Starting phenix.real_space_refine on Fri Jul 3 18:34:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sz7_55361/07_2026/9sz7_55361.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sz7_55361/07_2026/9sz7_55361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9sz7_55361/07_2026/9sz7_55361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sz7_55361/07_2026/9sz7_55361.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9sz7_55361/07_2026/9sz7_55361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sz7_55361/07_2026/9sz7_55361.map" } resolution = 3.87 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= -0.000 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: 5 Type Number sf(0) Gaussians P 205 5.49 5 S 29 5.16 5 C 9118 2.51 5 N 2656 2.21 5 O 3346 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15354 Number of models: 1 Model: "" Number of chains: 16 Chain: "C" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1128 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "A" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1137 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain: "Y" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 981 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Chain: "Z" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 965 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain: "E" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1128 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "F" Number of atoms: 1120 Number of conformers: 1 Conformer: "" Number of residues, atoms: 137, 1120 Classifications: {'peptide': 137} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain: "H" Number of atoms: 1127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1127 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "I" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1128 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "J" Number of atoms: 1104 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1104 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 3, 'TRANS': 131} Chain breaks: 1 Chain: "B" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1128 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "D" Number of atoms: 1128 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1128 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "y" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 604 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "z" Number of atoms: 585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 585 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "k" Number of atoms: 586 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 586 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "l" Number of atoms: 481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 481 Classifications: {'DNA': 24} Link IDs: {'rna3p': 23} Chain: "K" Number of atoms: 1024 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1024 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} Chain breaks: 1 Time building chain proxies: 3.24, per 1000 atoms: 0.21 Number of scatterers: 15354 At special positions: 0 Unit cell: (101.813, 163.982, 178.398, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 29 16.00 P 205 15.00 O 3346 8.00 N 2656 7.00 C 9118 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: 1.52 Conformation dependent library (CDL) restraints added in 584.8 milliseconds 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2670 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 17 sheets defined 39.9% alpha, 14.4% beta 90 base pairs and 170 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'C' and resid 19 through 23 Processing helix chain 'C' and resid 44 through 57 Processing helix chain 'C' and resid 61 through 73 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 117 through 125 Processing helix chain 'C' and resid 129 through 136 Processing helix chain 'A' and resid 19 through 24 removed outlier: 3.663A pdb=" N SER A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 56 removed outlier: 3.589A pdb=" N GLU A 49 " --> pdb=" O PRO A 45 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 74 Processing helix chain 'A' and resid 90 through 97 removed outlier: 3.627A pdb=" N SER A 95 " --> pdb=" O ASN A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 126 Processing helix chain 'A' and resid 129 through 137 Processing helix chain 'E' and resid 22 through 26 Processing helix chain 'E' and resid 47 through 58 removed outlier: 3.553A pdb=" N ASN E 57 " --> pdb=" O GLN E 53 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N PHE E 58 " --> pdb=" O THR E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 75 removed outlier: 3.995A pdb=" N ARG E 66 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ASN E 75 " --> pdb=" O LEU E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 96 removed outlier: 3.764A pdb=" N ASP E 96 " --> pdb=" O ASN E 92 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 126 Processing helix chain 'E' and resid 129 through 137 Processing helix chain 'F' and resid 47 through 56 removed outlier: 4.022A pdb=" N TYR F 51 " --> pdb=" O ASP F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 64 through 73 Processing helix chain 'F' and resid 90 through 98 removed outlier: 3.783A pdb=" N SER F 95 " --> pdb=" O ASN F 91 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ASP F 96 " --> pdb=" O ASN F 92 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ALA F 97 " --> pdb=" O LEU F 93 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 124 removed outlier: 3.639A pdb=" N TYR F 120 " --> pdb=" O ASP F 116 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N GLU F 121 " --> pdb=" O LYS F 117 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N GLN F 122 " --> pdb=" O VAL F 118 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR F 123 " --> pdb=" O GLN F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 130 through 135 removed outlier: 3.710A pdb=" N GLU F 135 " --> pdb=" O GLU F 131 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 23 removed outlier: 3.531A pdb=" N ARG H 23 " --> pdb=" O ALA H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 46 through 56 removed outlier: 4.283A pdb=" N SER H 50 " --> pdb=" O ALA H 46 " (cutoff:3.500A) Processing helix chain 'H' and resid 64 through 76 removed outlier: 3.551A pdb=" N ALA H 74 " --> pdb=" O ARG H 70 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ASN H 75 " --> pdb=" O LEU H 71 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA H 76 " --> pdb=" O ILE H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 97 Processing helix chain 'H' and resid 117 through 126 Processing helix chain 'H' and resid 129 through 138 Processing helix chain 'I' and resid 19 through 26 removed outlier: 3.550A pdb=" N SER I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE I 25 " --> pdb=" O LYS I 21 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE I 26 " --> pdb=" O LEU I 22 " (cutoff:3.500A) Processing helix chain 'I' and resid 47 through 56 Processing helix chain 'I' and resid 62 through 73 Processing helix chain 'I' and resid 81 through 86 removed outlier: 4.027A pdb=" N ASN I 85 " --> pdb=" O LEU I 81 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG I 86 " --> pdb=" O ASP I 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 81 through 86' Processing helix chain 'I' and resid 90 through 97 removed outlier: 3.687A pdb=" N SER I 95 " --> pdb=" O ASN I 91 " (cutoff:3.500A) Processing helix chain 'I' and resid 116 through 124 Processing helix chain 'I' and resid 130 through 137 Processing helix chain 'J' and resid 21 through 26 removed outlier: 3.770A pdb=" N PHE J 25 " --> pdb=" O LYS J 21 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N PHE J 26 " --> pdb=" O LEU J 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 21 through 26' Processing helix chain 'J' and resid 46 through 56 removed outlier: 3.996A pdb=" N THR J 54 " --> pdb=" O SER J 50 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N PHE J 55 " --> pdb=" O TYR J 51 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ASN J 56 " --> pdb=" O PHE J 52 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 74 removed outlier: 3.539A pdb=" N LEU J 71 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ILE J 72 " --> pdb=" O LEU J 68 " (cutoff:3.500A) Processing helix chain 'J' and resid 90 through 95 removed outlier: 3.881A pdb=" N SER J 95 " --> pdb=" O ASN J 91 " (cutoff:3.500A) Processing helix chain 'J' and resid 117 through 125 Processing helix chain 'J' and resid 129 through 137 removed outlier: 3.819A pdb=" N VAL J 133 " --> pdb=" O SER J 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 24 removed outlier: 3.744A pdb=" N SER B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 57 removed outlier: 3.532A pdb=" N ASN B 57 " --> pdb=" O GLN B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 75 removed outlier: 3.813A pdb=" N ASN B 75 " --> pdb=" O LEU B 71 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 98 Processing helix chain 'B' and resid 117 through 126 Processing helix chain 'B' and resid 129 through 136 Processing helix chain 'D' and resid 19 through 24 removed outlier: 3.743A pdb=" N SER D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 49 Processing helix chain 'D' and resid 49 through 55 removed outlier: 3.586A pdb=" N THR D 54 " --> pdb=" O SER D 50 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE D 55 " --> pdb=" O TYR D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 64 through 73 Processing helix chain 'D' and resid 90 through 95 removed outlier: 3.637A pdb=" N SER D 95 " --> pdb=" O ASN D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 126 Processing helix chain 'D' and resid 130 through 137 Processing helix chain 'K' and resid 19 through 23 Processing helix chain 'K' and resid 44 through 54 removed outlier: 3.730A pdb=" N THR K 54 " --> pdb=" O SER K 50 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 73 Processing helix chain 'K' and resid 90 through 97 removed outlier: 3.554A pdb=" N SER K 95 " --> pdb=" O ASN K 91 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 125 Processing helix chain 'K' and resid 129 through 136 removed outlier: 3.533A pdb=" N GLU K 135 " --> pdb=" O GLU K 131 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 5 through 9 Processing sheet with id=AA2, first strand: chain 'C' and resid 16 through 17 Processing sheet with id=AA3, first strand: chain 'A' and resid 5 through 9 removed outlier: 3.625A pdb=" N CYS A 39 " --> pdb=" O GLY A 35 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 6 through 9 removed outlier: 3.711A pdb=" N CYS E 39 " --> pdb=" O GLY E 35 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'F' and resid 76 through 79 removed outlier: 3.633A pdb=" N LEU F 40 " --> pdb=" O VAL F 114 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 7 through 9 removed outlier: 3.773A pdb=" N LEU H 40 " --> pdb=" O VAL H 114 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS H 39 " --> pdb=" O GLY H 35 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ILE H 30 " --> pdb=" O VAL H 79 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 6 through 7 Processing sheet with id=AA8, first strand: chain 'I' and resid 33 through 34 Processing sheet with id=AA9, first strand: chain 'J' and resid 6 through 9 Processing sheet with id=AB1, first strand: chain 'J' and resid 41 through 43 Processing sheet with id=AB2, first strand: chain 'B' and resid 6 through 8 removed outlier: 4.033A pdb=" N ILE B 103 " --> pdb=" O LEU B 8 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 16 through 17 Processing sheet with id=AB4, first strand: chain 'B' and resid 76 through 78 removed outlier: 3.644A pdb=" N CYS B 39 " --> pdb=" O GLY B 35 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 6 through 8 removed outlier: 3.640A pdb=" N CYS D 39 " --> pdb=" O GLY D 35 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 15 through 17 Processing sheet with id=AB7, first strand: chain 'K' and resid 6 through 9 removed outlier: 3.610A pdb=" N ILE K 30 " --> pdb=" O VAL K 79 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL K 79 " --> pdb=" O ILE K 30 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'K' and resid 15 through 17 420 hydrogen bonds defined for protein. 1149 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 205 hydrogen bonds 390 hydrogen bond angles 0 basepair planarities 90 basepair parallelities 170 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 1.97 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2846 1.33 - 1.45: 4688 1.45 - 1.57: 8066 1.57 - 1.69: 404 1.69 - 1.81: 48 Bond restraints: 16052 Sorted by residual: bond pdb=" C3' DT k 0 " pdb=" C2' DT k 0 " ideal model delta sigma weight residual 1.516 1.546 -0.030 8.00e-03 1.56e+04 1.44e+01 bond pdb=" C3' DT Z 1 " pdb=" C2' DT Z 1 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DT Z 41 " pdb=" C2' DT Z 41 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DT Z 12 " pdb=" C2' DT Z 12 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DG k 11 " pdb=" C2' DG k 11 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 ... (remaining 16047 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.72: 21047 1.72 - 3.44: 1368 3.44 - 5.16: 130 5.16 - 6.88: 21 6.88 - 8.59: 4 Bond angle restraints: 22570 Sorted by residual: angle pdb=" O4' DG k 9 " pdb=" C4' DG k 9 " pdb=" C3' DG k 9 " ideal model delta sigma weight residual 106.00 101.80 4.20 6.00e-01 2.78e+00 4.89e+01 angle pdb=" O4' DT y -16 " pdb=" C1' DT y -16 " pdb=" N1 DT y -16 " ideal model delta sigma weight residual 108.00 111.79 -3.79 7.00e-01 2.04e+00 2.93e+01 angle pdb=" O4' DG Y -1 " pdb=" C4' DG Y -1 " pdb=" C3' DG Y -1 " ideal model delta sigma weight residual 106.00 102.83 3.17 6.00e-01 2.78e+00 2.79e+01 angle pdb=" O4' DT l 15 " pdb=" C4' DT l 15 " pdb=" C3' DT l 15 " ideal model delta sigma weight residual 106.00 102.95 3.05 6.00e-01 2.78e+00 2.58e+01 angle pdb=" O4' DG Y 9 " pdb=" C4' DG Y 9 " pdb=" C3' DG Y 9 " ideal model delta sigma weight residual 106.00 102.98 3.02 6.00e-01 2.78e+00 2.54e+01 ... (remaining 22565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.25: 7943 34.25 - 68.50: 1231 68.50 - 102.75: 34 102.75 - 137.00: 15 137.00 - 171.25: 18 Dihedral angle restraints: 9241 sinusoidal: 5188 harmonic: 4053 Sorted by residual: dihedral pdb=" CA SER D 28 " pdb=" C SER D 28 " pdb=" N SER D 29 " pdb=" CA SER D 29 " ideal model delta harmonic sigma weight residual 180.00 -150.89 -29.11 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" CA ASP E 27 " pdb=" C ASP E 27 " pdb=" N SER E 28 " pdb=" CA SER E 28 " ideal model delta harmonic sigma weight residual 180.00 150.99 29.01 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA SER E 28 " pdb=" C SER E 28 " pdb=" N SER E 29 " pdb=" CA SER E 29 " ideal model delta harmonic sigma weight residual 180.00 152.92 27.08 0 5.00e+00 4.00e-02 2.93e+01 ... (remaining 9238 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1693 0.042 - 0.083: 598 0.083 - 0.125: 210 0.125 - 0.166: 49 0.166 - 0.208: 12 Chirality restraints: 2562 Sorted by residual: chirality pdb=" C3' DA Y -4 " pdb=" C4' DA Y -4 " pdb=" O3' DA Y -4 " pdb=" C2' DA Y -4 " both_signs ideal model delta sigma weight residual False -2.73 -2.52 -0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" C3' DT Z 42 " pdb=" C4' DT Z 42 " pdb=" O3' DT Z 42 " pdb=" C2' DT Z 42 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.40e-01 chirality pdb=" C3' DG k 11 " pdb=" C4' DG k 11 " pdb=" O3' DG k 11 " pdb=" C2' DG k 11 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.12e-01 ... (remaining 2559 not shown) Planarity restraints: 2195 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG k 9 " -0.035 2.00e-02 2.50e+03 1.53e-02 7.01e+00 pdb=" N9 DG k 9 " 0.036 2.00e-02 2.50e+03 pdb=" C8 DG k 9 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DG k 9 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DG k 9 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG k 9 " -0.001 2.00e-02 2.50e+03 pdb=" O6 DG k 9 " -0.011 2.00e-02 2.50e+03 pdb=" N1 DG k 9 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG k 9 " 0.001 2.00e-02 2.50e+03 pdb=" N2 DG k 9 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG k 9 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DG k 9 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT z 31 " -0.030 2.00e-02 2.50e+03 1.34e-02 4.48e+00 pdb=" N1 DT z 31 " 0.024 2.00e-02 2.50e+03 pdb=" C2 DT z 31 " -0.000 2.00e-02 2.50e+03 pdb=" O2 DT z 31 " 0.009 2.00e-02 2.50e+03 pdb=" N3 DT z 31 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DT z 31 " -0.005 2.00e-02 2.50e+03 pdb=" O4 DT z 31 " -0.010 2.00e-02 2.50e+03 pdb=" C5 DT z 31 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT z 31 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DT z 31 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA y -14 " 0.027 2.00e-02 2.50e+03 1.19e-02 3.87e+00 pdb=" N9 DA y -14 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DA y -14 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DA y -14 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA y -14 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DA y -14 " 0.004 2.00e-02 2.50e+03 pdb=" N6 DA y -14 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DA y -14 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA y -14 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DA y -14 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA y -14 " -0.001 2.00e-02 2.50e+03 ... (remaining 2192 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 37 2.57 - 3.15: 13261 3.15 - 3.74: 27877 3.74 - 4.32: 36030 4.32 - 4.90: 52860 Nonbonded interactions: 130065 Sorted by model distance: nonbonded pdb=" N2 DG k 9 " pdb=" O2 DC l 10 " model vdw 1.989 2.496 nonbonded pdb=" N7 DA y -27 " pdb=" O2 DT z 46 " model vdw 2.059 2.496 nonbonded pdb=" N2 DG Y 11 " pdb=" O2 DC Z 8 " model vdw 2.138 2.496 nonbonded pdb=" N1 DG k 9 " pdb=" N3 DC l 10 " model vdw 2.356 2.560 nonbonded pdb=" O5' DC Z 10 " pdb=" O4' DC Z 10 " model vdw 2.449 2.432 ... (remaining 130060 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 54 or resid 67 through 136)) selection = (chain 'B' and (resid 1 through 54 or resid 67 through 136)) selection = (chain 'C' and (resid 1 through 54 or resid 67 through 136)) selection = (chain 'D' and (resid 1 through 54 or resid 67 through 136)) selection = (chain 'E' and (resid 1 through 54 or resid 67 through 136)) selection = (chain 'F' and (resid 1 through 54 or resid 67 through 136)) selection = (chain 'H' and (resid 1 through 54 or resid 67 through 136)) selection = (chain 'I' and (resid 1 through 54 or resid 67 through 136)) selection = (chain 'J' and (resid 1 through 54 or resid 67 through 136)) selection = (chain 'K' and resid 1 through 136) } 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: 12.810 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.050 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6836 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 : 0.005 0.060 16052 Z= 0.438 Angle : 0.869 8.595 22570 Z= 0.670 Chirality : 0.050 0.208 2562 Planarity : 0.004 0.049 2195 Dihedral : 26.741 171.249 6571 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 17.02 Ramachandran Plot: Outliers : 1.64 % Allowed : 17.90 % Favored : 80.46 % Rotamer: Outliers : 11.63 % Allowed : 14.50 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.48 (0.21), residues: 1341 helix: -1.58 (0.21), residues: 480 sheet: -1.73 (0.29), residues: 310 loop : -3.26 (0.24), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 70 TYR 0.016 0.001 TYR B 51 PHE 0.014 0.001 PHE J 109 TRP 0.014 0.002 TRP F 115 HIS 0.004 0.001 HIS J 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00543 / 0.44 (16052) covalent geometry : angle 0.86938 / 0.67 (22570) hydrogen bonds : bond 0.18004 / 11.86 ( 625) hydrogen bonds : angle 7.94673 / 5.41 ( 1539) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 286 time to evaluate : 0.436 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 109 PHE cc_start: 0.8583 (OUTLIER) cc_final: 0.8134 (m-80) REVERT: C 132 THR cc_start: 0.8922 (OUTLIER) cc_final: 0.8529 (p) REVERT: A 21 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7987 (mtmm) REVERT: E 31 VAL cc_start: 0.8880 (OUTLIER) cc_final: 0.8655 (m) REVERT: F 89 ILE cc_start: 0.7210 (OUTLIER) cc_final: 0.6946 (pt) REVERT: F 110 ASP cc_start: 0.6590 (p0) cc_final: 0.6150 (p0) REVERT: J 3 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7795 (tt) REVERT: J 39 CYS cc_start: 0.5048 (OUTLIER) cc_final: 0.4799 (t) REVERT: J 70 ARG cc_start: 0.5768 (OUTLIER) cc_final: 0.5541 (mtt180) REVERT: D 130 LEU cc_start: 0.8326 (tp) cc_final: 0.8088 (tp) outliers start: 146 outliers final: 53 residues processed: 386 average time/residue: 0.1300 time to fit residues: 72.4867 Evaluate side-chains 220 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 159 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 109 PHE Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 69 LYS Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain E residue 5 THR Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 138 LYS Chi-restraints excluded: chain I residue 0 HIS Chi-restraints excluded: chain I residue 44 LYS Chi-restraints excluded: chain I residue 48 PHE Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 98 LYS Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain J residue 2 LEU Chi-restraints excluded: chain J residue 3 LEU Chi-restraints excluded: chain J residue 39 CYS Chi-restraints excluded: chain J residue 70 ARG Chi-restraints excluded: chain J residue 72 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 68 LEU Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain K residue 0 HIS Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 14 ASN C 33 ASN C 57 ASN C 92 ASN A 38 ASN ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 56 ASN ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 0 HIS F 57 ASN ** F 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 HIS ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 57 ASN ** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 0 HIS ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 57 ASN D 75 ASN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.049731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.038454 restraints weight = 129369.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.039401 restraints weight = 66260.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.039997 restraints weight = 43501.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.040388 restraints weight = 33167.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.040541 restraints weight = 27701.353| |-----------------------------------------------------------------------------| r_work (final): 0.3171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 16052 Z= 0.297 Angle : 0.912 12.579 22570 Z= 0.499 Chirality : 0.055 0.327 2562 Planarity : 0.006 0.051 2195 Dihedral : 30.903 166.468 3905 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 25.03 Ramachandran Plot: Outliers : 1.57 % Allowed : 17.23 % Favored : 81.21 % Rotamer: Outliers : 8.29 % Allowed : 20.24 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.15 % 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: -3.38 (0.21), residues: 1341 helix: -1.26 (0.21), residues: 497 sheet: -1.69 (0.28), residues: 347 loop : -3.60 (0.23), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 34 TYR 0.020 0.002 TYR B 51 PHE 0.029 0.002 PHE A 52 TRP 0.015 0.002 TRP H 115 HIS 0.010 0.002 HIS J 0 Details of bonding type rmsd/Z covalent geometry : bond 0.00606 / 0.30 (16052) covalent geometry : angle 0.91160 / 0.50 (22570) hydrogen bonds : bond 0.08358 / 5.23 ( 625) hydrogen bonds : angle 6.26058 / 4.27 ( 1539) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 176 time to evaluate : 0.449 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 30 ILE cc_start: 0.9235 (OUTLIER) cc_final: 0.9025 (pp) REVERT: C 132 THR cc_start: 0.9587 (OUTLIER) cc_final: 0.9202 (p) REVERT: A 70 ARG