Starting phenix.real_space_refine on Thu Aug 6 13:55:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9sz7_55361/08_2026/9sz7_55361.cif Found real_map, /net/cci-nas-00/data/ceres_data/9sz7_55361/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9sz7_55361/08_2026/9sz7_55361.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9sz7_55361/08_2026/9sz7_55361.map" model { file = "/net/cci-nas-00/data/ceres_data/9sz7_55361/08_2026/9sz7_55361.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9sz7_55361/08_2026/9sz7_55361.cif" } 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-2.2rc3-6140/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: 3.04, per 1000 atoms: 0.20 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: 0.85 Conformation dependent library (CDL) restraints added in 644.6 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: 1.99 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: 2.15 Time building geometry restraints manager: 1.20 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: 21035 1.72 - 3.44: 1378 3.44 - 5.16: 132 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: 9.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 13.560 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.730 ------------------------------------------------------------------------------- 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 : 0.874 8.595 22570 Z= 0.676 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 0.87373 / 0.68 (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 : 0.536 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: 0.8089 (tp) outliers start: 146 outliers final: 53 residues processed: 386 average time/residue: 0.1273 time to fit residues: 71.5168 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 : 0.532 ------------------------------------------------------------------------------- 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 33 ASN C 57 ASN C 92 ASN A 38 ASN ** A 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 GLN 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 = 0.3567 r_free = 0.3567 target = 0.049666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.038769 restraints weight = 129307.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.039681 restraints weight = 67386.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.040272 restraints weight = 44613.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.040615 restraints weight = 33930.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.040883 restraints weight = 28740.278| |-----------------------------------------------------------------------------| r_work (final): 0.3189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 16052 Z= 0.291 Angle : 0.915 11.913 22570 Z= 0.498 Chirality : 0.056 0.345 2562 Planarity : 0.006 0.051 2195 Dihedral : 30.856 166.880 3905 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 25.45 Ramachandran Plot: Outliers : 1.57 % Allowed : 17.38 % Favored : 81.06 % Rotamer: Outliers : 8.37 % Allowed : 20.32 % Favored : 71.31 % 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: -3.37 (0.21), residues: 1341 helix: -1.24 (0.21), residues: 497 sheet: -1.71 (0.28), residues: 347 loop : -3.59 (0.23), residues: 497 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 34 TYR 0.019 0.002 TYR B 51 PHE 0.030 0.003 PHE A 52 TRP 0.014 0.002 TRP H 115 HIS 0.008 0.002 HIS J 0 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.29 (16052) covalent geometry : angle 0.91486 / 0.50 (22570) hydrogen bonds : bond 0.08441 / 5.28 ( 625) hydrogen bonds : angle 6.28445 / 4.28 ( 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: 105 poor density : 175 time to evaluate : 0.534 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: C 30 ILE cc_start: 0.9240 (OUTLIER) cc_final: 0.9031 (pp) REVERT: A 70 ARG cc_start: 0.8005 (ttt180) cc_final: 0.7532 (ttm170) REVERT: E 3 LEU cc_start: 0.8113 (mt) cc_final: 0.7879 (mt) REVERT: E 31 VAL cc_start: 0.9168 (OUTLIER) cc_final: 0.8803 (m) REVERT: F 61 THR cc_start: 0.8357 (OUTLIER) cc_final: 0.8103 (p) REVERT: H 86 ARG cc_start: 0.7340 (OUTLIER) cc_final: 0.7127 (mtp85) REVERT: H 106 ILE cc_start: 0.9035 (mm) cc_final: 0.8531 (mt) REVERT: H 137 MET cc_start: 0.8466 (mmm) cc_final: 0.8243 (mmp) REVERT: J 6 PHE cc_start: 0.8817 (m-80) cc_final: 0.8579 (m-10) REVERT: J 25 PHE cc_start: 0.8689 (t80) cc_final: 0.8450 (t80) REVERT: J 41 GLU cc_start: 0.8191 (mt-10) cc_final: 0.7418 (mt-10) REVERT: J 86 ARG cc_start: 0.7161 (OUTLIER) cc_final: 0.6827 (mtp85) REVERT: J 98 LYS cc_start: 0.9387 (tppt) cc_final: 0.9176 (tptp) REVERT: B 86 ARG cc_start: 0.7937 (OUTLIER) cc_final: 0.7016 (mtp85) REVERT: D 1 MET cc_start: 0.8460 (mmm) cc_final: 0.8169 (tpt) REVERT: D 48 PHE cc_start: 0.9168 (OUTLIER) cc_final: 0.8843 (t80) REVERT: K 136 ARG cc_start: 0.8647 (ptm160) cc_final: 0.8310 (ptm-80) outliers start: 105 outliers final: 60 residues processed: 260 average time/residue: 0.1311 time to fit residues: 50.1855 Evaluate side-chains 209 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 142 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 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 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 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 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 86 ARG 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: 0.3980 chunk 12 optimal weight: 1.9990 chunk 67 optimal weight: 0.5980 chunk 96 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 133 optimal weight: 10.0000 chunk 53 optimal weight: 0.0370 chunk 78 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 overall best weight: 0.5660 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 85 ASN ** 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.050917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.039801 restraints weight = 127638.