Starting phenix.real_space_refine on Sat Sep 12 06:19:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9xdb_66761/09_2026/9xdb_66761.cif Found real_map, /net/cci-nas-00/data/ceres_data/9xdb_66761/09_2026/9xdb_66761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9xdb_66761/09_2026/9xdb_66761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9xdb_66761/09_2026/9xdb_66761.map" model { file = "/net/cci-nas-00/data/ceres_data/9xdb_66761/09_2026/9xdb_66761.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9xdb_66761/09_2026/9xdb_66761.cif" } resolution = 3.9 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= 0.012 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: 4 Type Number sf(0) Gaussians S 108 5.16 5 C 8751 2.51 5 N 2262 2.21 5 O 2577 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 13698 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4566 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 549} Chain breaks: 2 Chain: "B" Number of atoms: 4566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4566 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 549} Chain breaks: 2 Chain: "C" Number of atoms: 4566 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4566 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 549} Chain breaks: 2 Time building chain proxies: 3.08, per 1000 atoms: 0.22 Number of scatterers: 13698 At special positions: 0 Unit cell: (129.02, 127.108, 150.045, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 108 16.00 O 2577 8.00 N 2262 7.00 C 8751 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.06 Conformation dependent library (CDL) restraints added in 625.9 milliseconds 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3252 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 16 sheets defined 20.9% alpha, 28.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 464 through 468 removed outlier: 4.098A pdb=" N LYS A 468 " --> pdb=" O LEU A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 639 through 649 Processing helix chain 'A' and resid 663 through 671 Processing helix chain 'A' and resid 673 through 678 Processing helix chain 'A' and resid 679 through 690 removed outlier: 3.529A pdb=" N TRP A 683 " --> pdb=" O ASN A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 776 through 787 removed outlier: 3.790A pdb=" N ASN A 784 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS A 785 " --> pdb=" O ASN A 781 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER A 787 " --> pdb=" O ILE A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 800 No H-bonds generated for 'chain 'A' and resid 798 through 800' Processing helix chain 'A' and resid 803 through 823 Processing helix chain 'A' and resid 838 through 845 Processing helix chain 'A' and resid 860 through 864 removed outlier: 4.223A pdb=" N GLY A 863 " --> pdb=" O CYS A 860 " (cutoff:3.500A) Processing helix chain 'A' and resid 883 through 887 removed outlier: 3.977A pdb=" N GLY A 887 " --> pdb=" O ASN A 884 " (cutoff:3.500A) Processing helix chain 'A' and resid 957 through 963 removed outlier: 4.186A pdb=" N ALA A 961 " --> pdb=" O SER A 958 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN A 962 " --> pdb=" O SER A 959 " (cutoff:3.500A) Processing helix chain 'A' and resid 1001 through 1003 No H-bonds generated for 'chain 'A' and resid 1001 through 1003' Processing helix chain 'A' and resid 1022 through 1026 Processing helix chain 'A' and resid 1049 through 1057 removed outlier: 3.894A pdb=" N ALA A1053 " --> pdb=" O ASN A1049 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN A1055 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN A1056 " --> pdb=" O LYS A1052 " (cutoff:3.500A) Processing helix chain 'B' and resid 464 through 468 removed outlier: 4.099A pdb=" N LYS B 468 " --> pdb=" O LEU B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 639 through 649 Processing helix chain 'B' and resid 663 through 671 Processing helix chain 'B' and resid 673 through 678 Processing helix chain 'B' and resid 679 through 690 removed outlier: 3.529A pdb=" N TRP B 683 " --> pdb=" O ASN B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 776 through 787 removed outlier: 3.791A pdb=" N ASN B 784 " --> pdb=" O VAL B 780 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS B 785 " --> pdb=" O ASN B 781 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER B 787 " --> pdb=" O ILE B 783 " (cutoff:3.500A) Processing helix chain 'B' and resid 798 through 800 No H-bonds generated for 'chain 'B' and resid 798 through 800' Processing helix chain 'B' and resid 803 through 823 Processing helix chain 'B' and resid 838 through 845 Processing helix chain 'B' and resid 860 through 864 removed outlier: 4.223A pdb=" N GLY B 863 " --> pdb=" O CYS B 860 " (cutoff:3.500A) Processing helix chain 'B' and resid 883 through 887 removed outlier: 3.977A pdb=" N GLY B 887 " --> pdb=" O ASN B 884 " (cutoff:3.500A) Processing helix chain 'B' and resid 957 through 963 removed outlier: 4.186A pdb=" N ALA B 961 " --> pdb=" O SER B 958 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ASN B 962 " --> pdb=" O SER B 959 " (cutoff:3.500A) Processing helix chain 'B' and resid 1001 through 1003 No H-bonds generated for 'chain 'B' and resid 1001 through 1003' Processing helix chain 'B' and resid 1022 through 1026 Processing helix chain 'B' and resid 1049 through 1057 removed outlier: 3.894A pdb=" N ALA B1053 " --> pdb=" O ASN B1049 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN B1055 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN B1056 " --> pdb=" O LYS B1052 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 468 removed outlier: 4.099A pdb=" N LYS C 468 " --> pdb=" O LEU C 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 639 through 649 Processing helix chain 'C' and resid 663 through 671 Processing helix chain 'C' and resid 673 through 678 Processing helix chain 'C' and resid 679 through 690 removed outlier: 3.530A pdb=" N TRP C 683 " --> pdb=" O ASN C 679 " (cutoff:3.500A) Processing helix chain 'C' and resid 776 through 787 removed outlier: 3.790A pdb=" N ASN C 784 " --> pdb=" O VAL C 780 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS C 785 " --> pdb=" O ASN C 781 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER C 787 " --> pdb=" O ILE C 783 " (cutoff:3.500A) Processing helix chain 'C' and resid 798 through 800 No H-bonds generated for 'chain 'C' and resid 798 through 800' Processing helix chain 'C' and resid 803 through 823 Processing helix chain 'C' and resid 838 through 845 Processing helix chain 'C' and resid 860 through 864 removed outlier: 4.223A pdb=" N GLY C 863 " --> pdb=" O CYS C 860 " (cutoff:3.500A) Processing helix chain 'C' and resid 883 through 887 removed outlier: 3.977A pdb=" N GLY C 887 " --> pdb=" O ASN C 884 " (cutoff:3.500A) Processing helix chain 'C' and resid 957 through 963 removed outlier: 4.185A pdb=" N ALA C 961 " --> pdb=" O SER C 958 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N ASN C 962 " --> pdb=" O SER C 959 " (cutoff:3.500A) Processing helix chain 'C' and resid 1001 through 1003 No H-bonds generated for 'chain 'C' and resid 1001 through 1003' Processing helix chain 'C' and resid 1022 through 1026 Processing helix chain 'C' and resid 1049 through 1057 removed outlier: 3.895A pdb=" N ALA C1053 " --> pdb=" O ASN C1049 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASN C1055 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN C1056 " --> pdb=" O LYS C1052 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 472 through 474 removed outlier: 4.709A pdb=" N GLY A 495 " --> pdb=" O GLY A 473 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 493 through 496 current: chain 'A' and resid 596 through 624 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 596 through 624 current: chain 'A' and resid 693 through 729 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 739 through 762 current: chain 'B' and resid 493 through 496 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 493 through 496 current: chain 'B' and resid 596 through 624 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 596 through 624 current: chain 'B' and resid 693 through 729 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 739 through 762 current: chain 'C' and resid 493 through 496 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 493 through 496 current: chain 'C' and resid 596 through 624 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 596 through 624 current: chain 'C' and resid 693 through 729 Processing sheet with id=AA2, first strand: chain 'A' and resid 846 through 852 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 846 through 852 current: chain 'A' and resid 909 through 917 No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 925 through 931 removed outlier: 3.528A pdb=" N THR A 925 " --> pdb=" O CYS A 994 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLN A 987 " --> pdb=" O MET A 953 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N MET A 953 " --> pdb=" O GLN A 987 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N MET A 989 " --> pdb=" O ALA A 951 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA A 951 " --> pdb=" O MET A 989 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR A 991 " --> pdb=" O GLY A 949 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY A 949 " --> pdb=" O TYR A 991 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 935 through 939 Processing sheet with id=AA5, first strand: chain 'A' and resid 1005 through 1014 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1005 through 1014 current: chain 'A' and resid 1086 through 1095 No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 1027 through 1031 Processing sheet with id=AA7, first strand: chain 'B' and resid 846 through 852 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 846 through 852 current: chain 'B' and resid 909 through 917 No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 925 through 931 removed outlier: 3.528A pdb=" N THR B 925 " --> pdb=" O CYS B 994 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLN B 987 " --> pdb=" O MET B 953 