Starting phenix.real_space_refine on Sun Apr 7 03:50:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibx_35348/04_2024/8ibx_35348.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibx_35348/04_2024/8ibx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibx_35348/04_2024/8ibx_35348.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibx_35348/04_2024/8ibx_35348.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibx_35348/04_2024/8ibx_35348.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ibx_35348/04_2024/8ibx_35348.pdb" } 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 Residue "C GLU 575": "OE1" <-> "OE2" Residue "C GLU 867": "OE1" <-> "OE2" Residue "C GLU 929": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 6.00, per 1000 atoms: 0.63 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 - 3.50 Amino acid : False - 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: 4.53 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: 3.62 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: 4.81 Time building geometry restraints manager: 4.89 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: 99.26 - 106.22: 819 106.22 - 113.18: 5419 113.18 - 120.15: 3741 120.15 - 127.11: 3558 127.11 - 134.07: 336 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 2.440 nonbonded pdb=" NH1 ARG C 473 " pdb=" OP1 A D 247 " model vdw 2.080 2.520 nonbonded pdb=" OG SER C 406 " pdb=" OP1 A D 246 " model vdw 2.107 2.440 nonbonded pdb=" OD1 ASN C1028 " pdb=" N LYS C1029 " model vdw 2.128 2.520 nonbonded pdb=" NH1 ARG C 848 " pdb=" OP1 DT A 30 " model vdw 2.137 2.520 ... (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 ========== 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: 0.340 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: 0.010 Extract box with map and model: 2.220 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 35.050 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.090 ------------------------------------------------------------------------------- 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 9915 Z= 0.231 Angle : 0.589 6.072 13873 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 *********************** 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 fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 1.012 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: 0.2194 time to fit residues: 21.4530 Evaluate side-chains 61 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 1.041 ------------------------------------------------------------------------------- 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: 0.9990 chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 0.0870 chunk 79 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 overall best weight: 2.0166 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7984 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9915 Z= 0.233 Angle : 0.591 6.975 13873 Z= 0.316 Chirality : 0.038 0.159 1565 Planarity : 0.004 0.031 1402 Dihedral : 22.576 179.122 2392 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.50 % Favored : 96.39 % Rotamer: Outliers : 1.97 % Allowed : 24.61 % Favored : 73.42 % 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: 0.98 (0.28), residues: 914 helix: 1.66 (0.23), residues: 509 sheet: -0.92 (0.59), residues: 66 loop : -0.52 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 978 HIS 0.005 0.001 HIS C 744 PHE 0.014 0.001 PHE C 116 TYR 0.010 0.002 TYR C 628 ARG 0.003 0.000 ARG C1027 *********************** 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 76 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 61 time to evaluate : 0.915 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 147 MET cc_start: 0.9080 (mmm) cc_final: 0.8867 (mtt) REVERT: C 911 ILE cc_start: 0.8959 (tp) cc_final: 0.8749 (tp) outliers start: 15 outliers final: 8 residues processed: 74 average time/residue: 0.1879 time to fit residues: 21.0809 Evaluate side-chains 64 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.927 ------------------------------------------------------------------------------- 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 575 GLU Chi-restraints excluded: chain C residue 697 CYS Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 812 VAL Chi-restraints excluded: chain C residue 895 CYS 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 50 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 76 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 25 optimal weight: 7.9990 chunk 91 optimal weight: 2.9990 chunk 99 optimal weight: 8.9990 chunk 81 optimal weight: 7.9990 chunk 31 optimal weight: 3.9990 chunk 73 optimal weight: 10.0000 chunk 90 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1096 HIS C1098 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9915 Z= 0.321 Angle : 0.615 7.492 13873 Z= 0.331 Chirality : 0.039 0.144 1565 Planarity : 0.004 0.032 1402 Dihedral : 22.501 179.235 2390 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 12.96 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.60 % Favored : 95.30 % Rotamer: Outliers : 4.74 % Allowed : 23.42 % 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: 0.75 (0.28), residues: 914 helix: 1.50 (0.23), residues: 509 sheet: -1.02 (0.59), residues: 66 loop : -0.68 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 978 HIS 0.005 0.001 HIS C 868 PHE 0.014 0.002 PHE C 597 TYR 0.012 0.002 TYR C 628 ARG 0.005 0.000 ARG C 547 *********************** 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 94 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 58 time to evaluate : 0.933 Fit side-chains REVERT: C 668 MET cc_start: 0.8969 (tmm) cc_final: 0.7930 (tmm) REVERT: C 836 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8459 (ttp-110) REVERT: C 911 ILE cc_start: 0.9063 (tp) cc_final: 0.8849 (tp) outliers start: 36 outliers final: 23 residues processed: 89 average time/residue: 0.2246 time to fit residues: 28.4030 Evaluate side-chains 77 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 53 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 453 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 605 LEU 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 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 Chi-restraints excluded: chain C residue 1046 LEU Chi-restraints excluded: chain C residue 1058 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 9.9990 chunk 47 optimal weight: 4.9990 chunk 10 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 61 optimal weight: 0.0040 chunk 92 optimal weight: 10.0000 chunk 97 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 81 optimal weight: 30.0000 overall best weight: 3.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9915 Z= 0.346 Angle : 0.635 8.315 13873 Z= 0.340 Chirality : 0.040 0.209 1565 Planarity : 0.004 0.032 1402 Dihedral : 22.474 179.059 2384 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.72 % Favored : 96.17 % Rotamer: Outliers : 6.32 % Allowed : 22.63 % Favored : 71.05 % 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: 0.55 (0.28), residues: 914 helix: 1.36 (0.23), residues: 509 sheet: -1.18 (0.60), residues: 66 loop : -0.78 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP C1065 HIS 0.005 0.001 HIS C 868 PHE 0.016 0.002 PHE C 815 TYR 0.012 0.002 TYR C 628 ARG 0.008 0.000 ARG C 941 *********************** 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 103 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 55 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 549 ARG cc_start: 0.8101 (OUTLIER) cc_final: 0.7628 (tpp80) REVERT: C 668 MET cc_start: 0.9072 (tmm) cc_final: 0.8185 (tmm) REVERT: C 836 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8350 (mtm-85) outliers start: 48 outliers final: 35 residues processed: 94 average time/residue: 0.1969 time to fit residues: 27.2104 Evaluate side-chains 91 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 54 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 503 LEU Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 535 ASP Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 537 VAL Chi-restraints excluded: chain C residue 546 LEU Chi-restraints excluded: chain C residue 549 ARG Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 572 VAL Chi-restraints excluded: chain C residue 575 GLU 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 629 ASP Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 740 ILE 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 891 ILE Chi-restraints excluded: chain C residue 943 THR 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 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 55 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 72 optimal weight: 0.7980 chunk 40 optimal weight: 0.0060 chunk 83 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 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 : 0.003 0.033 9915 Z= 0.169 Angle : 0.553 8.157 13873 Z= 0.293 Chirality : 0.037 0.174 1565 Planarity : 0.003 0.033 1402 Dihedral : 22.289 177.081 2384 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.50 % Favored : 96.39 % Rotamer: Outliers : 3.82 % Allowed : 24.74 % 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: 0.96 (0.28), residues: 914 helix: 1.76 (0.23), residues: 503 sheet: -0.97 (0.60), residues: 66 loop : -0.69 (0.34), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 978 HIS 0.005 0.001 HIS C 744 PHE 0.008 0.001 PHE C 597 TYR 0.007 0.001 TYR C 202 ARG 0.005 0.000 ARG C1027 *********************** 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 99 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 70 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 437 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.6688 (mm-30) REVERT: C 561 HIS cc_start: 0.8047 (OUTLIER) cc_final: 0.7691 (t-170) REVERT: C 668 MET cc_start: 0.9056 (tmm) cc_final: 0.8352 (tmm) REVERT: C 836 ARG cc_start: 0.8895 (OUTLIER) cc_final: 0.8372 (mtm-85) outliers start: 29 outliers final: 19 residues processed: 94 average time/residue: 0.2061 time to fit residues: 28.1450 Evaluate side-chains 88 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 66 time to evaluate : 0.887 ------------------------------------------------------------------------------- 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 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 437 GLU Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 535 ASP Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain C residue 575 GLU Chi-restraints excluded: chain C residue 629 ASP 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 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 1046 LEU 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 87 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 81 optimal weight: 20.0000 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 94 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.107 9915 Z= 0.450 Angle : 0.714 9.736 13873 Z= 0.375 Chirality : 0.041 0.155 1565 Planarity : 0.005 0.046 1402 Dihedral : 22.487 179.075 2383 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.81 % Favored : 95.08 % Rotamer: Outliers : 5.92 % Allowed : 25.00 % Favored : 69.08 % 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: 0.54 (0.28), residues: 914 helix: 1.38 (0.23), residues: 509 sheet: -1.21 (0.59), residues: 66 loop : -0.83 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C1065 HIS 0.007 0.002 HIS C 868 PHE 0.016 0.002 PHE C 597 TYR 0.014 0.002 TYR C 628 ARG 0.013 0.001 ARG C 133 *********************** 