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.040805 restraints weight = 64051.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.041437 restraints weight = 41367.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.041864 restraints weight = 31195.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.042063 restraints weight = 25721.974| |-----------------------------------------------------------------------------| r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2569 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= 0.170 Angle : 0.840 11.065 22570 Z= 0.458 Chirality : 0.054 0.385 2562 Planarity : 0.005 0.066 2195 Dihedral : 30.814 163.381 3870 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 20.25 Ramachandran Plot: Outliers : 1.49 % Allowed : 16.48 % Favored : 82.03 % Rotamer: Outliers : 6.69 % Allowed : 21.35 % Favored : 71.95 % 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: -3.18 (0.21), residues: 1341 helix: -1.08 (0.22), residues: 501 sheet: -1.57 (0.28), residues: 337 loop : -3.51 (0.23), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 34 TYR 0.014 0.002 TYR C 51 PHE 0.028 0.002 PHE F 73 TRP 0.016 0.002 TRP I 115 HIS 0.006 0.001 HIS C 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.17 (16052) covalent geometry : angle 0.83965 / 0.46 (22570) hydrogen bonds : bond 0.06439 / 4.04 ( 625) hydrogen bonds : angle 5.88249 / 3.99 ( 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 262 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 178 time to evaluate : 0.540 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: A 49 GLU cc_start: 0.8667 (mp0) cc_final: 0.8431 (mp0) REVERT: A 135 GLU cc_start: 0.8492 (mm-30) cc_final: 0.8267 (mm-30) REVERT: E 3 LEU cc_start: 0.8634 (mt) cc_final: 0.8391 (mt) REVERT: E 100 ASP cc_start: 0.7969 (p0) cc_final: 0.7716 (m-30) REVERT: E 106 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8061 (mp) REVERT: F 49 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8782 (mm-30) REVERT: H 106 ILE cc_start: 0.8862 (mm) cc_final: 0.8407 (mt) REVERT: H 118 VAL cc_start: 0.9429 (OUTLIER) cc_final: 0.9085 (p) REVERT: I 49 GLU cc_start: 0.8733 (tm-30) cc_final: 0.8354 (tm-30) REVERT: I 53 GLN cc_start: 0.9259 (mm-40) cc_final: 0.8991 (mm-40) REVERT: J 6 PHE cc_start: 0.8750 (m-80) cc_final: 0.8385 (m-10) REVERT: J 86 ARG cc_start: 0.7165 (OUTLIER) cc_final: 0.6826 (mtp85) REVERT: J 98 LYS cc_start: 0.9435 (tppt) cc_final: 0.9113 (tptp) REVERT: B 86 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.6948 (mtp85) REVERT: D 1 MET cc_start: 0.8484 (mmm) cc_final: 0.8259 (tpt) REVERT: D 48 PHE cc_start: 0.9099 (OUTLIER) cc_final: 0.8806 (t80) REVERT: D 60 ASN cc_start: 0.6842 (t0) cc_final: 0.6263 (t0) REVERT: K 81 LEU cc_start: 0.8944 (OUTLIER) cc_final: 0.7049 (mt) REVERT: K 121 GLU cc_start: 0.9338 (tp30) cc_final: 0.9063 (tp30) REVERT: K 136 ARG cc_start: 0.8702 (ptm160) cc_final: 0.8374 (ptm-80) outliers start: 84 outliers final: 50 residues processed: 243 average time/residue: 0.1208 time to fit residues: 44.1442 Evaluate side-chains 202 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 146 time to evaluate : 0.490 ------------------------------------------------------------------------------- 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 114 VAL 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 5 THR 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 41 GLU Chi-restraints excluded: chain F residue 48 PHE 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 I residue 0 HIS 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 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 72 ILE Chi-restraints excluded: chain J residue 86 ARG 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 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 27 ASP Chi-restraints excluded: chain D residue 48 PHE Chi-restraints excluded: chain D residue 58 PHE 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: 9.9990 chunk 86 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 115 optimal weight: 0.2980 chunk 36 optimal weight: 6.9990 chunk 57 optimal weight: 8.9990 chunk 89 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 131 optimal weight: 40.0000 chunk 75 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN C 119 GLN ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 14 ASN I 85 ASN I 92 ASN I 108 GLN I 119 GLN ** J 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 ASN D 33 ASN D 60 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.050487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.039600 restraints weight = 128290.