Starting phenix.real_space_refine on Tue May 13 05:44:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ibx_35348/05_2025/8ibx_35348.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ibx_35348/05_2025/8ibx_35348.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ibx_35348/05_2025/8ibx_35348.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ibx_35348/05_2025/8ibx_35348.map" model { file = "/net/cci-nas-00/data/ceres_data/8ibx_35348/05_2025/8ibx_35348.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ibx_35348/05_2025/8ibx_35348.cif" } resolution = 3.74 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= 0.002 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 24 atoms to isotropic. 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 Zn 2 6.06 5 P 108 5.49 5 S 38 5.16 5 C 5584 2.51 5 N 1815 2.21 5 O 1955 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-5687/modules/chem_data/mon_lib" Total number of atoms: 9502 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 7250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 922, 7250 Classifications: {'peptide': 922} Link IDs: {'PTRANS': 44, 'TRANS': 877} Chain breaks: 3 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 5, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 26 Chain: "B" Number of atoms: 730 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 730 Classifications: {'DNA': 36} Link IDs: {'rna3p': 35} Chain: "A" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 687 Classifications: {'DNA': 33} Link IDs: {'rna3p': 32} Chain: "D" Number of atoms: 833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 833 Classifications: {'RNA': 39} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 3, 'rna3p_pur': 17, 'rna3p_pyr': 15} Link IDs: {'rna2p': 6, 'rna3p': 32} Chain breaks: 2 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 31 SG CYS C 114 16.419 86.790 77.796 1.00120.15 S ATOM 57 SG CYS C 117 17.245 85.475 81.375 1.00125.02 S ATOM 5880 SG CYS C 934 54.317 47.378 120.733 1.00132.83 S ATOM 5906 SG CYS C 938 57.626 46.389 122.449 1.00138.77 S Time building chain proxies: 6.31, per 1000 atoms: 0.66 Number of scatterers: 9502 At special positions: 0 Unit cell: (106.496, 121.867, 136.14, 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) Zn 2 29.99 S 38 16.00 P 108 15.00 O 1955 8.00 N 1815 7.00 C 5584 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: 2.78 Conformation dependent library (CDL) restraints added in 1.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN C1201 " pdb="ZN ZN C1201 " - pdb=" NE2 HIS C 135 " pdb="ZN ZN C1201 " - pdb=" NE2 HIS C 130 " pdb="ZN ZN C1201 " - pdb=" SG CYS C 114 " pdb="ZN ZN C1201 " - pdb=" SG CYS C 117 " pdb=" ZN C1202 " pdb="ZN ZN C1202 " - pdb=" NE2 HIS C 946 " pdb="ZN ZN C1202 " - pdb=" SG CYS C 938 " pdb="ZN ZN C1202 " - pdb=" SG CYS C 934 " Number of angles added : 2 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1698 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 60.2% alpha, 7.2% beta 42 base pairs and 68 stacking pairs defined. Time for finding SS restraints: 4.21 Creating SS restraints... Processing helix chain 'C' and resid 123 through 135 Processing helix chain 'C' and resid 135 through 143 Processing helix chain 'C' and resid 153 through 172 Processing helix chain 'C' and resid 175 through 183 removed outlier: 3.871A pdb=" N GLY C 181 " --> pdb=" O GLY C 177 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 197 Processing helix chain 'C' and resid 199 through 214 Processing helix chain 'C' and resid 261 through 283 Processing helix chain 'C' and resid 306 through 324 removed outlier: 3.574A pdb=" N LYS C 323 " --> pdb=" O GLU C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 324 through 334 removed outlier: 3.524A pdb=" N ALA C 328 " --> pdb=" O CYS C 324 " (cutoff:3.500A) Processing helix chain 'C' and resid 347 through 357 Proline residue: C 353 - end of helix Processing helix chain 'C' and resid 365 through 374 removed outlier: 3.538A pdb=" N ARG C 374 " --> pdb=" O HIS C 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 392 through 399 Processing helix chain 'C' and resid 413 through 420 removed outlier: 3.566A pdb=" N TRP C 417 " --> pdb=" O ARG C 413 " (cutoff:3.500A) Processing helix chain 'C' and resid 421 through 436 Processing helix chain 'C' and resid 439 through 444 removed outlier: 3.789A pdb=" N ARG C 443 " --> pdb=" O PRO C 439 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLN C 444 " --> pdb=" O GLU C 440 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 439 through 444' Processing helix chain 'C' and resid 458 through 462 removed outlier: 3.821A pdb=" N TYR C 462 " --> pdb=" O PRO C 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 469 through 487 removed outlier: 3.737A pdb=" N ILE C 478 " --> pdb=" O HIS C 474 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU C 479 " --> pdb=" O PHE C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 500 through 520 Processing helix chain 'C' and resid 532 through 537 removed outlier: 3.578A pdb=" N THR C 536 " --> pdb=" O ALA C 533 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N VAL C 537 " --> pdb=" O PHE C 534 " (cutoff:3.500A) Processing