Starting phenix.real_space_refine on Sun Jun 8 22:35:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bwt_44979/06_2025/9bwt_44979_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bwt_44979/06_2025/9bwt_44979.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bwt_44979/06_2025/9bwt_44979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bwt_44979/06_2025/9bwt_44979.map" model { file = "/net/cci-nas-00/data/ceres_data/9bwt_44979/06_2025/9bwt_44979_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bwt_44979/06_2025/9bwt_44979_trim.cif" } resolution = 2.5 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= -0.001 sd= 0.058 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 S 55 5.16 5 Cl 1 4.86 5 C 6402 2.51 5 N 1698 2.21 5 O 1790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9955 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 6891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 898, 6891 Classifications: {'peptide': 898} Incomplete info: {'truncation_to_alanine': 46} Link IDs: {'PTRANS': 41, 'TRANS': 856} Chain breaks: 2 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 176 Unresolved non-hydrogen angles: 214 Unresolved non-hydrogen dihedrals: 146 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 5, 'TPO:plan-1': 2, 'ASP:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 88 Chain: "B" Number of atoms: 2979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2979 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 17, 'TRANS': 355} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "A" Number of atoms: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 48 Unusual residues: {'ATP': 1, 'HCZ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 6.57, per 1000 atoms: 0.66 Number of scatterers: 9955 At special positions: 0 Unit cell: (143.55, 99.825, 111.375, 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) Cl 1 17.00 S 55 16.00 P 9 15.00 O 1790 8.00 N 1698 7.00 C 6402 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 415 " - pdb=" SG CYS A 420 " distance=2.03 Simple disulfide: pdb=" SG CYS A 429 " - pdb=" SG CYS A 435 " distance=2.03 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: 2.86 Conformation dependent library (CDL) restraints added in 1.4 seconds 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2350 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 2 sheets defined 59.1% alpha, 7.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 66 through 70 Processing helix chain 'A' and resid 85 through 90 Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 141 through 150 Processing helix chain 'A' and resid 152 through 157 Processing helix chain 'A' and resid 157 through 192 removed outlier: 6.760A pdb=" N ILE A 167 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 9.178A pdb=" N VAL A 168 " --> pdb=" O GLN A 164 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU A 169 " --> pdb=" O ALA A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 211 Processing helix chain 'A' and resid 211 through 248 removed outlier: 3.844A pdb=" N SER A 217 " --> pdb=" O GLU A 213 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ALA A 231 " --> pdb=" O ALA A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 276 removed outlier: 3.772A pdb=" N ILE A 259 " --> pdb=" O PRO A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 277 through 303 Processing helix chain 'A' and resid 308 through 313 Processing helix chain 'A' and resid 320 through 327 Processing helix chain 'A' and resid 338 through 347 Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 356 through 363 removed outlier: 3.592A pdb=" N ILE A 359 " --> pdb=" O GLY A 356 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER A 360 " --> pdb=" O ALA A 357 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N GLY A 361 " --> pdb=" O ASN A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 394 Proline residue: A 371 - end of helix Processing helix chain 'A' and resid 403 through 407 removed outlier: 4.081A pdb=" N THR A 407 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 421 Processing helix chain 'A' and resid 426 through 433 Processing helix chain 'A' and resid 444 through 450 Processing helix chain 'A' and resid 452 through 486 removed outlier: 3.597A pdb=" N ILE A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 490 through 494 Processing helix chain 'A' and resid 504 through 522 removed outlier: 3.754A pdb=" N ILE A 521 " --> pdb=" O ALA A 517 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA A 522 " --> pdb=" O PHE A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 553 Processing helix chain 'A' and resid 565 through 606 removed outlier: 3.694A pdb=" N THR A 584 " --> pdb=" O MET A 580 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N TRP A 586 " --> pdb=" O LEU A 582 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ALA A 587 " --> pdb=" O LEU A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 613 through 633 Processing helix chain 'A' and resid 636 through 640 removed outlier: 4.154A pdb=" N ASN A 639 " --> pdb=" O HIS A 636 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N TYR A 640 " --> pdb=" O ILE A 637 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 636 through 640' Processing helix chain 'A' and resid 654 through 666 removed outlier: 3.794A pdb=" N VAL A 658 " --> pdb=" O ARG A 654 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N PHE A 664 " --> pdb=" O PHE A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 685 through 702 Processing helix chain 'A' and resid 715 through 727 Processing helix chain 'A' and resid 749 through 766 removed outlier: 3.786A pdb=" N VAL A 753 " --> pdb=" O HIS A 749 " (cutoff:3.500A) Processing helix chain 'A' and resid 819 through 823 Processing helix chain 'A' and resid 840 through 850 Proline residue: A 846 - end of helix Processing helix chain 'A' and resid 875 through 885 removed outlier: 3.558A pdb=" N ILE A 879 " --> pdb=" O ARG A 875 " (cutoff:3.500A) Processing helix chain 'A' and resid 903 through 915 Processing helix chain 'A' and resid 916 through 918 No H-bonds generated for 'chain 'A' and resid 916 through 918' Processing helix chain 'A' and resid 925 through 934 removed outlier: 4.310A pdb=" N ASN A 930 " --> pdb=" O GLU A 926 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N GLU A 931 " --> pdb=" O ALA A 927 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N MET A 932 " --> pdb=" O THR A 928 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 948 Processing helix chain 'A' and resid 949 through 966 removed outlier: 3.726A pdb=" N GLN A 955 " --> pdb=" O LYS A 951 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N VAL A 956 " --> pdb=" O SER A 952 " (cutoff:3.500A) Processing helix chain 'A' and resid 985 through 997 Processing helix chain 'A' and resid 1013 through 1018 removed outlier: 3.942A pdb=" N THR A1016 " --> pdb=" O ASN A1013 " (cutoff:3.500A) Processing helix chain 'B' and resid 616 through 630 Processing helix chain 'B' and resid 654 through 666 removed outlier: 3.700A pdb=" N VAL B 658 " --> pdb=" O ARG B 654 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N PHE B 