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.040558 restraints weight = 65145.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.041180 restraints weight = 42489.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.041478 restraints weight = 31903.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.041808 restraints weight = 27362.629| |-----------------------------------------------------------------------------| r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.2938 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= 0.168 Angle : 0.817 11.256 22570 Z= 0.444 Chirality : 0.052 0.369 2562 Planarity : 0.005 0.055 2195 Dihedral : 30.765 162.298 3853 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 1.49 % Allowed : 16.03 % Favored : 82.48 % Rotamer: Outliers : 6.45 % Allowed : 22.31 % Favored : 71.24 % 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: -2.98 (0.21), residues: 1341 helix: -0.95 (0.22), residues: 502 sheet: -1.60 (0.29), residues: 330 loop : -3.22 (0.24), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 70 TYR 0.016 0.002 TYR J 120 PHE 0.027 0.002 PHE E 109 TRP 0.012 0.002 TRP I 115 HIS 0.008 0.001 HIS J 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.17 (16052) covalent geometry : angle 0.81722 / 0.44 (22570) hydrogen bonds : bond 0.06430 / 4.02 ( 625) hydrogen bonds : angle 5.63603 / 3.81 ( 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 252 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 171 time to evaluate : 0.490 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: 0.9174 (OUTLIER) cc_final: 0.8972 (pp) REVERT: A 49 GLU cc_start: 0.8661 (mp0) cc_final: 0.8441 (mp0) REVERT: E 106 ILE cc_start: 0.8256 (OUTLIER) cc_final: 0.7992 (mp) REVERT: F 49 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8790 (mm-30) REVERT: F 61 THR cc_start: 0.8553 (OUTLIER) cc_final: 0.8297 (p) REVERT: H 64 ASP cc_start: 0.8386 (m-30) cc_final: 0.8145 (t0) REVERT: H 86 ARG cc_start: 0.7342 (OUTLIER) cc_final: 0.7137 (mtp85) REVERT: H 106 ILE cc_start: 0.8952 (mm) cc_final: 0.8567 (mt) REVERT: I 49 GLU cc_start: 0.8781 (tm-30) cc_final: 0.8375 (tm-30) REVERT: I 53 GLN cc_start: 0.9379 (mm-40) cc_final: 0.9052 (mm-40) REVERT: I 93 LEU cc_start: 0.8520 (mt) cc_final: 0.8126 (mt) REVERT: I 109 PHE cc_start: 0.6230 (t80) cc_final: 0.5088 (t80) REVERT: J 6 PHE cc_start: 0.8801 (m-80) cc_final: 0.8390 (m-10) REVERT: J 25 PHE cc_start: 0.8825 (t80) cc_final: 0.8571 (t80) REVERT: B 86 ARG cc_start: 0.7870 (OUTLIER) cc_final: 0.6948 (mtp85) REVERT: B 95 SER cc_start: 0.9439 (t) cc_final: 0.9194 (p) REVERT: D 48 PHE cc_start: 0.9058 (OUTLIER) cc_final: 0.8632 (t80) REVERT: K 121 GLU cc_start: 0.9360 (tp30) cc_final: 0.9037 (tp30) REVERT: K 136 ARG cc_start: 0.8720 (ptm160) cc_final: 0.8410 (ptm-80) outliers start: 81 outliers final: 54 residues processed: 236 average time/residue: 0.1247 time to fit residues: 43.9444 Evaluate side-chains 212 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 152 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 48 PHE Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 104 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 103 ILE 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 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 121 GLU Chi-restraints excluded: chain I residue 130 LEU Chi-restraints excluded: chain I residue 133 VAL 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 110 ASP Chi-restraints excluded: chain B residue 115 TRP Chi-restraints excluded: chain D residue 27 ASP 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 110 ASP Chi-restraints excluded: chain K residue 0 HIS Chi-restraints excluded: chain K residue 31 VAL 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: 0.6980 chunk 56 optimal weight: 0.5980 chunk 40 optimal weight: 4.9990 chunk 62 optimal weight: 0.7980 chunk 76 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 31 optimal weight: 9.9990 chunk 138 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 114 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 HIS ** J 119 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 = 0.3600 r_free = 0.3600 target = 0.050690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.039856 restraints weight = 128281.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.040838 restraints weight = 64755.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.041487 restraints weight = 41835.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.041909 restraints weight = 31149.