Starting phenix.real_space_refine on Thu Jan 16 17:49:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9f6k_50227/01_2025/9f6k_50227.cif Found real_map, /net/cci-nas-00/data/ceres_data/9f6k_50227/01_2025/9f6k_50227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9f6k_50227/01_2025/9f6k_50227.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9f6k_50227/01_2025/9f6k_50227.map" model { file = "/net/cci-nas-00/data/ceres_data/9f6k_50227/01_2025/9f6k_50227.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9f6k_50227/01_2025/9f6k_50227.cif" } resolution = 4.2 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= 0.005 sd= 0.120 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 26 5.49 5 S 53 5.16 5 C 6066 2.51 5 N 1647 2.21 5 O 1841 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 9637 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9098 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1118, 9098 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: 246 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 246 Classifications: {'DNA': 12} Link IDs: {'rna3p': 11} 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 4834 SG CYS A 651 39.686 19.306 54.662 1.00106.69 S ATOM 4850 SG CYS A 654 38.377 17.719 49.063 1.00110.12 S ATOM 4916 SG CYS A 663 44.195 16.679 51.105 1.00102.11 S ATOM 5640 SG CYS A 747 42.848 22.430 50.219 1.00 96.95 S Time building chain proxies: 5.61, per 1000 atoms: 0.58 Number of scatterers: 9637 At special positions: 0 Unit cell: (106.58, 110.96, 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 26 15.00 O 1841 8.00 N 1647 7.00 C 6066 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: 2.26 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" SF4 A1301 " pdb="FE3 SF4 A1301 " - pdb=" SG CYS A 663 " pdb="FE4 SF4 A1301 " - pdb=" SG CYS A 747 " pdb="FE2 SF4 A1301 " - pdb=" SG CYS A 654 " pdb="FE1 SF4 A1301 " - pdb=" SG CYS A 651 " 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: 43 helices and 12 sheets defined 49.4% alpha, 14.5% beta 11 base pairs and 19 stacking pairs defined. Time for finding SS restraints: 3.19 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 removed outlier: 3.501A pdb=" N VAL A 146 " --> pdb=" O ASN A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 181 Proline residue: A 172 - end of helix Processing helix chain 'A' and resid 213 through 218 Processing helix chain 'A' and resid 227 through 237 removed outlier: 3.651A pdb=" N LEU A 232 " --> pdb=" O TYR A 228 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N SER A 233 " --> pdb=" O HIS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 355 Processing helix chain 'A' and resid 367 through 375 Processing helix chain 'A' and resid 376 through 380 Processing helix chain 'A' and resid 382 through 387 Processing helix chain 'A' and resid 407 through 415 Processing helix chain 'A' and resid 423 through 433 Processing helix chain 'A' and resid 440 through 451 removed outlier: 4.134A pdb=" N CYS A 445 " --> pdb=" O PRO A 441 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N ARG A 446 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N THR A 449 " --> pdb=" O CYS A 445 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU A 450 " --> pdb=" O ARG A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 451 through 460 removed outlier: 3.623A pdb=" N LEU A 455 " --> pdb=" O GLN A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 473 removed outlier: 3.683A pdb=" N VAL A 464 " --> pdb=" O VAL A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 483 removed outlier: 4.039A pdb=" N PHE A 477 " --> pdb=" O TYR A 473 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE A 479 " --> pdb=" O HIS A 475 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALA A 480 " --> pdb=" O PRO A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 495 removed outlier: 3.532A pdb=" N LEU A 493 " --> pdb=" O PRO A 489 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 512 removed outlier: 3.584A pdb=" N LEU A 500 " --> pdb=" O GLY A 496 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS A 501 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N GLU A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N VAL A 507 " --> pdb=" O ALA A 503 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N GLN A 508 " --> pdb=" O LEU A 504 " (cutoff:3.500A) Processing helix chain 'A' and resid 567 through 572 Processing helix chain 'A' and resid 573 through 586 removed outlier: 3.682A pdb=" N GLU A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 593 Processing helix chain 'A' and resid 595 through 613 removed outlier: 3.581A pdb=" N VAL A 599 " --> pdb=" O ASN A 595 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N