664 " --> pdb=" O PHE B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 684 through 702 removed outlier: 4.341A pdb=" N LEU B 688 " --> pdb=" O ARG B 684 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLN B 689 " --> pdb=" O MET B 685 " (cutoff:3.500A) Processing helix chain 'B' and resid 715 through 727 Processing helix chain 'B' and resid 749 through 766 removed outlier: 3.656A pdb=" N VAL B 753 " --> pdb=" O HIS B 749 " (cutoff:3.500A) Processing helix chain 'B' and resid 819 through 823 Processing helix chain 'B' and resid 840 through 851 Proline residue: B 846 - end of helix Processing helix chain 'B' and resid 867 through 869 No H-bonds generated for 'chain 'B' and resid 867 through 869' Processing helix chain 'B' and resid 870 through 886 Processing helix chain 'B' and resid 903 through 914 Processing helix chain 'B' and resid 915 through 918 Processing helix chain 'B' and resid 925 through 928 Processing helix chain 'B' and resid 929 through 934 removed outlier: 3.785A pdb=" N ARG B 933 " --> pdb=" O VAL B 929 " (cutoff:3.500A) Processing helix chain 'B' and resid 941 through 964 removed outlier: 5.165A pdb=" N VAL B 950 " --> pdb=" O THR B 946 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N LYS B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) Processing helix chain 'B' and resid 985 through 997 removed outlier: 3.515A pdb=" N SER B 997 " --> pdb=" O LEU B 993 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 707 through 712 removed outlier: 6.599A pdb=" N CYS A 644 " --> pdb=" O ILE A 672 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N GLY A 674 " --> pdb=" O CYS A 644 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL A 646 " --> pdb=" O GLY A 674 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N VAL A 676 " --> pdb=" O VAL A 646 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N GLY A 740 " --> pdb=" O LEU A 647 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ILE A 972 " --> pdb=" O ILE A1005 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N ILE A1007 " --> pdb=" O ILE A 972 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ILE A 974 " --> pdb=" O ILE A1007 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASP A 831 " --> pdb=" O VAL A 973 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N THR A 975 " --> pdb=" O ASP A 831 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N TYR A 833 " --> pdb=" O THR A 975 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE A 830 " --> pdb=" O ARG A 861 " (cutoff:3.500A) removed outlier: 7.270A pdb=" N PHE A 863 " --> pdb=" O ILE A 830 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE A 832 " --> pdb=" O PHE A 863 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ILE A 860 " --> pdb=" O GLU A 891 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N HIS A 893 " --> pdb=" O ILE A 860 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N VAL A 862 " --> pdb=" O HIS A 893 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 707 through 713 removed outlier: 6.638A pdb=" N CYS B 644 " --> pdb=" O ILE B 672 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N GLY B 674 " --> pdb=" O CYS B 644 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL B 646 " --> pdb=" O GLY B 674 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N VAL B 676 " --> pdb=" O VAL B 646 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N GLY B 740 " --> pdb=" O LEU B 647 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ILE B 972 " --> pdb=" O ILE B1005 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ILE B1007 " --> pdb=" O ILE B 972 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N ILE B 974 " --> pdb=" O ILE B1007 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU B 971 " --> pdb=" O THR B 829 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE B 830 " --> pdb=" O ARG B 861 " (cutoff:3.500A) removed outlier: 7.514A pdb=" N PHE B 863 " --> pdb=" O ILE B 830 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE B 832 " --> pdb=" O PHE B 863 " (cutoff:3.500A) removed outlier: 8.298A pdb=" N GLY B 865 " --> pdb=" O ILE B 832 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ILE B 860 " --> pdb=" O GLU B 891 " (cutoff:3.500A) removed outlier: 8.032A pdb=" N HIS B 893 " --> pdb=" O ILE B 860 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N VAL B 862 " --> pdb=" O HIS B 893 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LEU B 895 " --> pdb=" O VAL B 862 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL B 864 " --> pdb=" O LEU B 895 " (cutoff:3.500A) 538 hydrogen bonds defined for protein. 1554 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.32 Time building geometry restraints manager: 3.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3178 1.34 - 1.46: 2319 1.46 - 1.58: 4576 1.58 - 1.69: 28 1.69 - 1.81: 85 Bond restraints: 10186 Sorted by residual: bond pdb=" O1A ATP A1301 " pdb=" PA ATP A1301 " ideal model delta sigma weight residual 1.477 1.608 -0.131 1.10e-02 8.26e+03 1.42e+02 bond pdb=" O1A ATP B1101 " pdb=" PA ATP B1101 " ideal model delta sigma weight residual 1.477 1.605 -0.128 1.10e-02 8.26e+03 1.36e+02 bond pdb=" C6 ATP A1301 " pdb=" N6 ATP A1301 " ideal model delta sigma weight residual 1.337 1.440 -0.103 1.10e-02 8.26e+03 8.77e+01 bond pdb=" C6 ATP B1101 " pdb=" N6 ATP B1101 " ideal model delta sigma weight residual 1.337 1.440 -0.103 1.10e-02 8.26e+03 8.76e+01 bond pdb=" O1B ATP A1301 " pdb=" PB ATP A1301 " ideal model delta sigma weight residual 1.477 1.608 -0.131 2.20e-02 2.07e+03 3.57e+01 ... (remaining 10181 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.34: 13827 4.34 - 8.67: 31 8.67 - 13.01: 5 13.01 - 17.34: 2 17.34 - 21.68: 2 Bond angle restraints: 13867 Sorted by residual: angle pdb=" PB ATP A1301 " pdb=" O3B ATP A1301 " pdb=" PG ATP A1301 " ideal model delta sigma weight residual 139.87 118.19 21.68 1.00e+00 1.00e+00 4.70e+02 angle pdb=" PB ATP B1101 " pdb=" O3B ATP B1101 " pdb=" PG ATP B1101 " ideal model delta sigma weight residual 139.87 120.86 19.01 1.00e+00 1.00e+00 3.62e+02 angle pdb=" PA ATP A1301 " pdb=" O3A ATP A1301 " pdb=" PB ATP A1301 " ideal model delta sigma weight residual 136.83 119.75 17.08 1.00e+00 1.00e+00 2.92e+02 angle pdb=" PA ATP B1101 " pdb=" O3A ATP B1101 " pdb=" PB ATP B1101 " ideal model delta sigma weight residual 136.83 120.29 16.54 1.00e+00 1.00e+00 2.74e+02 angle pdb=" N1 ATP B1101 " pdb=" C2 ATP B1101 " pdb=" N3 ATP B1101 " ideal model delta sigma weight residual 128.69 120.70 7.99 1.00e+00 1.00e+00 6.39e+01 ... (remaining 13862 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 5131 17.76 - 35.52: 661 35.52 - 53.28: 181 53.28 - 71.05: 41 71.05 - 88.81: 15 Dihedral angle restraints: 6029 sinusoidal: 2369 harmonic: 3660 Sorted by residual: dihedral pdb=" CB CYS A 415 " pdb=" SG CYS A 415 " pdb=" SG CYS A 420 " pdb=" CB CYS A 420 " ideal model delta sinusoidal sigma weight residual -86.00 2.81 -88.81 1 1.00e+01 1.00e-02 9.40e+01 dihedral pdb=" CA PRO B1002 " pdb=" C PRO B1002 " pdb=" N PRO B1003 " pdb=" CA PRO B1003 " ideal model delta harmonic sigma weight residual 180.00 141.61 38.39 0 5.00e+00 4.00e-02 5.90e+01 