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.042059 restraints weight = 25635.323| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16052 Z= 0.161 Angle : 0.802 9.306 22570 Z= 0.436 Chirality : 0.052 0.376 2562 Planarity : 0.005 0.056 2195 Dihedral : 30.697 161.006 3847 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 1.49 % Allowed : 16.03 % Favored : 82.48 % Rotamer: Outliers : 5.90 % Allowed : 24.30 % Favored : 69.80 % 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: -2.87 (0.22), residues: 1341 helix: -0.78 (0.22), residues: 498 sheet: -1.58 (0.29), residues: 330 loop : -3.22 (0.24), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG H 70 TYR 0.016 0.001 TYR J 120 PHE 0.026 0.001 PHE C 52 TRP 0.014 0.002 TRP I 115 HIS 0.007 0.001 HIS J 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 (16052) covalent geometry : angle 0.80248 / 0.44 (22570) hydrogen bonds : bond 0.06040 / 3.82 ( 625) hydrogen bonds : angle 5.49869 / 3.73 ( 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 243 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 169 time to evaluate : 0.526 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: 0.9160 (OUTLIER) cc_final: 0.8948 (pp) REVERT: C 101 LYS cc_start: 0.8715 (tptt) cc_final: 0.8377 (tptt) REVERT: A 49 GLU cc_start: 0.8690 (mp0) cc_final: 0.8373 (mp0) REVERT: E 100 ASP cc_start: 0.8184 (p0) cc_final: 0.7932 (m-30) REVERT: E 106 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7980 (mp) REVERT: F 49 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8787 (mm-30) REVERT: F 52 PHE cc_start: 0.7773 (t80) cc_final: 0.7552 (t80) REVERT: F 61 THR cc_start: 0.8448 (OUTLIER) cc_final: 0.7963 (t) REVERT: H 64 ASP cc_start: 0.8388 (m-30) cc_final: 0.8122 (t0) REVERT: H 86 ARG cc_start: 0.7485 (OUTLIER) cc_final: 0.7244 (mtp85) REVERT: H 106 ILE cc_start: 0.8953 (mm) cc_final: 0.8572 (mt) REVERT: I 49 GLU cc_start: 0.8790 (tm-30) cc_final: 0.8365 (tm-30) REVERT: I 53 GLN cc_start: 0.9452 (mm-40) cc_final: 0.9109 (mm-40) REVERT: I 70 ARG cc_start: 0.8490 (mmm160) cc_final: 0.8133 (mmm160) REVERT: I 93 LEU cc_start: 0.8581 (mt) cc_final: 0.8019 (mt) REVERT: J 6 PHE cc_start: 0.8869 (m-80) cc_final: 0.8069 (m-10) REVERT: J 25 PHE cc_start: 0.8859 (t80) cc_final: 0.8521 (t80) REVERT: J 63 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7929 (tptt) REVERT: B 86 ARG cc_start: 0.7829 (OUTLIER) cc_final: 0.6966 (mtp85) REVERT: B 95 SER cc_start: 0.9429 (t) cc_final: 0.9190 (p) REVERT: D 23 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.8357 (tpm-80) REVERT: D 48 PHE cc_start: 0.9057 (OUTLIER) cc_final: 0.8615 (t80) REVERT: D 49 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8647 (mt-10) REVERT: K 121 GLU cc_start: 0.9401 (tp30) cc_final: 0.9001 (tp30) REVERT: K 136 ARG cc_start: 0.8687 (ptm160) cc_final: 0.8408 (ptm-80) outliers start: 74 outliers final: 53 residues processed: 224 average time/residue: 0.1228 time to fit residues: 40.4657 Evaluate side-chains 210 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 149 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 128 GLU 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 48 PHE 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 61 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 55 PHE Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain I residue 0 HIS 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 J residue 63 LYS 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 D residue 23 ARG Chi-restraints excluded: chain D residue 27 ASP 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 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: 2.9990 chunk 15 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 20.0000 chunk 98 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 123 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 120 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 53 GLN ** E 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 53 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 GLN ** I 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 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 57 ASN ** 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 = 0.3533 r_free = 0.3533 target = 0.048296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.037307 restraints weight = 132330.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.038206 restraints weight = 68847.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.038790 restraints weight = 45606.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.039166 restraints weight = 34850.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.039410 restraints weight = 29296.189| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 16052 Z= 0.290 Angle : 0.884 9.021 22570 Z= 0.474 Chirality : 0.053 0.357 2562 Planarity : 0.005 0.072 2195 Dihedral : 30.826 161.536 3836 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 25.45 Ramachandran Plot: Outliers : 1.42 % Allowed : 17.30 % Favored : 81.28 % Rotamer: Outliers : 7.09 % Allowed : 24.30 % Favored : 68.61 % 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: -2.94 (0.22), residues: 1341 helix: -0.72 (0.22), residues: 496 sheet: -1.59 (0.29), residues: 328 loop : -3.39 (0.23), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 34 TYR 0.020 0.002 TYR B 51 PHE 0.027 0.002 PHE A 52 TRP 0.022 0.003 TRP H 115 HIS 0.006 0.002 HIS E 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00600 / 0.29 (16052) covalent geometry : angle 0.88371 / 0.47 (22570) hydrogen bonds : bond 0.08469 / 5.29 ( 625) hydrogen bonds : angle 5.66468 / 3.84 ( 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 240 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 151 time to evaluate : 0.471 