cc_start: 0.8034 (ttt180) cc_final: 0.7736 (ttt180) REVERT: E 3 LEU cc_start: 0.8126 (mt) cc_final: 0.7876 (mt) REVERT: E 31 VAL cc_start: 0.9170 (OUTLIER) cc_final: 0.8806 (m) REVERT: F 61 THR cc_start: 0.8292 (OUTLIER) cc_final: 0.8038 (p) REVERT: H 86 ARG cc_start: 0.7389 (OUTLIER) cc_final: 0.6689 (mtp85) REVERT: H 106 ILE cc_start: 0.9045 (mm) cc_final: 0.8538 (mt) REVERT: H 137 MET cc_start: 0.8474 (mmm) cc_final: 0.8105 (mmp) REVERT: J 6 PHE cc_start: 0.8800 (m-80) cc_final: 0.8480 (m-10) REVERT: J 25 PHE cc_start: 0.8738 (t80) cc_final: 0.8500 (t80) REVERT: J 41 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7418 (mt-10) REVERT: J 98 LYS cc_start: 0.9405 (tppt) cc_final: 0.9156 (tptp) REVERT: B 86 ARG cc_start: 0.7881 (OUTLIER) cc_final: 0.6985 (mtp85) REVERT: D 1 MET cc_start: 0.8470 (mmm) cc_final: 0.8194 (tpt) REVERT: D 48 PHE cc_start: 0.9177 (OUTLIER) cc_final: 0.8904 (t80) REVERT: K 136 ARG cc_start: 0.8688 (ptm160) cc_final: 0.8344 (ptm-80) outliers start: 104 outliers final: 58 residues processed: 261 average time/residue: 0.1218 time to fit residues: 46.7924 Evaluate side-chains 209 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 144 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain F residue 41 GLU Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain I residue 0 HIS Chi-restraints excluded: chain I residue 48 PHE Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 2 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 72 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 94 ILE Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 13 optimal weight: 8.9990 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 96 optimal weight: 3.9990 chunk 105 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN A 85 ASN ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 119 GLN ** J 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 108 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.049558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.038607 restraints weight = 129021.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.039560 restraints weight = 65716.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.040155 restraints weight = 42874.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.040527 restraints weight = 32567.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.040804 restraints weight = 27214.242| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2727 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16052 Z= 0.216 Angle : 0.832 10.171 22570 Z= 0.459 Chirality : 0.053 0.350 2562 Planarity : 0.005 0.057 2195 Dihedral : 30.952 164.304 3867 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 22.47 Ramachandran Plot: Outliers : 1.49 % Allowed : 16.78 % Favored : 81.73 % Rotamer: Outliers : 7.33 % Allowed : 21.75 % Favored : 70.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -3.16 (0.21), residues: 1341 helix: -0.99 (0.22), residues: 501 sheet: -1.72 (0.28), residues: 342 loop : -3.46 (0.23), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 70 TYR 0.015 0.002 TYR B 51 PHE 0.031 0.002 PHE F 73 TRP 0.016 0.002 TRP H 115 HIS 0.007 0.001 HIS J 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.22 (16052) covalent geometry : angle 0.83224 / 0.46 (22570) hydrogen bonds : bond 0.06806 / 4.23 ( 625) hydrogen bonds : angle 5.93091 / 4.02 ( 1539) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 162 time to evaluate : 0.484 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 30 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.9016 (pp) REVERT: C 119 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8362 (mm-40) REVERT: C 132 THR cc_start: 0.9510 (OUTLIER) cc_final: 0.9154 (p) REVERT: A 33 ASN cc_start: 0.8045 (OUTLIER) cc_final: 0.7815 (m-40) REVERT: A 49 GLU cc_start: 0.8581 (mp0) cc_final: 0.8366 (mp0) REVERT: E 100 ASP cc_start: 0.7832 (p0) cc_final: 0.7554 (m-30) REVERT: E 106 ILE cc_start: 0.8395 (OUTLIER) cc_final: 0.8176 (mp) REVERT: F 49 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8819 (mm-30) REVERT: H 106 ILE cc_start: 0.9086 (mm) cc_final: 0.8705 (mt) REVERT: H 118 VAL cc_start: 0.9388 (OUTLIER) cc_final: 0.9080 (p) REVERT: I 53 GLN cc_start: 0.9289 (mm-40) cc_final: 0.8996 (mm-40) REVERT: I 137 MET cc_start: 0.6713 (OUTLIER) cc_final: 0.6451 (ttm) REVERT: J 6 PHE cc_start: 0.8778 (m-80) cc_final: 0.8437 (m-10) REVERT: J 25 PHE cc_start: 0.8782 (t80) cc_final: 0.8547 (t80) REVERT: J 98 LYS cc_start: 0.9429 (tppt) cc_final: 0.9111 (tptp) REVERT: B 86 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7039 (mtp85) REVERT: D 48 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8736 (t80) REVERT: D 109 PHE cc_start: 0.8242 (OUTLIER) cc_final: 0.7767 (t80) REVERT: K 81 LEU cc_start: 0.8992 (OUTLIER) cc_final: 0.7116 (mt) REVERT: K 121 GLU cc_start: 0.9305 (tp30) cc_final: 0.8998 (tp30) REVERT: K 136 ARG cc_start: 0.8660 (ptm160) cc_final: 0.8336 (ptm-80) outliers start: 92 outliers final: 58 residues processed: 235 average time/residue: 0.1120 time to fit residues: 39.4425 Evaluate side-chains 213 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 144 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 0 HIS Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 51 TYR Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 31 VAL Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain I residue 0 HIS Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 48 PHE Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain I residue 137 MET Chi-restraints excluded: chain J residue 2 LEU Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 72 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain B residue 6 PHE Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 109 PHE Chi-restraints excluded: chain K residue 0 HIS Chi-restraints excluded: chain K residue 81 LEU Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 31 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 81 optimal weight: 0.3980 chunk 115 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 89 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 131 optimal weight: 30.0000 chunk 75 optimal weight: 3.9990 overall best weight: 2.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 ASN ** I 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 HIS ** J 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 ASN ** 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 = 0.3556 r_free = 0.3556 target = 0.049100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.038096 restraints weight = 129484.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.039012 restraints weight = 66939.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.039611 restraints weight = 44055.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.039999 restraints weight = 33487.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.040225 restraints weight = 28005.303| |-----------------------------------------------------------------------------| r_work (final): 0.3176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 16052 Z= 0.216 Angle : 0.820 11.563 22570 Z= 0.449 Chirality : 0.052 0.347 2562 Planarity : 0.005 0.056 2195 Dihedral : 30.959 163.672 3858 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 21.64 Ramachandran Plot: Outliers : 1.49 % Allowed : 17.08 % Favored : 81.43 % Rotamer: Outliers : 7.01 % Allowed : 23.03 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.05 (0.21), residues: 1341 helix: -0.85 (0.22), residues: 507 sheet: -1.72 (0.28), residues: 338 loop : -3.42 (0.23), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 70 TYR 0.015 0.002 TYR J 120 PHE 0.030 0.002 PHE E 109 TRP 0.015 0.002 TRP H 115 HIS 0.008 0.001 HIS J 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.22 (16052) covalent geometry : angle 0.81970 / 0.45 (22570) hydrogen bonds : bond 0.06828 / 4.24 ( 625) hydrogen bonds : angle 5.77818 / 3.91 ( 1539) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 160 time to evaluate : 0.408 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 