Starting phenix.real_space_refine on Sat Aug 23 05:31:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bwt_44979/08_2025/9bwt_44979_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bwt_44979/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9bwt_44979/08_2025/9bwt_44979_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bwt_44979/08_2025/9bwt_44979_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9bwt_44979/08_2025/9bwt_44979.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bwt_44979/08_2025/9bwt_44979.map" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'TPO:plan-1': 2, 'GLN:plan1': 5, 'GLU:plan': 3, 'HIS:plan': 1, 'ARG:plan': 5, 'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 2} 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: {'HIS:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 1, 'GLU: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: 2.20, per 1000 atoms: 0.22 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: 0.93 Conformation dependent library (CDL) restraints added in 377.2 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.31 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: 1.20 Time building geometry restraints manager: 1.17 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: 3.210 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.540 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:6.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.100 ------------------------------------------------------------------------------- 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 : 23.27 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.008 0.000 ARG A 934 TYR 0.012 0.001 TYR A 965 PHE 0.014 0.001 PHE A 597 TRP 0.010 0.001 TRP A 586 HIS 0.003 0.001 HIS A 636 Details of bonding type rmsd covalent geometry : bond 0.00612 (10186) covalent geometry : angle 0.71055 (13867) SS BOND : bond 0.00191 ( 2) SS BOND : angle 1.63868 ( 4) hydrogen bonds : bond 0.13884 ( 538) hydrogen bonds : angle 5.82329 ( 1554) *********************** 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 : 0.243 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: 0.5320 time to fit residues: 122.1165 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 : 0.376 ------------------------------------------------------------------------------- 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 108 optimal weight: 0.7980 chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 9.9990 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.0020 overall best weight: 0.6588 ------------------------------------------------------------------------------- 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 667 ASN B 873 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.147679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.115470 restraints weight = 12321.436| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.92 r_work: 0.3282 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3184 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.1357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10188 Z= 0.133 Angle : 0.579 6.258 13871 Z= 0.302 Chirality : 0.043 0.178 1565 Planarity : 0.005 0.085 1741 Dihedral : 8.565 86.025 1486 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.75 % Favored : 96.09 % Rotamer: Outliers : 4.09 % Allowed : 25.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.25 (0.24), residues: 1252 helix: 2.01 (0.20), residues: 676 sheet: 0.38 (0.49), residues: 117 loop : -0.87 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 918 TYR 0.012 0.001 TYR A1018 PHE 0.010 0.001 PHE A 664 TRP 0.014 0.001 TRP A 137 HIS 0.005 0.001 HIS B 761 Details of bonding type rmsd covalent geometry : bond 0.00293 (10186) covalent geometry : angle 0.57771 (13867) SS BOND : bond 0.00922 ( 2) SS BOND : angle 2.13334 ( 4) hydrogen bonds : bond 0.04794 ( 538) hydrogen bonds : angle 4.57512 ( 1554) *********************** 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 214 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 172 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.7812 (m-30) cc_final: 0.7576 (m-30) REVERT: A 247 GLU cc_start: 0.7203 (tm-30) cc_final: 0.6933 (tt0) REVERT: A 331 ASP cc_start: 0.7956 (t0) cc_final: 0.7621 (t0) REVERT: A 345 ILE cc_start: 0.8428 (mt) cc_final: 0.8211 (mm) REVERT: A 416 GLU cc_start: 0.6424 (tm-30) cc_final: 0.5811 (tt0) REVERT: A 485 ASP cc_start: 0.8275 (m-30) cc_final: 0.8049 (m-30) REVERT: A 605 LYS cc_start: 0.8248 (tppp) cc_final: 0.7873 (tptt) REVERT: A 606 LYS cc_start: 0.7635 (mtmt) cc_final: 0.7302 (tttt) REVERT: A 718 ARG cc_start: 0.8443 (mpp80) cc_final: 0.7975 (mmp80) REVERT: A 731 ARG cc_start: 0.8335 (ttm-80) cc_final: 0.7981 (mtt90) REVERT: A 777 GLU cc_start: 0.7885 (mp0) cc_final: 0.7539 (pm20) REVERT: A 827 LYS cc_start: 0.8248 (mmtm) cc_final: 0.7994 (mmtm) REVERT: A 857 LYS cc_start: 0.8438 (mmmm) cc_final: 0.7526 (mppt) REVERT: A 898 ILE cc_start: 0.7324 (OUTLIER) cc_final: 0.7110 (tt) REVERT: A 947 LYS cc_start: 0.8007 (mttp) cc_final: 0.7760 (mttp) REVERT: A 949 ARG cc_start: 0.7559 (tpp80) cc_final: 0.7150 (tpp-160) REVERT: A 1012 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7987 (tt0) REVERT: A 1013 ASN cc_start: 0.8556 (t0) cc_final: 0.8309 (t0) REVERT: B 853 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7340 (pmt170) REVERT: B 875 ARG cc_start: 0.8055 (ttp80) cc_final: 0.7340 (ttm110) REVERT: B 905 GLU cc_start: 0.7535 (mp0) cc_final: 0.7106 (pm20) REVERT: B 947 LYS cc_start: 0.8508 (mtpt) cc_final: 0.8199 (mttt) REVERT: B 1001 ARG cc_start: 0.5170 (OUTLIER) cc_final: 0.3762 (mmt-90) outliers start: 42 outliers final: 13 residues processed: 197 average time/residue: 0.5581 time to fit residues: 117.6427 Evaluate side-chains 156 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 421 SER Chi-restraints excluded: chain A residue 530 ILE Chi-restraints excluded: chain A residue 658 VAL 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 667 ASN Chi-restraints excluded: chain B residue 853 ARG Chi-restraints excluded: chain B residue 872 ASP 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 54 optimal weight: 0.0470 chunk 5 optimal weight: 2.9990 chunk 113 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 106 optimal weight: 6.9990 chunk 121 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 overall best weight: 1.5482 ------------------------------------------------------------------------------- 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 667 ASN B 959 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.138913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.104114 restraints weight = 11524.786| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 1.91 r_work: 0.3068 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8587 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10188 Z= 0.179 Angle : 0.600 8.894 13871 Z= 0.311 Chirality : 0.044 0.188 1565 Planarity : 0.005 0.068 1741 Dihedral : 8.329 81.664 1465 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.67 % Favored : 96.17 % Rotamer: Outliers : 4.67 % Allowed : 23.93 % Favored : 71.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.24), residues: 1252 helix: 1.84 (0.20), residues: 676 sheet: 0.25 (0.47), residues: 120 loop : -0.92 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 949 TYR 0.014 0.002 TYR B 626 PHE 0.015 0.002 PHE A 340 TRP 0.012 0.001 TRP A 137 HIS 0.005 0.001 HIS B 761 Details of bonding type rmsd covalent geometry : bond 0.00421 (10186) covalent geometry : angle 0.59875 (13867) SS BOND : bond 0.00851 ( 2) SS BOND : angle 2.29079 ( 4) hydrogen bonds : bond 0.05236 ( 538) hydrogen bonds : angle 4.51530 ( 1554) *********************** 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 194 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 146 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.7768 (m-30) cc_final: 0.7442 (m-30) REVERT: A 247 GLU cc_start: 0.7079 (tm-30) cc_final: 0.6837 (tt0) REVERT: A 331 ASP cc_start: 0.8081 (t0) cc_final: 0.7735 (t0) REVERT: A 336 ASP cc_start: 0.7438 (OUTLIER) cc_final: 0.6650 (t0) REVERT: A 345 ILE cc_start: 0.8400 (OUTLIER) cc_final: 0.8142 (mm) REVERT: A 416 GLU cc_start: 0.6622 (tm-30) cc_final: 0.5550 (tt0) REVERT: A 421 SER cc_start: 0.7911 (OUTLIER) cc_final: 0.7507 (p) REVERT: A 605 LYS cc_start: 0.8139 (tppp) cc_final: 0.7748 (tptt) REVERT: A 606 LYS cc_start: 0.7557 (mtmt) cc_final: 0.7240 (tttt) REVERT: A 718 ARG cc_start: 0.8373 (mpp80) cc_final: 0.7760 (mmp80) REVERT: A 731 ARG cc_start: 0.8372 (ttm-80) cc_final: 0.7892 (mtt90) REVERT: A 777 GLU cc_start: 0.7911 (mp0) cc_final: 0.7469 (pm20) REVERT: A 824 GLU cc_start: 0.7189 (mp0) cc_final: 0.6786 (mm-30) REVERT: A 827 LYS cc_start: 0.8336 (mmtm) cc_final: 0.8077 (mmtm) REVERT: A 857 LYS cc_start: 0.8387 (mmmm) cc_final: 0.7657 (mmtt) REVERT: A 913 MET cc_start: 0.8425 (OUTLIER) cc_final: 0.8110 (ttp) REVERT: A 947 LYS cc_start: 0.7944 (mttp) cc_final: 0.7715 (mttp) REVERT: A 949 ARG cc_start: 0.7476 (tpp80) cc_final: 0.7034 (tpp-160) REVERT: A 967 ARG cc_start: 0.8099 (mtm-85) cc_final: 0.7894 (mtm-85) REVERT: A 1012 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7995 (tt0) REVERT: A 1013 ASN cc_start: 0.8608 (t0) cc_final: 0.8249 (t0) REVERT: B 827 LYS cc_start: 0.8313 (OUTLIER) cc_final: 0.7815 (mmtt) REVERT: B 853 ARG cc_start: 0.7959 (OUTLIER) cc_final: 0.7334 (pmt170) REVERT: B 871 MET cc_start: 0.8602 (mtm) cc_final: 0.8372 (mtm) REVERT: B 875 ARG cc_start: 0.7884 (ttp80) cc_final: 0.7033 (ttm110) REVERT: B 905 GLU cc_start: 0.7540 (mp0) cc_final: 0.6993 (pm20) REVERT: B 947 LYS cc_start: 0.8474 (mtpt) cc_final: 0.8051 (mmtp) REVERT: B 1001 ARG cc_start: 0.5112 (OUTLIER) cc_final: 0.3395 (mpt-90) outliers start: 48 outliers final: 15 residues processed: 175 average time/residue: 0.5028 time to fit