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N MET B 953 " --> pdb=" O GLN B 987 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N MET B 989 " --> pdb=" O ALA B 951 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA B 951 " --> pdb=" O MET B 989 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR B 991 " --> pdb=" O GLY B 949 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY B 949 " --> pdb=" O TYR B 991 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 935 through 939 Processing sheet with id=AB1, first strand: chain 'B' and resid 1005 through 1014 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1005 through 1014 current: chain 'B' and resid 1086 through 1095 No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 1027 through 1031 Processing sheet with id=AB3, first strand: chain 'C' and resid 846 through 852 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 846 through 852 current: chain 'C' and resid 909 through 917 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 925 through 931 removed outlier: 3.528A pdb=" N THR C 925 " --> pdb=" O CYS C 994 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLN C 987 " --> pdb=" O MET C 953 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N MET C 953 " --> pdb=" O GLN C 987 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N MET C 989 " --> pdb=" O ALA C 951 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N ALA C 951 " --> pdb=" O MET C 989 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR C 991 " --> pdb=" O GLY C 949 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N GLY C 949 " --> pdb=" O TYR C 991 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 935 through 939 Processing sheet with id=AB6, first strand: chain 'C' and resid 1005 through 1014 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 1005 through 1014 current: chain 'C' and resid 1086 through 1095 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'C' and resid 1027 through 1031 307 hydrogen bonds defined for protein. 867 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: 1.93 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.12 - 1.26: 2250 1.26 - 1.40: 2482 1.40 - 1.54: 8393 1.54 - 1.68: 717 1.68 - 1.83: 165 Bond restraints: 14007 Sorted by residual: bond pdb=" C PHE C 592 " pdb=" O PHE C 592 " ideal model delta sigma weight residual 1.238 1.118 0.120 1.28e-02 6.10e+03 8.72e+01 bond pdb=" C PHE B 592 " pdb=" O PHE B 592 " ideal model delta sigma weight residual 1.238 1.118 0.119 1.28e-02 6.10e+03 8.71e+01 bond pdb=" C PHE A 592 " pdb=" O PHE A 592 " ideal model delta sigma weight residual 1.238 1.118 0.119 1.28e-02 6.10e+03 8.70e+01 bond pdb=" CG PHE C 592 " pdb=" CD2 PHE C 592 " ideal model delta sigma weight residual 1.384 1.243 0.141 2.10e-02 2.27e+03 4.53e+01 bond pdb=" CG PHE B 592 " pdb=" CD2 PHE B 592 " ideal model delta sigma weight residual 1.384 1.243 0.141 2.10e-02 2.27e+03 4.53e+01 ... (remaining 14002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.80: 15934 2.80 - 5.60: 2660 5.60 - 8.39: 255 8.39 - 11.19: 33 11.19 - 13.99: 9 Bond angle restraints: 18891 Sorted by residual: angle pdb=" N ASN C 786 " pdb=" CA ASN C 786 " pdb=" C ASN C 786 " ideal model delta sigma weight residual 112.23 122.59 -10.36 1.26e+00 6.30e-01 6.76e+01 angle pdb=" N ASN A 786 " pdb=" CA ASN A 786 " pdb=" C ASN A 786 " ideal model delta sigma weight residual 112.23 122.55 -10.32 1.26e+00 6.30e-01 6.71e+01 angle pdb=" N ASN B 786 " pdb=" CA ASN B 786 " pdb=" C ASN B 786 " ideal model delta sigma weight residual 112.23 122.55 -10.32 1.26e+00 6.30e-01 6.71e+01 angle pdb=" C ILE A 946 " pdb=" N LEU A 947 " pdb=" CA LEU A 947 " ideal model delta sigma weight residual 122.74 136.73 -13.99 1.82e+00 3.02e-01 5.91e+01 angle pdb=" C ILE C 946 " pdb=" N LEU C 947 " pdb=" CA LEU C 947 " ideal model delta sigma weight residual 122.74 136.71 -13.97 1.82e+00 3.02e-01 5.89e+01 ... (remaining 18886 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.76: 7725 17.76 - 35.53: 592 35.53 - 53.29: 111 53.29 - 71.05: 35 71.05 - 88.81: 21 Dihedral angle restraints: 8484 sinusoidal: 3432 harmonic: 5052 Sorted by residual: dihedral pdb=" CA VAL B1039 " pdb=" C VAL B1039 " pdb=" N PHE B1040 " pdb=" CA PHE B1040 " ideal model delta harmonic sigma weight residual 180.00 150.42 29.58 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA VAL C1039 " pdb=" C VAL C1039 " pdb=" N PHE C1040 " pdb=" CA PHE C1040 " ideal model delta harmonic sigma weight residual 180.00 150.43 29.57 0 5.00e+00 4.00e-02 3.50e+01 dihedral pdb=" CA VAL A1039 " pdb=" C VAL A1039 " pdb=" N PHE A1040 " pdb=" CA PHE A1040 " ideal model delta harmonic sigma weight residual 180.00 150.44 29.56 0 5.00e+00 4.00e-02 3.50e+01 ... (remaining 8481 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 1435 0.115 - 0.230: 527 0.230 - 0.345: 63 0.345 - 0.459: 21 0.459 - 0.574: 12 Chirality restraints: 2058 Sorted by residual: chirality pdb=" CA HIS C 690 " pdb=" N HIS C 690 " pdb=" C HIS C 690 " pdb=" CB HIS C 690 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.24e+00 chirality pdb=" CA HIS A 690 " pdb=" N HIS A 690 " pdb=" C HIS A 690 " pdb=" CB HIS A 690 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.17e+00 chirality pdb=" CA HIS B 690 " pdb=" N HIS B 690 " pdb=" C HIS B 690 " pdb=" CB HIS B 690 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.16e+00 ... (remaining 2055 not shown) Planarity restraints: 2412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR C 817 " 0.147 2.00e-02 2.50e+03 8.50e-02 1.44e+02 pdb=" CG TYR C 817 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TYR C 817 " -0.072 2.00e-02 2.50e+03 pdb=" CD2 TYR C 817 " -0.062 2.00e-02 2.50e+03 pdb=" CE1 TYR C 817 " -0.053 2.00e-02 2.50e+03 pdb=" CE2 TYR C 817 " -0.066 2.00e-02 2.50e+03 pdb=" CZ TYR C 817 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 817 " 0.138 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 817 " 0.147 2.00e-02 2.50e+03 8.49e-02 1.44e+02 pdb=" CG TYR A 817 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR A 817 " -0.072 2.00e-02 2.50e+03 pdb=" CD2 TYR A 817 " -0.062 2.00e-02 2.50e+03 pdb=" CE1 TYR A 817 " -0.053 2.00e-02 2.50e+03 pdb=" CE2 TYR A 817 " -0.066 2.00e-02 2.50e+03 pdb=" CZ TYR A 817 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 817 " 0.138 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 817 " 0.146 2.00e-02 2.50e+03 8.48e-02 1.44e+02 pdb=" CG TYR B 817 " -0.029 2.00e-02 2.50e+03 pdb=" CD1 TYR B 817 " -0.072 2.00e-02 2.50e+03 pdb=" CD2 TYR B 817 " -0.062 2.00e-02 2.50e+03 pdb=" CE1 TYR B 817 " -0.054 2.00e-02 2.50e+03 pdb=" CE2 TYR B 817 " -0.066 2.00e-02 2.50e+03 pdb=" CZ TYR B 817 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 817 " 0.138 2.00e-02 2.50e+03 ... (remaining 2409 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 7 2.37 - 3.01: 6791 3.01 - 3.64: 18879 3.64 - 4.27: 28431 4.27 - 4.90: 48434 Nonbonded interactions: 102542 Sorted by model distance: nonbonded pdb=" NH2 ARG A 754 " pdb=" OE2 GLU B 568 " model vdw 1.743 3.120 nonbonded pdb=" NH2 ARG B 754 " pdb=" OE2 GLU C 568 " model vdw 1.814 3.120 nonbonded pdb=" OE2 GLU A 896 " pdb=" NH1 ARG B 970 " model vdw 2.015 3.120 nonbonded pdb=" OD1 ASN B 641 " pdb=" OG1 THR C 633 " model vdw 2.072 3.040 nonbonded pdb=" OE2 GLU B 896 " pdb=" NH1 ARG C 970 " model vdw 2.146 3.120 ... (remaining 102537 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.700 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: 0.020 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 12.760 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5683 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 : 0.014 0.162 14007 Z= 0.823 Angle : 2.069 13.989 18891 Z= 1.360 Chirality : 0.119 0.574 2058 Planarity : 0.016 0.111 2412 Dihedral : 14.634 88.813 5232 Min Nonbonded Distance : 1.743 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 1.92 % Allowed : 7.52 % Favored : 90.56 % Rotamer: Outliers : 2.32 % Allowed : 4.83 % Favored : 92.86 % Cbeta Deviations : 1.48 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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 are not related in a simple way. whole: -1.40 (0.19), residues: 1716 helix: -2.06 (0.25), residues: 240 sheet: 1.56 (0.19), residues: 597 loop : -2.56 (0.19), residues: 879 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 494 TYR 0.149 0.030 TYR C 664 PHE 0.108 0.015 PHE C 948 TRP 0.120 0.033 TRP A 779 HIS 0.019 0.004 HIS A 690 Details of bonding type rmsd/Z covalent geometry : bond 0.01372 / 0.82 (14007) covalent geometry : angle 2.06876 / 1.36 (18891) hydrogen bonds : bond 0.16096 / 9.74 ( 307) hydrogen bonds : angle 9.47056 / 6.46 ( 867) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 475 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 439 time to evaluate : 0.