30 ILE cc_start: 0.9223 (OUTLIER) cc_final: 0.8980 (pp) REVERT: C 119 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8420 (mm-40) REVERT: A 49 GLU cc_start: 0.8717 (mp0) cc_final: 0.8490 (mp0) REVERT: E 106 ILE cc_start: 0.8378 (OUTLIER) cc_final: 0.8151 (mp) REVERT: F 49 GLU cc_start: 0.9174 (mt-10) cc_final: 0.8837 (mm-30) REVERT: F 61 THR cc_start: 0.8551 (OUTLIER) cc_final: 0.8061 (t) REVERT: H 106 ILE cc_start: 0.9077 (mm) cc_final: 0.8735 (mt) REVERT: H 118 VAL cc_start: 0.9435 (OUTLIER) cc_final: 0.9103 (p) REVERT: I 53 GLN cc_start: 0.9433 (mm-40) cc_final: 0.9120 (mm-40) REVERT: I 137 MET cc_start: 0.6687 (tpp) cc_final: 0.6325 (ttm) REVERT: J 6 PHE cc_start: 0.8795 (m-80) cc_final: 0.8164 (m-10) REVERT: J 25 PHE cc_start: 0.8913 (t80) cc_final: 0.8597 (t80) REVERT: J 98 LYS cc_start: 0.9482 (tppt) cc_final: 0.9194 (tppt) REVERT: B 86 ARG cc_start: 0.7885 (OUTLIER) cc_final: 0.6887 (mtp85) REVERT: B 95 SER cc_start: 0.9436 (t) cc_final: 0.9235 (p) REVERT: D 1 MET cc_start: 0.8481 (tpt) cc_final: 0.8156 (mmm) REVERT: D 48 PHE cc_start: 0.9079 (OUTLIER) cc_final: 0.8668 (t80) REVERT: K 121 GLU cc_start: 0.9415 (tp30) cc_final: 0.8989 (tp30) REVERT: K 136 ARG cc_start: 0.8719 (ptm160) cc_final: 0.8400 (ptm-80) outliers start: 88 outliers final: 64 residues processed: 233 average time/residue: 0.1162 time to fit residues: 40.5187 Evaluate side-chains 215 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 144 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 0 HIS Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 126 SER Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain I residue 0 HIS Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 2 LEU Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 72 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 38 ASN Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain K residue 0 HIS Chi-restraints excluded: chain K residue 111 HIS Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 74 optimal weight: 0.9980 chunk 56 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 62 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 122 optimal weight: 2.9990 chunk 31 optimal weight: 10.0000 chunk 138 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 92 ASN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN ** D 108 GLN ** 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 = 0.3569 r_free = 0.3569 target = 0.049549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.038563 restraints weight = 128581.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.039511 restraints weight = 65950.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.040137 restraints weight = 43214.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.040542 restraints weight = 32578.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.040764 restraints weight = 26997.589| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.3337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16052 Z= 0.174 Angle : 0.787 9.581 22570 Z= 0.434 Chirality : 0.051 0.356 2562 Planarity : 0.005 0.052 2195 Dihedral : 30.868 162.896 3853 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 1.49 % Allowed : 16.48 % Favored : 82.03 % Rotamer: Outliers : 7.81 % Allowed : 23.51 % Favored : 68.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.84 (0.22), residues: 1341 helix: -0.66 (0.22), residues: 500 sheet: -1.62 (0.29), residues: 324 loop : -3.26 (0.24), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 34 TYR 0.016 0.002 TYR J 120 PHE 0.026 0.002 PHE A 52 TRP 0.013 0.002 TRP I 115 HIS 0.006 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.17 (16052) covalent geometry : angle 0.78717 / 0.43 (22570) hydrogen bonds : bond 0.06131 / 3.84 ( 625) hydrogen bonds : angle 5.61338 / 3.81 ( 1539) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 173 time to evaluate : 0.518 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 30 ILE cc_start: 0.9200 (OUTLIER) cc_final: 0.8966 (pp) REVERT: C 119 GLN cc_start: 0.8726 (OUTLIER) cc_final: 0.8396 (mm-40) REVERT: A 49 GLU cc_start: 0.8668 (mp0) cc_final: 0.8360 (mp0) REVERT: A 70 ARG cc_start: 0.8092 (ttt180) cc_final: 0.7774 (ttt180) REVERT: E 106 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8097 (mp) REVERT: F 49 GLU cc_start: 0.9181 (mt-10) cc_final: 0.8830 (mm-30) REVERT: F 61 THR cc_start: 0.8549 (OUTLIER) cc_final: 0.8050 (t) REVERT: H 106 ILE cc_start: 0.9075 (mm) cc_final: 0.8759 (mt) REVERT: H 118 VAL cc_start: 0.9432 (OUTLIER) cc_final: 0.9100 (p) REVERT: I 53 GLN cc_start: 0.9484 (mm-40) cc_final: 0.9176 (mm-40) REVERT: I 92 ASN cc_start: 0.9254 (OUTLIER) cc_final: 0.9043 (p0) REVERT: I 93 LEU cc_start: 0.8630 (mt) cc_final: 0.8069 (mt) REVERT: I 137 MET cc_start: 0.6721 (tpp) cc_final: 0.6467 (ttm) REVERT: J 6 PHE cc_start: 0.8833 (m-80) cc_final: 0.8137 (m-10) REVERT: J 25 PHE cc_start: 0.8907 (t80) cc_final: 0.8583 (t80) REVERT: J 63 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7941 (tptt) REVERT: J 98 LYS cc_start: 0.9475 (tppt) cc_final: 0.9155 (tppt) REVERT: J 108 GLN cc_start: 0.7344 (mm110) cc_final: 0.6973 (mm110) REVERT: B 86 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.6858 (mtp85) REVERT: D 23 ARG cc_start: 0.8822 (OUTLIER) cc_final: 0.8074 (tpm-80) REVERT: D 48 PHE cc_start: 0.9028 (OUTLIER) cc_final: 0.8553 (t80) REVERT: K 121 GLU cc_start: 0.9416 (tp30) cc_final: 0.9061 (tp30) REVERT: K 136 ARG cc_start: 0.8744 (ptm160) cc_final: 0.8438 (ptm-80) REVERT: K 137 MET cc_start: 0.6279 (tpt) cc_final: 0.5916 (mmm) outliers start: 98 outliers final: 68 residues processed: 254 average time/residue: 0.1171 time to fit residues: 44.0415 Evaluate side-chains 224 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 146 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 0 HIS Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 132 THR Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain I residue 0 HIS Chi-restraints excluded: chain I residue 15 ARG Chi-restraints excluded: chain I residue 28 SER Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 92 ASN Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 2 LEU Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 63 LYS Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 72 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain K residue 0 HIS Chi-restraints excluded: chain K residue 31 VAL Chi-restraints excluded: chain K residue 87 ILE Chi-restraints excluded: chain K residue 111 HIS Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 78 optimal weight: 5.9990 chunk 15 optimal weight: 6.9990 chunk 142 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 20.0000 chunk 98 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 123 optimal weight: 0.3980 chunk 45 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 49 optimal weight: 8.9990 overall best weight: 2.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 ASN A 119 GLN ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 119 GLN I 92 ASN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.048431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.037418 restraints weight = 130846.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.038313 restraints weight = 68905.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.038885 restraints weight = 45946.651| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.039264 restraints weight = 35376.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.039481 restraints weight = 29734.683| |-----------------------------------------------------------------------------| r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 16052 Z= 0.260 Angle : 0.826 9.106 22570 Z= 0.452 Chirality : 0.051 0.345 2562 Planarity : 0.005 0.069 2195 Dihedral : 30.909 163.065 3850 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 23.40 Ramachandran Plot: Outliers : 1.49 % Allowed : 16.93 % Favored : 81.58 % Rotamer: Outliers : 7.81 % Allowed : 25.90 % Favored : 66.