helix chain 'C' and resid 538 through 550 Processing helix chain 'C' and resid 552 through 565 Processing helix chain 'C' and resid 592 through 606 removed outlier: 3.625A pdb=" N ASN C 598 " --> pdb=" O PRO C 594 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL C 599 " --> pdb=" O ILE C 595 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N VAL C 600 " --> pdb=" O LEU C 596 " (cutoff:3.500A) Processing helix chain 'C' and resid 636 through 655 Processing helix chain 'C' and resid 719 through 730 Processing helix chain 'C' and resid 733 through 744 Processing helix chain 'C' and resid 744 through 756 removed outlier: 3.508A pdb=" N ARG C 748 " --> pdb=" O HIS C 744 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N HIS C 751 " --> pdb=" O PRO C 747 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N GLY C 752 " --> pdb=" O ARG C 748 " (cutoff:3.500A) Processing helix chain 'C' and resid 759 through 779 Processing helix chain 'C' and resid 786 through 791 removed outlier: 4.229A pdb=" N HIS C 790 " --> pdb=" O LYS C 786 " (cutoff:3.500A) Processing helix chain 'C' and resid 802 through 817 Proline residue: C 808 - end of helix removed outlier: 4.327A pdb=" N GLY C 817 " --> pdb=" O ARG C 813 " (cutoff:3.500A) Processing helix chain 'C' and resid 823 through 831 Processing helix chain 'C' and resid 832 through 849 Processing helix chain 'C' and resid 861 through 872 Processing helix chain 'C' and resid 873 through 879 removed outlier: 3.562A pdb=" N ARG C 876 " --> pdb=" O VAL C 873 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLU C 877 " --> pdb=" O ASP C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 884 through 889 removed outlier: 3.538A pdb=" N THR C 888 " --> pdb=" O PRO C 885 " (cutoff:3.500A) Processing helix chain 'C' and resid 899 through 911 Processing helix chain 'C' and resid 916 through 921 Processing helix chain 'C' and resid 928 through 932 Processing helix chain 'C' and resid 943 through 950 Processing helix chain 'C' and resid 951 through 953 No H-bonds generated for 'chain 'C' and resid 951 through 953' Processing helix chain 'C' and resid 954 through 976 Processing helix chain 'C' and resid 1018 through 1032 removed outlier: 3.855A pdb=" N LYS C1029 " --> pdb=" O GLU C1025 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N TYR C1030 " --> pdb=" O LYS C1026 " (cutoff:3.500A) Processing helix chain 'C' and resid 1034 through 1045 Processing helix chain 'C' and resid 1066 through 1076 Processing helix chain 'C' and resid 1080 through 1085 removed outlier: 3.662A pdb=" N LEU C1084 " --> pdb=" O ARG C1080 " (cutoff:3.500A) Processing helix chain 'C' and resid 1086 through 1105 Processing sheet with id=AA1, first strand: chain 'C' and resid 112 through 113 removed outlier: 3.768A pdb=" N TRP C 112 " --> pdb=" O PHE C 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 465 through 467 removed outlier: 3.505A pdb=" N ILE C 467 " --> pdb=" O ARG C 446 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG C 446 " --> pdb=" O ILE C 467 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N CYS C 445 " --> pdb=" O SER C 567 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 623 through 626 Processing sheet with id=AA4, first strand: chain 'C' and resid 614 through 616 Processing sheet with id=AA5, first strand: chain 'C' and resid 668 through 671 removed outlier: 3.629A pdb=" N HIS C 678 " --> pdb=" O ILE C 669 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 686 through 687 Processing sheet with id=AA7, first strand: chain 'C' and resid 700 through 703 Processing sheet with id=AA8, first strand: chain 'C' and resid 851 through 852 removed outlier: 3.519A pdb=" N ARG C 851 " --> pdb=" O SER C 860 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER C 860 " --> pdb=" O ARG C 851 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 981 through 982 removed outlier: 3.797A pdb=" N GLU C 981 " --> pdb=" O ILE C 998 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE C 998 " --> pdb=" O GLU C 981 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N GLY C1005 " --> pdb=" O ARG C1053 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N THR C1055 " --> pdb=" O GLY C1005 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ILE C1007 " --> pdb=" O THR C1055 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N CYS C1057 " --> pdb=" O ILE C1007 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N ASP C1009 " --> pdb=" O CYS C1057 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N ILE C1059 " --> pdb=" O ASP C1009 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLN C1011 " --> pdb=" O ILE C1059 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 986 through 987 removed outlier: 4.484A pdb=" N LEU C 986 " --> pdb=" O ARG C 993 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ARG C 993 " --> pdb=" O LEU C 986 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 386 hydrogen bonds defined for protein. 1101 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 111 hydrogen bonds 222 hydrogen bond angles 0 basepair planarities 42 basepair parallelities 68 stacking parallelities Total time for adding SS restraints: 5.05 Time building geometry restraints manager: 3.