Starting phenix.real_space_refine on Wed Sep 25 07:25:46 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f6j_50226/09_2024/9f6j_50226.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f6j_50226/09_2024/9f6j_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f6j_50226/09_2024/9f6j_50226.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f6j_50226/09_2024/9f6j_50226.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f6j_50226/09_2024/9f6j_50226.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9f6j_50226/09_2024/9f6j_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-5461/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: 5.70, per 1000 atoms: 0.58 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: 2.41 Conformation dependent library (CDL) restraints added in 1.1 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: 3.20 Creating SS restraints... Processing helix chain 'A' and resid 27 through 48 Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 143 through 147 Processing helix chain 'A' and resid 159 through 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: 4.12 Time building geometry restraints manager: 2.83 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: 1.050 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: 0.310 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 28.870 Find NCS groups from input model: 0.090 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.040 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 194 time to evaluate : 1.013 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: 0.3012 time to fit residues: 76.2143 Evaluate side-chains 85 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 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 fitting. rotamer outliers: 20 poor density : 110 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 TYR cc_start: 0.8867 (p90) cc_final: 0.8664 (p90) REVERT: A 138 ASP cc_start: 0.8437 (t0) cc_final: 0.7393 (p0) REVERT: A 157 PHE cc_start: 0.8837 (m-80) cc_final: 0.8406 (m-80) REVERT: A 444 MET cc_start: 0.7473 (ptp) cc_final: 0.7178 (ptp) REVERT: A 688 HIS cc_start: 0.8619 (t-170) cc_final: 0.8302 (m170) REVERT: A 779 LEU cc_start: 0.8084 (tt) cc_final: 0.7778 (tt) outliers start: 20 outliers final: 11 residues processed: 121 average time/residue: 0.2167 time to fit residues: 37.2666 Evaluate side-chains 93 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 1.114 ------------------------------------------------------------------------------- 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 57 optimal weight: 0.0570 chunk 31 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 69 optimal weight: 3.9990 chunk 28 optimal weight: 10.0000 chunk 102 optimal weight: 0.9990 chunk 111 optimal weight: 8.9990 chunk 91 optimal weight: 2.9990 chunk 101 optimal weight: 7.9990 chunk 35 optimal weight: 0.5980 chunk 82 optimal weight: 4.9990 overall best weight: 1.7304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10045 Z= 0.260 Angle : 0.594 7.196 13714 Z= 0.328 Chirality : 0.043 0.180 1480 Planarity : 0.005 0.044 1659 Dihedral : 15.245 82.380 1573 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 2.83 % Allowed : 9.70 % Favored : 87.47 % 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: 0.47 (0.25), residues: 1114 helix: 0.80 (0.24), residues: 460 sheet: 0.02 (0.35), residues: 201 loop : 0.13 (0.31), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 671 HIS 0.005 0.001 HIS A1163 PHE 0.037 0.002 PHE A 971 TYR 0.015 0.001 TYR A 754 ARG 0.004 0.000 ARG A 976 *********************** 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 118 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 90 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8931 (tpt) cc_final: 0.8683 (tpt) REVERT: A 47 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8586 (tmm-80) REVERT: A 83 ASP cc_start: 0.7768 (m-30) cc_final: 0.6735 (p0) REVERT: A 103 TYR cc_start: 0.8841 (p90) cc_final: 0.8500 (p90) REVERT: A 138 ASP cc_start: 0.8543 (t0) cc_final: 