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.90 (0.22), residues: 1341 helix: -0.61 (0.23), residues: 495 sheet: -1.69 (0.29), residues: 322 loop : -3.35 (0.23), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 70 TYR 0.027 0.002 TYR E 51 PHE 0.053 0.002 PHE I 48 TRP 0.020 0.002 TRP H 115 HIS 0.011 0.002 HIS D 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00532 / 0.26 (16052) covalent geometry : angle 0.82559 / 0.45 (22570) hydrogen bonds : bond 0.07198 / 4.49 ( 625) hydrogen bonds : angle 5.70952 / 3.87 ( 1539) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 150 time to evaluate : 0.505 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: symmetry clash revert: symmetry clash REVERT: C 30 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8986 (pp) REVERT: C 119 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8399 (mm-40) REVERT: A 49 GLU cc_start: 0.8713 (mp0) cc_final: 0.8391 (mp0) REVERT: E 106 ILE cc_start: 0.8459 (OUTLIER) cc_final: 0.8232 (mp) REVERT: F 49 GLU cc_start: 0.9183 (mt-10) cc_final: 0.8831 (mm-30) REVERT: H 106 ILE cc_start: 0.9129 (mm) cc_final: 0.8835 (mt) REVERT: H 118 VAL cc_start: 0.9429 (OUTLIER) cc_final: 0.9159 (p) REVERT: I 53 GLN cc_start: 0.9554 (mm-40) cc_final: 0.9327 (mm-40) REVERT: I 70 ARG cc_start: 0.8555 (mmm160) cc_final: 0.8160 (mmm160) REVERT: I 137 MET cc_start: 0.6718 (tpp) cc_final: 0.6452 (ttm) REVERT: J 6 PHE cc_start: 0.8907 (m-80) cc_final: 0.8097 (m-10) REVERT: J 25 PHE cc_start: 0.8973 (t80) cc_final: 0.8641 (t80) REVERT: J 63 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.8013 (tptt) REVERT: J 98 LYS cc_start: 0.9465 (tppt) cc_final: 0.9093 (tppt) REVERT: B 86 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.6864 (mtp85) REVERT: D 23 ARG cc_start: 0.8878 (OUTLIER) cc_final: 0.8111 (tpm-80) REVERT: D 48 PHE cc_start: 0.9101 (OUTLIER) cc_final: 0.8723 (t80) REVERT: D 58 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7574 (p90) REVERT: D 113 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7529 (mt-10) REVERT: K 121 GLU cc_start: 0.9359 (tp30) cc_final: 0.9037 (tp30) REVERT: K 136 ARG cc_start: 0.8695 (ptm160) cc_final: 0.8406 (ptm-80) outliers start: 98 outliers final: 74 residues processed: 231 average time/residue: 0.1167 time to fit residues: 40.0226 Evaluate side-chains 217 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 134 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 0 HIS Chi-restraints excluded: chain C residue 2 LEU Chi-restraints excluded: chain C residue 3 LEU Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 92 ASN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 14 ASN Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 27 ASP Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain E residue 104 VAL Chi-restraints excluded: chain E residue 106 ILE Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain I residue 0 HIS Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 2 LEU Chi-restraints excluded: chain J residue 63 LYS Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 72 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 29 SER Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain D residue 94 ILE Chi-restraints excluded: chain K residue 0 HIS Chi-restraints excluded: chain K residue 87 ILE Chi-restraints excluded: chain K residue 111 HIS Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 124 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 128 optimal weight: 20.0000 chunk 98 optimal weight: 0.7980 chunk 46 optimal weight: 7.9990 chunk 135 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 38 ASN ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 ASN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 GLN D 53 GLN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.049069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.038103 restraints weight = 128613.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.039033 restraints weight = 66162.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.039640 restraints weight = 43474.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.040035 restraints weight = 32971.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.040280 restraints weight = 27537.074| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 16052 Z= 0.173 Angle : 0.799 9.256 22570 Z= 0.437 Chirality : 0.051 0.357 2562 Planarity : 0.005 0.061 2195 Dihedral : 30.884 162.109 3841 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 20.63 Ramachandran Plot: Outliers : 1.34 % Allowed : 16.41 % Favored : 82.25 % Rotamer: Outliers : 7.49 % Allowed : 25.66 % Favored : 66.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.85 (0.22), residues: 1341 helix: -0.54 (0.23), residues: 496 sheet: -1.60 (0.31), residues: 294 loop : -3.35 (0.22), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 70 TYR 0.027 0.002 TYR E 51 PHE 0.045 0.002 PHE I 48 TRP 0.016 0.002 TRP H 115 HIS 0.006 0.001 HIS D 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.17 (16052) covalent geometry : angle 0.79885 / 0.44 (22570) hydrogen bonds : bond 0.06026 / 3.78 ( 625) hydrogen bonds : angle 5.58317 / 3.80 ( 1539) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 152 time to evaluate : 0.396 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 30 ILE cc_start: 0.9185 (OUTLIER) cc_final: 0.8954 (pp) REVERT: C 119 GLN cc_start: 0.8750 (OUTLIER) cc_final: 0.8388 (mm-40) REVERT: A 49 GLU cc_start: 0.8607 (mp0) cc_final: 0.8274 (mp0) REVERT: A 70 ARG cc_start: 0.8099 (ttt180) cc_final: 0.7766 (ttm170) REVERT: F 49 GLU cc_start: 0.9139 (mt-10) cc_final: 0.8844 (mm-30) REVERT: H 106 ILE cc_start: 0.9073 (mm) cc_final: 0.8782 (mt) REVERT: H 118 VAL cc_start: 0.9431 (OUTLIER) cc_final: 0.9015 (p) REVERT: I 1 MET cc_start: 0.8298 (mmm) cc_final: 0.7650 (tpp) REVERT: I 6 PHE cc_start: 0.7782 (m-80) cc_final: 0.7242 (m-80) REVERT: I 49 GLU cc_start: 0.8722 (tm-30) cc_final: 0.8381 (tm-30) REVERT: I 53 GLN cc_start: 0.9550 (mm-40) cc_final: 0.9305 (mm-40) REVERT: I 137 MET cc_start: 0.6800 (tpp) cc_final: 0.6559 (ttm) REVERT: J 6 PHE cc_start: 0.8917 (m-80) cc_final: 0.8071 (m-10) REVERT: J 25 PHE cc_start: 0.8923 (t80) cc_final: 0.8638 (t80) REVERT: J 63 LYS cc_start: 0.8214 (OUTLIER) cc_final: 0.7942 (tptt) REVERT: J 98 LYS cc_start: 0.9424 (tppt) cc_final: 0.9032 (tppt) REVERT: B 27 ASP cc_start: 0.8927 (OUTLIER) cc_final: 0.8554 (p0) REVERT: B 86 ARG cc_start: 0.7852 (OUTLIER) cc_final: 0.6879 (mtp85) REVERT: B 115 TRP cc_start: 0.8056 (OUTLIER) cc_final: 0.7006 (t60) REVERT: D 23 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8153 (tpm-80) REVERT: D 48 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.8677 (t80) REVERT: D 58 PHE cc_start: 0.7999 (OUTLIER) cc_final: 0.7584 (p90) REVERT: K 121 GLU cc_start: 0.9362 (tp30) cc_final: 0.9060 (tp30) REVERT: K 136 ARG cc_start: 0.8691 (ptm160) cc_final: 0.8383 (ptm-80) outliers start: 94 outliers final: 66 residues processed: 233 average time/residue: 0.1100 time to fit residues: 38.0494 Evaluate side-chains 214 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 138 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 0 HIS Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 30 ILE Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 14 ASN Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 130 LEU Chi-restraints excluded: chain I residue 0 HIS Chi-restraints excluded: chain I residue 38 ASN Chi-restraints excluded: chain I residue 81 LEU Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 99 LEU Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 2 LEU Chi-restraints excluded: chain J residue 63 LYS Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 72 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain K residue 87 ILE Chi-restraints excluded: chain K residue 111 HIS Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 65 optimal weight: 2.9990 chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 91 optimal weight: 0.3980 chunk 118 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 117 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN ** D 108 GLN ** 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 = 0.3546 r_free = 0.3546 target = 0.048694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.037775 restraints weight = 131580.