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2777 1.34 - 1.46: 2189 1.46 - 1.58: 4684 1.58 - 1.70: 211 1.70 - 1.82: 54 Bond restraints: 9915 Sorted by residual: bond pdb=" CA GLU C 575 " pdb=" C GLU C 575 " ideal model delta sigma weight residual 1.530 1.498 0.032 1.08e-02 8.57e+03 8.91e+00 bond pdb=" N GLY C 111 " pdb=" CA GLY C 111 " ideal model delta sigma weight residual 1.451 1.490 -0.039 1.60e-02 3.91e+03 6.08e+00 bond pdb=" CA ALA C 571 " pdb=" C ALA C 571 " ideal model delta sigma weight residual 1.522 1.500 0.022 1.08e-02 8.57e+03 4.13e+00 bond pdb=" N ALA C 571 " pdb=" CA ALA C 571 " ideal model delta sigma weight residual 1.461 1.438 0.023 1.19e-02 7.06e+03 3.68e+00 bond pdb=" CA ASN C 573 " pdb=" C ASN C 573 " ideal model delta sigma weight residual 1.523 1.498 0.026 1.34e-02 5.57e+03 3.67e+00 ... (remaining 9910 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 13241 1.21 - 2.43: 507 2.43 - 3.64: 93 3.64 - 4.86: 25 4.86 - 6.07: 7 Bond angle restraints: 13873 Sorted by residual: angle pdb=" N ALA C 571 " pdb=" CA ALA C 571 " pdb=" C ALA C 571 " ideal model delta sigma weight residual 107.61 112.82 -5.21 1.74e+00 3.30e-01 8.97e+00 angle pdb=" C GLU C 575 " pdb=" CA GLU C 575 " pdb=" CB GLU C 575 " ideal model delta sigma weight residual 111.70 107.82 3.88 1.31e+00 5.83e-01 8.76e+00 angle pdb=" N GLU C 575 " pdb=" CA GLU C 575 " pdb=" C GLU C 575 " ideal model delta sigma weight residual 107.32 112.11 -4.79 1.65e+00 3.67e-01 8.41e+00 angle pdb=" CA MET C 973 " pdb=" CB MET C 973 " pdb=" CG MET C 973 " ideal model delta sigma weight residual 114.10 119.56 -5.46 2.00e+00 2.50e-01 7.45e+00 angle pdb=" N LYS C 939 " pdb=" CA LYS C 939 " pdb=" CB LYS C 939 " ideal model delta sigma weight residual 113.65 109.69 3.96 1.47e+00 4.63e-01 7.27e+00 ... (remaining 13868 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.16: 5327 35.16 - 70.32: 490 70.32 - 105.48: 29 105.48 - 140.64: 2 140.64 - 175.80: 2 Dihedral angle restraints: 5850 sinusoidal: 3218 harmonic: 2632 Sorted by residual: dihedral pdb=" C4' DA B 25 " pdb=" C3' DA B 25 " pdb=" O3' DA B 25 " pdb=" P DG B 26 " ideal model delta sinusoidal sigma weight residual 220.00 44.20 175.80 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" O4' A D 247 " pdb=" C1' A D 247 " pdb=" N9 A D 247 " pdb=" C4 A D 247 " ideal model delta sinusoidal sigma weight residual -106.00 -162.87 56.87 1 1.70e+01 3.46e-03 1.51e+01 dihedral pdb=" CA ARG C 742 " pdb=" C ARG C 742 " pdb=" N ALA C 743 " pdb=" CA ALA C 743 " ideal model delta harmonic sigma weight residual -180.00 -160.68 -19.32 0 5.00e+00 4.00e-02 1.49e+01 ... (remaining 5847 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1050 0.031 - 0.062: 336 0.062 - 0.093: 122 0.093 - 0.124: 52 0.124 - 0.155: 5 Chirality restraints: 1565 Sorted by residual: chirality pdb=" CA ILE C 438 " pdb=" N ILE C 438 " pdb=" C ILE C 438 " pdb=" CB ILE C 438 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.04e-01 chirality pdb=" CA ILE C 800 " pdb=" N ILE C 800 " pdb=" C ILE C 800 " pdb=" CB ILE C 800 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" C1' A D 242 " pdb=" O4' A D 242 " pdb=" C2' A D 242 " pdb=" N9 A D 242 " both_signs ideal model delta sigma weight residual False 2.46 2.33 0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 1562 not shown) Planarity restraints: 1402 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' A D 242 " -0.024 2.00e-02 2.50e+03 1.06e-02 3.08e+00 pdb=" N9 A D 242 " 0.022 2.00e-02 2.50e+03 pdb=" C8 A D 242 " 0.004 2.00e-02 2.50e+03 pdb=" N7 A D 242 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A D 242 " 0.004 2.00e-02 2.50e+03 pdb=" C6 A D 242 " -0.004 2.00e-02 2.50e+03 pdb=" N6 A D 242 " -0.010 2.00e-02 2.50e+03 pdb=" N1 A D 242 " 0.002 2.00e-02 2.50e+03 pdb=" C2 A D 242 " 0.000 2.00e-02 2.50e+03 pdb=" N3 A D 242 " 0.003 2.00e-02 2.50e+03 pdb=" C4 A D 242 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE C 669 " 0.025 5.00e-02 4.00e+02 3.75e-02 2.25e+00 pdb=" N PRO C 670 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO C 670 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 670 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 593 " 0.024 5.00e-02 4.00e+02 3.72e-02 2.21e+00 pdb=" N PRO C 594 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 594 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 594 " 0.021 5.00e-02 4.00e+02 ... (remaining 1399 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 106 2.57 - 3.15: 8089 3.15 - 3.73: 16648 3.73 - 4.32: 20668 4.32 - 4.90: 32567 Nonbonded interactions: 78078 Sorted by model distance: nonbonded pdb=" OG SER C 175 " pdb=" OP2 DG A 8 " model vdw 1.982 3.040 nonbonded pdb=" NH1 ARG C 473 " pdb=" OP1 A D 247 " model vdw 2.080 3.120 nonbonded pdb=" OG SER C 406 " pdb=" OP1 A D 246 " model vdw 2.107 3.040 nonbonded pdb=" OD1 ASN C1028 " pdb=" N LYS C1029 " model vdw 2.128 3.120 nonbonded pdb=" NH1 ARG C 848 " pdb=" OP1 DT A 30 " model vdw 2.137 3.120 ... (remaining 78073 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: 0.