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 558 GLU cc_start: 0.6826 (mm-30) cc_final: 0.6177 (tt0) REVERT: A 570 ILE cc_start: 0.8347 (mt) cc_final: 0.8144 (mp) REVERT: A 603 LYS cc_start: 0.8381 (tttt) cc_final: 0.7555 (ttmm) REVERT: A 610 LYS cc_start: 0.8837 (tttt) cc_final: 0.8463 (mttm) REVERT: A 670 LYS cc_start: 0.7022 (mmtt) cc_final: 0.6812 (mttp) REVERT: A 684 MET cc_start: 0.6529 (mmp) cc_final: 0.6324 (mmp) REVERT: A 685 MET cc_start: 0.6056 (ttp) cc_final: 0.5689 (ttt) REVERT: A 703 LYS cc_start: 0.8428 (mtpt) cc_final: 0.8000 (mtmm) REVERT: A 712 LYS cc_start: 0.8389 (tttt) cc_final: 0.7968 (mttt) REVERT: A 715 TYR cc_start: 0.7345 (t80) cc_final: 0.6858 (t80) REVERT: A 733 PHE cc_start: 0.4812 (OUTLIER) cc_final: 0.4455 (p90) REVERT: A 735 LYS cc_start: -0.0923 (OUTLIER) cc_final: -0.1161 (ttpt) REVERT: A 757 LYS cc_start: 0.8961 (pttt) cc_final: 0.8522 (ptpp) REVERT: A 775 PHE cc_start: 0.5588 (t80) cc_final: 0.5280 (t80) REVERT: A 806 MET cc_start: 0.6485 (mtm) cc_final: 0.5784 (mtp) REVERT: A 910 ILE cc_start: 0.8952 (tt) cc_final: 0.8624 (tt) REVERT: A 916 CYS cc_start: 0.7284 (m) cc_final: 0.6230 (p) REVERT: A 990 ILE cc_start: 0.8732 (mt) cc_final: 0.8449 (mt) REVERT: A 1028 LEU cc_start: 0.6913 (tp) cc_final: 0.5950 (tt) REVERT: B 478 MET cc_start: 0.4857 (mtt) cc_final: 0.4653 (mtt) REVERT: B 565 LYS cc_start: 0.8648 (ttpt) cc_final: 0.8115 (tttp) REVERT: B 596 PHE cc_start: 0.7278 (t80) cc_final: 0.6585 (t80) REVERT: B 603 LYS cc_start: 0.8447 (tttt) cc_final: 0.7878 (tptm) REVERT: B 618 MET cc_start: 0.7869 (ttm) cc_final: 0.7451 (ttt) REVERT: B 685 MET cc_start: 0.4401 (ttp) cc_final: 0.2606 (mmt) REVERT: B 744 LYS cc_start: 0.7691 (ttpt) cc_final: 0.7459 (mttm) REVERT: B 788 MET cc_start: 0.2554 (ptt) cc_final: 0.2192 (ptm) REVERT: B 872 LEU cc_start: 0.8558 (mt) cc_final: 0.8239 (pp) REVERT: B 896 GLU cc_start: 0.6179 (tt0) cc_final: 0.5713 (mt-10) REVERT: B 898 CYS cc_start: 0.7049 (t) cc_final: 0.6350 (p) REVERT: B 912 ILE cc_start: 0.8321 (mt) cc_final: 0.7861 (pt) REVERT: B 950 PHE cc_start: 0.7461 (OUTLIER) cc_final: 0.7199 (p90) REVERT: B 1012 LYS cc_start: 0.6485 (tttt) cc_final: 0.6046 (mttt) REVERT: C 499 GLN cc_start: 0.5451 (mt0) cc_final: 0.4955 (mt0) REVERT: C 619 MET cc_start: 0.7687 (ttt) cc_final: 0.7434 (ttp) REVERT: C 677 GLU cc_start: 0.5716 (mm-30) cc_final: 0.5388 (tm-30) REVERT: C 754 ARG cc_start: 0.7714 (ppp-140) cc_final: 0.7207 (tpp-160) REVERT: C 757 LYS cc_start: 0.8081 (pttt) cc_final: 0.7453 (ptpt) REVERT: C 762 LEU cc_start: 0.7659 (mp) cc_final: 0.7331 (mp) REVERT: C 765 ASN cc_start: 0.0782 (OUTLIER) cc_final: 0.0459 (m-40) REVERT: C 806 MET cc_start: 0.6340 (mtm) cc_final: 0.6109 (tpp) REVERT: C 872 LEU cc_start: 0.8439 (mt) cc_final: 0.7927 (mt) REVERT: C 973 GLN cc_start: 0.5723 (mm-40) cc_final: 0.5268 (mm-40) REVERT: C 982 ASN cc_start: 0.7876 (t0) cc_final: 0.7353 (m-40) REVERT: C 1012 LYS cc_start: 0.6785 (tttt) cc_final: 0.6552 (ttpt) outliers start: 36 outliers final: 8 residues processed: 467 average time/residue: 0.1292 time to fit residues: 85.9254 Evaluate side-chains 284 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 272 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 730 ASN Chi-restraints excluded: chain A residue 731 LEU Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 735 LYS Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 950 PHE Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 950 PHE Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 765 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.0020 chunk 91 optimal weight: 6.9990 chunk 149 optimal weight: 9.9990 overall best weight: 3.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 572 ASN A 575 GLN ** A 672 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 784 ASN A 847 GLN A 873 ASN A 981 GLN B 501 ASN ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 572 ASN ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 612 GLN B 672 HIS B 784 ASN B 930 GLN B 973 GLN B1047 HIS C 488 ASN ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 563 GLN C 575 GLN C 612 GLN C 765 ASN C 784 ASN C1047 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.184145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.152482 restraints weight = 21045.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.153571 restraints weight = 19131.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.154450 restraints weight = 18109.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4222 r_free = 0.4222 target = 0.155360 restraints weight = 12091.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.155802 restraints weight = 10709.412| |-----------------------------------------------------------------------------| r_work (final): 0.4223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6091 moved from start: 0.4386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.078 14007 Z= 0.271 Angle : 1.034 14.173 18891 Z= 0.544 Chirality : 0.057 0.271 2058 Planarity : 0.007 0.068 2412 Dihedral : 9.853 59.975 1856 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.82 % Allowed : 8.28 % Favored : 90.91 % Rotamer: Outliers : 5.02 % Allowed : 14.35 % Favored : 80.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.49 % 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 are not related in a simple way. whole: -2.18 (0.19), residues: 1716 helix: -1.69 (0.27), residues: 267 sheet: -0.07 (0.18), residues: 648 loop : -2.58 (0.21), residues: 801 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 494 TYR 0.030 0.004 TYR B 666 PHE 0.034 0.004 PHE C1042 TRP 0.038 0.004 TRP A 779 HIS 0.013 0.002 HIS C 690 Details of bonding type rmsd/Z covalent geometry : bond 0.00611 / 0.27 (14007) covalent geometry : angle 1.03430 / 0.54 (18891) hydrogen bonds : bond 0.06082 / 3.90 ( 307) hydrogen bonds : angle 6.88686 / 4.67 ( 867) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 393 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 315 time to evaluate : 0.537 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 565 LYS cc_start: 0.7988 (tptp) cc_final: 0.7705 (tptt) REVERT: A 573 LEU cc_start: 0.8406 (tt) cc_final: 0.8031 (tp) REVERT: A 603 LYS cc_start: 0.8548 (tttt) cc_final: 0.7868 (ttmm) REVERT: A 607 LYS cc_start: 0.8603 (mptt) cc_final: 0.8319 (mmtm) REVERT: A 610 LYS cc_start: 0.8815 (tttt) cc_final: 0.8480 (mttm) REVERT: A 730 ASN cc_start: 0.6191 (OUTLIER) cc_final: 0.5223 (t0) REVERT: A 733 PHE cc_start: 0.4124 (OUTLIER) cc_final: 0.3665 (p90) REVERT: A 736 MET cc_start: 0.6229 (ppp) cc_final: 0.4814 (tpp) REVERT: A 757 LYS cc_start: 0.8870 (pttt) cc_final: 0.8339 (ptpp) REVERT: A 806 MET cc_start: 0.5871 (mtm) cc_final: 0.5378 (mtp) REVERT: A 916 CYS cc_start: 0.7660 (m) cc_final: 0.7130 (p) REVERT: A 977 SER cc_start: 0.8550 (m) cc_final: 0.8350 (m) REVERT: B 565 LYS cc_start: 0.8770 (ttpt) cc_final: 0.8082 (tttp) REVERT: B 573 LEU cc_start: 0.8157 (tt) cc_final: 0.7945 (mp) REVERT: B 579 GLU cc_start: 0.7483 (mt-10) cc_final: 0.7176 (mt-10) REVERT: B 588 THR cc_start: 0.4227 (OUTLIER) cc_final: 0.3712 (p) REVERT: B 685 MET cc_start: 0.4266 (ttp) cc_final: 0.2836 (mmt) REVERT: B 766 PRO cc_start: 0.3465 (OUTLIER) cc_final: 0.3265 (Cg_endo) REVERT: B 779 TRP cc_start: 0.7078 (t60) cc_final: 0.6613 (t60) REVERT: B 788 MET cc_start: 0.3232 (ptt) cc_final: 0.2465 (ptm) REVERT: B 848 LYS cc_start: 0.7653 (mmmt) cc_final: 0.7306 (pttp) REVERT: B 872 LEU cc_start: 0.8269 (mt) cc_final: 0.7872 (mt) REVERT: B 896 GLU cc_start: 0.5951 (tt0) cc_final: 0.5320 (mt-10) REVERT: B 1044 LEU cc_start: 0.5362 (OUTLIER) cc_final: 0.4875 (mt) REVERT: B 1095 ARG cc_start: 0.6922 (ppt170) cc_final: 0.6639 (ptt90) REVERT: C 569 GLU cc_start: 0.7760 (mp0) cc_final: 0.7421 (mp0) REVERT: C 610 LYS cc_start: 0.9045 (tttt) cc_final: 0.8831 (mptt) REVERT: C 762 LEU cc_start: 0.7992 (mp) cc_final: 0.7529 (mp) REVERT: C 800 PHE cc_start: 0.5393 (m-80) cc_final: 0.4967 (m-80) REVERT: C 870 PHE cc_start: 0.5680 (OUTLIER) cc_final: 0.5389 (p90) REVERT: C 953 MET cc_start: 0.4990 (ptp) cc_final: 0.4738 (ptp) REVERT: C 982 ASN cc_start: 0.7720 (t0) cc_final: 0.7014 (m-40) REVERT: C 1012 LYS cc_start: 0.7761 (tttt) cc_final: 0.7541 (mmtm) REVERT: C 1044 LEU cc_start: 0.6035 (OUTLIER) cc_final: 0.5797 (mt) outliers start: 78 outliers final: 47 residues processed: 369 average time/residue: 0.1191 time to fit residues: 64.0335 Evaluate side-chains 320 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 266 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 730 ASN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 765 ASN Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 923 PHE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 946 ILE Chi-restraints excluded: chain A residue 950 PHE Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain B residue 501 ASN Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 614 ASN Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 766 PRO Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 950 PHE Chi-restraints excluded: chain B residue 953 MET Chi-restraints excluded: chain B residue 973 GLN Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain B residue 1044 LEU Chi-restraints excluded: chain B residue 1047 HIS Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 669 ASN Chi-restraints excluded: chain C residue 694 VAL Chi-restraints excluded: chain C residue 718 LEU Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 838 ILE Chi-restraints excluded: chain C residue 846 THR Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 910 ILE Chi-restraints excluded: chain C residue 916 CYS Chi-restraints excluded: chain C residue 928 VAL Chi-restraints excluded: chain C residue 947 LEU Chi-restraints excluded: chain C residue 950 PHE Chi-restraints excluded: chain C residue 971 THR Chi-restraints excluded: chain C residue 979 VAL Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain C residue 1044 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 156 optimal weight: 7.9990 chunk 138 optimal weight: 9.9990 chunk 126 optimal weight: 0.9980 chunk 111 optimal weight: 5.9990 chunk 125 optimal weight: 6.9990 chunk 147 optimal weight: 4.9990 chunk 166 optimal weight: 0.0050 chunk 44 optimal weight: 4.9990 chunk 58 optimal weight: 0.9990 chunk 121 optimal weight: 7.9990 chunk 14 optimal weight: 6.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 672 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 ASN A 893 GLN A 943 ASN ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 930 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 973 GLN C 765 ASN C1047 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.185474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.152557 restraints weight = 21182.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.154948 restraints weight = 16076.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.155407 restraints weight = 14312.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.156703 restraints weight = 10029.