CYS A 600 " --> pdb=" O PHE A 596 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 613 " --> pdb=" O SER A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 629 through 639 removed outlier: 3.644A pdb=" N ARG A 639 " --> pdb=" O ILE A 635 " (cutoff:3.500A) Processing helix chain 'A' and resid 648 through 653 Processing helix chain 'A' and resid 679 through 691 Processing helix chain 'A' and resid 711 through 731 removed outlier: 4.335A pdb=" N LYS A 717 " --> pdb=" O GLU A 713 " (cutoff:3.500A) removed outlier: 3.620A 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: 4.166A pdb=" N TYR A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLY A 817 " --> pdb=" O ASN A 813 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N VAL A 819 " --> pdb=" O PHE A 815 " (cutoff:3.500A) Processing helix chain 'A' and resid 828 through 854 removed outlier: 4.044A pdb=" N ALA A 832 " --> pdb=" O SER A 828 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 835 " --> pdb=" O MET A 831 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN A 852 " --> pdb=" O GLU A 848 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N ILE A 853 " --> pdb=" O LEU A 849 " (cutoff:3.500A) Processing helix chain 'A' and resid 892 through 906 removed outlier: 4.308A pdb=" N LYS A 902 " --> pdb=" O ASN A 898 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLU A 903 " --> pdb=" O ILE A 899 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N GLY A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR A 906 " --> pdb=" O LYS A 902 " (cutoff:3.500A) Processing helix chain 'A' and resid 979 through 993 removed outlier: 3.673A pdb=" N LYS A 983 " --> pdb=" O LEU A 979 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE A 990 " --> pdb=" O GLN A 986 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU A 991 " --> pdb=" O SER A 987 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA A 992 " --> pdb=" O SER A 988 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N PHE A 993 " --> pdb=" O VAL A 989 " (cutoff:3.500A) Processing helix chain 'A' and resid 998 through 1020 removed outlier: 3.926A pdb=" N LYS A1008 " --> pdb=" O GLY A1004 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A1009 " --> pdb=" O SER A1005 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N TYR A1012 " --> pdb=" O LYS A1008 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N TRP A1013 " --> pdb=" O VAL A1009 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N LEU A1014 " --> pdb=" O ALA A1010 " (cutoff:3.500A) Processing helix chain 'A' and resid 1025 through 1033 removed outlier: 4.077A pdb=" N LEU A1029 " --> pdb=" O PRO A1025 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE A1030 " --> pdb=" O ASP A1026 " (cutoff:3.500A) Processing helix chain 'A' and resid 1042 through 1047 Processing helix chain 'A' and resid 1051 through 1062 removed outlier: 3.722A pdb=" N ALA A1061 " --> pdb=" O ALA A1057 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N GLU A1062 " --> pdb=" O LYS A1058 " (cutoff:3.500A) Processing helix chain 'A' and resid 1066 through 1071 Processing helix chain 'A' and resid 1088 through 1092 removed outlier: 3.572A pdb=" N ARG A1092 " --> pdb=" O PRO A1088 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1088 through 1092' Processing helix chain 'A' and resid 1096 through 1101 removed outlier: 4.242A pdb=" N GLN A1100 " --> pdb=" O LEU A1096 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA A1101 " --> pdb=" O ALA A1097 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 1096 through 1101' Processing helix chain 'A' and resid 1102 through 1114 removed outlier: 3.848A pdb=" N LEU A1114 " --> pdb=" O LEU A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1123 through 1128 Processing helix chain 'A' and resid 1129 through 1145 removed outlier: 4.188A pdb=" N TYR A1133 " --> pdb=" O ASP A1129 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N ILE A1134 " --> pdb=" O TRP A1130 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N LYS A1143 " --> pdb=" O SER A1139 " (cutoff:3.500A) Processing helix chain 'A' and resid 1145 through 1152 Processing helix chain 'A' and resid 1164 through 1175 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 99 removed outlier: 3.510A pdb=" N ASN A 65 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N ILE A 87 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 5.563A 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: 3.525A pdb=" N LYS A 130 " --> pdb=" O SER A 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 332 through 334 removed outlier: 6.332A pdb=" N LEU A 272 " --> pdb=" O VAL A 360 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N MET A 359 " --> pdb=" O