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.110 Process input model: 32.300 Find NCS groups from input model: 0.300 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 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 : 0.004 0.039 9922 Z= 0.179 Angle : 0.589 6.072 13875 Z= 0.334 Chirality : 0.038 0.155 1565 Planarity : 0.003 0.038 1402 Dihedral : 22.081 175.797 4152 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.22 % Allowed : 4.81 % Favored : 94.97 % Rotamer: Outliers : 0.79 % Allowed : 25.13 % Favored : 74.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.28), residues: 914 helix: 1.57 (0.23), residues: 497 sheet: -0.68 (0.61), residues: 66 loop : -0.55 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 701 HIS 0.003 0.001 HIS C1096 PHE 0.010 0.001 PHE C 116 TYR 0.011 0.001 TYR C 628 ARG 0.003 0.000 ARG C 549 Details of bonding type rmsd hydrogen bonds : bond 0.13936 ( 497) hydrogen bonds : angle 5.42580 ( 1323) metal coordination : bond 0.00619 ( 7) metal coordination : angle 1.02882 ( 2) covalent geometry : bond 0.00353 ( 9915) covalent geometry : angle 0.58920 (13873) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 59 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 573 ASN cc_start: 0.8163 (OUTLIER) cc_final: 0.7914 (m-40) outliers start: 6 outliers final: 3 residues processed: 64 average time/residue: 0.1808 time to fit residues: 17.5341 Evaluate side-chains 61 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 573 ASN Chi-restraints excluded: chain C residue 575 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 30 optimal weight: 8.9990 chunk 48 optimal weight: 7.9990 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 196 GLN C 694 GLN C1096 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.102549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.075906 restraints weight = 31227.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.078023 restraints weight = 17104.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.079328 restraints weight = 12210.090| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.1234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 9922 Z= 0.252 Angle : 0.681 7.869 13875 Z= 0.361 Chirality : 0.042 0.159 1565 Planarity : 0.005 0.040 1402 Dihedral : 22.750 177.888 2392 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.83 % Favored : 96.06 % Rotamer: Outliers : 3.68 % Allowed : 23.29 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.28), residues: 914 helix: 1.33 (0.23), residues: 509 sheet: -0.76 (0.63), residues: 66 loop : -0.59 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 152 HIS 0.006 0.001 HIS C1023 PHE 0.016 0.002 PHE C 116 TYR 0.013 0.002 TYR C 563 ARG 0.005 0.001 ARG C 919 Details of bonding type rmsd hydrogen bonds : bond 0.04759 ( 497) hydrogen bonds : angle 4.57233 ( 1323) metal coordination : bond 0.01897 ( 7) metal coordination : angle 2.69279 ( 2) covalent geometry : bond 0.00559 ( 9915) covalent geometry : angle 0.67980 (13873) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 0.990 Fit side-chains REVERT: C 437 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7731 (mm-30) REVERT: C 575 GLU cc_start: 0.7330 (OUTLIER) cc_final: 0.7081 (mp0) REVERT: C 836 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8556 (ttp-110) outliers start: 28 outliers final: 13 residues processed: 82 average time/residue: 0.1843 time to fit residues: 22.7365 Evaluate side-chains 69 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 437 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 575 GLU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 811 ILE Chi-restraints excluded: chain C residue 812 VAL Chi-restraints excluded: chain C residue 836 ARG Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 895 CYS Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 948 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 20 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 37 optimal weight: 0.0670 chunk 12 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.7920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 653 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.105368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.079198 restraints weight = 31207.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.081376 restraints weight = 16651.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.082749 restraints weight = 11698.557| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.1502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9922 Z= 0.125 Angle : 0.549 6.525 13875 Z= 0.296 Chirality : 0.037 0.221 1565 Planarity : 0.003 0.029 1402 Dihedral : 22.446 179.747 2390 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.95 % Favored : 96.94 % Rotamer: Outliers : 3.68 % Allowed : 21.97 % Favored : 74.