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.038692 restraints weight = 68677.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.039287 restraints weight = 45459.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.039672 restraints weight = 34635.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.039874 restraints weight = 29025.278| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 16052 Z= 0.202 Angle : 0.805 8.707 22570 Z= 0.441 Chirality : 0.051 0.347 2562 Planarity : 0.005 0.052 2195 Dihedral : 30.887 161.200 3841 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 20.53 Ramachandran Plot: Outliers : 1.34 % Allowed : 17.23 % Favored : 81.43 % Rotamer: Outliers : 7.01 % Allowed : 26.37 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.85 (0.22), residues: 1341 helix: -0.47 (0.23), residues: 500 sheet: -1.79 (0.30), residues: 314 loop : -3.35 (0.22), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E 43 TYR 0.017 0.002 TYR E 51 PHE 0.033 0.002 PHE A 52 TRP 0.019 0.002 TRP H 115 HIS 0.007 0.001 HIS D 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00407 / 0.20 (16052) covalent geometry : angle 0.80537 / 0.44 (22570) hydrogen bonds : bond 0.06377 / 3.99 ( 625) hydrogen bonds : angle 5.60187 / 3.80 ( 1539) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 148 time to evaluate : 0.516 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: symmetry clash revert: symmetry clash REVERT: C 119 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8323 (mm-40) REVERT: A 49 GLU cc_start: 0.8595 (mp0) cc_final: 0.8276 (mp0) REVERT: F 49 GLU cc_start: 0.9158 (mt-10) cc_final: 0.8819 (mm-30) REVERT: H 106 ILE cc_start: 0.9100 (mm) cc_final: 0.8833 (mt) REVERT: H 118 VAL cc_start: 0.9294 (OUTLIER) cc_final: 0.9046 (p) REVERT: I 1 MET cc_start: 0.8436 (mmm) cc_final: 0.7582 (tpp) REVERT: I 6 PHE cc_start: 0.7715 (m-80) cc_final: 0.7288 (m-80) REVERT: I 70 ARG cc_start: 0.8649 (mmm160) cc_final: 0.8293 (mmm160) REVERT: J 6 PHE cc_start: 0.8992 (m-80) cc_final: 0.8082 (m-10) REVERT: J 63 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.8004 (tptt) REVERT: J 98 LYS cc_start: 0.9426 (tppt) cc_final: 0.9023 (tppt) REVERT: B 27 ASP cc_start: 0.8940 (OUTLIER) cc_final: 0.8573 (p0) REVERT: B 86 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.6902 (mtp85) REVERT: B 115 TRP cc_start: 0.8083 (OUTLIER) cc_final: 0.6873 (t60) REVERT: D 23 ARG cc_start: 0.8845 (OUTLIER) cc_final: 0.8119 (tpm-80) REVERT: D 48 PHE cc_start: 0.9048 (OUTLIER) cc_final: 0.8755 (t80) REVERT: D 58 PHE cc_start: 0.8081 (OUTLIER) cc_final: 0.7670 (p90) REVERT: K 121 GLU cc_start: 0.9387 (tp30) cc_final: 0.9097 (tp30) REVERT: K 136 ARG cc_start: 0.8764 (ptm160) cc_final: 0.8464 (ptm-80) outliers start: 88 outliers final: 66 residues processed: 221 average time/residue: 0.1091 time to fit residues: 35.9286 Evaluate side-chains 212 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 137 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 0 HIS Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain A residue 21 LYS Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 89 ILE Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain H residue 128 GLU Chi-restraints excluded: chain I residue 0 HIS Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 2 LEU Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 63 LYS Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 29 SER Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 72 ILE Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain K residue 87 ILE Chi-restraints excluded: chain K residue 111 HIS Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 3 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 chunk 55 optimal weight: 0.0970 chunk 10 optimal weight: 3.9990 chunk 100 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 143 optimal weight: 8.9990 chunk 105 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 53 GLN D 108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.049537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.038653 restraints weight = 128933.383| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.039612 restraints weight = 65438.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.040236 restraints weight = 42608.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.040576 restraints weight = 32056.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.040844 restraints weight = 27180.676| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 16052 Z= 0.160 Angle : 0.810 9.696 22570 Z= 0.442 Chirality : 0.052 0.356 2562 Planarity : 0.005 0.054 2195 Dihedral : 30.810 159.757 3837 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 19.03 Ramachandran Plot: Outliers : 1.27 % Allowed : 15.59 % Favored : 83.15 % Rotamer: Outliers : 5.98 % Allowed : 27.89 % Favored : 66.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.79 (0.22), residues: 1341 helix: -0.43 (0.23), residues: 501 sheet: -1.59 (0.31), residues: 293 loop : -3.38 (0.22), residues: 547 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 70 TYR 0.016 0.002 TYR J 51 PHE 0.051 0.002 PHE J 25 TRP 0.015 0.002 TRP I 115 HIS 0.007 0.001 HIS D 0 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.16 (16052) covalent geometry : angle 0.80999 / 0.44 (22570) hydrogen bonds : bond 0.05605 / 3.55 ( 625) hydrogen bonds : angle 5.45460 / 3.73 ( 1539) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 168 time to evaluate : 0.528 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 119 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8370 (mm-40) REVERT: A 49 GLU cc_start: 0.8459 (mp0) cc_final: 0.8163 (mp0) REVERT: A 70 ARG cc_start: 0.7960 (ttt180) cc_final: 0.7685 (ttm170) REVERT: F 49 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8821 (mm-30) REVERT: H 106 ILE cc_start: 0.9077 (mm) cc_final: 0.8846 (mt) REVERT: I 1 MET cc_start: 0.8341 (mmm) cc_final: 0.7563 (tpp) REVERT: I 6 PHE cc_start: 0.7728 (m-80) cc_final: 0.7378 (m-80) REVERT: I 70 ARG cc_start: 0.8517 (mmm160) cc_final: 0.8229 (mmm160) REVERT: I 93 LEU cc_start: 0.8627 (mt) cc_final: 0.8225 (mt) REVERT: J 25 PHE cc_start: 0.8770 (t80) cc_final: 0.8565 (t80) REVERT: J 63 LYS cc_start: 0.8221 (OUTLIER) cc_final: 0.7961 (tptt) REVERT: J 98 LYS cc_start: 0.9363 (tppt) cc_final: 0.8995 (tppt) REVERT: B 27 ASP cc_start: 0.8859 (OUTLIER) cc_final: 0.8501 (p0) REVERT: B 86 ARG cc_start: 0.7883 (OUTLIER) cc_final: 0.6938 (mtp85) REVERT: B 115 TRP cc_start: 0.7854 (OUTLIER) cc_final: 0.7157 (t60) REVERT: D 23 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8087 (tpm-80) REVERT: D 30 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8649 (mm) REVERT: D 48 PHE cc_start: 0.8989 (OUTLIER) cc_final: 0.8677 (t80) REVERT: D 58 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7706 (p90) REVERT: K 121 GLU cc_start: 0.9354 (tp30) cc_final: 0.9096 (tp30) REVERT: K 136 ARG cc_start: 0.8731 (ptm160) cc_final: 0.8427 (ptm-80) outliers start: 75 outliers final: 60 residues processed: 231 average time/residue: 0.1083 time to fit residues: 37.5821 Evaluate side-chains 218 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 149 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 0 HIS Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 119 GLN Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain F residue 48 PHE Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 0 HIS Chi-restraints excluded: chain I residue 38 ASN Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 63 LYS Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 72 ILE Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain K residue 87 ILE Chi-restraints excluded: chain K residue 111 HIS Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 10 optimal weight: 0.6980 chunk 97 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 74 optimal weight: 0.9980 chunk 120 optimal weight: 4.9990 chunk 131 optimal weight: 30.0000 chunk 16 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 0.4980 chunk 83 optimal weight: 0.6980 chunk 54 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 77 ASN C 119 GLN ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 HIS ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN D 53 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.049536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.038694 restraints weight = 129814.