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: A 41 GLU cc_start: 0.7830 (mt-10) cc_final: 0.7312 (tt0) REVERT: A 49 GLU cc_start: 0.8699 (mp0) cc_final: 0.8387 (mp0) REVERT: E 106 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8216 (mp) REVERT: F 49 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8801 (mm-30) REVERT: F 61 THR cc_start: 0.8634 (OUTLIER) cc_final: 0.8376 (p) REVERT: H 64 ASP cc_start: 0.8451 (m-30) cc_final: 0.8147 (t0) REVERT: H 86 ARG cc_start: 0.7936 (OUTLIER) cc_final: 0.6978 (mtp180) REVERT: H 106 ILE cc_start: 0.9171 (mm) cc_final: 0.8826 (mt) REVERT: I 49 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8380 (tm-30) REVERT: I 53 GLN cc_start: 0.9542 (mm-40) cc_final: 0.9265 (mm-40) REVERT: I 93 LEU cc_start: 0.8666 (mt) cc_final: 0.8109 (mt) REVERT: J 6 PHE cc_start: 0.8890 (m-80) cc_final: 0.8086 (m-10) REVERT: J 25 PHE cc_start: 0.8912 (t80) cc_final: 0.8530 (t80) REVERT: J 63 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.8027 (tptt) REVERT: B 86 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.6932 (mtp85) REVERT: B 95 SER cc_start: 0.9451 (t) cc_final: 0.9243 (p) REVERT: D 48 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.8825 (t80) REVERT: D 49 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8581 (mt-10) REVERT: K 121 GLU cc_start: 0.9474 (tp30) cc_final: 0.9135 (tp30) REVERT: K 136 ARG cc_start: 0.8705 (ptm160) cc_final: 0.8401 (ptm-80) outliers start: 89 outliers final: 71 residues processed: 224 average time/residue: 0.1099 time to fit residues: 36.9609 Evaluate side-chains 213 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 136 time to evaluate : 0.438 ------------------------------------------------------------------------------- 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 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 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 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 3 LEU Chi-restraints excluded: chain H residue 30 ILE Chi-restraints excluded: chain H residue 55 PHE Chi-restraints excluded: chain H residue 82 ASP Chi-restraints excluded: chain H residue 86 ARG Chi-restraints excluded: chain H residue 103 ILE Chi-restraints excluded: chain I residue 0 HIS Chi-restraints excluded: chain I residue 28 SER 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 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 103 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 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 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 124 optimal weight: 0.8980 chunk 2 optimal weight: 0.9990 chunk 128 optimal weight: 20.0000 chunk 98 optimal weight: 6.9990 chunk 46 optimal weight: 7.9990 chunk 135 optimal weight: 0.5980 chunk 90 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 67 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 111 HIS ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 108 GLN J 111 HIS ** 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 Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.049576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.038645 restraints weight = 128345.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.039601 restraints weight = 65093.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.040203 restraints weight = 42525.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.040608 restraints weight = 32323.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.040818 restraints weight = 26842.562| |-----------------------------------------------------------------------------| r_work (final): 0.3196 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 16052 Z= 0.162 Angle : 0.808 8.973 22570 Z= 0.438 Chirality : 0.053 0.384 2562 Planarity : 0.005 0.049 2195 Dihedral : 30.747 159.995 3834 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 18.93 Ramachandran Plot: Outliers : 1.27 % Allowed : 15.81 % Favored : 82.92 % Rotamer: Outliers : 6.22 % Allowed : 25.10 % 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: -2.85 (0.22), residues: 1341 helix: -0.58 (0.23), residues: 496 sheet: -1.68 (0.29), residues: 333 loop : -3.31 (0.23), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 34 TYR 0.018 0.002 TYR J 120 PHE 0.032 0.002 PHE A 52 TRP 0.016 0.002 TRP H 115 HIS 0.005 0.001 HIS B 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.16 (16052) covalent geometry : angle 0.80782 / 0.44 (22570) hydrogen bonds : bond 0.05685 / 3.59 ( 625) hydrogen bonds : angle 5.43480 / 3.70 ( 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 241 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 163 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLU cc_start: 0.7756 (mt-10) cc_final: 0.7192 (tt0) REVERT: A 49 GLU cc_start: 0.8580 (mp0) cc_final: 0.8267 (mp0) REVERT: E 106 ILE cc_start: 0.8376 (OUTLIER) cc_final: 0.8131 (mp) REVERT: F 49 GLU cc_start: 0.9177 (mt-10) cc_final: 0.8776 (mm-30) REVERT: H 106 ILE cc_start: 0.9060 (mm) cc_final: 0.8737 (mt) REVERT: I 49 GLU cc_start: 0.8719 (tm-30) cc_final: 0.8383 (tm-30) REVERT: I 53 GLN cc_start: 0.9549 (mm-40) cc_final: 0.9326 (mm-40) REVERT: I 93 LEU cc_start: 0.8599 (mt) cc_final: 0.8008 (mt) REVERT: J 6 