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.29), residues: 914 helix: 1.72 (0.23), residues: 503 sheet: -0.74 (0.63), residues: 66 loop : -0.53 (0.35), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 978 HIS 0.005 0.001 HIS C 718 PHE 0.010 0.001 PHE C 597 TYR 0.010 0.001 TYR C 202 ARG 0.003 0.000 ARG C1027 Details of bonding type rmsd hydrogen bonds : bond 0.03776 ( 497) hydrogen bonds : angle 4.23734 ( 1323) metal coordination : bond 0.00586 ( 7) metal coordination : angle 2.58395 ( 2) covalent geometry : bond 0.00265 ( 9915) covalent geometry : angle 0.54782 (13873) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 60 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 836 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8392 (mtm-85) outliers start: 28 outliers final: 16 residues processed: 82 average time/residue: 0.2013 time to fit residues: 24.1447 Evaluate side-chains 75 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 ARG Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 575 GLU Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 811 ILE Chi-restraints excluded: chain C residue 836 ARG Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1079 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 98 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 3 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 60 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C1098 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.100559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.073529 restraints weight = 30788.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.075613 restraints weight = 17001.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.076872 restraints weight = 12236.076| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 9922 Z= 0.287 Angle : 0.689 8.179 13875 Z= 0.366 Chirality : 0.042 0.199 1565 Planarity : 0.005 0.034 1402 Dihedral : 22.544 177.767 2387 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.16 % Favored : 95.73 % Rotamer: Outliers : 6.05 % Allowed : 21.18 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.52 (0.28), residues: 914 helix: 1.21 (0.23), residues: 510 sheet: -1.00 (0.63), residues: 66 loop : -0.61 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 152 HIS 0.008 0.002 HIS C 868 PHE 0.020 0.002 PHE C 597 TYR 0.012 0.003 TYR C 628 ARG 0.008 0.001 ARG C 941 Details of bonding type rmsd hydrogen bonds : bond 0.05016 ( 497) hydrogen bonds : angle 4.50805 ( 1323) metal coordination : bond 0.01565 ( 7) metal coordination : angle 1.97202 ( 2) covalent geometry : bond 0.00630 ( 9915) covalent geometry : angle 0.68817 (13873) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 54 time to evaluate : 0.961 Fit side-chains REVERT: C 836 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8467 (mtm-85) outliers start: 46 outliers final: 34 residues processed: 92 average time/residue: 0.1989 time to fit residues: 26.8614 Evaluate side-chains 88 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 53 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 ARG Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 677 HIS Chi-restraints excluded: chain C residue 678 HIS Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 711 SER Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 740 ILE Chi-restraints excluded: chain C residue 750 GLN Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain C residue 811 ILE Chi-restraints excluded: chain C residue 812 VAL Chi-restraints excluded: chain C residue 836 ARG Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 895 CYS Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1058 THR Chi-restraints excluded: chain C residue 1064 VAL Chi-restraints excluded: chain C residue 1079 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 86 optimal weight: 20.0000 chunk 63 optimal weight: 0.3980 chunk 84 optimal weight: 20.0000 chunk 75 optimal weight: 9.9990 chunk 1 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 59 optimal weight: 0.9990 chunk 80 optimal weight: 20.0000 overall best weight: 2.0786 ------------------------------------------------------------------------------- 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 = 0.3934 r_free = 0.3934 target = 0.102820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.075984 restraints weight = 30763.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.078045 restraints weight = 16651.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.079415 restraints weight = 11927.378| |-----------------------------------------------------------------------------| r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9922 Z= 0.160 Angle : 0.581 8.284 13875 Z= 0.309 Chirality : 0.038 0.168 1565 Planarity : 0.004 0.029 1402 Dihedral : 22.423 179.479 2384 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.28 % Favored : 96.61 % Rotamer: Outliers : 4.34 % Allowed : 22.63 % Favored : 73.