0.7572 (p0) REVERT: A 293 ILE cc_start: 0.7933 (mt) cc_final: 0.7698 (tp) REVERT: A 473 TYR cc_start: 0.8532 (m-80) cc_final: 0.8315 (m-10) REVERT: A 688 HIS cc_start: 0.8688 (t-170) cc_final: 0.8363 (m170) REVERT: A 843 ILE cc_start: 0.9297 (OUTLIER) cc_final: 0.8997 (tp) REVERT: A 1094 ILE cc_start: 0.7766 (OUTLIER) cc_final: 0.7451 (pt) outliers start: 28 outliers final: 19 residues processed: 111 average time/residue: 0.2306 time to fit residues: 36.3085 Evaluate side-chains 98 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 76 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 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 387 ILE 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 843 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 1094 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 49 optimal weight: 0.2980 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 6.9990 chunk 109 optimal weight: 2.9990 chunk 97 optimal weight: 0.0970 chunk 29 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10045 Z= 0.227 Angle : 0.563 7.658 13714 Z= 0.307 Chirality : 0.042 0.142 1480 Planarity : 0.005 0.041 1659 Dihedral : 15.299 82.774 1573 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 2.83 % Allowed : 11.41 % Favored : 85.76 % 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: 0.53 (0.25), residues: 1114 helix: 0.96 (0.24), residues: 458 sheet: 0.01 (0.35), residues: 202 loop : 0.06 (0.31), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 671 HIS 0.004 0.001 HIS A1163 PHE 0.029 0.002 PHE A 971 TYR 0.012 0.001 TYR A 754 ARG 0.006 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 fitting. rotamer outliers: 28 poor density : 83 time to evaluate : 1.134 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8534 (tmm-80) REVERT: A 83 ASP cc_start: 0.7758 (m-30) cc_final: 0.6636 (p0) REVERT: A 103 TYR cc_start: 0.8780 (p90) cc_final: 0.8446 (p90) REVERT: A 138 ASP cc_start: 0.8593 (t0) cc_final: 0.7690 (p0) REVERT: A 221 MET cc_start: 0.8655 (ptm) cc_final: 0.8182 (ptp) REVERT: A 244 TYR cc_start: 0.8654 (m-80) cc_final: 0.7857 (m-80) REVERT: A 263 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8776 (mm) REVERT: A 293 ILE cc_start: 0.7981 (mt) cc_final: 0.7727 (tp) REVERT: A 359 MET cc_start: 0.8634 (tpp) cc_final: 0.8115 (mpp) REVERT: A 447 MET cc_start: 0.8277 (mmt) cc_final: 0.7971 (mmt) REVERT: A 473 TYR cc_start: 0.8594 (m-80) cc_final: 0.8317 (m-10) REVERT: A 526 LYS cc_start: 0.8824 (ptmt) cc_final: 0.8507 (pttt) REVERT: A 688 HIS cc_start: 0.8718 (t-170) cc_final: 0.8350 (m170) REVERT: A 1094 ILE cc_start: 0.7698 (OUTLIER) cc_final: 0.7311 (pt) outliers start: 28 outliers final: 22 residues processed: 105 average time/residue: 0.2133 time to fit residues: 32.0573 Evaluate side-chains 101 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 76 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ARG Chi-restraints excluded: chain A residue 130 LYS Chi-restraints excluded: chain A residue 163 LEU Chi-restraints excluded: chain A residue 263 LEU Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 354 THR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 366 PHE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 627 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 880 THR 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 1094 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 75 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 36 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 10045 Z= 0.232 Angle : 0.561 8.151 13714 Z= 0.303 Chirality : 0.042 0.213 1480 Planarity : 0.005 0.042 1659 Dihedral : 15.230 82.363 1573 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 3.43 % Allowed : 12.22 % 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: 0.49 (0.25), residues: 1114 helix: 1.00 (0.24), residues: 457 sheet: 0.03 (0.36), residues: 202 loop : -0.07 (0.31), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 671 HIS 0.004 0.001 HIS A1163 PHE 0.031 0.002 PHE A 971 TYR 0.012 0.001 TYR