PHE cc_start: 0.8900 (m-80) cc_final: 0.8050 (m-10) REVERT: J 25 PHE cc_start: 0.8866 (t80) cc_final: 0.8645 (t80) REVERT: J 63 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7920 (tptt) REVERT: J 98 LYS cc_start: 0.9235 (tppt) cc_final: 0.8907 (tptp) REVERT: J 103 ILE cc_start: 0.8595 (OUTLIER) cc_final: 0.8264 (pt) REVERT: B 86 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.6939 (mtp85) REVERT: B 115 TRP cc_start: 0.7945 (OUTLIER) cc_final: 0.6757 (t60) REVERT: D 1 MET cc_start: 0.8197 (tpt) cc_final: 0.7431 (mmm) REVERT: D 23 ARG cc_start: 0.8812 (OUTLIER) cc_final: 0.8125 (tpm-80) REVERT: D 48 PHE cc_start: 0.9047 (OUTLIER) cc_final: 0.8739 (t80) REVERT: D 49 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8519 (mt-10) REVERT: D 58 PHE cc_start: 0.7954 (OUTLIER) cc_final: 0.7582 (p90) REVERT: K 80 GLU cc_start: 0.8538 (mp0) cc_final: 0.8248 (pm20) REVERT: K 121 GLU cc_start: 0.9457 (tp30) cc_final: 0.9127 (tp30) REVERT: K 136 ARG cc_start: 0.8722 (ptm160) cc_final: 0.8463 (ptm-80) REVERT: K 137 MET cc_start: 0.6347 (tpt) cc_final: 0.6015 (mmm) outliers start: 78 outliers final: 53 residues processed: 225 average time/residue: 0.1059 time to fit residues: 35.2326 Evaluate side-chains 200 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 139 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 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 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 104 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain H residue 3 LEU 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 I residue 0 HIS 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 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 103 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 23 ARG 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 65 optimal weight: 1.9990 chunk 30 optimal weight: 20.0000 chunk 16 optimal weight: 4.9990 chunk 77 optimal weight: 2.9990 chunk 112 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 118 optimal weight: 3.9990 chunk 122 optimal weight: 3.9990 chunk 117 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 39 optimal weight: 0.8980 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 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** B 122 GLN 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 = 0.3531 r_free = 0.3531 target = 0.048183 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.037200 restraints weight = 132420.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.038102 restraints weight = 69174.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.038695 restraints weight = 45921.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.039062 restraints weight = 35024.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.039276 restraints weight = 29571.738| |-----------------------------------------------------------------------------| r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 16052 Z= 0.258 Angle : 0.856 10.110 22570 Z= 0.464 Chirality : 0.052 0.361 2562 Planarity : 0.005 0.062 2195 Dihedral : 30.814 160.132 3834 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 1.27 % Allowed : 17.97 % Favored : 80.76 % Rotamer: Outliers : 6.29 % Allowed : 25.42 % Favored : 68.29 % 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: -2.89 (0.22), residues: 1341 helix: -0.64 (0.22), residues: 503 sheet: -1.60 (0.31), residues: 306 loop : -3.37 (0.23), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 70 TYR 0.019 0.002 TYR A 120 PHE 0.042 0.002 PHE I 48 TRP 0.017 0.002 TRP H 115 HIS 0.010 0.001 HIS J 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00531 / 0.26 (16052) covalent geometry : angle 0.85572 / 0.46 (22570) hydrogen bonds : bond 0.07331 / 4.56 ( 625) hydrogen bonds : angle 5.58528 / 3.79 ( 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 217 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 138 time to evaluate : 0.514 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: A 41 GLU cc_start: 0.7788 (mt-10) cc_final: 0.7207 (tt0) REVERT: A 49 GLU cc_start: 0.8615 (mp0) cc_final: 0.8301 (mp0) REVERT: E 106 ILE cc_start: 0.8504 (OUTLIER) cc_final: 0.8266 (mp) REVERT: F 26 PHE cc_start: 0.8227 (t80) cc_final: 0.7897 (t80) REVERT: F 49 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8826 (mm-30) REVERT: H 106 ILE cc_start: 0.9140 (mm) cc_final: 0.8843 (mt) REVERT: I 93 LEU cc_start: 0.8682 (mt) cc_final: 0.8100 (mt) REVERT: J 6 PHE cc_start: 0.8969 (m-80) cc_final: 0.8071 (m-10) REVERT: J 25 PHE cc_start: 0.8951 (t80) cc_final: 0.8702 (t80) REVERT: J 63 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.8042 (tptt) REVERT: J 98 LYS cc_start: 0.9351 (tppt) cc_final: 0.8982 (tptp) REVERT: B 86 ARG cc_start: 0.7815 (OUTLIER) cc_final: 0.6884 (mtp85) REVERT: B 115 TRP cc_start: 0.8125 (OUTLIER) cc_final: 0.6867 (t60) REVERT: D 23 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8101 (tpm-80) REVERT: D 48 PHE cc_start: 0.9055 (OUTLIER) cc_final: 0.8810 (t80) REVERT: D 58 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7677 (p90) REVERT: K 80 GLU cc_start: 0.8668 (mp0) cc_final: 0.8369 (pm20) REVERT: K 121 GLU cc_start: 0.9500 (tp30) cc_final: 0.9153 (tp30) REVERT: K 136 ARG cc_start: 0.8729 (ptm160) cc_final: 0.8476 (ptm-80) outliers start: 79 outliers final: 60 residues processed: 204 average time/residue: 0.1127 time to fit residues: 34.1668 Evaluate side-chains 198 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 131 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 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 E residue 106 ILE 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 30 ILE 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 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 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 23 ARG 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 106 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 145 random chunks: chunk 3 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 143 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 119 optimal weight: 0.5980 chunk 46 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 119 GLN ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 122 GLN ** 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** B 119 GLN D 53 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.049440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.038525 restraints weight = 128705.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.039465 restraints weight = 66284.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.040072 restraints weight = 43544.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.040462 restraints weight = 33004.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.040701 restraints weight = 27568.177| |-----------------------------------------------------------------------------| r_work (final): 0.3194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4213 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= 0.163 Angle : 0.822 10.352 22570 Z= 0.446 Chirality : 0.053 0.384 2562 Planarity : 0.005 0.045 2195 Dihedral : 30.732 159.113 3832 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 18.24 Ramachandran Plot: Outliers : 1.19 % Allowed : 16.11 % Favored : 82.70 % Rotamer: Outliers : 5.42 % Allowed : 26.37 % Favored : 68.21 % 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: -2.86 (0.22), residues: 1341 helix: -0.57 (0.23), residues: 501 sheet: -1.69 (0.30), residues: 309 loop : -3.32 (0.23), residues: 531 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 70 TYR 0.016 0.002 TYR J 120 PHE 0.070 0.002 PHE I 48 TRP 0.016 0.002 TRP I 115 HIS 0.011 0.002 HIS J 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.16 (16052) covalent geometry : angle 0.82206 / 0.45 (22570) hydrogen bonds : bond 0.05570 / 3.51 ( 625) hydrogen bonds : angle 5.45932 / 3.70 ( 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 230 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 162 time to evaluate : 0.589 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: A 49 GLU cc_start: 0.8571 (mp0) cc_final: 0.8239 (mp0) REVERT: F 49 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8805 (mm-30) REVERT: H 106 ILE cc_start: 0.9056 (mm) cc_final: 0.8769 (mt) REVERT: I 6 PHE cc_start: 0.7817 (m-80) cc_final: 0.7360 (m-80) REVERT: I 93 LEU cc_start: 0.8644 (mt) cc_final: 0.8051 (mt) REVERT: J 25 PHE cc_start: 0.8882 (t80) cc_final: 0.8673 (t80) REVERT: J 63 LYS cc_start: 0.8235 (OUTLIER) cc_final: 0.8003 (tptt) REVERT: B 86 ARG cc_start: 0.7750 (OUTLIER) cc_final: 0.6840 (mtp85) REVERT: B 115 TRP cc_start: 0.7845 (OUTLIER) cc_final: 0.6810 (t60) REVERT: D 23 ARG cc_start: 0.8836 (OUTLIER) cc_final: 0.8166 (tpm-80) REVERT: D 48 PHE cc_start: 0.9029 (OUTLIER) cc_final: 0.8745 (t80) REVERT: D 58 PHE cc_start: 0.8032 (OUTLIER) cc_final: 0.7651 (p90) REVERT: K 80 GLU cc_start: 0.8605 (mp0) cc_final: 0.8296 (pm20) REVERT: K 121 GLU cc_start: 0.9473 (tp30) cc_final: 0.9128 (tp30) outliers start: 68 outliers final: 52 residues processed: 218 average time/residue: 0.1235 time to fit residues: 40.0176 Evaluate side-chains 203 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 145 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASN 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 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 104 VAL Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 30 ILE 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 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 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 23 ARG 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: 0.3980 chunk 97 optimal weight: 2.9990 chunk 90 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 120 optimal weight: 0.7980 chunk 131 optimal weight: 30.0000 chunk 16 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 62 GLN ** H 122 GLN ** 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** B 122 GLN D 53 GLN ** D 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.049620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.038789 restraints weight = 130204.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.039736 restraints weight = 66912.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.040340 restraints weight = 43973.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.040727 restraints weight = 33382.