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.77 (0.28), residues: 914 helix: 1.47 (0.23), residues: 509 sheet: -0.95 (0.64), residues: 66 loop : -0.59 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 978 HIS 0.004 0.001 HIS C 130 PHE 0.013 0.001 PHE C 597 TYR 0.010 0.002 TYR C 202 ARG 0.004 0.000 ARG C 941 Details of bonding type rmsd hydrogen bonds : bond 0.03984 ( 497) hydrogen bonds : angle 4.24522 ( 1323) metal coordination : bond 0.01062 ( 7) metal coordination : angle 2.89837 ( 2) covalent geometry : bond 0.00352 ( 9915) covalent geometry : angle 0.57963 (13873) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 59 time to evaluate : 0.877 Fit side-chains REVERT: C 561 HIS cc_start: 0.8188 (OUTLIER) cc_final: 0.7856 (t-90) REVERT: C 836 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8470 (mtm-85) outliers start: 33 outliers final: 26 residues processed: 83 average time/residue: 0.2061 time to fit residues: 24.6773 Evaluate side-chains 85 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 57 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 ARG Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain C residue 569 THR Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 766 LEU Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 811 ILE Chi-restraints excluded: chain C residue 812 VAL Chi-restraints excluded: chain C residue 836 ARG Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 891 ILE Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1012 VAL Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1058 THR Chi-restraints excluded: chain C residue 1079 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 18 optimal weight: 1.9990 chunk 48 optimal weight: 8.9990 chunk 52 optimal weight: 0.0030 chunk 50 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 71 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 33 optimal weight: 3.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 308 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.105002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.078619 restraints weight = 30681.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.080856 restraints weight = 16145.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.082168 restraints weight = 11277.592| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9922 Z= 0.121 Angle : 0.547 7.979 13875 Z= 0.291 Chirality : 0.037 0.167 1565 Planarity : 0.003 0.033 1402 Dihedral : 22.232 176.591 2383 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.28 % Favored : 96.61 % Rotamer: Outliers : 3.16 % Allowed : 25.00 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.02 (0.29), residues: 914 helix: 1.79 (0.23), residues: 503 sheet: -1.22 (0.55), residues: 86 loop : -0.50 (0.36), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 978 HIS 0.004 0.001 HIS C 744 PHE 0.010 0.001 PHE C 597 TYR 0.010 0.001 TYR C 202 ARG 0.019 0.000 ARG C 133 Details of bonding type rmsd hydrogen bonds : bond 0.03506 ( 497) hydrogen bonds : angle 4.07292 ( 1323) metal coordination : bond 0.00514 ( 7) metal coordination : angle 3.38130 ( 2) covalent geometry : bond 0.00258 ( 9915) covalent geometry : angle 0.54522 (13873) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 69 time to evaluate : 0.872 Fit side-chains revert: symmetry clash REVERT: C 561 HIS cc_start: 0.8138 (t-90) cc_final: 0.7781 (t-90) REVERT: C 668 MET cc_start: 0.8903 (tpt) cc_final: 0.8677 (tpt) REVERT: C 836 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8408 (mtm-85) outliers start: 24 outliers final: 15 residues processed: 88 average time/residue: 0.1962 time to fit residues: 25.4651 Evaluate side-chains 81 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 65 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 374 ARG Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain C residue 836 ARG Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1046 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 39 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 67 optimal weight: 7.9990 chunk 95 optimal weight: 10.0000 chunk 85 optimal weight: 8.9990 chunk 17 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 54 optimal weight: 0.9980 overall best weight: 3.3986 ------------------------------------------------------------------------------- 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 = 0.3915 r_free = 0.3915 target = 0.101678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.074782 restraints weight = 30915.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.076905 restraints weight = 16735.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.078192 restraints weight = 11866.721| |-----------------------------------------------------------------------------| r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9922 Z= 0.228 Angle : 0.629 9.782 13875 Z= 0.331 Chirality : 0.039 0.189 1565 Planarity : 0.004 0.039 1402 Dihedral : 22.304 178.994 2383 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.27 % Favored : 95.62 % Rotamer: Outliers : 5.26 % Allowed : 23.82 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.29), residues: 914 helix: 1.60 (0.23), residues: 510 sheet: -0.90 (0.63), residues: 67 loop : -0.62 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 777 HIS 0.005 0.001 HIS C 868 PHE 0.015 0.002 PHE C 597 TYR 0.014 0.002 TYR C 202 ARG 0.009 0.000 ARG C1027 Details of bonding type rmsd hydrogen bonds : bond 0.04210 ( 497) hydrogen bonds : angle 4.20223 ( 1323) metal coordination : bond 0.01131 ( 7) metal coordination : angle 1.90238 ( 2) covalent geometry : bond 0.00503 ( 9915) covalent geometry : angle 0.62842 (13873) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 58 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: C 433 MET cc_start: 0.8673 (mmm) cc_final: 0.8230 (mmm) REVERT: C 561 HIS cc_start: 0.8203 (OUTLIER) cc_final: 0.7853 (t-90) REVERT: C 836 