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.157539 restraints weight = 8654.324| |-----------------------------------------------------------------------------| r_work (final): 0.4250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6019 moved from start: 0.5188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 14007 Z= 0.190 Angle : 0.866 10.015 18891 Z= 0.449 Chirality : 0.051 0.229 2058 Planarity : 0.006 0.071 2412 Dihedral : 8.630 58.951 1848 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.29 % Allowed : 8.33 % Favored : 91.38 % Rotamer: Outliers : 5.15 % Allowed : 16.28 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % 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 are not related in a simple way. whole: -2.38 (0.18), residues: 1716 helix: -1.40 (0.27), residues: 267 sheet: -0.51 (0.18), residues: 645 loop : -2.58 (0.20), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 970 TYR 0.024 0.002 TYR C 967 PHE 0.024 0.003 PHE A 617 TRP 0.031 0.003 TRP C 779 HIS 0.015 0.002 HIS B1047 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.19 (14007) covalent geometry : angle 0.86609 / 0.45 (18891) hydrogen bonds : bond 0.04735 / 2.98 ( 307) hydrogen bonds : angle 6.38688 / 4.33 ( 867) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 291 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 603 LYS cc_start: 0.8660 (tttt) cc_final: 0.7897 (ttmm) REVERT: A 607 LYS cc_start: 0.8673 (mptt) cc_final: 0.8344 (mmtm) REVERT: A 610 LYS cc_start: 0.8786 (tttt) cc_final: 0.8491 (mttm) REVERT: A 684 MET cc_start: 0.6828 (mmp) cc_final: 0.6409 (mmt) REVERT: A 733 PHE cc_start: 0.4042 (OUTLIER) cc_final: 0.3713 (p90) REVERT: A 736 MET cc_start: 0.5877 (ppp) cc_final: 0.5195 (ptm) REVERT: A 757 LYS cc_start: 0.8875 (pttt) cc_final: 0.8472 (ptpp) REVERT: A 806 MET cc_start: 0.6177 (mtm) cc_final: 0.5575 (mtp) REVERT: A 916 CYS cc_start: 0.7389 (m) cc_final: 0.7037 (p) REVERT: A 991 TYR cc_start: 0.6172 (t80) cc_final: 0.5798 (t80) REVERT: A 1086 TYR cc_start: 0.5865 (OUTLIER) cc_final: 0.5038 (p90) REVERT: B 565 LYS cc_start: 0.8819 (ttpt) cc_final: 0.7921 (tttt) REVERT: B 568 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8142 (mp0) REVERT: B 573 LEU cc_start: 0.8297 (tt) cc_final: 0.7916 (mp) REVERT: B 579 GLU cc_start: 0.7458 (mt-10) cc_final: 0.7211 (mt-10) REVERT: B 685 MET cc_start: 0.4036 (ttp) cc_final: 0.2581 (mmt) REVERT: B 726 LYS cc_start: 0.7597 (mtpt) cc_final: 0.7278 (pttm) REVERT: B 779 TRP cc_start: 0.7206 (t60) cc_final: 0.6706 (t60) REVERT: B 788 MET cc_start: 0.2846 (ptt) cc_final: 0.2226 (ptm) REVERT: B 848 LYS cc_start: 0.7468 (mmmt) cc_final: 0.7241 (pttm) REVERT: B 896 GLU cc_start: 0.5879 (tt0) cc_final: 0.5105 (mt-10) REVERT: B 990 ILE cc_start: 0.8678 (mt) cc_final: 0.8450 (mt) REVERT: B 1012 LYS cc_start: 0.7660 (tttt) cc_final: 0.6881 (ttmt) REVERT: B 1044 LEU cc_start: 0.5315 (OUTLIER) cc_final: 0.4899 (mt) REVERT: C 554 TRP cc_start: 0.4726 (OUTLIER) cc_final: 0.4384 (p-90) REVERT: C 558 GLU cc_start: 0.7683 (mp0) cc_final: 0.7377 (mt-10) REVERT: C 569 GLU cc_start: 0.7986 (mp0) cc_final: 0.7622 (mp0) REVERT: C 610 LYS cc_start: 0.9047 (tttt) cc_final: 0.8724 (mptt) REVERT: C 754 ARG cc_start: 0.7423 (OUTLIER) cc_final: 0.7146 (tmm-80) REVERT: C 762 LEU cc_start: 0.7867 (mp) cc_final: 0.7437 (mp) REVERT: C 779 TRP cc_start: 0.7308 (t60) cc_final: 0.6391 (t60) REVERT: C 800 PHE cc_start: 0.5236 (m-80) cc_final: 0.4978 (m-80) REVERT: C 848 LYS cc_start: 0.8408 (mttt) cc_final: 0.8110 (mttt) REVERT: C 868 MET cc_start: 0.6375 (mmt) cc_final: 0.6161 (mmt) REVERT: C 870 PHE cc_start: 0.5918 (OUTLIER) cc_final: 0.5458 (p90) REVERT: C 982 ASN cc_start: 0.7857 (t0) cc_final: 0.7222 (m-40) REVERT: C 1044 LEU cc_start: 0.6017 (OUTLIER) cc_final: 0.5379 (mp) outliers start: 80 outliers final: 51 residues processed: 344 average time/residue: 0.1186 time to fit residues: 59.4349 Evaluate side-chains 321 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 262 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 726 LYS Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 788 MET Chi-restraints excluded: chain A residue 864 SER Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 923 PHE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain A residue 950 PHE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 999 THR Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1086 TYR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 663 SER Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 733 PHE Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 757 LYS Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 871 SER Chi-restraints excluded: chain B residue 888 ILE Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 950 PHE Chi-restraints excluded: chain B residue 953 MET Chi-restraints excluded: chain B residue 979 VAL Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain B residue 1044 LEU Chi-restraints excluded: chain C residue 554 TRP Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 694 VAL Chi-restraints excluded: chain C residue 754 ARG Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 870 PHE Chi-restraints excluded: chain C residue 912 ILE Chi-restraints excluded: chain C residue 915 LEU Chi-restraints excluded: chain C residue 916 CYS Chi-restraints excluded: chain C residue 947 LEU Chi-restraints excluded: chain C residue 950 PHE Chi-restraints excluded: chain C residue 971 THR Chi-restraints excluded: chain C residue 979 VAL Chi-restraints excluded: chain C residue 1028 LEU Chi-restraints excluded: chain C residue 1044 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 40 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 164 optimal weight: 0.2980 chunk 142 optimal weight: 3.9990 chunk 37 optimal weight: 0.4980 chunk 27 optimal weight: 1.9990 chunk 99 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 chunk 134 optimal weight: 9.9990 chunk 136 optimal weight: 9.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 672 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 693 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 847 GLN A 943 ASN B 501 ASN ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 930 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.185548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.152596 restraints weight = 20957.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.154000 restraints weight = 16174.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.154890 restraints weight = 14534.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4237 r_free = 0.4237 target = 0.156470 restraints weight = 10311.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.156986 restraints weight = 8932.720| |-----------------------------------------------------------------------------| r_work (final): 0.4241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6034 moved from start: 0.5759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14007 Z= 0.175 Angle : 0.816 9.534 18891 Z= 0.419 Chirality : 0.049 0.171 2058 Planarity : 0.005 0.051 2412 Dihedral : 7.961 56.580 1844 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.23 % Allowed : 8.51 % Favored : 91.26 % Rotamer: Outliers : 5.60 % Allowed : 17.12 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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 are not related in a simple way. whole: -2.57 (0.18), residues: 1716 helix: -1.20 (0.28), residues: 264 sheet: -0.92 (0.18), residues: 675 loop : -2.60 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 791 TYR 0.017 0.002 TYR B 967 PHE 0.026 0.003 PHE A 617 TRP 0.027 0.003 TRP A 779 HIS 0.005 0.001 HIS C 690 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (14007) covalent geometry : angle 0.81573 / 0.42 (18891) hydrogen bonds : bond 0.04235 / 2.66 ( 307) hydrogen bonds : angle 6.31914 / 4.25 ( 867) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 359 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 272 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 603 LYS cc_start: 0.8776 (tttt) cc_final: 0.8101 (ttmm) REVERT: A 607 LYS cc_start: 0.8642 (mptt) cc_final: 0.8286 (mmtm) REVERT: A 610 LYS cc_start: 0.8804 (tttt) cc_final: 0.8449 (mttm) REVERT: A 733 PHE cc_start: 0.3956 (OUTLIER) cc_final: 0.3683 (p90) REVERT: A 736 MET cc_start: 0.5701 (ppp) cc_final: 0.5289 (ptm) REVERT: A 757 LYS cc_start: 0.8939 (pttt) cc_final: 0.8383 (ptpp) REVERT: A 806 MET cc_start: 0.6222 (mtm) cc_final: 0.5555 (mtp) REVERT: A 916 CYS cc_start: 0.7477 (m) cc_final: 0.7187 (p) REVERT: A 1086 TYR cc_start: 0.6034 (OUTLIER) cc_final: 0.4213 (p90) REVERT: B 565 LYS cc_start: 0.8609 (ttpt) cc_final: 0.7976 (tttp) REVERT: B 568 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.8137 (mp0) REVERT: B 573 LEU cc_start: 0.8338 (tt) cc_final: 0.7838 (mp) REVERT: B 685 MET cc_start: 0.3981 (ttp) cc_final: 0.2520 (mmt) REVERT: B 779 TRP cc_start: 0.7348 (t60) cc_final: 0.6801 (t60) REVERT: B 848 LYS cc_start: 0.7266 (mmmt) cc_final: 0.6982 (pttm) REVERT: B 868 MET cc_start: 0.5892 (ptp) cc_final: 0.4387 (ttm) REVERT: B 896 GLU cc_start: 0.5920 (tt0) cc_final: 0.5143 (mt-10) REVERT: B 915 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.6529 (tt) REVERT: B 990 ILE cc_start: 0.8635 (mt) cc_final: 0.8346 (mt) REVERT: B 1012 LYS cc_start: 0.7898 (tttt) cc_final: 0.7275 (ttmt) REVERT: B 1044 LEU cc_start: 0.5444 (OUTLIER) cc_final: 0.4919 (mt) REVERT: B 1095 ARG cc_start: 0.7170 (ptt180) cc_final: 0.6806 (ptt180) REVERT: C 569 GLU cc_start: 0.8109 (mp0) cc_final: 0.7796 (mp0) REVERT: C 610 LYS cc_start: 0.9061 (tttt) cc_final: 0.8714 (mptt) REVERT: C 619 MET cc_start: 0.7751 (ttm) cc_final: 0.7341 (ttm) REVERT: C 669 ASN cc_start: 0.2960 (OUTLIER) cc_final: 0.2629 (m-40) REVERT: C 754 ARG cc_start: 0.7317 (OUTLIER) cc_final: 0.7110 (tmm-80) REVERT: C 762 LEU cc_start: 0.7782 (mp) cc_final: 0.7402 (mp) REVERT: C 779 TRP cc_start: 0.7254 (t60) cc_final: 0.6422 (t60) REVERT: C 847 GLN cc_start: 0.6404 (pp30) cc_final: 0.5972 (pp30) REVERT: C 872 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8012 (mt) REVERT: C 956 LYS cc_start: 0.6887 (mtpt) cc_final: 0.6379 (tppt) REVERT: C 982 ASN cc_start: 0.7629 (t0) cc_final: 0.7068 (m-40) outliers start: 87 outliers final: 52 residues processed: 333 average time/residue: 0.1087 time to fit residues: 53.6391 Evaluate side-chains 313 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 253 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 498 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 788 MET Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 847 GLN Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 864 SER Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 