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.039635 restraints weight = 67090.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.040244 restraints weight = 44099.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.040599 restraints weight = 33372.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.040866 restraints weight = 28113.869| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.4337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16052 Z= 0.160 Angle : 0.813 16.752 22570 Z= 0.442 Chirality : 0.051 0.349 2562 Planarity : 0.005 0.051 2195 Dihedral : 30.753 159.679 3835 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 1.19 % Allowed : 16.33 % Favored : 82.48 % Rotamer: Outliers : 5.82 % Allowed : 28.37 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.80 (0.22), residues: 1341 helix: -0.48 (0.23), residues: 501 sheet: -1.64 (0.29), residues: 330 loop : -3.39 (0.23), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 70 TYR 0.014 0.002 TYR J 120 PHE 0.048 0.002 PHE J 25 TRP 0.014 0.002 TRP H 115 HIS 0.020 0.002 HIS K 0 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.16 (16052) covalent geometry : angle 0.81257 / 0.44 (22570) hydrogen bonds : bond 0.05684 / 3.59 ( 625) hydrogen bonds : angle 5.36981 / 3.67 ( 1539) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2682 Ramachandran restraints generated. 1341 Oldfield, 0 Emsley, 1341 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 163 time to evaluate : 0.365 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7502 (tt0) REVERT: A 49 GLU cc_start: 0.8556 (mp0) cc_final: 0.8243 (mp0) REVERT: A 70 ARG cc_start: 0.8018 (ttt180) cc_final: 0.7746 (ttm170) REVERT: F 49 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8829 (mm-30) REVERT: H 106 ILE cc_start: 0.9071 (mm) cc_final: 0.8818 (mt) REVERT: I 1 MET cc_start: 0.8230 (mmm) cc_final: 0.7539 (tpp) REVERT: I 6 PHE cc_start: 0.7804 (m-80) cc_final: 0.7406 (m-80) REVERT: I 70 ARG cc_start: 0.8545 (mmm160) cc_final: 0.8262 (mmm160) REVERT: I 93 LEU cc_start: 0.8642 (mt) cc_final: 0.8241 (mt) REVERT: J 6 PHE cc_start: 0.9120 (m-80) cc_final: 0.8822 (m-80) REVERT: J 63 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.8014 (tptt) REVERT: J 98 LYS cc_start: 0.9369 (tppt) cc_final: 0.9003 (tppt) REVERT: B 27 ASP cc_start: 0.8928 (OUTLIER) cc_final: 0.8559 (p0) REVERT: B 86 ARG cc_start: 0.7785 (OUTLIER) cc_final: 0.7557 (mtm-85) REVERT: B 115 TRP cc_start: 0.7777 (OUTLIER) cc_final: 0.7068 (t60) REVERT: D 23 ARG cc_start: 0.8807 (OUTLIER) cc_final: 0.8047 (tpm-80) REVERT: D 30 ILE cc_start: 0.8989 (OUTLIER) cc_final: 0.8639 (mm) REVERT: D 48 PHE cc_start: 0.8994 (OUTLIER) cc_final: 0.8647 (t80) REVERT: K 121 GLU cc_start: 0.9366 (tp30) cc_final: 0.9106 (tp30) REVERT: K 136 ARG cc_start: 0.8750 (ptm160) cc_final: 0.8465 (ptm-80) outliers start: 73 outliers final: 59 residues processed: 222 average time/residue: 0.1084 time to fit residues: 36.0592 Evaluate side-chains 217 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 151 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 0 HIS Chi-restraints excluded: chain C residue 14 ASN Chi-restraints excluded: chain C residue 26 PHE Chi-restraints excluded: chain C residue 55 PHE Chi-restraints excluded: chain C residue 63 LYS Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain A residue 29 SER Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 63 LYS Chi-restraints excluded: chain A residue 64 ASP Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 109 PHE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 129 SER Chi-restraints excluded: chain E residue 11 ASP Chi-restraints excluded: chain E residue 22 LEU Chi-restraints excluded: chain E residue 66 ARG Chi-restraints excluded: chain E residue 77 ASN Chi-restraints excluded: chain E residue 103 ILE Chi-restraints excluded: chain F residue 67 THR Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 31 VAL Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 87 ILE Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain H residue 114 VAL Chi-restraints excluded: chain I residue 0 HIS Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 95 SER Chi-restraints excluded: chain I residue 103 ILE Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 106 ILE Chi-restraints excluded: chain I residue 119 GLN Chi-restraints excluded: chain I residue 121 GLU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 133 VAL Chi-restraints excluded: chain J residue 16 ILE Chi-restraints excluded: chain J residue 63 LYS Chi-restraints excluded: chain J residue 71 LEU Chi-restraints excluded: chain J residue 105 LEU Chi-restraints excluded: chain J residue 118 VAL Chi-restraints excluded: chain J residue 132 THR Chi-restraints excluded: chain J residue 133 VAL Chi-restraints excluded: chain B residue 8 LEU Chi-restraints excluded: chain B residue 12 ASN Chi-restraints excluded: chain B residue 27 ASP Chi-restraints excluded: chain B residue 55 PHE Chi-restraints excluded: chain B residue 63 LYS Chi-restraints excluded: chain B residue 86 ARG Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 99 LEU Chi-restraints excluded: chain B residue 110 ASP Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 27 ASP Chi-restraints excluded: chain D residue 30 ILE Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 58 PHE Chi-restraints excluded: chain D residue 92 ASN Chi-restraints excluded: chain K residue 87 ILE Chi-restraints excluded: chain K residue 114 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 41 optimal weight: 0.0870 chunk 13 optimal weight: 8.9990 chunk 82 optimal weight: 0.2980 chunk 57 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 22 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 140 optimal weight: 1.9990 chunk 102 optimal weight: 0.3980 chunk 137 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 62 GLN ** I 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 77 ASN ** 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 = 0.3585 r_free = 0.3585 target = 0.049991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.039197 restraints weight = 128835.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.040172 restraints weight = 65380.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.040797 restraints weight = 42431.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.041166 restraints weight = 31955.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.041436 restraints weight = 26691.401| |-----------------------------------------------------------------------------| r_work (final): 0.3215 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16052 Z= 0.158 Angle : 0.821 9.741 22570 Z= 0.446 Chirality : 0.051 0.350 2562 Planarity : 0.005 0.049 2195 Dihedral : 30.677 159.556 3830 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 1.12 % Allowed : 15.73 % Favored : 83.15 % Rotamer: Outliers : 5.34 % Allowed : 28.84 % Favored : 65.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.78 (0.22), residues: 1341 helix: -0.53 (0.23), residues: 502 sheet: -1.61 (0.29), residues: 333 loop : -3.33 (0.23), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 136 TYR 0.024 0.002 TYR J 120 PHE 0.037 0.002 PHE A 52 TRP 0.020 0.002 TRP E 115 HIS 0.010 0.002 HIS J 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 (16052) covalent geometry : angle 0.82117 / 0.45 (22570) hydrogen bonds : bond 0.05591 / 3.56 ( 625) hydrogen bonds : angle 5.35449 / 3.65 ( 1539) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2644.58 seconds wall clock time: 46 minutes 32.58 seconds (2792.58 seconds total)