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8467 (mtm-85) outliers start: 40 outliers final: 24 residues processed: 87 average time/residue: 0.1924 time to fit residues: 24.9283 Evaluate side-chains 82 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 56 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 ARG Chi-restraints excluded: chain C residue 422 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 607 SER Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain C residue 812 VAL Chi-restraints excluded: chain C residue 836 ARG Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1012 VAL Chi-restraints excluded: chain C residue 1058 THR Chi-restraints excluded: chain C residue 1079 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 91 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 5 optimal weight: 0.8980 chunk 50 optimal weight: 4.9990 chunk 88 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 58 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 574 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.104153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.077665 restraints weight = 30601.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.079861 restraints weight = 16159.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.081246 restraints weight = 11310.771| |-----------------------------------------------------------------------------| r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9922 Z= 0.124 Angle : 0.576 9.913 13875 Z= 0.302 Chirality : 0.037 0.232 1565 Planarity : 0.003 0.033 1402 Dihedral : 22.219 177.254 2383 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.17 % Favored : 96.72 % Rotamer: Outliers : 3.16 % Allowed : 25.26 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.29), residues: 914 helix: 1.77 (0.23), residues: 504 sheet: -1.29 (0.54), residues: 87 loop : -0.55 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 978 HIS 0.009 0.001 HIS C 677 PHE 0.010 0.001 PHE C 597 TYR 0.009 0.001 TYR C1070 ARG 0.009 0.000 ARG C1027 Details of bonding type rmsd hydrogen bonds : bond 0.03581 ( 497) hydrogen bonds : angle 4.05994 ( 1323) metal coordination : bond 0.00727 ( 7) metal coordination : angle 3.12481 ( 2) covalent geometry : bond 0.00266 ( 9915) covalent geometry : angle 0.57455 (13873) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 561 HIS cc_start: 0.8295 (t-90) cc_final: 0.7864 (t-90) REVERT: C 668 MET cc_start: 0.8864 (tpt) cc_final: 0.8555 (tpt) REVERT: C 836 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.7920 (mtm-85) outliers start: 24 outliers final: 20 residues processed: 85 average time/residue: 0.2031 time to fit residues: 25.8510 Evaluate side-chains 82 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 61 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 213 PHE Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 ARG Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 812 VAL Chi-restraints excluded: chain C residue 836 ARG Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1046 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 82 optimal weight: 7.9990 chunk 36 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 4 optimal weight: 8.9990 chunk 34 optimal weight: 9.9990 chunk 47 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.098866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.070979 restraints weight = 30560.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.073091 restraints weight = 16595.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.074428 restraints weight = 11769.494| |-----------------------------------------------------------------------------| r_work (final): 0.3309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 9922 Z= 0.204 Angle : 0.644 12.624 13875 Z= 0.334 Chirality : 0.039 0.184 1565 Planarity : 0.004 0.031 1402 Dihedral : 22.278 178.821 2383 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.05 % Favored : 95.84 % Rotamer: Outliers : 3.82 % Allowed : 24.61 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.86 (0.29), residues: 914 helix: 1.58 (0.23), residues: 509 sheet: -0.92 (0.63), residues: 67 loop : -0.62 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 978 HIS 0.008 0.001 HIS C 677 PHE 0.013 0.002 PHE C 597 TYR 0.009 0.002 TYR C 628 ARG 0.008 0.000 ARG C1027 Details of bonding type rmsd hydrogen bonds : bond 0.04112 ( 497) hydrogen bonds : angle 4.16945 ( 1323) metal coordination : bond 0.01117 ( 7) metal coordination : angle 2.26746 ( 2) covalent geometry : bond 0.00450 ( 9915) covalent geometry : angle 0.64353 (13873) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 57 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: C 347 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8192 (mmm) REVERT: C 561 HIS cc_start: 0.8436 (t-90) cc_final: 0.7973 (t-90) REVERT: C 836 ARG cc_start: 0.8914 (OUTLIER) cc_final: 0.8323 (mtm-85) outliers start: 29 outliers final: 23 residues processed: 80 average time/residue: 0.1843 time to fit residues: 22.1446 Evaluate side-chains 81 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 56 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 189 THR Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 