950 PHE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1086 TYR Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 734 HIS Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 769 ASN Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 871 SER Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 916 CYS Chi-restraints excluded: chain B residue 923 PHE Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 950 PHE Chi-restraints excluded: chain B residue 979 VAL Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain B residue 1044 LEU Chi-restraints excluded: chain B residue 1047 HIS Chi-restraints excluded: chain C residue 554 TRP Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 669 ASN Chi-restraints excluded: chain C residue 694 VAL Chi-restraints excluded: chain C residue 754 ARG Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 858 LEU Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 912 ILE Chi-restraints excluded: chain C residue 916 CYS Chi-restraints excluded: chain C residue 950 PHE Chi-restraints excluded: chain C residue 971 THR Chi-restraints excluded: chain C residue 979 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 147 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 chunk 70 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 111 optimal weight: 6.9990 chunk 163 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 747 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 ASN ** A1056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 488 ASN ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 563 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 575 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 943 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.181299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.149974 restraints weight = 21148.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.150194 restraints weight = 18852.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.151520 restraints weight = 17658.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.152344 restraints weight = 11708.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.153023 restraints weight = 10683.413| |-----------------------------------------------------------------------------| r_work (final): 0.4192 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6205 moved from start: 0.6363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 14007 Z= 0.241 Angle : 0.908 10.288 18891 Z= 0.466 Chirality : 0.052 0.188 2058 Planarity : 0.006 0.053 2412 Dihedral : 8.265 58.966 1842 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 14.31 Ramachandran Plot: Outliers : 0.29 % Allowed : 10.84 % Favored : 88.87 % Rotamer: Outliers : 6.63 % Allowed : 18.08 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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 are not related in a simple way. whole: -3.00 (0.18), residues: 1716 helix: -1.38 (0.28), residues: 264 sheet: -1.45 (0.18), residues: 714 loop : -2.70 (0.21), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 637 TYR 0.028 0.003 TYR C 967 PHE 0.029 0.004 PHE A 686 TRP 0.029 0.004 TRP A 636 HIS 0.009 0.002 HIS C 690 Details of bonding type rmsd/Z covalent geometry : bond 0.00540 / 0.24 (14007) covalent geometry : angle 0.90835 / 0.47 (18891) hydrogen bonds : bond 0.04887 / 3.12 ( 307) hydrogen bonds : angle 6.66769 / 4.50 ( 867) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 270 time to evaluate : 0.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 LEU cc_start: 0.8262 (OUTLIER) cc_final: 0.8045 (tt) REVERT: A 603 LYS cc_start: 0.8751 (tttt) cc_final: 0.8139 (ttmm) REVERT: A 607 LYS cc_start: 0.8691 (mptt) cc_final: 0.8333 (mmtm) REVERT: A 626 TYR cc_start: 0.6132 (OUTLIER) cc_final: 0.5411 (t80) REVERT: A 733 PHE cc_start: 0.3776 (OUTLIER) cc_final: 0.3479 (p90) REVERT: A 736 MET cc_start: 0.5740 (ppp) cc_final: 0.4451 (mpp) REVERT: A 738 LEU cc_start: 0.7338 (mt) cc_final: 0.6756 (mt) REVERT: A 754 ARG cc_start: 0.8655 (ptm160) cc_final: 0.8391 (mtp-110) REVERT: A 806 MET cc_start: 0.6005 (mtm) cc_final: 0.5248 (tpt) REVERT: A 1086 TYR cc_start: 0.5913 (OUTLIER) cc_final: 0.3800 (p90) REVERT: B 568 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: B 573 LEU cc_start: 0.8490 (tt) cc_final: 0.7915 (mp) REVERT: B 685 MET cc_start: 0.4376 (ttp) cc_final: 0.2854 (mmt) REVERT: B 779 TRP cc_start: 0.7442 (t60) cc_final: 0.6865 (t60) REVERT: B 791 ARG cc_start: 0.5022 (OUTLIER) cc_final: 0.4785 (mpt180) REVERT: B 848 LYS cc_start: 0.7361 (mmmt) cc_final: 0.7161 (pttp) REVERT: B 868 MET cc_start: 0.6319 (ptp) cc_final: 0.4674 (ttm) REVERT: B 896 GLU cc_start: 0.6003 (tt0) cc_final: 0.5429 (mt-10) REVERT: B 915 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.6866 (tt) REVERT: B 990 ILE cc_start: 0.8534 (mt) cc_final: 0.8328 (mt) REVERT: B 1044 LEU cc_start: 0.6149 (OUTLIER) cc_final: 0.5629 (mt) REVERT: B 1095 ARG cc_start: 0.7007 (ptt180) cc_final: 0.6726 (ptt180) REVERT: C 610 LYS cc_start: 0.9096 (tttt) cc_final: 0.8780 (mptt) REVERT: C 619 MET cc_start: 0.7717 (ttm) cc_final: 0.7332 (ttm) REVERT: C 626 TYR cc_start: 0.5460 (OUTLIER) cc_final: 0.5115 (t80) REVERT: C 690 HIS cc_start: 0.4616 (OUTLIER) cc_final: 0.2473 (m170) REVERT: C 762 LEU cc_start: 0.7815 (mp) cc_final: 0.7443 (mp) REVERT: C 768 LEU cc_start: 0.6643 (OUTLIER) cc_final: 0.6319 (mp) REVERT: C 779 TRP cc_start: 0.7221 (t60) cc_final: 0.6534 (t60) REVERT: C 847 GLN cc_start: 0.6525 (OUTLIER) cc_final: 0.6077 (pp30) REVERT: C 848 LYS cc_start: 0.8144 (mttt) cc_final: 0.7915 (mttt) REVERT: C 943 ASN cc_start: 0.7267 (t0) cc_final: 0.6915 (t0) REVERT: C 956 LYS cc_start: 0.6911 (mtpt) cc_final: 0.6521 (tppt) REVERT: C 982 ASN cc_start: 0.7560 (t0) cc_final: 0.6872 (m-40) outliers start: 103 outliers final: 67 residues processed: 344 average time/residue: 0.1120 time to fit residues: 57.2435 Evaluate side-chains 337 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 258 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 788 MET Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 859 THR Chi-restraints excluded: chain A residue 864 SER Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 910 ILE Chi-restraints excluded: chain A residue 912 ILE Chi-restraints excluded: chain A residue 923 PHE Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain A residue 950 PHE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1086 TYR Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 487 ILE Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 637 ARG Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 757 LYS Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 769 ASN Chi-restraints excluded: chain B residue 781 ASN Chi-restraints excluded: chain B residue 791 ARG Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 801 MET Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 871 SER Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 916 CYS Chi-restraints excluded: chain B residue 923 PHE Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 979 VAL Chi-restraints excluded: chain B residue 992 ILE Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain B residue 1044 LEU Chi-restraints excluded: chain B residue 1047 HIS Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 554 TRP Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 626 TYR Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 669 ASN Chi-restraints excluded: chain C residue 685 MET Chi-restraints excluded: chain C residue 690 HIS Chi-restraints excluded: chain C residue 694 VAL Chi-restraints excluded: chain C residue 709 ASN Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 773 SER Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 847 GLN Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 912 ILE Chi-restraints excluded: chain C residue 950 PHE Chi-restraints excluded: chain C residue 971 THR Chi-restraints excluded: chain C residue 979 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 145 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 33 optimal weight: 0.9990 chunk 71 optimal weight: 0.0970 chunk 77 optimal weight: 9.9990 chunk 152 optimal weight: 0.7980 chunk 42 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 10.0000 chunk 37 optimal weight: 7.9990 chunk 148 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 873 ASN ** A1056 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN C 612 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.187733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.156194 restraints weight = 20376.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.156858 restraints weight = 14690.744| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4258 r_free = 0.4258 target = 0.158135 restraints weight = 12961.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.158910 restraints weight = 9996.