ILE A 403 " (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 539 removed outlier: 3.945A pdb=" N SER A 536 " --> pdb=" O GLU A 674 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLU A 674 " --> pdb=" O SER A 536 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N THR A 538 " --> pdb=" O ARG A 672 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 545 through 546 removed outlier: 3.861A pdb=" N GLU A 545 " --> pdb=" O LEU A 859 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N LEU A 859 " --> pdb=" O GLU A 545 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N GLU A 858 " --> pdb=" O TRP A 865 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 550 through 553 removed outlier: 3.678A pdb=" N ALA A 939 " --> pdb=" O PHE A 959 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 558 through 561 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: 6.263A pdb=" N ASP A 908 " --> pdb=" O GLU A 926 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N GLU A 926 " --> pdb=" O ASP A 908 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 912 " --> pdb=" O VAL A 922 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 1078 through 1080 426 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 54 hydrogen bond angles 0 basepair planarities 11 basepair parallelities 19 stacking parallelities Total time for adding SS restraints: 4.14 Time building geometry restraints manager: 2.57 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: 4235 1.43 - 1.64: 5593 1.64 - 1.85: 78 1.85 - 2.07: 0 2.07 - 2.28: 12 Bond restraints: 9918 Sorted by residual: bond pdb=" CA LYS A 355 " pdb=" CB LYS A 355 " ideal model delta sigma weight residual 1.522 1.533 -0.011 8.90e-03 1.26e+04 1.42e+00 bond pdb=" C LYS A 355 " pdb=" O LYS A 355 " ideal model delta sigma weight residual 1.233 1.238 -0.005 4.80e-03 4.34e+04 9.91e-01 bond pdb=" C4' DC P 25 " pdb=" O4' DC P 25 " ideal model delta sigma weight residual 1.450 1.430 0.020 2.00e-02 2.50e+03 9.60e-01 bond pdb=" C1' DC T 12 " pdb=" N1 DC T 12 " ideal model delta sigma weight residual 1.490 1.517 -0.027 3.00e-02 1.11e+03 8.11e-01 bond pdb=" C2' DG P 20 " pdb=" C1' DG P 20 " ideal model delta sigma weight residual 1.525 1.508 0.017 2.00e-02 2.50e+03 7.46e-01 ... (remaining 9913 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 12133 0.99 - 1.98: 1101 1.98 - 2.97: 216 2.97 - 3.97: 56 3.97 - 4.96: 10 Bond angle restraints: 13516 Sorted by residual: angle pdb=" N TYR A 473 " pdb=" CA TYR A 473 " pdb=" C TYR A 473 " ideal model delta sigma weight residual 112.04 116.90 -4.86 1.44e+00 4.82e-01 1.14e+01 angle pdb=" C4' DA P 21 " pdb=" C3' DA P 21 " pdb=" O3' DA P 21 " ideal model delta sigma weight residual 110.00 105.33 4.67 1.50e+00 4.44e-01 9.71e+00 angle pdb=" O3' DA P 21 " pdb=" C3' DA P 21 " pdb=" C2' DA P 21 " ideal model delta sigma weight residual 111.50 115.86 -4.36 1.50e+00 4.44e-01 8.46e+00 angle pdb=" N ASN A 217 " pdb=" CA ASN A 217 " pdb=" C ASN A 217 " ideal model delta sigma weight residual 111.82 114.94 -3.12 1.16e+00 7.43e-01 7.24e+00 angle pdb=" O3' DA P 29 " pdb=" C3' DA P 29 " pdb=" C2' DA P 29 " ideal model delta sigma weight residual 111.50 115.40 -3.90 1.50e+00 4.44e-01 6.75e+00 ... (remaining 13511 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.46: 5697 31.46 - 62.93: 241 62.93 - 94.39: 21 94.39 - 125.86: 0 125.86 - 157.32: 1 Dihedral angle restraints: 5960 sinusoidal: 2661 harmonic: 3299 Sorted by residual: dihedral pdb=" CA PHE A 367 " pdb=" C PHE A 367 " pdb=" N ASP A 368 " pdb=" CA ASP A 368 " ideal model delta harmonic sigma weight residual 180.00 -151.36 -28.64 0 5.00e+00 4.00e-02 3.28e+01 dihedral pdb=" CA GLU A 329 " pdb=" C GLU A 329 " pdb=" N GLY A 330 " pdb=" CA GLY A 330 " ideal model delta harmonic sigma weight residual -180.00 -153.21 -26.79 0 5.00e+00 4.00e-02 2.87e+01 dihedral pdb=" CA LEU A1114 " pdb=" C LEU A1114 " pdb=" N LYS A1115 " pdb=" CA LYS A1115 " ideal model delta harmonic sigma weight residual 180.00 -153.37 -26.63 0 5.00e+00 4.00e-02 2.84e+01 ... (remaining 5957 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1199 0.051 - 0.101: 211 0.101 - 0.152: 43 0.152 - 0.202: 2 0.202 - 0.253: 1 Chirality restraints: 1456 Sorted by residual: chirality pdb=" C3' DA P 29 " pdb=" C4' DA P 29 " pdb=" O3' DA P 29 " pdb=" C2' DA P 29 " both_signs ideal model delta sigma weight residual False -2.66 -2.41 -0.25 2.00e-01 2.50e+01 1.60e+00 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 2.32 0.19 2.00e-01 2.50e+01 9.39e-01 chirality pdb=" CA PRO A1103 " pdb=" N PRO A1103 " pdb=" C PRO A1103 " pdb=" CB PRO A1103 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.03e-01 ... (remaining 1453 not shown) Planarity restraints: 1655 