dihedral pdb=" CB CYS A 429 " pdb=" SG CYS A 429 " pdb=" SG CYS A 435 " pdb=" CB CYS A 435 " ideal model delta sinusoidal sigma weight residual 93.00 38.27 54.73 1 1.00e+01 1.00e-02 4.06e+01 ... (remaining 6026 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 951 0.029 - 0.058: 392 0.058 - 0.087: 141 0.087 - 0.116: 71 0.116 - 0.145: 10 Chirality restraints: 1565 Sorted by residual: chirality pdb=" C2' ATP A1301 " pdb=" C1' ATP A1301 " pdb=" C3' ATP A1301 " pdb=" O2' ATP A1301 " both_signs ideal model delta sigma weight residual False -2.68 -2.54 -0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" C2' ATP B1101 " pdb=" C1' ATP B1101 " pdb=" C3' ATP B1101 " pdb=" O2' ATP B1101 " both_signs ideal model delta sigma weight residual False -2.68 -2.54 -0.14 2.00e-01 2.50e+01 5.06e-01 chirality pdb=" CB THR A 179 " pdb=" CA THR A 179 " pdb=" OG1 THR A 179 " pdb=" CG2 THR A 179 " both_signs ideal model delta sigma weight residual False 2.55 2.43 0.12 2.00e-01 2.50e+01 3.89e-01 ... (remaining 1562 not shown) Planarity restraints: 1741 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 984 " 0.031 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO A 985 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 985 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 985 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B1002 " 0.030 5.00e-02 4.00e+02 4.57e-02 3.34e+00 pdb=" N PRO B1003 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO B1003 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B1003 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 915 " -0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO A 916 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 916 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 916 " -0.020 5.00e-02 4.00e+02 ... (remaining 1738 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 63 2.46 - 3.07: 7257 3.07 - 3.68: 15242 3.68 - 4.29: 23198 4.29 - 4.90: 38504 Nonbonded interactions: 84264 Sorted by model distance: nonbonded pdb=" O THR A 351 " pdb=" OH TYR A 539 " model vdw 1.847 3.040 nonbonded pdb=" O ASP A 88 " pdb=" NH2 ARG B 980 " model vdw 2.014 3.120 nonbonded pdb=" O PRO A 977 " pdb=" OH TYR A 989 " model vdw 2.038 3.040 nonbonded pdb=" OH TYR A 67 " pdb=" O HOH A1401 " model vdw 2.052 3.040 nonbonded pdb=" O GLY A 166 " pdb=" OG1 THR A 170 " model vdw 2.054 3.040 ... (remaining 84259 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 individual isotropic 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: 3.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 27.170 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 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 : 0.006 0.131 10188 Z= 0.356 Angle : 0.711 21.679 13871 Z= 0.485 Chirality : 0.040 0.145 1565 Planarity : 0.004 0.048 1741 Dihedral : 17.533 84.610 3673 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 23.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.23 % Favored : 95.61 % Rotamer: Outliers : 2.72 % Allowed : 28.89 % Favored : 68.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.75 % 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: 1.32 (0.25), residues: 1252 helix: 2.20 (0.21), residues: 658 sheet: 0.54 (0.51), residues: 113 loop : -0.96 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 586 HIS 0.003 0.001 HIS A 636 PHE 0.014 0.001 PHE A 597 TYR 0.012 0.001 TYR A 965 ARG 0.008 0.000 ARG A 934 Details of bonding type rmsd hydrogen bonds : bond 0.13884 ( 538) hydrogen bonds : angle 5.82329 ( 1554) SS BOND : bond 0.00191 ( 2) SS BOND : angle 1.63868 ( 4) covalent geometry : bond 0.00612 (10186) covalent geometry : angle 0.71055 (13867) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 195 time to evaluate : 1.113 Fit side-chains revert: symmetry clash REVERT: A 154 LEU cc_start: 0.8275 (tp) cc_final: 0.7888 (tt) REVERT: A 164 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7373 (mm-40) REVERT: A 196 LYS cc_start: 0.7380 (ttmm) cc_final: 0.7066 (ttmt) REVERT: A 213 GLU cc_start: 0.6730 (mp0) cc_final: 0.6431 (mp0) REVERT: A 243 ASP cc_start: 0.7247 (m-30) cc_final: 0.6856 (m-30) REVERT: A 247 GLU cc_start: 0.6915 (tm-30) cc_final: 0.6676 (tt0) REVERT: A 310 ASP cc_start: 0.7508 (t0) cc_final: 0.7291 (t70) REVERT: A 331 ASP cc_start: 0.7297 (t0) cc_final: 0.6914 (t0) REVERT: A 345 ILE cc_start: 0.7261 (mt) cc_final: 0.6999 (mm) REVERT: A 416 GLU cc_start: 0.5942 (tm-30) cc_final: 0.5224 (tt0) REVERT: A 484 GLU cc_start: 0.6264 (mm-30) cc_final: 0.5884 (mt-10) REVERT: A 603 ILE cc_start: 0.7273 (tt) cc_final: 0.6933 (mt) REVERT: A 605 LYS cc_start: 0.7493 (tppp) cc_final: 0.7133 (tptt) REVERT: A 606 LYS cc_start: 0.6718 (mtmt) cc_final: 0.6198 (mmmt) REVERT: A 718 ARG cc_start: 0.7009 (mpp80) cc_final: 0.6169 (mmp80) REVERT: A 752 THR cc_start: 0.7945 (m) cc_final: 0.7655 (p) REVERT: A 767 ASN cc_start: 0.7918 (t0) cc_final: 0.7497 (t0) REVERT: A 777 GLU cc_start: 0.7134 (mp0) cc_final: 0.6677 (pm20) REVERT: A 827 LYS cc_start: 0.8130 (mmtm) cc_final: 0.7906 (mmtm) REVERT: A 857 LYS cc_start: 0.7846 (mmmm) cc_final: 0.6920 (mmtt) REVERT: A 947 LYS cc_start: 0.7146 (mttp) cc_final: 0.6800 (mttp) REVERT: A 949 ARG cc_start: 0.7013 (tpp80) cc_final: 0.6530 (tpp-160) REVERT: A 981 LYS cc_start: 0.6703 (OUTLIER) cc_final: 0.6204 (tptt) REVERT: A 999 ASP cc_start: 0.8194 (m-30) cc_final: 0.7970 (m-30) REVERT: A 1001 ARG cc_start: 0.7841 (ttm-80) cc_final: 0.7458 (ttm-80) REVERT: A 1011 GLN cc_start: 0.7953 (tp-100) cc_final: 0.7555 (mm-40) REVERT: A 1013 ASN cc_start: 0.8298 (t0) cc_final: 0.7864 (t0) REVERT: B 714 GLU cc_start: 0.7322 (mp0) cc_final: 0.6895 (mm-30) REVERT: B 820 ILE cc_start: 0.8191 (mp) cc_final: 0.7873 (pt) REVERT: B 827 LYS cc_start: 0.7927 (tppp) cc_final: 0.7270 (mmmt) REVERT: B 853 ARG cc_start: 0.7349 (OUTLIER) cc_final: 0.5981 (mtm-85) REVERT: B 857 LYS cc_start: 0.7801 (mmtt) cc_final: 0.7430 (tppt) REVERT: B 875 ARG cc_start: 0.6506 (ttp80) cc_final: 0.6115 (ttp-110) REVERT: B 903 ARG cc_start: 0.7516 (mmm-85) cc_final: 0.7262 (mtp-110) REVERT: B 905 GLU cc_start: 0.6778 (mp0) cc_final: 0.6405 (mp0) REVERT: B 911 GLU cc_start: 0.7122 (mt-10) cc_final: 0.6891 (mt-10) REVERT: B 947 LYS cc_start: 0.7643 (mtpt) cc_final: 0.7236 (mmtt) REVERT: B 967 ARG cc_start: 0.7590 (tpp80) cc_final: 0.7248 (tpt170) REVERT: B 1001 ARG cc_start: 0.5569 (pmt-80) cc_final: 0.3151 (mmt90) outliers start: 28 outliers final: 15 residues processed: 215 average time/residue: 1.2768 time to fit residues: 293.7570 Evaluate side-chains 174 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 164 GLN Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 325 VAL Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 614 SER Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 981 LYS Chi-restraints excluded: chain B residue 853 ARG Chi-restraints excluded: chain B residue 864 VAL Chi-restraints excluded: chain B residue 923 PHE Chi-restraints excluded: chain B residue 928 THR Chi-restraints excluded: chain B residue 950 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN A 431 GLN A 900 GLN B 616 GLN B 873 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.145165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.112623 restraints weight = 12207.033| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.90 r_work: 0.3234 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3136 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10188 Z= 0.172 Angle : 0.610 6.229 13871 Z= 0.319 Chirality : 0.044 0.183 1565 Planarity : 0.005 0.087 1741 Dihedral : 8.700 84.935 1486 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.07 % Favored : 95.77 % Rotamer: Outliers : 4.57 % Allowed : 24.51 % Favored : 70.