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.159578 restraints weight = 9247.690| |-----------------------------------------------------------------------------| r_work (final): 0.4280 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 moved from start: 0.6504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14007 Z= 0.130 Angle : 0.750 9.473 18891 Z= 0.378 Chirality : 0.048 0.173 2058 Planarity : 0.005 0.044 2412 Dihedral : 7.204 56.854 1840 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.04 % Favored : 91.84 % Rotamer: Outliers : 4.63 % Allowed : 20.08 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % 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 are not related in a simple way. whole: -2.69 (0.19), residues: 1716 helix: -0.86 (0.30), residues: 264 sheet: -1.19 (0.18), residues: 690 loop : -2.66 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 911 TYR 0.020 0.002 TYR B 666 PHE 0.019 0.002 PHE B 596 TRP 0.023 0.002 TRP C 779 HIS 0.003 0.001 HIS C 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (14007) covalent geometry : angle 0.75003 / 0.38 (18891) hydrogen bonds : bond 0.03565 / 2.22 ( 307) hydrogen bonds : angle 6.23614 / 4.18 ( 867) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 272 time to evaluate : 0.522 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 603 LYS cc_start: 0.8691 (tttt) cc_final: 0.8132 (ttmm) REVERT: A 607 LYS cc_start: 0.8604 (mptt) cc_final: 0.8270 (mmtm) REVERT: A 626 TYR cc_start: 0.5697 (OUTLIER) cc_final: 0.5141 (t80) REVERT: A 684 MET cc_start: 0.6926 (mmp) cc_final: 0.6526 (mmt) REVERT: A 733 PHE cc_start: 0.3787 (OUTLIER) cc_final: 0.3495 (p90) REVERT: A 738 LEU cc_start: 0.7148 (mt) cc_final: 0.6701 (mt) REVERT: A 757 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8756 (mttp) REVERT: A 806 MET cc_start: 0.5836 (mtm) cc_final: 0.5255 (mtp) REVERT: A 1086 TYR cc_start: 0.5764 (OUTLIER) cc_final: 0.4052 (p90) REVERT: B 565 LYS cc_start: 0.8417 (ttpt) cc_final: 0.7775 (tttp) REVERT: B 568 GLU cc_start: 0.8442 (OUTLIER) cc_final: 0.8056 (mp0) REVERT: B 573 LEU cc_start: 0.8407 (tt) cc_final: 0.7859 (mp) REVERT: B 609 LEU cc_start: 0.8493 (tp) cc_final: 0.8283 (tt) REVERT: B 684 MET cc_start: 0.5720 (mmt) cc_final: 0.5266 (mmt) REVERT: B 685 MET cc_start: 0.4152 (ttp) cc_final: 0.2679 (mmt) REVERT: B 779 TRP cc_start: 0.7344 (t60) cc_final: 0.6777 (t60) REVERT: B 848 LYS cc_start: 0.7226 (mmmt) cc_final: 0.7022 (pttm) REVERT: B 868 MET cc_start: 0.6186 (ptp) cc_final: 0.4866 (ttm) REVERT: B 896 GLU cc_start: 0.5876 (tt0) cc_final: 0.5199 (mt-10) REVERT: B 915 LEU cc_start: 0.7558 (OUTLIER) cc_final: 0.7031 (tt) REVERT: B 990 ILE cc_start: 0.8488 (mt) cc_final: 0.8231 (mt) REVERT: B 1044 LEU cc_start: 0.5832 (OUTLIER) cc_final: 0.5400 (mt) REVERT: B 1095 ARG cc_start: 0.7039 (ptt180) cc_final: 0.6797 (ptt180) REVERT: C 569 GLU cc_start: 0.7991 (mp0) cc_final: 0.7591 (mp0) REVERT: C 610 LYS cc_start: 0.9053 (tttt) cc_final: 0.8721 (mptt) REVERT: C 619 MET cc_start: 0.7646 (ttm) cc_final: 0.7287 (ttm) REVERT: C 622 TYR cc_start: 0.7385 (OUTLIER) cc_final: 0.6397 (t80) REVERT: C 762 LEU cc_start: 0.8062 (mp) cc_final: 0.7668 (mp) REVERT: C 779 TRP cc_start: 0.7084 (t60) cc_final: 0.6410 (t60) REVERT: C 848 LYS cc_start: 0.7931 (mttt) cc_final: 0.7717 (mttt) REVERT: C 857 LEU cc_start: 0.8049 (tp) cc_final: 0.7816 (pt) REVERT: C 894 MET cc_start: 0.6163 (mmm) cc_final: 0.5113 (mmt) REVERT: C 956 LYS cc_start: 0.6796 (mtpt) cc_final: 0.6403 (tppt) REVERT: C 982 ASN cc_start: 0.7528 (t0) cc_final: 0.6993 (m-40) outliers start: 72 outliers final: 46 residues processed: 318 average time/residue: 0.1122 time to fit residues: 53.0460 Evaluate side-chains 313 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 259 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 757 LYS Chi-restraints excluded: chain A residue 785 LYS Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 872 LEU Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 927 VAL Chi-restraints excluded: chain A residue 950 PHE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1086 TYR Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 567 VAL Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 582 SER Chi-restraints excluded: chain B residue 616 ILE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 757 LYS Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 801 MET Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain B residue 1044 LEU Chi-restraints excluded: chain B residue 1047 HIS Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 554 TRP Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 622 TYR Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 669 ASN Chi-restraints excluded: chain C residue 694 VAL Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 912 ILE Chi-restraints excluded: chain C residue 946 ILE Chi-restraints excluded: chain C residue 950 PHE Chi-restraints excluded: chain C residue 971 THR Chi-restraints excluded: chain C residue 979 VAL Chi-restraints excluded: chain C residue 1047 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 17 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 67 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 127 optimal weight: 7.9990 chunk 29 optimal weight: 0.9990 chunk 6 optimal weight: 10.0000 chunk 121 optimal weight: 0.9980 chunk 69 optimal weight: 0.0010 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 693 HIS A1056 ASN ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 690 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4596 r_free = 0.4596 target = 0.190416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.159108 restraints weight = 20127.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4289 r_free = 0.4289 target = 0.160532 restraints weight = 14646.923| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.161615 restraints weight = 12173.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.163962 restraints weight = 9504.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.164182 restraints weight = 7931.739| |-----------------------------------------------------------------------------| r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5943 moved from start: 0.6706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14007 Z= 0.120 Angle : 0.718 9.290 18891 Z= 0.361 Chirality : 0.047 0.198 2058 Planarity : 0.004 0.045 2412 Dihedral : 6.681 56.116 1840 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.22 % Favored : 91.67 % Rotamer: Outliers : 3.93 % Allowed : 21.36 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 are not related in a simple way. whole: -2.52 (0.19), residues: 1716 helix: -0.59 (0.31), residues: 264 sheet: -1.07 (0.19), residues: 687 loop : -2.61 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 791 TYR 0.019 0.001 TYR B 967 PHE 0.023 0.002 PHE B 617 TRP 0.018 0.002 TRP C 779 HIS 0.003 0.001 HIS C 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (14007) covalent geometry : angle 0.71756 / 0.36 (18891) hydrogen bonds : bond 0.03380 / 2.10 ( 307) hydrogen bonds : angle 6.01790 / 4.04 ( 867) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 266 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 603 LYS cc_start: 0.8654 (tttt) cc_final: 0.8122 (ttmm) REVERT: A 607 LYS cc_start: 0.8588 (mptt) cc_final: 0.8238 (mmtm) REVERT: A 626 TYR cc_start: 0.5668 (OUTLIER) cc_final: 0.5234 (t80) REVERT: A 684 MET cc_start: 0.7012 (mmp) cc_final: 0.6619 (mmt) REVERT: A 719 LYS cc_start: 0.8769 (tttt) cc_final: 0.8330 (tttm) REVERT: A 733 PHE cc_start: 0.3674 (OUTLIER) cc_final: 0.3402 (p90) REVERT: A 738 LEU cc_start: 0.7055 (mt) cc_final: 0.6648 (mt) REVERT: A 806 MET cc_start: 0.5524 (mtm) cc_final: 0.5052 (mtp) REVERT: A 812 ASP cc_start: 0.7249 (m-30) cc_final: 0.7036 (t0) REVERT: A 923 PHE cc_start: 0.5939 (p90) cc_final: 0.5583 (p90) REVERT: A 950 PHE cc_start: 0.7822 (OUTLIER) cc_final: 0.7017 (m-80) REVERT: A 980 LEU cc_start: 0.8128 (mt) cc_final: 0.7898 (pt) REVERT: A 1052 LYS cc_start: 0.8324 (mmmt) cc_final: 0.8121 (mtmm) REVERT: A 1086 TYR cc_start: 0.5605 (OUTLIER) cc_final: 0.4282 (p90) REVERT: B 565 LYS cc_start: 0.8433 (ttpt) cc_final: 0.7733 (tttp) REVERT: B 568 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8090 (mp0) REVERT: B 573 LEU cc_start: 0.8366 (tt) cc_final: 0.7793 (mp) REVERT: B 625 ARG cc_start: 0.7120 (ttt-90) cc_final: 0.6559 (mtp-110) REVERT: B 685 MET cc_start: 0.4052 (ttp) cc_final: 0.2476 (mmt) REVERT: B 719 LYS cc_start: 0.8865 (tttt) cc_final: 0.8041 (ttmm) REVERT: B 779 TRP cc_start: 0.7228 (t60) cc_final: 0.6761 (t60) REVERT: B 817 TYR cc_start: 0.4282 (t80) cc_final: 0.3984 (t80) REVERT: B 848 LYS cc_start: 0.7170 (mmmt) cc_final: 0.6898 (pttm) REVERT: B 868 MET cc_start: 0.5953 (ptp) cc_final: 0.4585 (ttm) REVERT: B 896 GLU cc_start: 0.5942 (tt0) cc_final: 0.5259 (mt-10) REVERT: B 915 LEU cc_start: 0.7382 (OUTLIER) cc_final: 0.6880 (tt) REVERT: B 990 ILE cc_start: 0.8410 (mt) cc_final: 0.8202 (mt) REVERT: B 1095 ARG cc_start: 0.7113 (ptt180) cc_final: 0.6843 (ptt180) REVERT: C 569 GLU cc_start: 0.7978 (mp0) cc_final: 0.7559 (mp0) REVERT: C 610 LYS cc_start: 0.9020 (tttt) cc_final: 0.8752 (mptt) REVERT: C 622 TYR cc_start: 0.7369 (OUTLIER) cc_final: 0.6230 (t80) REVERT: C 762 LEU cc_start: 0.8016 (mp) cc_final: 0.7649 (mp) REVERT: C 779 TRP cc_start: 0.7050 (t60) cc_final: 0.6445 (t60) outliers start: 61 outliers final: 45 residues processed: 304 average time/residue: 0.1127 time to fit residues: 50.6026 Evaluate side-chains 314 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 262 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 671 ILE Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 933 SER Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain A residue 950 PHE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1086 TYR Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 757 LYS Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 857 LEU Chi-restraints excluded: chain B residue 910 ILE Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 916 CYS Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 979 VAL Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain B residue 1047 HIS Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 554 TRP Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 622 TYR Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 626 TYR Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 669 ASN Chi-restraints excluded: chain C residue 694 VAL Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain C residue 846 THR Chi-restraints excluded: chain C residue 912 ILE Chi-restraints excluded: chain C residue 950 PHE Chi-restraints excluded: chain C residue 971 THR Chi-restraints excluded: chain C residue 979 VAL Chi-restraints excluded: chain C residue 1047 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 163 optimal weight: 10.0000 chunk 155 optimal weight: 0.0970 chunk 50 optimal weight: 30.0000 chunk 113 optimal weight: 0.0270 chunk 140 optimal weight: 0.0170 overall best weight: 0.8278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 873 ASN ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4612 r_free = 0.4612 target = 0.191900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.160061 restraints weight = 20187.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.162612 restraints weight = 14440.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.163150 restraints weight = 12915.