A 754 ARG 0.006 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 114 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 80 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8585 (tmm-80) REVERT: A 83 ASP cc_start: 0.7795 (m-30) cc_final: 0.6638 (p0) REVERT: A 103 TYR cc_start: 0.8811 (p90) cc_final: 0.8398 (p90) REVERT: A 138 ASP cc_start: 0.8689 (t0) cc_final: 0.7832 (p0) REVERT: A 221 MET cc_start: 0.8672 (ptm) cc_final: 0.8175 (ptp) REVERT: A 244 TYR cc_start: 0.8750 (m-80) cc_final: 0.7886 (m-80) REVERT: A 263 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8796 (mm) REVERT: A 359 MET cc_start: 0.8639 (tpp) cc_final: 0.8150 (mpp) REVERT: A 447 MET cc_start: 0.8263 (mmt) cc_final: 0.8021 (mmt) REVERT: A 526 LYS cc_start: 0.8803 (ptmt) cc_final: 0.8544 (pttt) REVERT: A 528 THR cc_start: 0.6571 (OUTLIER) cc_final: 0.6239 (p) REVERT: A 688 HIS cc_start: 0.8761 (t-170) cc_final: 0.8369 (m170) REVERT: A 843 ILE cc_start: 0.9314 (OUTLIER) cc_final: 0.9002 (tp) REVERT: A 1068 MET cc_start: 0.6933 (mmm) cc_final: 0.6598 (mmm) REVERT: A 1094 ILE cc_start: 0.7688 (OUTLIER) cc_final: 0.7249 (pt) outliers start: 34 outliers final: 25 residues processed: 108 average time/residue: 0.2242 time to fit residues: 34.7064 Evaluate side-chains 99 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 69 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 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 387 ILE 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 627 VAL Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 736 ILE Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 843 ILE Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 880 THR 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 1094 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 64 optimal weight: 0.3980 chunk 26 optimal weight: 5.9990 chunk 109 optimal weight: 0.9980 chunk 90 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10045 Z= 0.209 Angle : 0.551 8.302 13714 Z= 0.297 Chirality : 0.041 0.154 1480 Planarity : 0.004 0.043 1659 Dihedral : 15.186 80.735 1573 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 3.23 % Allowed : 12.63 % 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: 0.47 (0.25), residues: 1114 helix: 1.08 (0.24), residues: 458 sheet: -0.08 (0.36), residues: 204 loop : -0.14 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 671 HIS 0.003 0.001 HIS A1163 PHE 0.040 0.002 PHE A 971 TYR 0.012 0.001 TYR A 397 ARG 0.007 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 110 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 78 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8598 (tmm-80) REVERT: A 83 ASP cc_start: 0.7628 (m-30) cc_final: 0.6495 (p0) REVERT: A 103 TYR cc_start: 0.8764 (p90) cc_final: 0.8352 (p90) REVERT: A 138 ASP cc_start: 0.8661 (t0) cc_final: 0.7844 (p0) REVERT: A 221 MET cc_start: 0.8622 (ptm) cc_final: 0.8191 (ptp) REVERT: A 244 TYR cc_start: 0.8761 (m-80) cc_final: 0.7948 (m-80) REVERT: A 263 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8780 (mm) REVERT: A 359 MET cc_start: 0.8787 (tpp) cc_final: 0.8345 (mpp) REVERT: A 526 LYS cc_start: 0.8774 (ptmt) cc_final: 0.8550 (pttt) REVERT: A 528 THR cc_start: 0.6626 (OUTLIER) cc_final: 0.6322 (p) REVERT: A 688 HIS cc_start: 0.8637 (t-170) cc_final: 0.8335 (m170) REVERT: A 993 PHE cc_start: 0.8538 (OUTLIER) cc_final: 0.7146 (t80) REVERT: A 1068 MET cc_start: 0.6721 (mmm) cc_final: 0.6322 (mmm) REVERT: A 1094 ILE cc_start: 0.7610 (OUTLIER) cc_final: 0.7169 (pt) REVERT: A 1119 LEU cc_start: 0.4754 (mm) cc_final: 0.4483 (mm) outliers start: 32 outliers final: 21 residues processed: 104 average time/residue: 0.2299 time to fit residues: 33.9063 Evaluate side-chains 93 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 67 time to evaluate : 1.166 ------------------------------------------------------------------------------- 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 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 387 ILE Chi-restraints excluded: chain