residues: 94.2081 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 : 0.379 ------------------------------------------------------------------------------- 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 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 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 895 LEU Chi-restraints excluded: chain A residue 913 MET 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 667 ASN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 83 optimal weight: 5.9990 chunk 122 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 119 optimal weight: 0.7980 chunk 48 optimal weight: 0.6980 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 24 optimal weight: 0.0060 overall best weight: 0.5796 ------------------------------------------------------------------------------- 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 667 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.141652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.107210 restraints weight = 11584.704| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 1.90 r_work: 0.3111 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2994 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10188 Z= 0.120 Angle : 0.536 7.862 13871 Z= 0.279 Chirality : 0.041 0.152 1565 Planarity : 0.004 0.059 1741 Dihedral : 8.036 76.485 1463 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.67 % Favored : 96.25 % Rotamer: Outliers : 3.79 % Allowed : 24.12 % Favored : 72.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.24), residues: 1252 helix: 1.91 (0.20), residues: 678 sheet: 0.26 (0.47), residues: 120 loop : -0.92 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 949 TYR 0.011 0.001 TYR A 626 PHE 0.013 0.001 PHE A 597 TRP 0.013 0.001 TRP A 137 HIS 0.003 0.001 HIS B 761 Details of bonding type rmsd covalent geometry : bond 0.00265 (10186) covalent geometry : angle 0.53452 (13867) SS BOND : bond 0.00296 ( 2) SS BOND : angle 2.17177 ( 4) hydrogen bonds : bond 0.04444 ( 538) hydrogen bonds : angle 4.32497 ( 1554) *********************** 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 193 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.8830 (ttp) cc_final: 0.8626 (ttt) REVERT: A 243 ASP cc_start: 0.7764 (m-30) cc_final: 0.7449 (m-30) REVERT: A 247 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6748 (tt0) REVERT: A 331 ASP cc_start: 0.7963 (t0) cc_final: 0.7610 (t0) REVERT: A 336 ASP cc_start: 0.7487 (OUTLIER) cc_final: 0.6799 (t0) REVERT: A 345 ILE cc_start: 0.8387 (OUTLIER) cc_final: 0.8164 (mm) REVERT: A 416 GLU cc_start: 0.6471 (tm-30) cc_final: 0.5984 (tt0) REVERT: A 446 MET cc_start: 0.8744 (ttt) cc_final: 0.8363 (ttt) REVERT: A 605 LYS cc_start: 0.8101 (tppp) cc_final: 0.7791 (tptt) REVERT: A 606 LYS cc_start: 0.7535 (mtmt) cc_final: 0.7232 (ttmt) REVERT: A 718 ARG cc_start: 0.8369 (mpp80) cc_final: 0.7811 (mmp80) REVERT: A 731 ARG cc_start: 0.8345 (ttm-80) cc_final: 0.7862 (mtt90) REVERT: A 777 GLU cc_start: 0.7917 (mp0) cc_final: 0.7434 (pm20) REVERT: A 779 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8182 (mm) REVERT: A 824 GLU cc_start: 0.7145 (mp0) cc_final: 0.6769 (mm-30) REVERT: A 827 LYS cc_start: 0.8342 (mmtm) cc_final: 0.8081 (mmtm) REVERT: A 857 LYS cc_start: 0.8399 (mmmm) cc_final: 0.7686 (mmtt) REVERT: A 913 MET cc_start: 0.8366 (ttm) cc_final: 0.8124 (ttp) REVERT: A 947 LYS cc_start: 0.8003 (mttp) cc_final: 0.7798 (mttp) REVERT: A 949 ARG cc_start: 0.7461 (tpp80) cc_final: 0.7040 (tpp-160) REVERT: A 967 ARG cc_start: 0.8043 (mtm-85) cc_final: 0.7810 (mtm-85) REVERT: A 1012 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.7971 (tt0) REVERT: A 1013 ASN cc_start: 0.8593 (t0) cc_final: 0.8233 (t0) REVERT: B 827 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7725 (mmmt) REVERT: B 853 ARG cc_start: 0.7833 (OUTLIER) cc_final: 0.7270 (pmt170) REVERT: B 871 MET cc_start: 0.8573 (mtm) cc_final: 0.8331 (mtm) REVERT: B 875 ARG cc_start: 0.7906 (ttp80) cc_final: 0.7122 (ttm110) REVERT: B 905 GLU cc_start: 0.7568 (mp0) cc_final: 0.7058 (pm20) REVERT: B 947 LYS cc_start: 0.8474 (mtpt) cc_final: 0.8048 (mmtp) REVERT: B 1001 ARG cc_start: 0.4865 (OUTLIER) cc_final: 0.3443 (mpt-90) outliers start: 39 outliers final: 16 residues processed: 177 average time/residue: 0.5385 time to fit residues: 101.7878 Evaluate side-chains 169 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 146 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 421 SER 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 1012 GLU Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 667 ASN 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 85 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 101 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 61 optimal weight: 0.1980 chunk 60 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 120 optimal weight: 3.9990 chunk 29 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.9984 ------------------------------------------------------------------------------- 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 B 667 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.140820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.106303 restraints weight = 11544.443| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.89 r_work: 0.3103 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2983 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10188 Z= 0.137 Angle : 0.545 7.234 13871 Z= 0.283 Chirality : 0.042 0.199 1565 Planarity : 0.004 0.051 1741 Dihedral : 7.979 71.780 1463 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.75 % Favored : 96.17 % Rotamer: Outliers : 4.47 % Allowed : 22.86 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.24), residues: 1252 helix: 1.94 (0.20), residues: 672 sheet: 0.31 (0.47), residues: 120 loop : -0.92 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 918 TYR 0.011 0.001 TYR B 626 PHE 0.015 0.001 PHE A 597 TRP 0.012 0.001 TRP A 137 HIS 0.003 0.001 HIS B 761 Details of bonding type rmsd covalent geometry : bond 0.00314 (10186) covalent geometry : angle 0.54354 (13867) SS BOND : bond 0.00268 ( 2) SS BOND : angle 2.18746 ( 4) hydrogen bonds : bond 0.04631 ( 538) hydrogen bonds : angle 4.32491 ( 1554) *********************** 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: 46 poor density : 148 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.7695 (m-30) cc_final: 0.7389 (m-30) REVERT: A 247 GLU cc_start: 0.7063 (tm-30) cc_final: 0.6753 (tt0) REVERT: A 331 ASP cc_start: 0.8073 (t0) cc_final: 0.7735 (t0) REVERT: A 336 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.6792 (t0) REVERT: A 345 ILE cc_start: 0.8403 (OUTLIER) cc_final: 0.8199 (mm) REVERT: A 416 GLU cc_start: 0.6458 (tm-30) cc_final: 0.5876 (tt0) REVERT: A 530 ILE cc_start: 0.7855 (OUTLIER) cc_final: 0.7417 (mm) REVERT: A 605 LYS cc_start: 0.8090 (tppp) cc_final: 0.7789 (tptt) REVERT: A 606 LYS cc_start: 0.7559 (mtmt) cc_final: 0.7262 (ttmt) REVERT: A 718 ARG cc_start: 0.8342 (mpp80) cc_final: 0.7777 (mmp80) REVERT: A 731 ARG cc_start: 0.8358 (ttm-80) cc_final: 0.7826 (mtt90) REVERT: A 777 GLU cc_start: 0.7904 (mp0) cc_final: 0.7408 (pm20) REVERT: A 779 LEU cc_start: 0.8416 (OUTLIER) cc_final: 0.8156 (mm) REVERT: A 824 GLU cc_start: 0.7038 (mp0) cc_final: 0.6658 (mm-30) REVERT: A 827 LYS cc_start: 0.8326 (mmtm) cc_final: 0.8080 (mmtm) REVERT: A 853 ARG cc_start: 0.7979 (pmm150) cc_final: 0.7155 (mtm-85) REVERT: A 857 LYS cc_start: 0.8444 (mmmm) cc_final: 0.7720 (mmtt) REVERT: A 947 LYS cc_start: 0.8026 (mttp) cc_final: 0.7808 (mttp) REVERT: A 949 ARG cc_start: 0.7456 (tpp80) cc_final: 0.7043 (tpp-160) REVERT: A 967 ARG cc_start: 0.8073 (mtm-85) cc_final: 0.7837 (mtm-85) REVERT: B 827 LYS cc_start: 0.8301 (OUTLIER) cc_final: 0.7808 (mmtt) REVERT: B 853 ARG cc_start: 0.7849 (OUTLIER) cc_final: 0.7284 (pmt170) REVERT: B 871 MET cc_start: 0.8577 (mtm) cc_final: 0.8367 (mtm) REVERT: B 875 ARG cc_start: 0.7886 (ttp80) cc_final: 0.7122 (ttm110) REVERT: B 905 GLU cc_start: 0.7567 (mp0) cc_final: 0.7055 (pm20) REVERT: B 947 LYS cc_start: 0.8451 (mtpt) cc_final: 0.8017 (mmtp) REVERT: B 1001 ARG cc_start: 0.4884 (OUTLIER) cc_final: 0.3413 (mmm160) outliers start: 46 outliers final: 20 residues processed: 174 average time/residue: 0.5007 time to fit residues: 93.6175 Evaluate side-chains 168 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 141 time to evaluate : 0.254 ------------------------------------------------------------------------------- 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 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 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 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 779 LEU Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 914 ILE Chi-restraints excluded: chain A residue 945 ILE Chi-restraints excluded: chain A residue 965 TYR Chi-restraints excluded: chain A residue 1014 VAL Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 667 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 68 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 76 optimal weight: 6.9990 chunk 52 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 B 667 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.138406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.103535 restraints weight = 11567.748| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.91 r_work: 0.3058 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10188 Z= 0.188 Angle : 0.594 6.834 13871 Z= 0.309 Chirality : 0.044 0.187 1565 Planarity : 0.005 0.062 1741 Dihedral : 8.145 68.297 1463 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.91 % Favored : 96.01 % Rotamer: Outliers : 4.18 % Allowed : 22.47 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.05 (0.24), residues: 1252 helix: 1.84 (0.20), residues: 670 sheet: 0.35 (0.47), residues: 