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 847 " -0.016 2.00e-02 2.50e+03 3.26e-02 1.06e+01 pdb=" C ARG A 847 " 0.056 2.00e-02 2.50e+03 pdb=" O ARG A 847 " -0.021 2.00e-02 2.50e+03 pdb=" N GLU A 848 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 843 " -0.015 2.00e-02 2.50e+03 3.04e-02 9.27e+00 pdb=" C ILE A 843 " 0.053 2.00e-02 2.50e+03 pdb=" O ILE A 843 " -0.020 2.00e-02 2.50e+03 pdb=" N THR A 844 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 838 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.76e+00 pdb=" C THR A 838 " -0.051 2.00e-02 2.50e+03 pdb=" O THR A 838 " 0.019 2.00e-02 2.50e+03 pdb=" N GLY A 839 " 0.017 2.00e-02 2.50e+03 ... (remaining 1652 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 2743 2.82 - 3.34: 9460 3.34 - 3.86: 14779 3.86 - 4.38: 16470 4.38 - 4.90: 27822 Nonbonded interactions: 71274 Sorted by model distance: nonbonded pdb=" OG SER A 549 " pdb=" O LEU A 942 " model vdw 2.304 3.040 nonbonded pdb=" OD2 ASP A 287 " pdb=" OG1 THR A 290 " model vdw 2.310 3.040 nonbonded pdb=" OH TYR A 105 " pdb=" NH2 ARG A 154 " model vdw 2.330 3.120 nonbonded pdb=" OE2 GLU A 991 " pdb=" NZ LYS A 995 " model vdw 2.346 3.120 nonbonded pdb=" OE1 GLU A 674 " pdb=" OG1 THR A 737 " model vdw 2.355 3.040 ... (remaining 71269 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: 0.800 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 28.320 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 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 0.027 9918 Z= 0.174 Angle : 0.656 4.957 13516 Z= 0.400 Chirality : 0.042 0.253 1456 Planarity : 0.009 0.107 1655 Dihedral : 16.571 157.322 3824 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 2.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 0.10 % Allowed : 5.85 % Favored : 94.05 % 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: -1.36 (0.22), residues: 1114 helix: -1.03 (0.20), residues: 440 sheet: 0.14 (0.36), residues: 158 loop : -0.98 (0.25), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.007 TRP A 410 HIS 0.007 0.002 HIS A 67 PHE 0.032 0.004 PHE A 905 TYR 0.027 0.005 TYR A 683 ARG 0.022 0.003 ARG A 375 *********************** 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 191 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 190 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8045 (tpp) cc_final: 0.7768 (tpp) REVERT: A 83 ASP cc_start: 0.8006 (t0) cc_final: 0.7509 (t0) REVERT: A 266 ARG cc_start: 0.7993 (mtp-110) cc_final: 0.7354 (mtm180) REVERT: A 401 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.8412 (pp30) REVERT: A 431 LYS cc_start: 0.9316 (mmpt) cc_final: 0.8701 (mmpt) REVERT: A 447 MET cc_start: 0.7769 (ttp) cc_final: 0.7529 (ttt) REVERT: A 491 GLU cc_start: 0.8624 (mm-30) cc_final: 0.7676 (mm-30) REVERT: A 569 PHE cc_start: 0.8828 (t80) cc_final: 0.8209 (t80) REVERT: A 627 VAL cc_start: 0.8356 (t) cc_final: 0.7759 (p) REVERT: A 630 MET cc_start: 0.8364 (ttp) cc_final: 0.7819 (ttp) REVERT: A 637 THR cc_start: 0.8021 (m) cc_final: 0.7615 (p) REVERT: A 667 MET cc_start: 0.8202 (mtp) cc_final: 0.7974 (mtt) REVERT: A 827 TYR cc_start: 0.9045 (t80) cc_final: 0.8685 (t80) REVERT: A 829 MET cc_start: 0.8765 (mmm) cc_final: 0.8486 (mmm) REVERT: A 860 ASP cc_start: 0.7745 (t0) cc_final: 0.7341 (t70) REVERT: A 940 MET cc_start: 0.8815 (ttt) cc_final: 0.8505 (ttm) REVERT: A 1024 MET cc_start: 0.7902 (ttm) cc_final: 0.7549 (mmm) REVERT: A 1050 LYS cc_start: 0.7826 (ptmt) cc_final: 0.7020 (ptmt) REVERT: A 1151 LEU cc_start: 0.9090 (mt) cc_final: 0.8749 (mt) outliers start: 1 outliers final: 0 residues processed: 191 average time/residue: 0.2907 time to fit residues: 75.4324 Evaluate side-chains 102 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 101 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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: 4.9990 chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.0870 chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 102 optimal weight: 0.0020 overall best weight: 1.3770 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 GLN A 177 ASN A 239 HIS A 342 HIS ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 522 GLN A 592 GLN A 735 HIS A1049 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.112134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.091383 restraints weight = 24929.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.094654 restraints weight = 13441.