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.164147 restraints weight = 9049.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.165613 restraints weight = 8043.832| |-----------------------------------------------------------------------------| r_work (final): 0.4342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5918 moved from start: 0.6893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14007 Z= 0.120 Angle : 0.723 11.374 18891 Z= 0.359 Chirality : 0.046 0.191 2058 Planarity : 0.004 0.044 2412 Dihedral : 6.423 58.575 1840 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.99 % Favored : 92.89 % Rotamer: Outliers : 4.12 % Allowed : 21.94 % Favored : 73.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 are not related in a simple way. whole: -2.44 (0.19), residues: 1716 helix: -0.39 (0.31), residues: 264 sheet: -1.02 (0.19), residues: 687 loop : -2.62 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 791 TYR 0.019 0.001 TYR B 666 PHE 0.018 0.002 PHE B 596 TRP 0.017 0.002 TRP B 779 HIS 0.003 0.001 HIS C 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.12 (14007) covalent geometry : angle 0.72346 / 0.36 (18891) hydrogen bonds : bond 0.03257 / 2.03 ( 307) hydrogen bonds : angle 5.93297 / 3.99 ( 867) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 274 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 603 LYS cc_start: 0.8720 (tttt) cc_final: 0.8253 (ttmt) REVERT: A 607 LYS cc_start: 0.8624 (mptt) cc_final: 0.8294 (mmtm) REVERT: A 619 MET cc_start: 0.7533 (OUTLIER) cc_final: 0.7165 (tpp) REVERT: A 626 TYR cc_start: 0.5559 (OUTLIER) cc_final: 0.5149 (t80) REVERT: A 684 MET cc_start: 0.6982 (mmp) cc_final: 0.5765 (mmt) REVERT: A 719 LYS cc_start: 0.8739 (tttt) cc_final: 0.8310 (tttp) REVERT: A 733 PHE cc_start: 0.3719 (OUTLIER) cc_final: 0.3445 (p90) REVERT: A 738 LEU cc_start: 0.7108 (mt) cc_final: 0.6639 (mt) REVERT: A 812 ASP cc_start: 0.7424 (m-30) cc_final: 0.7144 (t0) REVERT: A 980 LEU cc_start: 0.8173 (mt) cc_final: 0.7953 (pt) REVERT: A 1086 TYR cc_start: 0.5686 (OUTLIER) cc_final: 0.4505 (p90) REVERT: B 565 LYS cc_start: 0.8411 (ttpt) cc_final: 0.7729 (tttp) REVERT: B 568 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8106 (mp0) REVERT: B 573 LEU cc_start: 0.8391 (tt) cc_final: 0.7896 (mp) REVERT: B 625 ARG cc_start: 0.7059 (ttt-90) cc_final: 0.6475 (mtp-110) REVERT: B 685 MET cc_start: 0.3887 (ttp) cc_final: 0.2418 (mmt) REVERT: B 719 LYS cc_start: 0.8841 (tttt) cc_final: 0.7978 (ttmm) REVERT: B 726 LYS cc_start: 0.7493 (mmtt) cc_final: 0.6889 (mmmt) REVERT: B 736 MET cc_start: 0.1827 (ttp) cc_final: 0.0133 (ttp) REVERT: B 779 TRP cc_start: 0.7244 (t60) cc_final: 0.6775 (t60) REVERT: B 817 TYR cc_start: 0.4326 (t80) cc_final: 0.4004 (t80) REVERT: B 848 LYS cc_start: 0.7092 (mmmt) cc_final: 0.6763 (pttm) REVERT: B 868 MET cc_start: 0.5960 (ptp) cc_final: 0.4623 (ttm) REVERT: B 896 GLU cc_start: 0.5901 (tt0) cc_final: 0.5186 (mt-10) REVERT: B 915 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.6844 (tt) REVERT: B 1095 ARG cc_start: 0.7136 (ptt180) cc_final: 0.6819 (ptt180) REVERT: C 569 GLU cc_start: 0.7984 (mp0) cc_final: 0.7554 (mp0) REVERT: C 610 LYS cc_start: 0.9060 (tttt) cc_final: 0.8727 (mptt) REVERT: C 622 TYR cc_start: 0.7336 (OUTLIER) cc_final: 0.6162 (t80) REVERT: C 762 LEU cc_start: 0.7973 (mp) cc_final: 0.7605 (mp) REVERT: C 894 MET cc_start: 0.6162 (mmm) cc_final: 0.5706 (mmt) REVERT: C 953 MET cc_start: 0.4176 (ptp) cc_final: 0.3936 (ptp) REVERT: C 1012 LYS cc_start: 0.7722 (tttt) cc_final: 0.6980 (mmtm) outliers start: 64 outliers final: 47 residues processed: 316 average time/residue: 0.1157 time to fit residues: 54.0983 Evaluate side-chains 322 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 268 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 933 SER Chi-restraints excluded: chain A residue 950 PHE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1058 THR Chi-restraints excluded: chain A residue 1086 TYR Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 568 GLU Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 757 LYS Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 910 ILE Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 916 CYS Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 950 PHE Chi-restraints excluded: chain B residue 979 VAL Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain B residue 1047 HIS Chi-restraints excluded: chain C residue 554 TRP Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 622 TYR Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 626 TYR Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 694 VAL Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 846 THR Chi-restraints excluded: chain C residue 912 ILE Chi-restraints excluded: chain C residue 950 PHE Chi-restraints excluded: chain C residue 971 THR Chi-restraints excluded: chain C residue 979 VAL Chi-restraints excluded: chain C residue 990 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 29 optimal weight: 4.9990 chunk 127 optimal weight: 6.9990 chunk 88 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 138 optimal weight: 10.0000 chunk 61 optimal weight: 1.9990 chunk 107 optimal weight: 0.5980 chunk 160 optimal weight: 6.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 730 ASN A1065 ASN A1073 GLN ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 GLN C 873 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.182753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.151508 restraints weight = 21152.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.151319 restraints weight = 19044.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.152228 restraints weight = 20509.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.153678 restraints weight = 13342.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.154173 restraints weight = 11438.690| |-----------------------------------------------------------------------------| r_work (final): 0.4201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6187 moved from start: 0.7178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 14007 Z= 0.223 Angle : 0.866 12.955 18891 Z= 0.438 Chirality : 0.051 0.297 2058 Planarity : 0.005 0.049 2412 Dihedral : 7.517 55.821 1840 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.78 % Favored : 88.99 % Rotamer: Outliers : 4.44 % Allowed : 21.94 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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 are not related in a simple way. whole: -2.91 (0.19), residues: 1716 helix: -0.89 (0.30), residues: 264 sheet: -1.48 (0.19), residues: 678 loop : -2.69 (0.21), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 791 TYR 0.023 0.003 TYR C 967 PHE 0.032 0.003 PHE B1042 TRP 0.024 0.003 TRP A 779 HIS 0.008 0.001 HIS C 690 Details of bonding type rmsd/Z covalent geometry : bond 0.00508 / 0.22 (14007) covalent geometry : angle 0.86607 / 0.44 (18891) hydrogen bonds : bond 0.04465 / 2.87 ( 307) hydrogen bonds : angle 6.55432 / 4.43 ( 867) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 269 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 573 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8239 (tt) REVERT: A 579 GLU cc_start: 0.7866 (tt0) cc_final: 0.7610 (mp0) REVERT: A 603 LYS cc_start: 0.8657 (tttt) cc_final: 0.8191 (ttmm) REVERT: A 607 LYS cc_start: 0.8609 (mptt) cc_final: 0.8289 (mmtm) REVERT: A 626 TYR cc_start: 0.6119 (OUTLIER) cc_final: 0.5372 (t80) REVERT: A 730 ASN cc_start: 0.6804 (OUTLIER) cc_final: 0.5866 (t0) REVERT: A 733 PHE cc_start: 0.3831 (OUTLIER) cc_final: 0.3559 (p90) REVERT: A 736 MET cc_start: 0.5254 (ppp) cc_final: 0.4126 (mpp) REVERT: A 738 LEU cc_start: 0.7342 (mt) cc_final: 0.6656 (mt) REVERT: A 806 MET cc_start: 0.6142 (mtt) cc_final: 0.5221 (mtp) REVERT: A 1086 TYR cc_start: 0.5828 (OUTLIER) cc_final: 0.4181 (p90) REVERT: B 469 TYR cc_start: 0.6151 (m-10) cc_final: 0.5548 (m-80) REVERT: B 573 LEU cc_start: 0.8536 (tt) cc_final: 0.8018 (mp) REVERT: B 577 LYS cc_start: 0.8620 (tttt) cc_final: 0.8115 (tttp) REVERT: B 626 TYR cc_start: 0.6155 (OUTLIER) cc_final: 0.5522 (t80) REVERT: B 685 MET cc_start: 0.4343 (ttp) cc_final: 0.2781 (mmt) REVERT: B 736 MET cc_start: 0.2780 (ttp) cc_final: 0.1301 (ttp) REVERT: B 779 TRP cc_start: 0.7432 (t60) cc_final: 0.6889 (t60) REVERT: B 791 ARG cc_start: 0.5333 (mpt180) cc_final: 0.4663 (mmt90) REVERT: B 848 LYS cc_start: 0.7411 (mmmt) cc_final: 0.7079 (pttp) REVERT: B 868 MET cc_start: 0.6141 (ptp) cc_final: 0.4504 (ttm) REVERT: B 896 GLU cc_start: 0.6115 (tt0) cc_final: 0.5469 (mt-10) REVERT: B 915 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7301 (tt) REVERT: C 569 GLU cc_start: 0.8025 (mp0) cc_final: 0.7823 (mp0) REVERT: C 610 LYS cc_start: 0.9088 (tttt) cc_final: 0.8761 (mptt) REVERT: C 619 MET cc_start: 0.7721 (ttm) cc_final: 0.7362 (ttm) REVERT: C 762 LEU cc_start: 0.7834 (mp) cc_final: 0.7460 (mp) REVERT: C 768 LEU cc_start: 0.6766 (OUTLIER) cc_final: 0.6404 (mt) REVERT: C 779 TRP cc_start: 0.7078 (t60) cc_final: 0.6573 (t60) REVERT: C 956 LYS cc_start: 0.6759 (mtpt) cc_final: 0.6484 (tppt) outliers start: 69 outliers final: 51 residues processed: 317 average time/residue: 0.1069 time to fit residues: 50.7712 Evaluate side-chains 318 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 259 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 573 LEU Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 730 ASN Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 933 SER Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain A residue 950 PHE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1086 TYR Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain B residue 630 ILE Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 757 LYS Chi-restraints excluded: chain B residue 759 VAL Chi-restraints excluded: chain B residue 792 THR Chi-restraints excluded: chain B residue 859 THR Chi-restraints excluded: chain B residue 910 ILE Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 916 CYS Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 946 ILE Chi-restraints excluded: chain B residue 979 VAL Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain B residue 1047 HIS Chi-restraints excluded: chain C residue 554 TRP Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 626 TYR Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 694 VAL Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 846 THR Chi-restraints excluded: chain C residue 912 ILE Chi-restraints excluded: chain C residue 933 SER Chi-restraints excluded: chain C residue 950 PHE Chi-restraints excluded: chain C residue 971 THR Chi-restraints excluded: chain C residue 979 VAL Chi-restraints excluded: chain C residue 990 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 84 optimal weight: 2.9990 chunk 15 optimal weight: 10.0000 chunk 13 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 113 optimal weight: 0.0970 chunk 122 optimal weight: 0.0970 chunk 142 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 156 optimal weight: 5.9990 chunk 99 optimal weight: 0.2980 chunk 11 optimal weight: 5.9990 overall best weight: 1.2980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 873 ASN ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 566 ASN ** C 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 612 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.187687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.155682 restraints weight = 20426.