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % 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: 1.24 (0.24), residues: 1252 helix: 1.98 (0.20), residues: 670 sheet: 0.42 (0.49), residues: 117 loop : -0.79 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 137 HIS 0.005 0.001 HIS B 761 PHE 0.014 0.002 PHE A 340 TYR 0.013 0.002 TYR B 626 ARG 0.007 0.001 ARG B1001 Details of bonding type rmsd hydrogen bonds : bond 0.05326 ( 538) hydrogen bonds : angle 4.66886 ( 1554) SS BOND : bond 0.00028 ( 2) SS BOND : angle 1.97679 ( 4) covalent geometry : bond 0.00399 (10186) covalent geometry : angle 0.60934 (13867) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 166 time to evaluate : 1.317 Fit side-chains revert: symmetry clash REVERT: A 191 ILE cc_start: 0.8564 (OUTLIER) cc_final: 0.8361 (mp) REVERT: A 243 ASP cc_start: 0.7883 (m-30) cc_final: 0.7647 (m-30) REVERT: A 247 GLU cc_start: 0.7215 (tm-30) cc_final: 0.6965 (tt0) REVERT: A 258 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7234 (m-30) REVERT: A 331 ASP cc_start: 0.8027 (t0) cc_final: 0.7699 (t0) REVERT: A 336 ASP cc_start: 0.7431 (OUTLIER) cc_final: 0.6744 (t0) REVERT: A 345 ILE cc_start: 0.8452 (mt) cc_final: 0.8223 (mm) REVERT: A 416 GLU cc_start: 0.6353 (tm-30) cc_final: 0.5750 (tt0) REVERT: A 530 ILE cc_start: 0.8239 (OUTLIER) cc_final: 0.7918 (mm) REVERT: A 605 LYS cc_start: 0.8240 (tppp) cc_final: 0.7863 (tptt) REVERT: A 606 LYS cc_start: 0.7676 (mtmt) cc_final: 0.7353 (tttt) REVERT: A 718 ARG cc_start: 0.8458 (mpp80) cc_final: 0.8006 (mmp80) REVERT: A 731 ARG cc_start: 0.8423 (ttm-80) cc_final: 0.8053 (mtt90) REVERT: A 777 GLU cc_start: 0.7916 (mp0) cc_final: 0.7522 (pm20) REVERT: A 824 GLU cc_start: 0.7271 (mp0) cc_final: 0.6904 (mm-30) REVERT: A 827 LYS cc_start: 0.8269 (mmtm) cc_final: 0.8015 (mmtm) REVERT: A 857 LYS cc_start: 0.8446 (mmmm) cc_final: 0.7833 (mmtt) REVERT: A 898 ILE cc_start: 0.7378 (OUTLIER) cc_final: 0.7149 (tt) REVERT: A 947 LYS cc_start: 0.7986 (mttp) cc_final: 0.7721 (mttp) REVERT: A 949 ARG cc_start: 0.7530 (tpp80) cc_final: 0.7133 (tpp-160) REVERT: A 1012 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7974 (tt0) REVERT: A 1013 ASN cc_start: 0.8557 (t0) cc_final: 0.8310 (t0) REVERT: B 667 ASN cc_start: 0.8033 (p0) cc_final: 0.7743 (p0) REVERT: B 853 ARG cc_start: 0.7998 (OUTLIER) cc_final: 0.7349 (pmt170) REVERT: B 875 ARG cc_start: 0.8076 (ttp80) cc_final: 0.7345 (ttm110) REVERT: B 905 GLU cc_start: 0.7556 (mp0) cc_final: 0.7349 (mp0) REVERT: B 947 LYS cc_start: 0.8515 (mtpt) cc_final: 0.8212 (mmtt) REVERT: B 967 ARG cc_start: 0.8101 (tpp80) cc_final: 0.7866 (tpt170) REVERT: B 1001 ARG cc_start: 0.5302 (OUTLIER) cc_final: 0.3667 (mmt90) outliers start: 47 outliers final: 15 residues processed: 197 average time/residue: 1.3820 time to fit residues: 291.8018 Evaluate side-chains 164 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 421 SER Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 987 SER Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 853 ARG Chi-restraints excluded: chain B residue 872 ASP Chi-restraints excluded: chain B residue 923 PHE Chi-restraints excluded: chain B residue 1001 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 111 optimal weight: 0.0020 chunk 70 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 105 optimal weight: 6.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 GLN B 959 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.139712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.104999 restraints weight = 11527.141| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.90 r_work: 0.3081 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2963 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10188 Z= 0.152 Angle : 0.571 6.091 13871 Z= 0.298 Chirality : 0.043 0.187 1565 Planarity : 0.005 0.069 1741 Dihedral : 8.473 81.859 1471 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.59 % Favored : 96.25 % Rotamer: Outliers : 3.99 % Allowed : 24.42 % Favored : 71.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % 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: 1.08 (0.24), residues: 1252 helix: 1.87 (0.20), residues: 675 sheet: 0.27 (0.46), residues: 120 loop : -0.92 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 137 HIS 0.004 0.001 HIS B 761 PHE 0.012 0.001 PHE A 340 TYR 0.012 0.002 TYR A1018 ARG 0.006 0.001 ARG B1001 Details of bonding type rmsd hydrogen bonds : bond 0.04950 ( 538) hydrogen bonds : angle 4.47974 ( 1554) SS BOND : bond 0.00964 ( 2) SS BOND : angle 2.13242 ( 4) covalent geometry : bond 0.00349 (10186) covalent geometry : angle 0.56981 (13867) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 147 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 191 ILE cc_start: 0.8613 (OUTLIER) cc_final: 0.8381 (mp) REVERT: A 243 ASP cc_start: 0.7774 (m-30) cc_final: 0.7452 (m-30) REVERT: A 247 GLU cc_start: 0.7083 (tm-30) cc_final: 0.6822 (tt0) REVERT: A 309 GLU cc_start: 0.7916 (tp30) cc_final: 0.7542 (mp0) REVERT: A 331 ASP cc_start: 0.8055 (t0) cc_final: 0.7705 (t0) REVERT: A 336 ASP cc_start: 0.7416 (OUTLIER) cc_final: 0.6582 (t0) REVERT: A 345 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8134 (mm) REVERT: A 416 GLU cc_start: 0.6621 (tm-30) cc_final: 0.5489 (tt0) REVERT: A 530 ILE cc_start: 0.7931 (OUTLIER) cc_final: 0.7677 (mm) REVERT: A 605 LYS cc_start: 0.8144 (tppp) cc_final: 0.7815 (tptt) REVERT: A 606 LYS cc_start: 0.7564 (mtmt) cc_final: 0.7258 (mttt) REVERT: A 718 ARG cc_start: 0.8377 (mpp80) cc_final: 0.7801 (mmp80) REVERT: A 731 ARG cc_start: 0.8379 (ttm-80) cc_final: 0.7912 (mtt90) REVERT: A 777 GLU cc_start: 0.7928 (mp0) cc_final: 0.7401 (pm20) REVERT: A 824 GLU cc_start: 0.7183 (mp0) cc_final: 0.6796 (mm-30) REVERT: A 827 LYS cc_start: 0.8335 (mmtm) cc_final: 0.8080 (mmtm) REVERT: A 857 LYS cc_start: 0.8411 (mmmm) cc_final: 0.7674 (mmtt) REVERT: A 898 ILE cc_start: 0.7276 (OUTLIER) cc_final: 0.7073 (tt) REVERT: A 913 MET cc_start: 0.8413 (ttm) cc_final: 0.8153 (ttp) REVERT: A 947 LYS cc_start: 0.7969 (mttp) cc_final: 0.7748 (mttp) REVERT: A 949 ARG cc_start: 0.7490 (tpp80) cc_final: 0.7019 (tpp-160) REVERT: A 967 ARG cc_start: 0.8074 (mtm-85) cc_final: 0.7872 (mtm-85) REVERT: A 1012 GLU cc_start: 0.8166 (OUTLIER) cc_final: 0.7962 (tt0) REVERT: B 827 LYS cc_start: 0.8323 (tppp) cc_final: 0.7857 (mmtt) REVERT: B 853 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7345 (pmt170) REVERT: B 875 ARG cc_start: 0.7910 (ttp80) cc_final: 0.7087 (ttm110) REVERT: B 905 GLU cc_start: 0.7543 (mp0) cc_final: 0.7003 (pm20) REVERT: B 947 LYS cc_start: 0.8484 (mtpt) cc_final: 0.8076 (mmtt) REVERT: B 967 ARG cc_start: 0.8069 (tpp80) cc_final: 0.7795 (tpt170) REVERT: B 1001 ARG cc_start: 0.5173 (OUTLIER) cc_final: 0.3382 (mpt-90) outliers start: 41 outliers final: 14 residues processed: 173 average time/residue: 1.3274 time to fit residues: 246.6721 Evaluate side-chains 163 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 141 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 191 ILE Chi-restraints excluded: chain A residue 192 SER Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 898 ILE Chi-restraints excluded: chain A residue 1012 GLU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 853 ARG Chi-restraints excluded: chain B residue 923 PHE Chi-restraints excluded: chain B residue 1001 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 81 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 chunk 116 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 54 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 23 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.140048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.105488 restraints weight = 11401.873| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 1.89 r_work: 0.3088 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2970 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10188 Z= 0.141 Angle : 0.554 6.228 13871 Z= 0.289 Chirality : 0.042 0.155 1565 Planarity : 0.005 0.062 1741 Dihedral : 8.282 75.698 1469 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.83 % Favored : 96.09 % Rotamer: Outliers : 3.70 % Allowed : 24.03 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % 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: 1.07 (0.24), residues: 1252 helix: 1.84 (0.20), residues: 678 sheet: 0.34 (0.47), residues: 119 loop : -0.94 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 137 HIS 0.003 0.001 HIS B 761 PHE 0.012 0.001 PHE B 664 TYR 0.011 0.001 TYR B 626 ARG 0.006 0.001 ARG B 949 Details of bonding type rmsd hydrogen bonds : bond 0.04748 ( 538) hydrogen bonds : angle 4.40122 ( 1554) SS BOND : bond 0.00666 ( 2) SS BOND : angle 2.32376 ( 4) covalent geometry : bond 0.00324 (10186) covalent geometry : angle 0.55246 (13867) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 141 time to evaluate : 1.191 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.7777 (m-30) cc_final: 0.7469 (m-30) REVERT: A 247 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6768 (tt0) REVERT: A 331 ASP cc_start: 0.8024 (t0) cc_final: 0.7668 (t0) REVERT: A 336 ASP cc_start: 0.7458 (OUTLIER) cc_final: 0.6777 (t0) REVERT: A 345 ILE cc_start: 0.8402 (OUTLIER) cc_final: 0.8161 (mm) REVERT: A 416 GLU cc_start: 0.6432 (tm-30) cc_final: 0.5932 (tt0) REVERT: A 605 LYS cc_start: 0.8115 (tppp) cc_final: 0.7811 (tptt) REVERT: A 606 LYS cc_start: 0.7566 (mtmt) cc_final: 0.7242 (ttmt) REVERT: A 718 ARG cc_start: 0.8366 (mpp80) cc_final: 0.7797 (mmp80) REVERT: A 731 ARG cc_start: 0.8386 (ttm-80) cc_final: 0.7886 (mtt90) REVERT: A 777 GLU cc_start: 0.7917 (mp0) cc_final: 0.7384 (pm20) REVERT: A 779 LEU cc_start: 0.8428 (OUTLIER) cc_final: 0.8181 (mm) REVERT: A 824 GLU cc_start: 0.7162 (mp0) cc_final: 0.6785 (mm-30) REVERT: A 827 LYS cc_start: 0.8348 (mmtm) cc_final: 0.8091 (mmtm) REVERT: A 853 ARG cc_start: 0.7998 (pmm150) cc_final: 0.7105 (mtm-85) REVERT: A 857 LYS cc_start: 0.8444 (mmmm) cc_final: 0.7704 (mmtt) REVERT: A 913 MET cc_start: 0.8323 (ttm) cc_final: 0.8119 (ttp) REVERT: A 947 LYS cc_start: 0.8009 (mttp) cc_final: 0.7806 (mttp) REVERT: A 949 ARG cc_start: 0.7479 (tpp80) cc_final: 0.7070 (tpp-160) REVERT: A 967 ARG cc_start: 0.8099 (mtm-85) cc_final: 0.7837 (mtm-85) REVERT: B 776 ARG cc_start: 0.8331 (OUTLIER) cc_final: 0.7392 (mtm180) REVERT: B 827 LYS cc_start: 0.8354 (tppp) cc_final: 0.7758 (mmmt) REVERT: B 853 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7329 (pmt170) REVERT: B 875 ARG cc_start: 0.7914 (ttp80) cc_final: 0.7138 (ttm110) REVERT: B 905 GLU cc_start: 0.7561 (mp0) cc_final: 0.7024 (pm20) REVERT: B 947 LYS cc_start: 0.8483 (mtpt) cc_final: 0.8094 (mmtt) REVERT: B 967 ARG cc_start: 0.8110 (tpp80) cc_final: 0.7774 (tpt170) REVERT: B 1001 ARG cc_start: 0.5047 (OUTLIER) cc_final: 0.3341 (mmt90) outliers start: 38 outliers final: 16 residues processed: 166 average time/residue: 1.6776 time to fit residues: 298.2817 Evaluate side-chains 164 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 958 LEU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain A residue 1016 THR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 776 ARG Chi-restraints excluded: chain B residue 853 ARG Chi-restraints excluded: chain B residue 923 PHE Chi-restraints excluded: chain B residue 1001 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 125 optimal weight: 5.9990 chunk 80 optimal weight: 10.0000 chunk 104 optimal weight: 0.7980 chunk 16 optimal weight: 6.9990 chunk 17 optimal weight: 4.9990 chunk 43 optimal weight: 0.0870 chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 96 optimal weight: 6.9990 chunk 1 optimal weight: 0.9980 overall best weight: 1.2960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 GLN B 616 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.139421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.104749 restraints weight = 11335.544| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.89 r_work: 0.3076 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10188 Z= 0.156 Angle : 0.563 6.126 13871 Z= 0.293 Chirality : 0.043 0.203 1565 Planarity : 0.005 0.054 1741 Dihedral : 8.191 69.879 1467 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.99 % Favored : 95.93 % Rotamer: Outliers : 4.57 % Allowed : 23.05 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % 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: 1.07 (0.24), residues: 1252 helix: 1.86 (0.20), residues: 670 sheet: 0.37 (0.47), residues: 119 loop : -0.93 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 137 HIS 0.003 0.001 HIS B 761 PHE 0.013 0.001 PHE B 664 TYR 0.012 0.002 TYR B 626 ARG 0.005 0.001 ARG B 949 Details of bonding type rmsd hydrogen bonds : bond 0.04925 ( 538) hydrogen bonds : angle 4.40907 ( 1554) SS BOND : bond 0.00198 ( 2) SS BOND : angle 2.44982 ( 4) covalent geometry : bond 0.00366 (10186) covalent geometry : angle 0.56195 (13867) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 147 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.7681 (m-30) cc_final: 0.7390 (m-30) REVERT: A 247 GLU cc_start: 0.7076 (tm-30) cc_final: 0.6748 (tt0) REVERT: A 331 ASP cc_start: 0.8101 (t0) cc_final: 0.7761 (t0) REVERT: A 336 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.6710 (t0) REVERT: A 345 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.8177 (mm) REVERT: A 416 GLU cc_start: 0.6486 (tm-30) cc_final: 0.5925 (tt0) REVERT: A 562 GLN cc_start: 0.8223 (OUTLIER) cc_final: 0.7831 (mt0) REVERT: A 605 LYS cc_start: 0.8091 (tppp) cc_final: 0.7795 (tptt) REVERT: A 606 LYS cc_start: 0.7533 (mtmt) cc_final: 0.7237 (ttmt) REVERT: A 718 ARG cc_start: 0.8334 (tpp80) cc_final: 0.7776 (mmp80) REVERT: A 731 ARG cc_start: 0.8396 (ttm-80) cc_final: 0.8034 (mtt90) REVERT: A 777 GLU cc_start: 0.7912 (mp0) cc_final: 0.7372 (pm20) REVERT: A 779 LEU cc_start: 0.8435 (OUTLIER) cc_final: 0.8191 (mm) REVERT: A 824 GLU cc_start: 0.7055 (mp0) cc_final: 0.6670 (mm-30) REVERT: A 827 LYS cc_start: 0.8355 (mmtm) cc_final: 0.8124 (mmtm) REVERT: A 853 ARG cc_start: 0.8009 (pmm150) cc_final: 0.7169 (mtm-85) REVERT: A 857 LYS cc_start: 0.8439 (mmmm) cc_final: 0.7701 (mmtt) REVERT: A 949 ARG cc_start: 0.7451 (tpp80) cc_final: 0.7077 (tpp-160) REVERT: B 667 ASN cc_start: 0.8082 (p0) cc_final: 0.7264 (m110) REVERT: B 827 LYS cc_start: 0.8400 (OUTLIER) cc_final: 0.7787 (mmmt) REVERT: B 853 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7341 (pmt170) REVERT: B 875 ARG cc_start: 0.7923 (ttp80) cc_final: 0.7133 (ttm110) REVERT: B 905 GLU cc_start: 0.7582 (mp0) cc_final: 0.7019 (pm20) REVERT: B 947 LYS cc_start: 0.8471 (mtpt) cc_final: 0.8085 (mmtt) REVERT: B 1001 ARG cc_start: 0.5121 (OUTLIER) cc_final: 0.3443 (mpt-90) outliers start: 47 outliers final: 18 residues processed: 174 average time/residue: 1.3843 time to fit residues: 257.9331 Evaluate side-chains 164 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 139 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 562 GLN Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 699 LEU Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 965 TYR Chi-restraints excluded: chain A residue 1016 THR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 827 LYS Chi-restraints excluded: chain B residue 853 ARG Chi-restraints excluded: chain B residue 1001 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 20 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 68 optimal weight: 5.9990 chunk 26 optimal weight: 0.6980 chunk 90 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 76 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 14 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 744 ASN B 616 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.146393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.114124 restraints weight = 12277.761| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 1.92 r_work: 0.3256 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10188 Z= 0.130 Angle : 0.540 6.048 13871 Z= 0.282 Chirality : 0.041 0.180 1565 Planarity : 0.004 0.050 1741 Dihedral : 8.052 68.586 1465 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.75 % Favored : 96.17 % Rotamer: Outliers : 3.40 % Allowed : 23.83 % Favored : 72.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % 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: 1.14 (0.24), residues: 1252 helix: 1.94 (0.20), residues: 672 sheet: 0.39 (0.47), residues: 119 loop : -0.96 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 137 HIS 0.003 0.001 HIS B 761 PHE 0.014 0.001 PHE A 597 TYR 0.011 0.001 TYR A 626 ARG 0.006 0.001 ARG A 918 Details of bonding type rmsd hydrogen bonds : bond 0.04563 ( 538) hydrogen bonds : angle 4.32754 ( 1554) SS BOND : bond 0.00269 ( 2) SS BOND : angle 2.56713 ( 4) covalent geometry : bond 0.00295 (10186) covalent geometry : angle 0.53784 (13867) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 146 time to evaluate : 1.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.7682 (m-30) cc_final: 0.7403 (m-30) REVERT: A 247 GLU cc_start: 0.7090 (tm-30) cc_final: 0.6766 (tt0) REVERT: A 331 ASP cc_start: 0.8029 (t0) cc_final: 0.7693 (t0) REVERT: A 336 ASP cc_start: 0.7447 (OUTLIER) cc_final: 0.6807 (t0) REVERT: A 345 ILE cc_start: 0.8441 (OUTLIER) cc_final: 0.8231 (mm) REVERT: A 416 GLU cc_start: 0.6767 (tm-30) cc_final: 0.6045 (tt0) REVERT: A 605 LYS cc_start: 0.8125 (tppp) cc_final: 0.7826 (tptt) REVERT: A 606 LYS cc_start: 0.7604 (mtmt) cc_final: 0.7287 (mttt) REVERT: A 718 ARG cc_start: 0.8350 (tpp80) cc_final: 0.7845 (mmp80) REVERT: A 731 ARG cc_start: 0.8360 (ttm-80) cc_final: 0.8002 (mtt90) REVERT: A 777 GLU cc_start: 0.7862 (mp0) cc_final: 0.7373 (pm20) REVERT: A 779 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8223 (mm) REVERT: A 824 GLU cc_start: 0.7009 (mp0) cc_final: 0.6746 (mm-30) REVERT: A 827 LYS cc_start: 0.8304 (mmtm) cc_final: 0.8086 (mmtm) REVERT: A 853 ARG cc_start: 0.7963 (pmm150) cc_final: 0.7281 (mtm-85) REVERT: A 857 LYS cc_start: 0.8452 (mmmm) cc_final: 0.7796 (mmtt) REVERT: A 949 ARG cc_start: 0.7512 (tpp80) cc_final: 0.7184 (tpp-160) REVERT: B 667 ASN cc_start: 0.7935 (p0) cc_final: 0.7454 (m-40) REVERT: B 827 LYS cc_start: 0.8383 (tppp) cc_final: 0.7796 (mmmt) REVERT: B 853 ARG cc_start: 0.7891 (OUTLIER) cc_final: 0.7322 (pmt170) REVERT: B 875 ARG cc_start: 0.7962 (ttp80) cc_final: 0.7249 (ttm110) REVERT: B 905 GLU cc_start: 0.7585 (mp0) cc_final: 0.7034 (pm20) REVERT: B 947 LYS cc_start: 0.8463 (mtpt) cc_final: 0.8090 (mmtp) REVERT: B 1001 ARG cc_start: 0.5014 (OUTLIER) cc_final: 0.3545 (mpt-90) outliers start: 35 outliers final: 16 residues processed: 168 average time/residue: 1.3590 time to fit residues: 244.2105 Evaluate side-chains 163 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 HIS Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 345 ILE Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 1016 THR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 853 ARG Chi-restraints excluded: chain B residue 923 PHE Chi-restraints excluded: chain B residue 1001 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 81 optimal weight: 0.5980 chunk 83 optimal weight: 6.9990 chunk 67 optimal weight: 5.9990 chunk 84 optimal weight: 0.9980 chunk 102 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 93 optimal weight: 0.9980 chunk 59 optimal weight: 8.9990 chunk 92 optimal weight: 0.2980 chunk 90 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.147318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.115102 restraints weight = 12397.890| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.93 r_work: 0.3272 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3174 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3174 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10188 Z= 0.122 Angle : 0.528 6.310 13871 Z= 0.277 Chirality : 0.041 0.168 1565 Planarity : 0.004 0.046 1741 Dihedral : 7.968 68.932 1465 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.75 % Favored : 96.17 % Rotamer: Outliers : 3.60 % Allowed : 23.54 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % 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: 1.19 (0.24), residues: 1252 helix: 2.02 (0.20), residues: 671 sheet: 0.47 (0.47), residues: 119 loop : -1.00 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 137 HIS 0.003 0.001 HIS B 761 PHE 0.018 0.001 PHE A 597 TYR 0.011 0.001 TYR A 626 ARG 0.007 0.001 ARG A 918 Details of bonding type rmsd hydrogen bonds : bond 0.04373 ( 538) hydrogen bonds : angle 4.26385 ( 1554) SS BOND : bond 0.00233 ( 2) SS BOND : angle 2.07055 ( 4) covalent geometry : bond 0.00275 (10186) covalent geometry : angle 0.52661 (13867) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 144 time to evaluate : 1.138 Fit side-chains revert: symmetry clash REVERT: A 243 ASP cc_start: 0.7632 (m-30) cc_final: 0.7336 (m-30) REVERT: A 247 GLU cc_start: 0.7054 (tm-30) cc_final: 0.6692 (tt0) REVERT: A 331 ASP cc_start: 0.8032 (t0) cc_final: 0.7706 (t0) REVERT: A 336 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.6900 (t0) REVERT: A 416 GLU cc_start: 0.6739 (tm-30) cc_final: 0.6194 (tt0) REVERT: A 605 LYS cc_start: 0.8136 (tppp) cc_final: 0.7836 (tptt) REVERT: A 606 LYS cc_start: 0.7583 (mtmt) cc_final: 0.7258 (mttt) REVERT: A 718 ARG cc_start: 0.8342 (tpp80) cc_final: 0.7839 (mmp80) REVERT: A 731 ARG cc_start: 0.8290 (ttm-80) cc_final: 0.7905 (mtt90) REVERT: A 777 GLU cc_start: 0.7844 (mp0) cc_final: 0.7382 (pm20) REVERT: A 779 LEU cc_start: 0.8418 (OUTLIER) cc_final: 0.8172 (mm) REVERT: A 824 GLU cc_start: 0.7031 (mp0) cc_final: 0.6732 (mm-30) REVERT: A 853 ARG cc_start: 0.7942 (pmm150) cc_final: 0.7303 (mtm-85) REVERT: A 949 ARG cc_start: 0.7514 (tpp80) cc_final: 0.7197 (tpp-160) REVERT: B 667 ASN cc_start: 0.7911 (p0) cc_final: 0.7564 (m-40) REVERT: B 827 LYS cc_start: 0.8390 (OUTLIER) cc_final: 0.7800 (mmmt) REVERT: B 853 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.7262 (pmt170) REVERT: B 875 ARG cc_start: 0.7952 (ttp80) cc_final: 0.7232 (ttm110) REVERT: B 905 GLU cc_start: 0.7531 (mp0) cc_final: 0.6997 (pm20) REVERT: B 947 LYS cc_start: 0.8475 (mtpt) cc_final: 0.8086 (mmtt) REVERT: B 1001 ARG cc_start: 0.4864 (OUTLIER) cc_final: 0.3558 (mpt-90) outliers start: 37 outliers final: 14 residues processed: 169 average time/residue: 1.3025 time to fit residues: 235.7199 Evaluate side-chains 157 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 HIS Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 1016 THR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 827 LYS Chi-restraints excluded: chain B residue 853 ARG Chi-restraints excluded: chain B residue 923 PHE Chi-restraints excluded: chain B residue 1001 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 103 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 116 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 99 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 54 optimal weight: 0.1980 chunk 2 optimal weight: 6.9990 chunk 106 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 GLN B 616 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.145592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.112410 restraints weight = 12180.565| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.95 r_work: 0.3234 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10188 Z= 0.124 Angle : 0.534 6.067 13871 Z= 0.281 Chirality : 0.041 0.207 1565 Planarity : 0.004 0.059 1741 Dihedral : 7.927 67.181 1464 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.01 % Rotamer: Outliers : 2.92 % Allowed : 24.12 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % 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: 1.23 (0.24), residues: 1252 helix: 2.05 (0.20), residues: 671 sheet: 0.52 (0.47), residues: 119 loop : -1.00 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 137 HIS 0.002 0.001 HIS B 761 PHE 0.021 0.001 PHE A 597 TYR 0.011 0.001 TYR A 626 ARG 0.008 0.000 ARG A 918 Details of bonding type rmsd hydrogen bonds : bond 0.04365 ( 538) hydrogen bonds : angle 4.28891 ( 1554) SS BOND : bond 0.00281 ( 2) SS BOND : angle 2.60571 ( 4) covalent geometry : bond 0.00283 (10186) covalent geometry : angle 0.53239 (13867) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 140 time to evaluate : 1.027 Fit side-chains revert: symmetry clash REVERT: A 243 ASP cc_start: 0.7661 (m-30) cc_final: 0.7379 (m-30) REVERT: A 247 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6714 (tt0) REVERT: A 331 ASP cc_start: 0.8032 (t0) cc_final: 0.7714 (t0) REVERT: A 336 ASP cc_start: 0.7522 (OUTLIER) cc_final: 0.7002 (t0) REVERT: A 416 GLU cc_start: 0.6755 (tm-30) cc_final: 0.6105 (tt0) REVERT: A 605 LYS cc_start: 0.8181 (tppp) cc_final: 0.7865 (tptt) REVERT: A 606 LYS cc_start: 0.7588 (mtmt) cc_final: 0.7318 (mttt) REVERT: A 718 ARG cc_start: 0.8313 (tpp80) cc_final: 0.7829 (mmp80) REVERT: A 731 ARG cc_start: 0.8313 (ttm-80) cc_final: 0.7923 (mtt90) REVERT: A 777 GLU cc_start: 0.7861 (mp0) cc_final: 0.7388 (pm20) REVERT: A 824 GLU cc_start: 0.7057 (mp0) cc_final: 0.6764 (mm-30) REVERT: A 853 ARG cc_start: 0.7951 (pmm150) cc_final: 0.7254 (mtm-85) REVERT: A 857 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.7843 (mmtt) REVERT: A 949 ARG cc_start: 0.7515 (tpp80) cc_final: 0.7139 (tpp-160) REVERT: B 667 ASN cc_start: 0.7923 (p0) cc_final: 0.7604 (m-40) REVERT: B 827 LYS cc_start: 0.8402 (OUTLIER) cc_final: 0.7819 (mmmt) REVERT: B 853 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7259 (pmt170) REVERT: B 875 ARG cc_start: 0.7989 (ttp80) cc_final: 0.7306 (ttm110) REVERT: B 905 GLU cc_start: 0.7539 (mp0) cc_final: 0.7034 (pm20) REVERT: B 947 LYS cc_start: 0.8469 (mtpt) cc_final: 0.8101 (mmtt) REVERT: B 1001 ARG cc_start: 0.4891 (OUTLIER) cc_final: 0.3663 (mpt-90) outliers start: 30 outliers final: 15 residues processed: 158 average time/residue: 1.3730 time to fit residues: 231.9074 Evaluate side-chains 156 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 HIS Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 1016 THR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 827 LYS Chi-restraints excluded: chain B residue 853 ARG Chi-restraints excluded: chain B residue 923 PHE Chi-restraints excluded: chain B residue 1001 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 106 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 112 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 89 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 616 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.144311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.111105 restraints weight = 12250.768| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 1.94 r_work: 0.3219 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10188 Z= 0.145 Angle : 0.555 6.454 13871 Z= 0.291 Chirality : 0.042 0.209 1565 Planarity : 0.004 0.049 1741 Dihedral : 8.002 65.750 1464 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.99 % Favored : 95.93 % Rotamer: Outliers : 2.82 % Allowed : 24.12 % Favored : 73.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % 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: 1.21 (0.24), residues: 1252 helix: 2.00 (0.20), residues: 672 sheet: 0.54 (0.48), residues: 119 loop : -0.94 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 137 HIS 0.003 0.001 HIS B 761 PHE 0.023 0.001 PHE A 597 TYR 0.011 0.001 TYR A 203 ARG 0.008 0.001 ARG A 918 Details of bonding type rmsd hydrogen bonds : bond 0.04626 ( 538) hydrogen bonds : angle 4.32507 ( 1554) SS BOND : bond 0.00290 ( 2) SS BOND : angle 2.18291 ( 4) covalent geometry : bond 0.00337 (10186) covalent geometry : angle 0.55433 (13867) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 137 time to evaluate : 1.083 Fit side-chains revert: symmetry clash REVERT: A 243 ASP cc_start: 0.7686 (m-30) cc_final: 0.7410 (m-30) REVERT: A 247 GLU cc_start: 0.7108 (tm-30) cc_final: 0.6739 (tt0) REVERT: A 331 ASP cc_start: 0.8054 (t0) cc_final: 0.7738 (t0) REVERT: A 336 ASP cc_start: 0.7535 (OUTLIER) cc_final: 0.7010 (t0) REVERT: A 416 GLU cc_start: 0.6659 (tm-30) cc_final: 0.6107 (tt0) REVERT: A 605 LYS cc_start: 0.8177 (tppp) cc_final: 0.7863 (tptt) REVERT: A 606 LYS cc_start: 0.7626 (mtmt) cc_final: 0.7356 (mttt) REVERT: A 718 ARG cc_start: 0.8339 (tpp80) cc_final: 0.7868 (mmp80) REVERT: A 731 ARG cc_start: 0.8356 (ttm-80) cc_final: 0.7939 (mtt90) REVERT: A 777 GLU cc_start: 0.7859 (mp0) cc_final: 0.7378 (pm20) REVERT: A 824 GLU cc_start: 0.7067 (mp0) cc_final: 0.6790 (mm-30) REVERT: A 853 ARG cc_start: 0.7961 (pmm150) cc_final: 0.7280 (mtm-85) REVERT: A 857 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7840 (mmtt) REVERT: A 949 ARG cc_start: 0.7557 (tpp80) cc_final: 0.7199 (tpp-160) REVERT: B 667 ASN cc_start: 0.7977 (p0) cc_final: 0.7629 (m-40) REVERT: B 827 LYS cc_start: 0.8420 (OUTLIER) cc_final: 0.7793 (mmmt) REVERT: B 853 ARG cc_start: 0.7877 (OUTLIER) cc_final: 0.7288 (pmt170) REVERT: B 875 ARG cc_start: 0.7998 (ttp80) cc_final: 0.7331 (ttm110) REVERT: B 905 GLU cc_start: 0.7570 (mp0) cc_final: 0.7068 (pm20) REVERT: B 947 LYS cc_start: 0.8493 (mtpt) cc_final: 0.8116 (mmtp) REVERT: B 1001 ARG cc_start: 0.4933 (OUTLIER) cc_final: 0.3775 (mpt-90) outliers start: 29 outliers final: 18 residues processed: 155 average time/residue: 1.3314 time to fit residues: 220.7902 Evaluate side-chains 156 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 133 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 HIS Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 431 GLN Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 732 MET Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 1016 THR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 827 LYS Chi-restraints excluded: chain B residue 853 ARG Chi-restraints excluded: chain B residue 923 PHE Chi-restraints excluded: chain B residue 1001 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 30 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 108 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.142940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.109374 restraints weight = 12102.895| |-----------------------------------------------------------------------------| r_work (start): 0.3289 rms_B_bonded: 1.95 r_work: 0.3197 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10188 Z= 0.164 Angle : 0.579 6.790 13871 Z= 0.304 Chirality : 0.043 0.211 1565 Planarity : 0.005 0.056 1741 Dihedral : 8.146 65.112 1464 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.07 % Favored : 95.85 % Rotamer: Outliers : 2.33 % Allowed : 25.00 % Favored : 72.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % 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: 1.15 (0.24), residues: 1252 helix: 1.92 (0.20), residues: 672 sheet: 0.52 (0.48), residues: 119 loop : -0.92 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 137 HIS 0.003 0.001 HIS B 761 PHE 0.023 0.002 PHE A 597 TYR 0.013 0.002 TYR A 203 ARG 0.007 0.001 ARG A 918 Details of bonding type rmsd hydrogen bonds : bond 0.04937 ( 538) hydrogen bonds : angle 4.38976 ( 1554) SS BOND : bond 0.00263 ( 2) SS BOND : angle 2.10882 ( 4) covalent geometry : bond 0.00388 (10186) covalent geometry : angle 0.57832 (13867) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2504 Ramachandran restraints generated. 1252 Oldfield, 0 Emsley, 1252 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 136 time to evaluate : 1.032 Fit side-chains REVERT: A 243 ASP cc_start: 0.7721 (m-30) cc_final: 0.7417 (m-30) REVERT: A 247 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6724 (tt0) REVERT: A 258 ASP cc_start: 0.7755 (OUTLIER) cc_final: 0.7124 (m-30) REVERT: A 331 ASP cc_start: 0.8117 (t0) cc_final: 0.7804 (t0) REVERT: A 336 ASP cc_start: 0.7510 (OUTLIER) cc_final: 0.6897 (t0) REVERT: A 416 GLU cc_start: 0.6784 (tm-30) cc_final: 0.5992 (tt0) REVERT: A 605 LYS cc_start: 0.8177 (tppp) cc_final: 0.7869 (tptt) REVERT: A 606 LYS cc_start: 0.7640 (mtmt) cc_final: 0.7371 (mttt) REVERT: A 718 ARG cc_start: 0.8362 (tpp80) cc_final: 0.7858 (mmp80) REVERT: A 731 ARG cc_start: 0.8383 (ttm-80) cc_final: 0.7922 (mtt90) REVERT: A 777 GLU cc_start: 0.7851 (mp0) cc_final: 0.7346 (pm20) REVERT: A 824 GLU cc_start: 0.7066 (mp0) cc_final: 0.6751 (mm-30) REVERT: A 853 ARG cc_start: 0.7950 (pmm150) cc_final: 0.7291 (mtm-85) REVERT: A 857 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.7804 (mmtt) REVERT: A 949 ARG cc_start: 0.7523 (tpp80) cc_final: 0.7150 (tpp-160) REVERT: B 667 ASN cc_start: 0.8002 (p0) cc_final: 0.7592 (m-40) REVERT: B 827 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.7805 (mmmt) REVERT: B 853 ARG cc_start: 0.7947 (OUTLIER) cc_final: 0.7293 (pmt170) REVERT: B 875 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7281 (ttm110) REVERT: B 905 GLU cc_start: 0.7572 (mp0) cc_final: 0.7055 (pm20) REVERT: B 947 LYS cc_start: 0.8493 (mtpt) cc_final: 0.8098 (mmtp) REVERT: B 1001 ARG cc_start: 0.5096 (OUTLIER) cc_final: 0.3618 (mpt-90) outliers start: 24 outliers final: 16 residues processed: 150 average time/residue: 1.3143 time to fit residues: 210.8163 Evaluate side-chains 157 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 THR Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 181 THR Chi-restraints excluded: chain A residue 197 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 258 ASP Chi-restraints excluded: chain A residue 318 SER Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 431 GLN Chi-restraints excluded: chain A residue 658 VAL Chi-restraints excluded: chain A residue 665 THR Chi-restraints excluded: chain A residue 779 LEU Chi-restraints excluded: chain A residue 857 LYS Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 1016 THR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 827 LYS Chi-restraints excluded: chain B residue 853 ARG Chi-restraints excluded: chain B residue 923 PHE Chi-restraints excluded: chain B residue 1001 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 82 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 57 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.144541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.111482 restraints weight = 12118.739| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.94 r_work: 0.3223 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10188 Z= 0.132 Angle : 0.550 6.815 13871 Z= 0.288 Chirality : 0.042 0.206 1565 Planarity : 0.004 0.047 1741 Dihedral : 8.024 65.836 1464 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.83 % Favored : 96.09 % Rotamer: Outliers : 2.24 % Allowed : 24.90 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % 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: 1.19 (0.24), residues: 1252 helix: 2.00 (0.20), residues: 672 sheet: 0.36 (0.47), residues: 121 loop : -0.96 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 137 HIS 0.002 0.001 HIS B 761 PHE 0.023 0.001 PHE A 597 TYR 0.011 0.001 TYR A 626 ARG 0.008 0.001 ARG A 918 Details of bonding type rmsd hydrogen bonds : bond 0.04513 ( 538) hydrogen bonds : angle 4.30861 ( 1554) SS BOND : bond 0.00305 ( 2) SS BOND : angle 1.92649 ( 4) covalent geometry : bond 0.00302 (10186) covalent geometry : angle 0.54879 (13867) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9351.42 seconds wall clock time: 162 minutes 44.38 seconds (9764.38 seconds total)