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.095210 restraints weight = 8302.293| |-----------------------------------------------------------------------------| r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9918 Z= 0.230 Angle : 0.635 6.117 13516 Z= 0.350 Chirality : 0.044 0.161 1456 Planarity : 0.005 0.046 1655 Dihedral : 15.574 150.143 1509 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 0.10 % Allowed : 2.52 % Favored : 97.38 % 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: 0.13 (0.24), residues: 1114 helix: 0.65 (0.24), residues: 456 sheet: 0.19 (0.36), residues: 174 loop : -0.38 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 671 HIS 0.006 0.001 HIS A 342 PHE 0.020 0.002 PHE A1122 TYR 0.019 0.002 TYR A 683 ARG 0.006 0.001 ARG A 955 *********************** 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 124 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 123 time to evaluate : 1.084 Fit side-chains revert: symmetry clash REVERT: A 177 ASN cc_start: 0.7804 (OUTLIER) cc_final: 0.7598 (m-40) REVERT: A 221 MET cc_start: 0.8910 (pmm) cc_final: 0.8701 (pmm) REVERT: A 247 ARG cc_start: 0.8356 (tpt170) cc_final: 0.8120 (tpt170) REVERT: A 328 TYR cc_start: 0.7327 (m-80) cc_final: 0.6625 (m-80) REVERT: A 491 GLU cc_start: 0.8409 (mm-30) cc_final: 0.7984 (mm-30) REVERT: A 569 PHE cc_start: 0.8792 (t80) cc_final: 0.8194 (t80) REVERT: A 637 THR cc_start: 0.8280 (m) cc_final: 0.7834 (p) REVERT: A 1024 MET cc_start: 0.7563 (ttm) cc_final: 0.7290 (mtm) REVERT: A 1028 GLU cc_start: 0.9164 (mt-10) cc_final: 0.8919 (mp0) outliers start: 1 outliers final: 0 residues processed: 124 average time/residue: 0.2390 time to fit residues: 41.1032 Evaluate side-chains 80 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 79 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 105 optimal weight: 0.7980 chunk 104 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 12 optimal weight: 0.2980 chunk 13 optimal weight: 0.7980 chunk 73 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 109 optimal weight: 0.0970 chunk 77 optimal weight: 3.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.113835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.093724 restraints weight = 24596.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.095996 restraints weight = 13494.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.097910 restraints weight = 8851.179| |-----------------------------------------------------------------------------| r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.3039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 9918 Z= 0.158 Angle : 0.552 7.465 13516 Z= 0.300 Chirality : 0.041 0.157 1456 Planarity : 0.004 0.042 1655 Dihedral : 15.024 148.442 1509 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % 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: 0.59 (0.25), residues: 1114 helix: 1.16 (0.25), residues: 452 sheet: 0.30 (0.36), residues: 174 loop : -0.20 (0.28), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A1130 HIS 0.001 0.001 HIS A 229 PHE 0.019 0.001 PHE A 815 TYR 0.009 0.001 TYR A 328 ARG 0.004 0.000 ARG A 821 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 ASP cc_start: 0.8334 (t0) cc_final: 0.7834 (t70) REVERT: A 569 PHE cc_start: 0.8792 (t80) cc_final: 0.8180 (t80) REVERT: A 1024 MET cc_start: 0.7404 (ttm) cc_final: 0.7145 (mtm) REVERT: A 1153 GLN cc_start: 0.8428 (mp10) cc_final: 0.8137 (mp10) outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.2319 time to fit residues: 37.4969 Evaluate side-chains 84 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 75 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 6 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 1 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 385 GLN ** A 401 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 451 GLN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1142 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.112121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.091939 restraints weight = 24672.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.094198 restraints weight = 13549.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.095956 restraints weight = 8911.079| |-----------------------------------------------------------------------------| r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9918 Z= 0.182 Angle : 0.543 7.179 13516 Z= 0.295 Chirality : 0.042 0.275 1456 Planarity : 0.004 0.044 1655 Dihedral : 14.879 147.462 1509 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % 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: 0.74 (0.25), residues: 1114 helix: 1.38 (0.25), residues: 451 sheet: 0.38 (0.36), residues: 174 loop : -0.22 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A1130 HIS 0.002 0.001 HIS A 580 PHE 0.016 0.001 PHE A 104 TYR 0.011 0.001 TYR A 726 ARG 0.003 0.000 ARG A 742 *********************** 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 100 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 