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 102 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 57 time to evaluate : 0.843 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 549 ARG cc_start: 0.8001 (OUTLIER) cc_final: 0.7611 (tpt-90) REVERT: C 668 MET cc_start: 0.9119 (tmm) cc_final: 0.8361 (tmm) REVERT: C 818 LEU cc_start: 0.9069 (OUTLIER) cc_final: 0.8826 (mp) REVERT: C 836 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8374 (mtm-85) outliers start: 45 outliers final: 36 residues processed: 95 average time/residue: 0.2043 time to fit residues: 28.4827 Evaluate side-chains 92 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 53 time to evaluate : 0.981 ------------------------------------------------------------------------------- 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 213 PHE 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 422 VAL Chi-restraints excluded: chain C residue 453 VAL Chi-restraints excluded: chain C residue 503 LEU Chi-restraints excluded: chain C residue 519 LYS Chi-restraints excluded: chain C residue 536 THR Chi-restraints excluded: chain C residue 549 ARG Chi-restraints excluded: chain C residue 561 HIS Chi-restraints excluded: chain C residue 568 THR Chi-restraints excluded: chain C residue 575 GLU 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 629 ASP Chi-restraints excluded: chain C residue 638 VAL Chi-restraints excluded: chain C residue 677 HIS 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 811 ILE Chi-restraints excluded: chain C residue 812 VAL Chi-restraints excluded: chain C residue 818 LEU 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 943 THR 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 1064 VAL Chi-restraints excluded: chain C residue 1079 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 8.9990 chunk 54 optimal weight: 0.7980 chunk 97 optimal weight: 6.9990 chunk 60 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 58 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 308 GLN ** C 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9915 Z= 0.198 Angle : 0.588 10.004 13873 Z= 0.308 Chirality : 0.037 0.177 1565 Planarity : 0.004 0.031 1402 Dihedral : 22.396 178.474 2383 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 12.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.72 % Favored : 96.17 % Rotamer: Outliers : 4.21 % Allowed : 27.11 % Favored : 68.68 % 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: 0.78 (0.28), residues: 914 helix: 1.60 (0.23), residues: 509 sheet: -1.23 (0.58), residues: 67 loop : -0.74 (0.34), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 978 HIS 0.005 0.001 HIS C 130 PHE 0.011 0.001 PHE C 597 TYR 0.008 0.001 TYR C 628 ARG 0.007 0.000 ARG C 133 *********************** 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 94 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 62 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 668 MET cc_start: 0.9129 (tmm) cc_final: 0.8508 (tmm) REVERT: C 836 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8379 (mtm-85) outliers start: 32 outliers final: 24 residues processed: 90 average time/residue: 0.2002 time to fit residues: 26.4940 Evaluate side-chains 86 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 61 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 213 PHE 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 561 HIS Chi-restraints excluded: chain C residue 575 GLU 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 629 ASP Chi-restraints excluded: chain C residue 713 CYS Chi-restraints excluded: chain C residue 784 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 891 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 48 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 76 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 85 optimal weight: 20.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 9915 Z= 0.243 Angle : 0.590 9.697 13873 Z= 0.312 Chirality : 0.037 0.163 1565 Planarity : 0.004 0.042 1402 Dihedral : 22.352 178.590 2383 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.60 % Favored : 95.30 % Rotamer: Outliers : 4.47 % Allowed : 27.11 % Favored : 68.42 % 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 (0.28), residues: 914 helix: 1.69 (0.23), residues: 509 sheet: -1.27 (0.58), residues: 67 loop : -0.73 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C1065 HIS 0.004 0.001 HIS C 130 PHE 0.011 0.001 PHE C 597 TYR 0.009 0.002 TYR C 628 ARG 0.008 0.000 ARG C 894 *********************** 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 92 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 58 time to evaluate : 0.892 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 668 MET cc_start: 0.9137 (tmm) cc_final: 0.8558 (tmm) REVERT: C 836 ARG cc_start: 0.8906 (OUTLIER) cc_final: 0.8301 (mtm-85) REVERT: C 1011 GLN cc_start: 0.8287 (pp30) cc_final: 0.7793 (pm20) outliers start: 34 outliers final: 30 residues processed: 84 average time/residue: 0.2071 time to fit residues: 25.3289 Evaluate side-chains 89 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 58 time to evaluate : 0.994 ------------------------------------------------------------------------------- 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 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 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 629 ASP Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 673 HIS 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 855 THR 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 943 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 54 optimal weight: 0.7980 chunk 39 optimal weight: 20.0000 chunk 71 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 85 optimal weight: 20.0000 chunk 