119 loop : -0.92 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 918 TYR 0.014 0.002 TYR B 626 PHE 0.018 0.002 PHE A 597 TRP 0.011 0.001 TRP A 137 HIS 0.004 0.001 HIS B 761 Details of bonding type rmsd covalent geometry : bond 0.00449 (10186) covalent geometry : angle 0.59269 (13867) SS BOND : bond 0.00336 ( 2) SS BOND : angle 2.51585 ( 4) hydrogen bonds : bond 0.05236 ( 538) hydrogen bonds : angle 4.43880 ( 1554) *********************** 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 190 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 147 time to evaluate : 0.566 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 ASP cc_start: 0.7684 (m-30) cc_final: 0.7391 (m-30) REVERT: A 247 GLU cc_start: 0.7075 (tm-30) cc_final: 0.6762 (tt0) REVERT: A 331 ASP cc_start: 0.8130 (t0) cc_final: 0.7786 (t0) REVERT: A 336 ASP cc_start: 0.7456 (OUTLIER) cc_final: 0.6730 (t0) REVERT: A 345 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8200 (mm) REVERT: A 416 GLU cc_start: 0.6776 (tm-30) cc_final: 0.6099 (tt0) REVERT: A 530 ILE cc_start: 0.7903 (OUTLIER) cc_final: 0.7464 (mm) REVERT: A 562 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7842 (mt0) REVERT: A 605 LYS cc_start: 0.8088 (tppp) cc_final: 0.7804 (tptt) REVERT: A 606 LYS cc_start: 0.7523 (mtmt) cc_final: 0.7215 (ttmt) REVERT: A 718 ARG cc_start: 0.8336 (tpp80) cc_final: 0.7742 (mmp80) REVERT: A 731 ARG cc_start: 0.8407 (ttm-80) cc_final: 0.8012 (mtt90) REVERT: A 777 GLU cc_start: 0.7902 (mp0) cc_final: 0.7386 (pm20) REVERT: A 779 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8179 (mm) REVERT: A 824 GLU cc_start: 0.7053 (mp0) cc_final: 0.6684 (mm-30) REVERT: A 827 LYS cc_start: 0.8353 (mmtm) cc_final: 0.8127 (mmtm) REVERT: A 853 ARG cc_start: 0.8005 (pmm150) cc_final: 0.7206 (mtm-85) REVERT: A 857 LYS cc_start: 0.8455 (mmmm) cc_final: 0.7736 (mmtt) REVERT: A 949 ARG cc_start: 0.7459 (tpp80) cc_final: 0.7084 (tpp-160) REVERT: B 827 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7778 (mmmt) REVERT: B 853 ARG cc_start: 0.7999 (OUTLIER) cc_final: 0.7375 (pmt170) REVERT: B 875 ARG cc_start: 0.7912 (ttp80) cc_final: 0.7123 (ttm110) REVERT: B 905 GLU cc_start: 0.7581 (mp0) cc_final: 0.7024 (pm20) REVERT: B 947 LYS cc_start: 0.8472 (mtpt) cc_final: 0.8044 (mmtp) REVERT: B 1001 ARG cc_start: 0.5259 (OUTLIER) cc_final: 0.3470 (mpt-90) outliers start: 43 outliers final: 21 residues processed: 172 average time/residue: 0.6071 time to fit residues: 111.6564 Evaluate side-chains 173 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 0.362 ------------------------------------------------------------------------------- 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 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 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 421 SER 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 779 LEU Chi-restraints excluded: chain A residue 895 LEU Chi-restraints excluded: chain A residue 898 ILE 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 667 ASN 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 929 VAL 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 21 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 34 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 667 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.140171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.105588 restraints weight = 11456.480| |-----------------------------------------------------------------------------| r_work (start): 0.3206 rms_B_bonded: 1.89 r_work: 0.3091 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2120 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= 0.136 Angle : 0.551 6.368 13871 Z= 0.288 Chirality : 0.042 0.171 1565 Planarity : 0.004 0.049 1741 Dihedral : 8.038 69.127 1463 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.83 % Favored : 96.09 % Rotamer: Outliers : 3.50 % Allowed : 23.64 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.24), residues: 1252 helix: 1.94 (0.20), residues: 671 sheet: 0.32 (0.47), residues: 119 loop : -0.96 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 851 TYR 0.011 0.001 TYR A 626 PHE 0.018 0.001 PHE A 597 TRP 0.013 0.001 TRP A 137 HIS 0.003 0.001 HIS B 761 Details of bonding type rmsd covalent geometry : bond 0.00312 (10186) covalent geometry : angle 0.55033 (13867) SS BOND : bond 0.00344 ( 2) SS BOND : angle 2.00465 ( 4) hydrogen bonds : bond 0.04700 ( 538) hydrogen bonds : angle 4.32839 ( 1554) *********************** 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: 36 poor density : 145 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 243 ASP cc_start: 0.7617 (m-30) cc_final: 0.7324 (m-30) REVERT: A 247 GLU cc_start: 0.7041 (tm-30) cc_final: 0.6709 (tt0) REVERT: A 331 ASP cc_start: 0.8048 (t0) cc_final: 0.7703 (t0) REVERT: A 336 ASP cc_start: 0.7468 (OUTLIER) cc_final: 0.6830 (t0) REVERT: A 345 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8187 (mm) REVERT: A 416 GLU cc_start: 0.6729 (tm-30) cc_final: 0.6055 (tt0) REVERT: A 562 GLN cc_start: 0.8229 (OUTLIER) cc_final: 0.7804 (mt0) REVERT: A 605 LYS cc_start: 0.8070 (tppp) cc_final: 0.7776 (tptt) REVERT: A 606 LYS cc_start: 0.7539 (mtmt) cc_final: 0.7219 (mttt) REVERT: A 718 ARG cc_start: 0.8306 (tpp80) cc_final: 0.7731 (mmp80) REVERT: A 731 ARG cc_start: 0.8294 (ttm-80) cc_final: 0.7874 (mtt90) REVERT: A 777 GLU cc_start: 0.7894 (mp0) cc_final: 0.7379 (pm20) REVERT: A 779 LEU cc_start: 0.8369 (OUTLIER) cc_final: 0.8107 (mm) REVERT: A 824 GLU cc_start: 0.7009 (mp0) cc_final: 0.6678 (mm-30) REVERT: A 827 LYS cc_start: 0.8335 (mmtm) cc_final: 0.8122 (mmtm) REVERT: A 853 ARG cc_start: 0.7943 (pmm150) cc_final: 0.7239 (mtm-85) REVERT: A 857 LYS cc_start: 0.8439 (mmmm) cc_final: 0.7723 (mmtt) REVERT: A 949 ARG cc_start: 0.7483 (tpp80) cc_final: 0.7143 (tpp-160) REVERT: B 827 LYS cc_start: 0.8331 (OUTLIER) cc_final: 0.7750 (mmmt) REVERT: B 853 ARG cc_start: 0.7935 (OUTLIER) cc_final: 0.7322 (pmt170) REVERT: B 875 ARG cc_start: 0.7898 (ttp80) cc_final: 0.7130 (ttm110) REVERT: B 905 GLU cc_start: 0.7566 (mp0) cc_final: 0.7038 (pm20) REVERT: B 947 LYS cc_start: 0.8451 (mtpt) cc_final: 0.8014 (mmtp) REVERT: B 1001 ARG cc_start: 0.5140 (OUTLIER) cc_final: 0.3568 (mpt-90) outliers start: 36 outliers final: 19 residues processed: 168 average time/residue: 0.6420 time to fit residues: 115.4559 Evaluate side-chains 167 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 141 time to evaluate : 0.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 181 THR 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 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 421 SER 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 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 667 ASN 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 929 VAL 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 4 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 77 optimal weight: 8.9990 chunk 57 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 667 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.141214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.107860 restraints weight = 12002.708| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 1.92 r_work: 0.3172 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3071 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 10188 Z= 0.208 Angle : 0.619 6.340 13871 Z= 0.322 Chirality : 0.045 0.220 1565 Planarity : 0.005 0.056 1741 Dihedral : 8.251 67.822 1463 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.99 % Favored : 95.85 % Rotamer: Outliers : 3.70 % Allowed : 22.86 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.99 (0.24), residues: 1252 helix: 1.80 (0.20), residues: 668 sheet: 0.34 (0.47), residues: 119 loop : -0.96 (0.27), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 918 TYR 0.014 0.002 TYR B 626 PHE 0.019 0.002 PHE A 597 TRP 0.011 0.001 TRP A 137 HIS 0.004 0.001 HIS B 890 Details of bonding type rmsd covalent geometry : bond 0.00499 (10186) covalent geometry : angle 0.61696 (13867) SS BOND : bond 0.00215 ( 2) SS BOND : angle 2.69725 ( 4) hydrogen bonds : bond 0.05433 ( 538) hydrogen bonds : angle 4.48987 ( 1554) *********************** 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 178 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 140 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: A 243 ASP cc_start: 0.7764 (m-30) cc_final: 0.7470 (m-30) REVERT: A 247 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6794 (tt0) REVERT: A 331 ASP cc_start: 0.8150 (t0) cc_final: 0.7835 (t0) REVERT: A 336 ASP cc_start: 0.7518 (OUTLIER) cc_final: 0.6876 (t0) REVERT: A 345 ILE cc_start: 0.8506 (mt) cc_final: 0.8283 (mm) REVERT: A 416 GLU cc_start: 0.6857 (tm-30) cc_final: 0.6047 (tt0) REVERT: A 562 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7878 (mt0) REVERT: A 605 LYS cc_start: 0.8222 (tppp) cc_final: 0.7943 (tptt) REVERT: A 606 LYS cc_start: 0.7643 (mtmt) cc_final: 0.7325 (mttt) REVERT: A 718 ARG cc_start: 0.8346 (tpp80) cc_final: 0.7832 (mmp80) REVERT: A 731 ARG cc_start: 0.8357 (ttm-80) cc_final: 0.7975 (mtt90) REVERT: A 777 GLU cc_start: 0.7861 (mp0) cc_final: 0.7352 (pm20) REVERT: A 824 GLU cc_start: 0.7075 (mp0) cc_final: 0.6787 (mm-30) REVERT: A 827 LYS cc_start: 0.8350 (mmtm) cc_final: 0.8145 (mmtm) REVERT: A 853 ARG cc_start: 0.8016 (pmm150) cc_final: 0.7300 (mtm-85) REVERT: A 857 LYS cc_start: 0.8434 (mmmm) cc_final: 0.7814 (mmtt) REVERT: A 949 ARG cc_start: 0.7550 (tpp80) cc_final: 0.7150 (tpp-160) REVERT: B 827 LYS cc_start: 0.8379 (OUTLIER) cc_final: 0.7822 (mmmt) REVERT: B 853 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7277 (pmt170) REVERT: B 857 LYS cc_start: 0.8807 (OUTLIER) cc_final: 0.8003 (mppt) REVERT: B 875 ARG cc_start: 0.7966 (ttp80) cc_final: 0.7288 (ttm110) REVERT: B 903 ARG cc_start: 0.7985 (mmm-85) cc_final: 