275 ASP cc_start: 0.8339 (t0) cc_final: 0.7808 (t70) REVERT: A 295 MET cc_start: 0.8492 (ptp) cc_final: 0.8289 (ptp) REVERT: A 569 PHE cc_start: 0.8845 (t80) cc_final: 0.8236 (t80) REVERT: A 1024 MET cc_start: 0.7413 (ttm) cc_final: 0.7071 (mtm) outliers start: 0 outliers final: 0 residues processed: 100 average time/residue: 0.2307 time to fit residues: 32.9621 Evaluate side-chains 79 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 86 optimal weight: 0.5980 chunk 111 optimal weight: 5.9990 chunk 85 optimal weight: 0.9990 chunk 36 optimal weight: 0.0670 chunk 24 optimal weight: 1.9990 chunk 11 optimal weight: 7.9990 chunk 76 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 401 GLN A 451 GLN ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.113349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.093931 restraints weight = 25361.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.095976 restraints weight = 14055.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.097243 restraints weight = 9370.289| |-----------------------------------------------------------------------------| r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9918 Z= 0.155 Angle : 0.531 8.429 13516 Z= 0.284 Chirality : 0.041 0.227 1456 Planarity : 0.004 0.045 1655 Dihedral : 14.820 146.878 1509 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.20 % Allowed : 2.52 % Favored : 97.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.25), residues: 1114 helix: 1.52 (0.25), residues: 451 sheet: 0.47 (0.36), residues: 174 loop : -0.18 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 347 HIS 0.002 0.001 HIS A 404 PHE 0.012 0.001 PHE A 104 TYR 0.014 0.001 TYR A 473 ARG 0.009 0.000 ARG A 266 *********************** 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 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 112 time to evaluate : 1.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 266 ARG cc_start: 0.8205 (mtm110) cc_final: 0.7843 (mtm180) REVERT: A 275 ASP cc_start: 0.8347 (t0) cc_final: 0.7810 (t70) REVERT: A 487 MET cc_start: 0.7763 (mtt) cc_final: 0.7559 (mtm) REVERT: A 520 GLN cc_start: 0.8112 (tm-30) cc_final: 0.7875 (tm-30) REVERT: A 569 PHE cc_start: 0.8814 (t80) cc_final: 0.8220 (t80) REVERT: A 797 MET cc_start: 0.8997 (mmm) cc_final: 0.8701 (mpp) REVERT: A 1024 MET cc_start: 0.7454 (ttm) cc_final: 0.7194 (mtm) REVERT: A 1153 GLN cc_start: 0.8374 (mp-120) cc_final: 0.8151 (mp-120) outliers start: 2 outliers final: 1 residues processed: 114 average time/residue: 0.2352 time to fit residues: 37.4032 Evaluate side-chains 82 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 110 optimal weight: 0.0970 chunk 55 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 chunk 79 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 2 optimal weight: 0.0470 chunk 18 optimal weight: 4.9990 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 HIS ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 735 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.115177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.093751 restraints weight = 24604.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.096305 restraints weight = 13498.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.098741 restraints weight = 8630.711| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 9918 Z= 0.161 Angle : 0.536 8.474 13516 Z= 0.286 Chirality : 0.040 0.205 1456 Planarity : 0.004 0.047 1655 Dihedral : 14.802 146.038 1509 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % 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: 1.51 (0.25), residues: 451 sheet: 0.50 (0.36), residues: 176 loop : -0.17 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 62 HIS 0.004 0.001 HIS A 144 PHE 0.015 0.001 PHE A 905 TYR 0.024 0.001 TYR A 105 ARG 0.007 0.000 ARG A 721 *********************** 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 108 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 247 ARG cc_start: 0.8426 (tpt170) cc_final: 0.8067 (tpt170) REVERT: A 275 ASP cc_start: 0.8294 (t0) cc_final: 0.7806 (t70) REVERT: A 295 MET cc_start: 0.8194 (ptp) cc_final: 0.7993 (ptp) REVERT: A 562 MET cc_start: 0.7584 (mmt) cc_final: 0.7070 (mmt) REVERT: A 569 PHE cc_start: 0.8819 (t80) cc_final: 0.8285 (t80) REVERT: A 797 MET cc_start: 0.8921 (mmm) cc_final: 0.8711 (mpp) REVERT: A 1024 MET cc_start: 0.7431 (ttm) cc_final: 0.7136 (mtm) REVERT: A 1153 GLN cc_start: 0.8434 (mp-120) cc_final: 0.8207 (mp-120) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2110 time to fit residues: 32.9308 Evaluate side-chains 80 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 31 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 22 optimal weight: 0.7980 chunk 40 optimal weight: 0.2980 chunk 37 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 54 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 HIS ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.113313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.091974 restraints weight = 24841.