A residue 445 CYS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 571 LEU Chi-restraints excluded: chain A residue 723 LEU Chi-restraints excluded: chain A residue 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 1016 VAL Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1094 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 79 optimal weight: 0.5980 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 67 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10045 Z= 0.230 Angle : 0.558 8.717 13714 Z= 0.302 Chirality : 0.042 0.137 1480 Planarity : 0.004 0.043 1659 Dihedral : 15.208 79.041 1573 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.03 % Allowed : 13.43 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.43 (0.25), residues: 1114 helix: 1.12 (0.24), residues: 456 sheet: -0.23 (0.35), residues: 207 loop : -0.19 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 671 HIS 0.004 0.001 HIS A1163 PHE 0.029 0.002 PHE A 971 TYR 0.012 0.001 TYR A 754 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 101 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 71 time to evaluate : 1.091 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8571 (tmm-80) REVERT: A 83 ASP cc_start: 0.7785 (m-30) cc_final: 0.6627 (p0) REVERT: A 103 TYR cc_start: 0.8757 (p90) cc_final: 0.8345 (p90) REVERT: A 138 ASP cc_start: 0.8654 (t0) cc_final: 0.7872 (p0) REVERT: A 221 MET cc_start: 0.8557 (ptm) cc_final: 0.8119 (ptp) REVERT: A 244 TYR cc_start: 0.8788 (m-80) cc_final: 0.7971 (m-80) REVERT: A 263 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8707 (mm) REVERT: A 293 ILE cc_start: 0.7469 (tp) cc_final: 0.7222 (mp) REVERT: A 294 MET cc_start: 0.5212 (mmm) cc_final: 0.4959 (tpp) REVERT: A 359 MET cc_start: 0.8803 (tpp) cc_final: 0.8362 (mpp) REVERT: A 526 LYS cc_start: 0.8576 (ptmt) cc_final: 0.8332 (pttt) REVERT: A 528 THR cc_start: 0.6952 (OUTLIER) cc_final: 0.6646 (p) REVERT: A 688 HIS cc_start: 0.8647 (t-170) cc_final: 0.8331 (m170) REVERT: A 993 PHE cc_start: 0.8506 (OUTLIER) cc_final: 0.7026 (t80) REVERT: A 1094 ILE cc_start: 0.7629 (OUTLIER) cc_final: 0.7152 (pt) REVERT: A 1119 LEU cc_start: 0.4818 (mm) cc_final: 0.4560 (mm) outliers start: 30 outliers final: 23 residues processed: 96 average time/residue: 0.2369 time to fit residues: 32.2260 Evaluate side-chains 93 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 65 time to evaluate : 1.183 ------------------------------------------------------------------------------- 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 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 387 ILE 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 771 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 995 LYS Chi-restraints excluded: chain A residue 999 LEU Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1094 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 53 optimal weight: 0.0970 chunk 10 optimal weight: 0.7980 chunk 85 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 chunk 104 optimal weight: 0.7980 chunk 95 optimal weight: 0.9980 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10045 Z= 0.161 Angle : 0.526 8.806 13714 Z= 0.282 Chirality : 0.040 0.134 1480 Planarity : 0.004 0.042 1659 Dihedral : 15.065 78.754 1573 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 2.42 % Allowed : 14.04 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.29 (0.25), residues: 459 sheet: 0.02 (0.37), residues: 197 loop : -0.24 (0.29), residues: 458 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 0.009 0.001 PHE A 971 TYR 0.010 0.001 TYR A 754 ARG 0.008 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 97 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 73 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8170 (tmm-80) REVERT: A 83 ASP cc_start: 0.7575 (m-30) cc_final: 0.6551 (p0) REVERT: A 138 ASP cc_start: 0.8739 (t0) cc_final: 0.7886 (p0) REVERT: A 244 TYR cc_start: 0.8680 (m-80) cc_final: 0.7938 (m-80) REVERT: A 263 LEU cc_start: 0.8962 (OUTLIER) cc_final: 0.8754 (mm) REVERT: A 359 MET cc_start: 0.8776 (tpp) cc_final: 0.8278 (mpp) REVERT: A 383 MET cc_start: 0.5580 (ttp) cc_final: 0.5254 (ttm) REVERT: A 397 TYR cc_start: 0.6411 (m-10) cc_final: 0.6152 (m-10) REVERT: A 528 THR cc_start: 0.6897 (OUTLIER) cc_final: 0.6598 (p) REVERT: A 562 MET cc_start: 0.8767 (tpp) cc_final: 0.8308 (mmm) REVERT: A 688 HIS cc_start: 0.8673 (t-170) cc_final: 0.8358 (m170) REVERT: A 993 PHE cc_start: 0.8367 (OUTLIER) cc_final: 0.7295 (t80) REVERT: A 1068 MET cc_start: 0.6489 (mmp) cc_final: 0.5912 (mmm) REVERT: A 1094 ILE cc_start: 0.7519 (OUTLIER) cc_final: 0.7201 (pt) REVERT: A 1119 LEU cc_start: 0.4989 (mm) cc_final: 0.4743 (mm) outliers start: 24 outliers final: 16 residues processed: 93 average time/residue: 0.2209 time to fit residues: 29.3660 Evaluate side-chains 88 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 67 time to evaluate : 1.137 ------------------------------------------------------------------------------- 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 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 445 CYS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 543 HIS Chi-restraints excluded: chain A residue 551 VAL Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 850 ILE Chi-restraints excluded: chain A residue 973 VAL Chi-restraints excluded: chain A residue 993 PHE Chi-restraints excluded: chain A residue 1052 THR Chi-restraints excluded: chain A residue 1094 ILE Chi-restraints excluded: chain A residue 1145 ILE Chi-restraints excluded: chain A residue 1151 LEU Chi-restraints excluded: chain A residue 1171 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 107 optimal weight: 3.9990 chunk 65 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7994 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10045 Z= 0.242 Angle : 0.565 8.363 13714 Z= 0.304 Chirality : 0.042 0.202 1480 Planarity : 0.005 0.041 1659 Dihedral : 15.149 76.837 1573 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.53 % Allowed : 14.14 % Favored : 83.33 % 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: 0.51 (0.25), residues: 1114 helix: 1.19 (0.24), residues: 458 sheet: -0.01 (0.36), residues: 203 loop : -0.27 (0.30), 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 0.040 0.002 PHE A 971 TYR 0.012 0.001 TYR A 754 ARG 0.010 0.000 ARG A 247 *********************** 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 96 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 71 time to evaluate : 1.098 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8594 (tmm-80) REVERT: A 83 ASP cc_start: 0.7647 (m-30) cc_final: 0.6518 (p0) REVERT: A 138 ASP cc_start: 0.8765 (t0) cc_final: 0.7978 (p0) REVERT: A 244 TYR cc_start: 0.8803 (m-80) cc_final: 0.8020 (m-80) REVERT: A 263 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8725 (mm) REVERT: A 359 MET cc_start: 0.8802 (tpp) cc_final: 0.8374 (mpp) REVERT: A 528 THR cc_start: 0.6794 (OUTLIER) cc_final: 0.6530 (p) REVERT: A 562 MET cc_start: 0.8811 (tpp) cc_final: 0.8584 (mmm) REVERT: A 688 HIS cc_start: 0.8669 (t-170) cc_final: 0.8322 (m170) REVERT: A 872 PHE cc_start: 0.8021 (OUTLIER) cc_final: 0.7640 (t80) REVERT: A 993 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.7036 (t80) REVERT: A 1068 MET cc_start: 0.6574 (mmp) cc_final: 0.6043 (mmm) REVERT: A 1094 ILE cc_start: 0.7640 (OUTLIER) cc_final: 0.7145 (pt) REVERT: A 1119 LEU cc_start: 0.5212 (mm) cc_final: 0.4974 (mm) outliers start: 25 outliers final: 18 residues processed: 92 average time/residue: 0.2183 time to fit residues: 28.8730 Evaluate side-chains 90 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 66 time to evaluate : 1.075 ------------------------------------------------------------------------------- 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 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 445 CYS Chi-restraints excluded: chain A residue 528 THR Chi-restraints excluded: chain A residue 543 HIS 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 872 PHE Chi-restraints excluded: chain A residue 906 THR Chi-restraints excluded: chain A residue 973 VAL 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 1094 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 50 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 112 optimal weight: 8.9990 chunk 103 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 54 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 95 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 moved from start: 0.4622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10045 Z= 0.238 Angle : 0.569 8.542 13714 Z= 0.307 Chirality : 0.042 0.211 1480 Planarity : 0.005 0.042 1659 Dihedral : 15.251 78.282 1573 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 2.63 % Allowed : 13.74 % Favored : 83.64 % 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: 0.40 (0.25), residues: 1114 helix: 1.21 (0.24), residues: 455 sheet: -0.16 (0.37), residues: 197 loop : -0.39 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 671 HIS 0.004 0.001 HIS A1163 PHE 0.018 0.002 PHE A 104 TYR 0.020 0.001 TYR A 397 ARG 0.009 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 93 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 67 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 47 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8561 (tmm-80) REVERT: A 138 ASP cc_start: 0.8755 (t0) cc_final: 0.8025 (p0) REVERT: A 244 TYR cc_start: 0.8777 (m-80) cc_final: 0.7963 (m-80) REVERT: A 263 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8755 (mm) REVERT: A 359 MET cc_start: 0.8833 (tpp) cc_final: 0.8376 (mpp) REVERT: A 528 THR cc_start: 0.6789 (OUTLIER) cc_final: 0.6533 (p) REVERT: A 562 MET cc_start: 0.8798 (tpp) cc_final: 0.8580 (mmm) REVERT: A 688 HIS cc_start: 0.8583 (t-170) cc_final: 0.8315 (m170) REVERT: A 872 PHE cc_start: 0.8041 (OUTLIER) cc_final: 0.7612 (t80) REVERT: A 993 PHE cc_start: 0.8509 (OUTLIER) cc_final: 0.7120 (t80) REVERT: A 1068 MET cc_start: 0.6554 (mmp) cc_final: 0.5986 (mmm) REVERT: A 1094 ILE cc_start: 0.7455 (OUTLIER) cc_final: 0.6885 (pt) outliers start: 26 outliers final: 18 residues processed: 88 average time/residue: 0.1996 time to fit residues: 26.0268 Evaluate side-chains 89 residues out of total 990 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 65 time to evaluate : 1.062 ------------------------------------------------------------------------------- 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 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 528 THR Chi-restraints excluded: chain A residue 543 HIS 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 872 PHE 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 1094 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 82 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 37 optimal weight: 0.3980 chunk 92 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 78 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3767 r_free = 0.3767 target = 0.128411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.097132 restraints weight = 19809.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.097018 restraints weight = 13471.341| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.097503 restraints weight = 11215.359| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7977 moved from start: 0.4755 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= 0.160 Angle : 0.531 8.240 13714 Z= 0.283 Chirality : 0.040 0.207 1480 Planarity : 0.004 0.042 1659 Dihedral : 15.119 80.645 1573 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.02 % Allowed : 14.55 % Favored : 83.43 % 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: 0.64 (0.25), residues: 1114 helix: 1.42 (0.25), residues: 456 sheet: -0.03 (0.36), residues: 205 loop : -0.28 (0.29), residues: 453 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 0.035 0.001 PHE A 971 TYR 0.015 0.001 TYR A1133 ARG 0.010 0.000 ARG A 446 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1800.88 seconds wall clock time: 33 minutes 1.27 seconds (1981.27 seconds total)