 20650.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.106994 restraints weight = 14548.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.107937 restraints weight = 10516.156| |-----------------------------------------------------------------------------| r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10045 Z= 0.155 Angle : 0.512 7.392 13714 Z= 0.272 Chirality : 0.039 0.205 1480 Planarity : 0.004 0.051 1659 Dihedral : 14.737 75.379 1573 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.63 % Allowed : 13.43 % 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: 0.96 (0.25), residues: 1114 helix: 1.54 (0.24), residues: 460 sheet: 0.22 (0.36), residues: 205 loop : 0.01 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 671 HIS 0.002 0.001 HIS A 242 PHE 0.013 0.001 PHE A 119 TYR 0.009 0.001 TYR A 754 ARG 0.009 0.000 ARG A 446 *********************** 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 105 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 79 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8191 (tmm-80) REVERT: A 83 ASP cc_start: 0.7438 (m-30) cc_final: 0.6914 (p0) REVERT: A 138 ASP cc_start: 0.8455 (t0) cc_final: 0.7773 (p0) REVERT: A 244 TYR cc_start: 0.8593 (m-80) cc_final: 0.8093 (m-80) REVERT: A 263 LEU cc_start: 0.8948 (OUTLIER) cc_final: 0.8641 (mm) REVERT: A 359 MET cc_start: 0.8658 (tpp) cc_final: 0.8065 (mpp) REVERT: A 383 MET cc_start: 0.5564 (ttp) cc_final: 0.5284 (ttm) REVERT: A 559 ARG cc_start: 0.7440 (tmm-80) cc_final: 0.6650 (ptt-90) REVERT: A 645 MET cc_start: 0.8341 (mpp) cc_final: 0.8027 (mpp) REVERT: A 993 PHE cc_start: 0.8352 (OUTLIER) cc_final: 0.7207 (t80) REVERT: A 1068 MET cc_start: 0.6131 (mmp) cc_final: 0.5661 (mmm) REVERT: A 1141 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7615 (tt) outliers start: 26 outliers final: 19 residues processed: 99 average time/residue: 0.2178 time to fit residues: 31.1662 Evaluate side-chains 98 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 75 time to evaluate : 1.029 ------------------------------------------------------------------------------- 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 215 LEU Chi-restraints excluded: chain A residue 218 ILE 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 551 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1141 ILE Chi-restraints excluded: chain A residue 1145 ILE 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: 1.9990 chunk 34 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 43 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 88 optimal weight: 0.2980 chunk 55 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 58 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 = 0.3884 r_free = 0.3884 target = 0.134731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.101831 restraints weight = 20800.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.103210 restraints weight = 14639.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.104204 restraints weight = 10181.110| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10045 Z= 0.162 Angle : 0.520 7.364 13714 Z= 0.278 Chirality : 0.040 0.209 1480 Planarity : 0.004 0.050 1659 Dihedral : 14.754 73.754 1573 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.42 % Allowed : 13.74 % 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: 0.96 (0.25), residues: 1114 helix: 1.59 (0.24), residues: 460 sheet: 0.29 (0.37), residues: 195 loop : -0.09 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 671 HIS 0.002 0.001 HIS A 242 PHE 0.012 0.001 PHE A 104 TYR 0.009 0.001 TYR A 754 ARG 0.010 0.000 ARG A 446 ********************** 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 101 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 1.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8197 (tmm-80) REVERT: A 83 ASP cc_start: 0.7435 (m-30) cc_final: 0.6845 (p0) REVERT: A 138 ASP cc_start: 0.8509 (t0) cc_final: 0.8018 (p0) REVERT: A 244 TYR cc_start: 0.8641 (m-80) cc_final: 0.8107 (m-80) REVERT: A 263 LEU cc_start: 0.8952 (OUTLIER) cc_final: 0.8656 (mm) REVERT: A 359 MET cc_start: 0.8684 (tpp) cc_final: 0.8087 (mpp) REVERT: A 383 MET cc_start: 0.5574 (ttp) cc_final: 0.5290 (ttm) REVERT: A 559 ARG cc_start: 0.7442 (tmm-80) cc_final: 0.6663 (ptt-90) REVERT: A 645 MET cc_start: 0.8354 (mpp) cc_final: 0.8006 (mpp) REVERT: A 993 PHE cc_start: 0.8346 (OUTLIER) cc_final: 0.7109 (t80) REVERT: A 1068 MET cc_start: 0.5919 (mmp) cc_final: 0.5593 (mmm) outliers start: 24 outliers final: 19 residues processed: 95 average time/residue: 0.2477 time to fit residues: 34.3661 Evaluate side-chains 99 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 215 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 551 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 990 PHE Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1145 ILE 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: 0.8980 chunk 95 optimal weight: 1.9990 chunk 100 optimal weight: 0.1980 chunk 52 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 92 optimal weight: 0.2980 chunk 103 optimal weight: 7.9990 chunk 78 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 7 optimal weight: 0.0370 overall best weight: 0.3858 ------------------------------------------------------------------------------- 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 = 0.3844 r_free = 0.3844 target = 0.133996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.103608 restraints weight = 19841.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.103568 restraints weight = 14318.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.103972 restraints weight = 12497.706| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10045 Z= 0.141 Angle : 0.511 7.590 13714 Z= 0.271 Chirality : 0.039 0.208 1480 Planarity : 0.004 0.049 1659 Dihedral : 14.679 72.179 1573 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.12 % Allowed : 14.04 % 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: 1.03 (0.25), residues: 1114 helix: 1.66 (0.25), residues: 467 sheet: 0.22 (0.36), residues: 205 loop : -0.04 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 671 HIS 0.002 0.000 HIS A 242 PHE 0.031 0.001 PHE A 971 TYR 0.010 0.001 TYR A1133 ARG 0.009 0.000 ARG A 446 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2579.30 seconds wall clock time: 47 minutes 19.76 seconds (2839.76 seconds total)