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.040953 restraints weight = 27917.144| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 16052 Z= 0.165 Angle : 0.831 11.038 22570 Z= 0.451 Chirality : 0.053 0.373 2562 Planarity : 0.005 0.066 2195 Dihedral : 30.692 159.009 3832 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 18.86 Ramachandran Plot: Outliers : 1.19 % Allowed : 16.33 % Favored : 82.48 % Rotamer: Outliers : 5.18 % Allowed : 26.77 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.88 (0.22), residues: 1341 helix: -0.60 (0.23), residues: 502 sheet: -1.72 (0.30), residues: 310 loop : -3.31 (0.23), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 43 TYR 0.014 0.002 TYR J 120 PHE 0.038 0.002 PHE A 52 TRP 0.017 0.002 TRP I 115 HIS 0.015 0.002 HIS J 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.16 (16052) covalent geometry : angle 0.83068 / 0.45 (22570) hydrogen bonds : bond 0.05737 / 3.59 ( 625) hydrogen bonds : angle 5.43314 / 3.68 ( 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 216 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 151 time to evaluate : 0.406 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: A 41 GLU cc_start: 0.7603 (mt-10) cc_final: 0.7007 (tt0) REVERT: A 49 GLU cc_start: 0.8555 (mp0) cc_final: 0.8242 (mp0) REVERT: F 49 GLU cc_start: 0.9184 (mt-10) cc_final: 0.8806 (mm-30) REVERT: H 106 ILE cc_start: 0.9060 (mm) cc_final: 0.8788 (mt) REVERT: I 6 PHE cc_start: 0.7803 (m-80) cc_final: 0.7433 (m-80) REVERT: I 93 LEU cc_start: 0.8646 (mt) cc_final: 0.8048 (mt) REVERT: J 6 PHE cc_start: 0.9095 (m-80) cc_final: 0.8614 (m-80) REVERT: J 25 PHE cc_start: 0.8843 (t80) cc_final: 0.8574 (t80) REVERT: J 63 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7997 (tptt) REVERT: J 98 LYS cc_start: 0.9156 (tppt) cc_final: 0.8843 (tptt) REVERT: B 86 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.6920 (mtp85) REVERT: B 115 TRP cc_start: 0.7735 (OUTLIER) cc_final: 0.6783 (t60) REVERT: D 23 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.8079 (tpm-80) REVERT: D 30 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8604 (mm) REVERT: D 48 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8702 (t80) REVERT: D 58 PHE cc_start: 0.8013 (OUTLIER) cc_final: 0.7636 (p90) REVERT: K 80 GLU cc_start: 0.8600 (mp0) cc_final: 0.8271 (pm20) REVERT: K 121 GLU cc_start: 0.9462 (tp30) cc_final: 0.9103 (tp30) outliers start: 65 outliers final: 52 residues processed: 204 average time/residue: 0.1298 time to fit residues: 39.1595 Evaluate side-chains 202 residues out of total 1255 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 143 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ASN 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 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 104 VAL Chi-restraints excluded: chain F residue 115 TRP Chi-restraints excluded: chain H residue 3 LEU Chi-restraints excluded: chain H residue 30 ILE 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 81 LEU 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 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 23 ARG 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 41 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 82 optimal weight: 0.9980 chunk 57 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 140 optimal weight: 0.2980 chunk 102 optimal weight: 0.9980 chunk 137 optimal weight: 7.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** H 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 38 ASN ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.049744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.038777 restraints weight = 128732.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.039734 restraints weight = 65418.479| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.040351 restraints weight = 42702.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.040752 restraints weight = 32275.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.040957 restraints weight = 26898.231| |-----------------------------------------------------------------------------| r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16052 Z= 0.165 Angle : 0.826 10.981 22570 Z= 0.448 Chirality : 0.052 0.370 2562 Planarity : 0.005 0.065 2195 Dihedral : 30.637 158.963 3830 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 18.65 Ramachandran Plot: Outliers : 1.12 % Allowed : 16.41 % Favored : 82.48 % Rotamer: Outliers : 5.34 % Allowed : 26.37 % Favored : 68.29 % 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: -2.86 (0.22), residues: 1341 helix: -0.59 (0.23), residues: 501 sheet: -1.69 (0.30), residues: 307 loop : -3.29 (0.23), residues: 533 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 136 TYR 0.017 0.002 TYR E 51 PHE 0.039 0.001 PHE A 52 TRP 0.016 0.002 TRP I 115 HIS 0.012 0.001 HIS J 111 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.16 (16052) covalent geometry : angle 0.82606 / 0.45 (22570) hydrogen bonds : bond 0.05692 / 3.59 ( 625) hydrogen bonds : angle 5.38457 / 3.64 ( 1539) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2719.55 seconds wall clock time: 47 minutes 46.58 seconds (2866.58 seconds total)