59 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 574 ASN ** C 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8021 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9915 Z= 0.208 Angle : 0.580 9.568 13873 Z= 0.305 Chirality : 0.037 0.164 1565 Planarity : 0.003 0.032 1402 Dihedral : 22.296 178.098 2383 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.05 % Favored : 95.84 % Rotamer: Outliers : 4.47 % Allowed : 26.71 % Favored : 68.82 % 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: 0.92 (0.28), residues: 914 helix: 1.75 (0.23), residues: 509 sheet: -1.25 (0.57), residues: 67 loop : -0.73 (0.35), residues: 338 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 0.011 0.001 PHE C 597 TYR 0.008 0.001 TYR C 628 ARG 0.008 0.000 ARG C1027 *********************** 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 96 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 62 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: C 561 HIS cc_start: 0.8010 (OUTLIER) cc_final: 0.7405 (t-170) REVERT: C 668 MET cc_start: 0.9143 (tmm) cc_final: 0.8654 (tmm) REVERT: C 836 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8374 (mtm-85) REVERT: C 1011 GLN cc_start: 0.8261 (pp30) cc_final: 0.7815 (pm20) outliers start: 34 outliers final: 29 residues processed: 88 average time/residue: 0.2069 time to fit residues: 26.8023 Evaluate side-chains 90 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 59 time to evaluate : 0.966 ------------------------------------------------------------------------------- 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 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 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 629 ASP Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 673 HIS 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 891 ILE Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 974 GLU 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 45 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 chunk 100 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 8 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 85 optimal weight: 8.9990 chunk 24 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9915 Z= 0.244 Angle : 0.596 9.287 13873 Z= 0.314 Chirality : 0.037 0.163 1565 Planarity : 0.004 0.032 1402 Dihedral : 22.299 178.975 2383 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.57 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.60 % Favored : 95.30 % Rotamer: Outliers : 4.34 % Allowed : 26.97 % Favored : 68.68 % 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: 0.93 (0.28), residues: 914 helix: 1.77 (0.23), residues: 509 sheet: -1.26 (0.58), residues: 67 loop : -0.75 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 978 HIS 0.004 0.001 HIS C 130 PHE 0.012 0.001 PHE C 597 TYR 0.009 0.002 TYR C 628 ARG 0.009 0.000 ARG C1027 ********************** 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 92 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 59 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: C 561 HIS cc_start: 0.7933 (OUTLIER) cc_final: 0.7320 (t-170) REVERT: C 668 MET cc_start: 0.9135 (tmm) cc_final: 0.8571 (tmm) REVERT: C 836 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8317 (mtm-85) REVERT: C 1011 GLN cc_start: 0.8244 (pp30) cc_final: 0.7835 (pm20) outliers start: 33 outliers final: 30 residues processed: 87 average time/residue: 0.1969 time to fit residues: 25.2295 Evaluate side-chains 91 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 59 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 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 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 629 ASP Chi-restraints excluded: chain C residue 630 LEU Chi-restraints excluded: chain C residue 644 ILE Chi-restraints excluded: chain C residue 673 HIS 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 891 ILE Chi-restraints excluded: chain C residue 943 THR Chi-restraints excluded: chain C residue 948 LEU Chi-restraints excluded: chain C residue 974 GLU 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 73 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 82 optimal weight: 8.9990 chunk 10 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 70 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 57 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 694 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 857 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 949 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3878 r_free = 0.3878 target = 0.099633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.072807 restraints weight = 30576.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.074822 restraints weight = 17021.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.076113 restraints weight = 12239.081| |-----------------------------------------------------------------------------| r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 9915 Z= 0.369 Angle : 0.679 8.962 13873 Z= 0.357 Chirality : 0.040 0.187 1565 Planarity : 0.005 0.037 1402 Dihedral : 22.433 177.453 2383 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 16.39 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.47 % Favored : 94.42 % Rotamer: Outliers : 4.61 % Allowed : 26.58 % Favored : 68.82 % 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: 0.62 (0.28), residues: 914 helix: 1.49 (0.23), residues: 510 sheet: -1.48 (0.58), residues: 67 loop : -0.81 (0.35), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C1099 HIS 0.005 0.001 HIS C 130 PHE 0.016 0.002 PHE C 597 TYR 0.011 0.002 TYR C 628 ARG 0.010 0.001 ARG C1027 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1668.20 seconds wall clock time: 31 minutes 35.82 seconds (1895.82 seconds total)