0.7738 (mtp-110) REVERT: B 905 GLU cc_start: 0.7612 (mp0) cc_final: 0.7268 (mp0) REVERT: B 947 LYS cc_start: 0.8522 (mtpt) cc_final: 0.8138 (mmtp) REVERT: B 1001 ARG cc_start: 0.5438 (OUTLIER) cc_final: 0.3722 (mpt-90) outliers start: 38 outliers final: 21 residues processed: 164 average time/residue: 0.5958 time to fit residues: 104.3133 Evaluate side-chains 165 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 PHE Chi-restraints excluded: chain A residue 133 VAL Chi-restraints excluded: chain A residue 181 THR 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 318 SER Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 421 SER 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 732 MET 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 945 ILE Chi-restraints excluded: chain A residue 1016 THR Chi-restraints excluded: chain B residue 665 THR Chi-restraints excluded: chain B residue 667 ASN Chi-restraints excluded: chain B residue 827 LYS Chi-restraints excluded: chain B residue 853 ARG Chi-restraints excluded: chain B residue 857 LYS 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 83 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 2 optimal weight: 7.9990 chunk 70 optimal weight: 0.1980 chunk 76 optimal weight: 4.9990 chunk 92 optimal weight: 0.0670 chunk 24 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.2524 ------------------------------------------------------------------------------- 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 667 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.142521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.109292 restraints weight = 12010.451| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 1.93 r_work: 0.3195 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10188 Z= 0.157 Angle : 0.578 6.477 13871 Z= 0.302 Chirality : 0.043 0.217 1565 Planarity : 0.005 0.053 1741 Dihedral : 8.157 68.302 1463 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.75 % Favored : 96.09 % Rotamer: Outliers : 3.11 % Allowed : 23.54 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.24), residues: 1252 helix: 1.85 (0.20), residues: 670 sheet: 0.23 (0.46), residues: 121 loop : -0.95 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 918 TYR 0.012 0.002 TYR A 626 PHE 0.021 0.001 PHE A 597 TRP 0.013 0.001 TRP A 137 HIS 0.003 0.001 HIS B 761 Details of bonding type rmsd covalent geometry : bond 0.00368 (10186) covalent geometry : angle 0.57663 (13867) SS BOND : bond 0.00301 ( 2) SS BOND : angle 2.36124 ( 4) hydrogen bonds : bond 0.04962 ( 538) hydrogen bonds : angle 4.41615 ( 1554) *********************** 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 173 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 141 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 243 ASP cc_start: 0.7695 (m-30) cc_final: 0.7421 (m-30) REVERT: A 247 GLU cc_start: 0.7114 (tm-30) cc_final: 0.6766 (tt0) REVERT: A 331 ASP cc_start: 0.8076 (t0) cc_final: 0.7744 (t0) REVERT: A 336 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.6897 (t0) REVERT: A 345 ILE cc_start: 0.8500 (mt) cc_final: 0.8294 (mm) REVERT: A 416 GLU cc_start: 0.6752 (tm-30) cc_final: 0.6220 (tt0) REVERT: A 605 LYS cc_start: 0.8227 (tppp) cc_final: 0.7938 (tptt) REVERT: A 606 LYS cc_start: 0.7594 (mtmt) cc_final: 0.7280 (mttt) REVERT: A 718 ARG cc_start: 0.8327 (tpp80) cc_final: 0.7827 (mmp80) REVERT: A 731 ARG cc_start: 0.8339 (ttm-80) cc_final: 0.7860 (mtt90) REVERT: A 777 GLU cc_start: 0.7867 (mp0) cc_final: 0.7383 (pm20) REVERT: A 824 GLU cc_start: 0.7084 (mp0) cc_final: 0.6740 (mm-30) REVERT: A 827 LYS cc_start: 0.8355 (mmtm) cc_final: 0.8154 (mmtm) REVERT: A 853 ARG cc_start: 0.8006 (pmm150) cc_final: 0.7278 (mtm-85) REVERT: A 857 LYS cc_start: 0.8439 (OUTLIER) cc_final: 0.7813 (mmtt) REVERT: A 949 ARG cc_start: 0.7529 (tpp80) cc_final: 0.7142 (tpp-160) REVERT: B 827 LYS cc_start: 0.8369 (OUTLIER) cc_final: 0.7796 (mmmt) REVERT: B 853 ARG cc_start: 0.7902 (OUTLIER) cc_final: 0.7316 (pmt170) REVERT: B 875 ARG cc_start: 0.7963 (ttp80) cc_final: 0.7294 (ttm110) REVERT: B 905 GLU cc_start: 0.7603 (mp0) cc_final: 0.7070 (pm20) REVERT: B 947 LYS cc_start: 0.8496 (mtpt) cc_final: 0.8106 (mmtp) REVERT: B 1001 ARG cc_start: 0.5360 (OUTLIER) cc_final: 0.3780 (mpt-90) outliers start: 32 outliers final: 20 residues processed: 161 average time/residue: 0.5758 time to fit residues: 99.1710 Evaluate side-chains 162 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 133 VAL Chi-restraints excluded: chain A residue 181 THR 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 318 SER Chi-restraints excluded: chain A residue 336 ASP Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 421 SER 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 667 ASN 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 95 optimal weight: 3.9990 chunk 111 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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 667 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.143525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.110507 restraints weight = 12122.985| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.93 r_work: 0.3204 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10188 Z= 0.141 Angle : 0.571 6.238 13871 Z= 0.297 Chirality : 0.042 0.212 1565 Planarity : 0.004 0.052 1741 Dihedral : 8.076 67.704 1463 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.83 % Favored : 96.01 % Rotamer: Outliers : 2.33 % Allowed : 24.32 % Favored : 73.