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.157602 restraints weight = 14398.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.158646 restraints weight = 11433.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.160205 restraints weight = 9297.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.160928 restraints weight = 8599.579| |-----------------------------------------------------------------------------| r_work (final): 0.4296 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6016 moved from start: 0.7275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14007 Z= 0.139 Angle : 0.784 12.990 18891 Z= 0.389 Chirality : 0.048 0.316 2058 Planarity : 0.005 0.051 2412 Dihedral : 6.815 55.218 1840 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.22 % Favored : 91.61 % Rotamer: Outliers : 3.86 % Allowed : 22.78 % Favored : 73.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 are not related in a simple way. whole: -2.73 (0.19), residues: 1716 helix: -0.65 (0.30), residues: 264 sheet: -1.36 (0.19), residues: 690 loop : -2.63 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 791 TYR 0.030 0.002 TYR B 666 PHE 0.019 0.002 PHE C 948 TRP 0.023 0.002 TRP C 779 HIS 0.003 0.001 HIS A 693 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (14007) covalent geometry : angle 0.78378 / 0.39 (18891) hydrogen bonds : bond 0.03576 / 2.24 ( 307) hydrogen bonds : angle 6.25245 / 4.22 ( 867) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3432 Ramachandran restraints generated. 1716 Oldfield, 0 Emsley, 1716 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 276 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 603 LYS cc_start: 0.8693 (tttt) cc_final: 0.8154 (ttmm) REVERT: A 607 LYS cc_start: 0.8623 (mptt) cc_final: 0.8257 (mmtm) REVERT: A 626 TYR cc_start: 0.5789 (OUTLIER) cc_final: 0.5173 (t80) REVERT: A 684 MET cc_start: 0.7013 (mmp) cc_final: 0.6612 (mmt) REVERT: A 719 LYS cc_start: 0.8813 (tttt) cc_final: 0.8321 (tttp) REVERT: A 733 PHE cc_start: 0.3841 (OUTLIER) cc_final: 0.3529 (p90) REVERT: A 736 MET cc_start: 0.4986 (ppp) cc_final: 0.4007 (mpp) REVERT: A 738 LEU cc_start: 0.6944 (mt) cc_final: 0.6481 (mt) REVERT: A 806 MET cc_start: 0.6225 (mtt) cc_final: 0.5051 (mtp) REVERT: A 1086 TYR cc_start: 0.5849 (OUTLIER) cc_final: 0.4202 (p90) REVERT: B 573 LEU cc_start: 0.8482 (tt) cc_final: 0.7935 (mp) REVERT: B 577 LYS cc_start: 0.8625 (tttt) cc_final: 0.8103 (tttp) REVERT: B 626 TYR cc_start: 0.5825 (OUTLIER) cc_final: 0.5281 (t80) REVERT: B 680 VAL cc_start: 0.5421 (OUTLIER) cc_final: 0.5198 (p) REVERT: B 685 MET cc_start: 0.4014 (ttp) cc_final: 0.2501 (mmt) REVERT: B 728 PHE cc_start: 0.6917 (t80) cc_final: 0.6668 (t80) REVERT: B 736 MET cc_start: 0.2879 (ttp) cc_final: 0.1643 (ttp) REVERT: B 779 TRP cc_start: 0.7373 (t60) cc_final: 0.6845 (t60) REVERT: B 791 ARG cc_start: 0.5208 (mpt180) cc_final: 0.4657 (mmt90) REVERT: B 848 LYS cc_start: 0.7159 (mmmt) cc_final: 0.6914 (pttm) REVERT: B 868 MET cc_start: 0.6087 (ptp) cc_final: 0.4735 (ttm) REVERT: B 896 GLU cc_start: 0.6156 (tt0) cc_final: 0.5462 (mt-10) REVERT: B 915 LEU cc_start: 0.7553 (OUTLIER) cc_final: 0.7046 (tt) REVERT: B 1095 ARG cc_start: 0.7029 (ptt180) cc_final: 0.6752 (ptt180) REVERT: C 569 GLU cc_start: 0.8086 (mp0) cc_final: 0.7842 (mp0) REVERT: C 610 LYS cc_start: 0.9089 (tttt) cc_final: 0.8710 (mptt) REVERT: C 619 MET cc_start: 0.7688 (ttm) cc_final: 0.7409 (ttm) REVERT: C 762 LEU cc_start: 0.7921 (mp) cc_final: 0.7558 (mp) REVERT: C 768 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6335 (mt) REVERT: C 894 MET cc_start: 0.6170 (mmt) cc_final: 0.5670 (mmt) REVERT: C 956 LYS cc_start: 0.6530 (mtpt) cc_final: 0.6291 (tppt) outliers start: 60 outliers final: 45 residues processed: 314 average time/residue: 0.1113 time to fit residues: 51.8099 Evaluate side-chains 318 residues out of total 1554 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 266 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 555 VAL Chi-restraints excluded: chain A residue 619 MET Chi-restraints excluded: chain A residue 626 TYR Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain A residue 680 VAL Chi-restraints excluded: chain A residue 694 VAL Chi-restraints excluded: chain A residue 733 PHE Chi-restraints excluded: chain A residue 792 THR Chi-restraints excluded: chain A residue 823 VAL Chi-restraints excluded: chain A residue 873 ASN Chi-restraints excluded: chain A residue 933 SER Chi-restraints excluded: chain A residue 943 ASN Chi-restraints excluded: chain A residue 950 PHE Chi-restraints excluded: chain A residue 992 ILE Chi-restraints excluded: chain A residue 1005 ILE Chi-restraints excluded: chain A residue 1039 VAL Chi-restraints excluded: chain A residue 1086 TYR Chi-restraints excluded: chain B residue 472 LEU Chi-restraints excluded: chain B residue 555 VAL Chi-restraints excluded: chain B residue 626 TYR Chi-restraints excluded: chain B residue 633 THR Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 680 VAL Chi-restraints excluded: chain B residue 694 VAL Chi-restraints excluded: chain B residue 757 LYS Chi-restraints excluded: chain B residue 915 LEU Chi-restraints excluded: chain B residue 916 CYS Chi-restraints excluded: chain B residue 928 VAL Chi-restraints excluded: chain B residue 945 VAL Chi-restraints excluded: chain B residue 979 VAL Chi-restraints excluded: chain B residue 1039 VAL Chi-restraints excluded: chain B residue 1047 HIS Chi-restraints excluded: chain C residue 472 LEU Chi-restraints excluded: chain C residue 554 TRP Chi-restraints excluded: chain C residue 555 VAL Chi-restraints excluded: chain C residue 567 VAL Chi-restraints excluded: chain C residue 624 LEU Chi-restraints excluded: chain C residue 626 TYR Chi-restraints excluded: chain C residue 630 ILE Chi-restraints excluded: chain C residue 634 THR Chi-restraints excluded: chain C residue 694 VAL Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 756 SER Chi-restraints excluded: chain C residue 768 LEU Chi-restraints excluded: chain C residue 792 THR Chi-restraints excluded: chain C residue 846 THR Chi-restraints excluded: chain C residue 872 LEU Chi-restraints excluded: chain C residue 912 ILE Chi-restraints excluded: chain C residue 946 ILE Chi-restraints excluded: chain C residue 950 PHE Chi-restraints excluded: chain C residue 971 THR Chi-restraints excluded: chain C residue 990 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 171 random chunks: chunk 19 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 122 optimal weight: 0.5980 chunk 169 optimal weight: 9.9990 chunk 104 optimal weight: 8.9990 chunk 162 optimal weight: 0.6980 chunk 33 optimal weight: 0.0030 chunk 45 optimal weight: 0.0770 chunk 58 optimal weight: 4.9990 chunk 68 optimal weight: 5.9990 overall best weight: 0.8750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 571 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 559 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 973 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 893 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 981 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4595 r_free = 0.4595 target = 0.189893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.157097 restraints weight = 20615.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.160509 restraints weight = 14124.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.161348 restraints weight = 10831.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.162059 restraints weight = 8261.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.162595 restraints weight = 7670.815| |-----------------------------------------------------------------------------| r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5945 moved from start: 0.7391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14007 Z= 0.128 Angle : 0.763 12.801 18891 Z= 0.376 Chirality : 0.047 0.314 2058 Planarity : 0.004 0.045 2412 Dihedral : 6.431 56.482 1840 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.17 % Allowed : 8.92 % Favored : 90.91 % Rotamer: Outliers : 3.35 % Allowed : 23.49 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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 are not related in a simple way. whole: -2.58 (0.19), residues: 1716 helix: -0.43 (0.31), residues: 264 sheet: -1.25 (0.19), residues: 717 loop : -2.62 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 791 TYR 0.027 0.001 TYR B 666 PHE 0.028 0.002 PHE B 753 TRP 0.020 0.002 TRP C 779 HIS 0.003 0.001 HIS C 559 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.13 (14007) covalent geometry : angle 0.76329 / 0.38 (18891) hydrogen bonds : bond 0.03301 / 2.06 ( 307) hydrogen bonds : angle 6.09245 / 4.11 ( 867) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2624.17 seconds wall clock time: 46 minutes 20.25 seconds (2780.25 seconds total)