ARG Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain C residue 812 VAL Chi-restraints excluded: chain C residue 836 ARG Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1046 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 37 optimal weight: 0.6980 chunk 1 optimal weight: 0.0270 chunk 53 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 57 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 chunk 18 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 overall best weight: 0.8840 ------------------------------------------------------------------------------- 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 = 0.3843 r_free = 0.3843 target = 0.101054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.073481 restraints weight = 30368.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.075668 restraints weight = 16137.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.077064 restraints weight = 11278.808| |-----------------------------------------------------------------------------| r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9922 Z= 0.124 Angle : 0.571 10.089 13875 Z= 0.299 Chirality : 0.037 0.177 1565 Planarity : 0.003 0.032 1402 Dihedral : 22.196 176.967 2383 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.39 % Favored : 96.50 % Rotamer: Outliers : 3.29 % Allowed : 25.26 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.01 (0.29), residues: 914 helix: 1.76 (0.23), residues: 503 sheet: -0.90 (0.62), residues: 67 loop : -0.59 (0.35), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 978 HIS 0.008 0.001 HIS C 677 PHE 0.011 0.001 PHE C 597 TYR 0.008 0.001 TYR C 788 ARG 0.011 0.000 ARG C1027 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 497) hydrogen bonds : angle 4.02579 ( 1323) metal coordination : bond 0.00724 ( 7) metal coordination : angle 2.93086 ( 2) covalent geometry : bond 0.00266 ( 9915) covalent geometry : angle 0.57044 (13873) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1828 Ramachandran restraints generated. 914 Oldfield, 0 Emsley, 914 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 347 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8180 (mmm) REVERT: C 561 HIS cc_start: 0.8446 (t-90) cc_final: 0.7940 (t-90) REVERT: C 668 MET cc_start: 0.8891 (tpt) cc_final: 0.8546 (tpt) REVERT: C 836 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.7864 (mtm-85) outliers start: 25 outliers final: 22 residues processed: 83 average time/residue: 0.2124 time to fit residues: 25.2527 Evaluate side-chains 83 residues out of total 769 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 183 LEU Chi-restraints excluded: chain C residue 190 LEU Chi-restraints excluded: chain C residue 347 MET Chi-restraints excluded: chain C residue 349 THR Chi-restraints excluded: chain C residue 365 THR Chi-restraints excluded: chain C residue 374 ARG Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 582 VAL Chi-restraints excluded: chain C residue 605 LEU Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 768 VAL Chi-restraints excluded: chain C residue 784 VAL Chi-restraints excluded: chain C residue 807 ILE Chi-restraints excluded: chain C residue 812 VAL Chi-restraints excluded: chain C residue 836 ARG Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 868 HIS Chi-restraints excluded: chain C residue 872 SER Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 1010 VAL Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1079 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 23 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 4 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 85 optimal weight: 20.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3796 r_free = 0.3796 target = 0.098515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.070893 restraints weight = 30469.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.072982 restraints weight = 16706.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.074282 restraints weight = 11896.705| |-----------------------------------------------------------------------------| r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.2849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 9922 Z= 0.220 Angle : 0.648 11.038 13875 Z= 0.337 Chirality : 0.039 0.222 1565 Planarity : 0.004 0.030 1402 Dihedral : 22.291 179.081 2383 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.27 % Favored : 95.62 % Rotamer: Outliers : 3.82 % Allowed : 25.26 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.86 (0.29), residues: 914 helix: 1.58 (0.23), residues: 509 sheet: -0.89 (0.63), residues: 67 loop : -0.62 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 978 HIS 0.007 0.001 HIS C 677 PHE 0.014 0.002 PHE C 597 TYR 0.009 0.002 TYR C 628 ARG 0.016 0.001 ARG C 307 Details of bonding type rmsd hydrogen bonds : bond 0.04132 ( 497) hydrogen bonds : angle 4.15742 ( 1323) metal coordination : bond 0.01173 ( 7) metal coordination : angle 2.32526 ( 2) covalent geometry : bond 0.00489 ( 9915) covalent geometry : angle 0.64768 (13873) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2919.23 seconds wall clock time: 51 minutes 48.35 seconds (3108.35 seconds total)