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.094565 restraints weight = 13513.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.096204 restraints weight = 8535.409| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9918 Z= 0.181 Angle : 0.534 9.009 13516 Z= 0.283 Chirality : 0.040 0.213 1456 Planarity : 0.004 0.046 1655 Dihedral : 14.783 145.442 1509 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % 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: 1.55 (0.26), residues: 451 sheet: 0.55 (0.36), residues: 176 loop : -0.24 (0.28), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 40 HIS 0.003 0.001 HIS A 404 PHE 0.016 0.001 PHE A 104 TYR 0.010 0.001 TYR A 328 ARG 0.005 0.000 ARG A 721 *********************** 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 99 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 1.062 Fit side-chains REVERT: A 247 ARG cc_start: 0.8367 (tpt170) cc_final: 0.8166 (tpt170) REVERT: A 275 ASP cc_start: 0.8333 (t0) cc_final: 0.7780 (t70) REVERT: A 295 MET cc_start: 0.8098 (ptp) cc_final: 0.7802 (ptp) REVERT: A 440 ASP cc_start: 0.8156 (t0) cc_final: 0.7930 (t0) REVERT: A 569 PHE cc_start: 0.8847 (t80) cc_final: 0.8290 (t80) REVERT: A 571 LEU cc_start: 0.9027 (pp) cc_final: 0.8711 (tp) REVERT: A 797 MET cc_start: 0.9117 (mmm) cc_final: 0.8913 (mpp) REVERT: A 1024 MET cc_start: 0.7544 (ttm) cc_final: 0.7196 (mtm) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.1893 time to fit residues: 28.1277 Evaluate side-chains 78 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.076 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 63 optimal weight: 7.9990 chunk 54 optimal weight: 0.2980 chunk 48 optimal weight: 5.9990 chunk 61 optimal weight: 0.9980 chunk 19 optimal weight: 0.0060 chunk 75 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 4 optimal weight: 0.4980 chunk 40 optimal weight: 0.7980 chunk 105 optimal weight: 3.9990 overall best weight: 0.4196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 HIS ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.113626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.093882 restraints weight = 26055.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.095857 restraints weight = 14562.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.097116 restraints weight = 9974.821| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 9918 Z= 0.143 Angle : 0.523 8.742 13516 Z= 0.275 Chirality : 0.040 0.227 1456 Planarity : 0.004 0.046 1655 Dihedral : 14.715 144.129 1509 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % 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: 1.62 (0.26), residues: 448 sheet: 0.71 (0.36), residues: 176 loop : -0.25 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 40 HIS 0.003 0.001 HIS A 144 PHE 0.011 0.001 PHE A 104 TYR 0.013 0.001 TYR A 248 ARG 0.004 0.000 ARG A 721 *********************** 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 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8363 (mmm-85) cc_final: 0.8084 (mtp180) REVERT: A 275 ASP cc_start: 0.8458 (t0) cc_final: 0.7946 (t70) REVERT: A 294 MET cc_start: 0.8793 (tpp) cc_final: 0.8580 (tpt) REVERT: A 569 PHE cc_start: 0.8829 (t80) cc_final: 0.8265 (t80) REVERT: A 797 MET cc_start: 0.9074 (mmm) cc_final: 0.8855 (mpp) REVERT: A 980 GLN cc_start: 0.8060 (mp10) cc_final: 0.7634 (tp40) REVERT: A 1024 MET cc_start: 0.7540 (ttm) cc_final: 0.7206 (mtm) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2136 time to fit residues: 32.7858 Evaluate side-chains 78 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 25 optimal weight: 0.0670 chunk 42 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 37 optimal weight: 0.2980 chunk 79 optimal weight: 0.0050 chunk 57 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 overall best weight: 0.4532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.113681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.093976 restraints weight = 25681.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.095910 restraints weight = 14332.