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.10 (0.24), residues: 1252 helix: 1.92 (0.20), residues: 671 sheet: 0.38 (0.47), residues: 119 loop : -0.98 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 918 TYR 0.012 0.001 TYR A 626 PHE 0.023 0.001 PHE A 597 TRP 0.013 0.001 TRP A 137 HIS 0.003 0.001 HIS B 761 Details of bonding type rmsd covalent geometry : bond 0.00325 (10186) covalent geometry : angle 0.56636 (13867) SS BOND : bond 0.00160 ( 2) SS BOND : angle 4.23007 ( 4) hydrogen bonds : bond 0.04731 ( 538) hydrogen bonds : angle 4.35971 ( 1554) ********************** 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 164 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 0.409 Fit side-chains revert: symmetry clash REVERT: A 243 ASP cc_start: 0.7703 (m-30) cc_final: 0.7414 (m-30) REVERT: A 247 GLU cc_start: 0.7111 (tm-30) cc_final: 0.6761 (tt0) REVERT: A 331 ASP cc_start: 0.8107 (t0) cc_final: 0.7796 (t0) REVERT: A 336 ASP cc_start: 0.7478 (OUTLIER) cc_final: 0.6920 (t0) REVERT: A 416 GLU cc_start: 0.6452 (tm-30) cc_final: 0.5892 (tt0) REVERT: A 605 LYS cc_start: 0.8238 (tppp) cc_final: 0.7949 (tptt) REVERT: A 606 LYS cc_start: 0.7600 (mtmt) cc_final: 0.7303 (mttt) REVERT: A 718 ARG cc_start: 0.8333 (tpp80) cc_final: 0.7843 (mmp80) REVERT: A 731 ARG cc_start: 0.8358 (ttm-80) cc_final: 0.8087 (mtt90) REVERT: A 777 GLU cc_start: 0.7879 (mp0) cc_final: 0.7468 (pm20) REVERT: A 824 GLU cc_start: 0.7104 (mp0) cc_final: 0.6775 (mm-30) REVERT: A 827 LYS cc_start: 0.8353 (mmtm) cc_final: 0.8113 (mmtm) REVERT: A 853 ARG cc_start: 0.8002 (pmm150) cc_final: 0.7399 (mtm-85) REVERT: A 857 LYS cc_start: 0.8460 (mmmm) cc_final: 0.7854 (mmtt) REVERT: A 949 ARG cc_start: 0.7556 (tpp80) cc_final: 0.7195 (tpp-160) REVERT: A 958 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8453 (tm) REVERT: B 827 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7810 (mmmt) REVERT: B 853 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7330 (pmt170) REVERT: B 875 ARG cc_start: 0.7997 (ttp80) cc_final: 0.7346 (ttm110) REVERT: B 905 GLU cc_start: 0.7605 (mp0) cc_final: 0.7105 (pm20) REVERT: B 947 LYS cc_start: 0.8498 (mtpt) cc_final: 0.8137 (mmtp) REVERT: B 1001 ARG cc_start: 0.5237 (OUTLIER) cc_final: 0.3803 (mpt-90) outliers start: 24 outliers final: 18 residues processed: 154 average time/residue: 0.6050 time to fit residues: 99.6210 Evaluate side-chains 158 residues out of total 1084 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 135 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 133 VAL Chi-restraints excluded: chain A residue 181 THR 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 336 ASP Chi-restraints excluded: chain A residue 403 VAL Chi-restraints excluded: chain A residue 421 SER 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 958 LEU 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 27 optimal weight: 0.7980 chunk 102 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 124 optimal weight: 0.3980 chunk 14 optimal weight: 5.9990 chunk 119 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3714 r_free = 0.3714 target = 0.144835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.111954 restraints weight = 12232.517| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.93 r_work: 0.3232 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10188 Z= 0.124 Angle : 0.548 6.880 13871 Z= 0.286 Chirality : 0.041 0.205 1565 Planarity : 0.004 0.049 1741 Dihedral : 7.939 67.117 1463 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.67 % Favored : 96.17 % Rotamer: Outliers : 2.43 % Allowed : 24.42 % Favored : 73.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.51 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.24), residues: 1252 helix: 2.00 (0.20), residues: 672 sheet: 0.40 (0.47), residues: 119 loop : -0.98 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 918 TYR 0.011 0.001 TYR A 626 PHE 0.025 0.001 PHE A 597 TRP 0.013 0.001 TRP A 137 HIS 0.002 0.001 HIS B 761 Details of bonding type rmsd covalent geometry : bond 0.00277 (10186) covalent geometry : angle 0.54558 (13867) SS BOND : bond 0.00137 ( 2) SS BOND : angle 3.16645 ( 4) hydrogen bonds : bond 0.04401 ( 538) hydrogen bonds : angle 4.28836 ( 1554) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4125.38 seconds wall clock time: 70 minutes 50.80 seconds (4250.80 seconds total)