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.097221 restraints weight = 9803.538| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.4322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9918 Z= 0.145 Angle : 0.536 8.740 13516 Z= 0.279 Chirality : 0.040 0.225 1456 Planarity : 0.004 0.046 1655 Dihedral : 14.688 143.939 1509 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: 0.99 (0.25), residues: 1114 helix: 1.62 (0.26), residues: 449 sheet: 0.80 (0.36), residues: 182 loop : -0.26 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 40 HIS 0.004 0.000 HIS A 404 PHE 0.012 0.001 PHE A 104 TYR 0.010 0.001 TYR A 248 ARG 0.004 0.000 ARG A 721 *********************** 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 102 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 1.085 Fit side-chains revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8286 (mmm-85) cc_final: 0.7980 (mtp180) REVERT: A 275 ASP cc_start: 0.8493 (t0) cc_final: 0.7908 (t70) REVERT: A 294 MET cc_start: 0.8781 (tpp) cc_final: 0.8553 (tpt) REVERT: A 569 PHE cc_start: 0.8850 (t80) cc_final: 0.8324 (t80) REVERT: A 797 MET cc_start: 0.9076 (mmm) cc_final: 0.8869 (mpp) REVERT: A 1024 MET cc_start: 0.7528 (ttm) cc_final: 0.7215 (mtm) outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.2242 time to fit residues: 33.3221 Evaluate side-chains 80 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 44 optimal weight: 0.9980 chunk 53 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 110 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 109 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 84 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 144 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.112845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.093067 restraints weight = 26059.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.094895 restraints weight = 14282.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.096107 restraints weight = 9959.386| |-----------------------------------------------------------------------------| r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9918 Z= 0.175 Angle : 0.554 10.845 13516 Z= 0.288 Chirality : 0.040 0.238 1456 Planarity : 0.004 0.060 1655 Dihedral : 14.677 144.058 1509 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.72 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.97 (0.25), residues: 1114 helix: 1.60 (0.26), residues: 449 sheet: 0.79 (0.35), residues: 182 loop : -0.27 (0.28), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 40 HIS 0.003 0.001 HIS A 404 PHE 0.015 0.001 PHE A 104 TYR 0.010 0.001 TYR A 298 ARG 0.003 0.000 ARG A 721 ********************** 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 96 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: A 34 ARG cc_start: 0.8304 (mmm-85) cc_final: 0.8029 (mtp180) REVERT: A 275 ASP cc_start: 0.8253 (t0) cc_final: 0.7648 (t70) REVERT: A 294 MET cc_start: 0.8765 (tpp) cc_final: 0.8466 (tpt) REVERT: A 569 PHE cc_start: 0.8787 (t80) cc_final: 0.8448 (t80) REVERT: A 627 VAL cc_start: 0.8485 (p) cc_final: 0.8276 (p) REVERT: A 797 MET cc_start: 0.9095 (mmm) cc_final: 0.8892 (mpp) REVERT: A 898 ASN cc_start: 0.8762 (m-40) cc_final: 0.8537 (m-40) REVERT: A 980 GLN cc_start: 0.8072 (mp10) cc_final: 0.7607 (tp40) REVERT: A 1024 MET cc_start: 0.7519 (ttm) cc_final: 0.7205 (mtm) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2169 time to fit residues: 30.7124 Evaluate side-chains 75 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 1.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 103 optimal weight: 0.0870 chunk 95 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 92 optimal weight: 0.8980 chunk 101 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 chunk 82 optimal weight: 8.9990 chunk 85 optimal weight: 0.4980 chunk 36 optimal weight: 0.9990 overall best weight: 0.8962 ------------------------------------------------------------------------------- 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 = 0.3641 r_free = 0.3641 target = 0.112339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.092538 restraints weight = 25923.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.094167 restraints weight = 14567.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.095361 restraints weight = 10329.248| |-----------------------------------------------------------------------------| r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9918 Z= 0.169 Angle : 0.541 8.269 13516 Z= 0.284 Chirality : 0.040 0.219 1456 Planarity : 0.004 0.047 1655 Dihedral : 14.659 143.602 1509 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: 0.95 (0.25), residues: 1114 helix: 1.62 (0.26), residues: 448 sheet: 0.76 (0.35), residues: 182 loop : -0.31 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 40 HIS 0.002 0.001 HIS A 404 PHE 0.015 0.001 PHE A 104 TYR 0.010 0.001 TYR A 298 ARG 0.003 0.000 ARG A 721 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2480.88 seconds wall clock time: 45 minutes 34.61 seconds (2734.61 seconds total)