Starting phenix.real_space_refine on Thu Mar 5 02:56:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7af5_11753/03_2026/7af5_11753_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7af5_11753/03_2026/7af5_11753.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7af5_11753/03_2026/7af5_11753_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7af5_11753/03_2026/7af5_11753_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7af5_11753/03_2026/7af5_11753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7af5_11753/03_2026/7af5_11753.map" } resolution = 2.96 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= 0.002 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 456 5.49 5 Mg 52 5.21 5 S 28 5.16 5 C 9824 2.51 5 N 3444 2.21 5 O 4726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18531 Number of models: 1 Model: "" Number of chains: 11 Chain: "1" Number of atoms: 9758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 9758 Classifications: {'RNA': 456} Modifications used: {'rna2p_pur': 36, 'rna2p_pyr': 35, 'rna3p': 3, 'rna3p_pur': 212, 'rna3p_pyr': 170} Link IDs: {'rna2p': 71, 'rna3p': 384} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1653 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 7, 'TRANS': 203} Chain: "G" Number of atoms: 1151 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1151 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 5, 'TRANS': 141} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 795 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "M" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "S" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "1" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Unusual residues: {' MG': 52} Classifications: {'undetermined': 52} Link IDs: {None: 51} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.68, per 1000 atoms: 0.20 Number of scatterers: 18531 At special positions: 0 Unit cell: (116.55, 151.2, 121.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 28 16.00 P 456 15.00 Mg 52 11.99 O 4726 8.00 N 3444 7.00 C 9824 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 481.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2044 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 9 sheets defined 48.8% alpha, 16.1% beta 138 base pairs and 249 stacking pairs defined. Time for finding SS restraints: 2.55 Creating SS restraints... Processing helix chain 'B' and resid 5 through 13 removed outlier: 3.707A pdb=" N ALA B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 42 through 63 Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 76 through 86 Processing helix chain 'B' and resid 103 through 124 removed outlier: 3.570A pdb=" N VAL B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLN B 122 " --> pdb=" O GLU B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 149 Processing helix chain 'B' and resid 169 through 180 Processing helix chain 'B' and resid 192 through 196 removed outlier: 4.226A pdb=" N GLY B 195 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 206 through 227 Processing helix chain 'C' and resid 25 through 47 removed outlier: 4.706A pdb=" N ALA C 30 " --> pdb=" O THR C 26 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ASP C 31 " --> pdb=" O LYS C 27 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 81 through 96 Processing helix chain 'C' and resid 112 through 126 removed outlier: 3.565A pdb=" N ARG C 126 " --> pdb=" O SER C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 129 through 144 Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'G' and resid 21 through 31 Processing helix chain 'G' and resid 35 through 54 removed outlier: 3.505A pdb=" N GLN G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 70 removed outlier: 3.959A pdb=" N GLU G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 110 removed outlier: 3.508A pdb=" N ARG G 96 " --> pdb=" O ARG G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 129 Processing helix chain 'G' and resid 133 through 144 Processing helix chain 'I' and resid 35 through 39 Processing helix chain 'I' and resid 41 through 55 removed outlier: 3.623A pdb=" N ARG I 45 " --> pdb=" O ARG I 41 " (cutoff:3.500A) Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 71 through 91 Processing helix chain 'I' and resid 91 through 101 removed outlier: 3.935A pdb=" N ARG I 95 " --> pdb=" O ASP I 91 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N SER I 96 " --> pdb=" O GLU I 92 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N GLU I 97 " --> pdb=" O SER I 93 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 32 Processing helix chain 'J' and resid 80 through 89 removed outlier: 3.703A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 20 Processing helix chain 'M' and resid 26 through 37 Processing helix chain 'M' and resid 49 through 61 removed outlier: 3.676A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 83 Processing helix chain 'M' and resid 85 through 93 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 20 Processing helix chain 'N' and resid 20 through 33 Processing helix chain 'N' and resid 39 through 49 Processing helix chain 'N' and resid 50 through 51 No H-bonds generated for 'chain 'N' and resid 50 through 51' Processing helix chain 'N' and resid 52 through 60 Proline residue: N 57 - end of helix Processing helix chain 'N' and resid 80 through 91 removed outlier: 3.866A pdb=" N ARG N 85 " --> pdb=" O ARG N 81 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 25 Processing helix chain 'S' and resid 63 through 67 Processing helix chain 'S' and resid 70 through 75 removed outlier: 3.516A pdb=" N ALA S 75 " --> pdb=" O GLY S 72 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 35 removed outlier: 3.567A pdb=" N GLY B 33 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.721A pdb=" N ILE B 67 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL B 92 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N PHE B 69 " --> pdb=" O VAL B 92 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ALA B 185 " --> pdb=" O PHE B 198 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 52 through 58 removed outlier: 7.770A pdb=" N ALA C 104 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ILE C 68 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 166 through 171 removed outlier: 3.536A pdb=" N GLY C 194 " --> pdb=" O THR C 191 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 73 through 75 Processing sheet with id=AA6, first strand: chain 'I' and resid 6 through 11 removed outlier: 6.191A pdb=" N VAL I 29 " --> pdb=" O ILE I 65 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N VAL I 67 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 36 through 52 removed outlier: 4.013A pdb=" N ASP J 75 " --> pdb=" O ARG J 37 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU J 73 " --> pdb=" O PRO J 39 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU J 71 " --> pdb=" O PRO J 41 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR J 69 " --> pdb=" O PRO J 43 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ARG J 45 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE J 67 " --> pdb=" O ARG J 45 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU J 47 " --> pdb=" O TYR J 65 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TYR J 65 " --> pdb=" O GLU J 47 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE J 49 " --> pdb=" O ASP J 63 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP J 63 " --> pdb=" O PHE J 49 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 36 through 52 removed outlier: 4.013A pdb=" N ASP J 75 " --> pdb=" O ARG J 37 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LEU J 73 " --> pdb=" O PRO J 39 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU J 71 " --> pdb=" O PRO J 41 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N THR J 69 " --> pdb=" O PRO J 43 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N ARG J 45 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N ILE J 67 " --> pdb=" O ARG J 45 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU J 47 " --> pdb=" O TYR J 65 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TYR J 65 " --> pdb=" O GLU J 47 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N PHE J 49 " --> pdb=" O ASP J 63 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ASP J 63 " --> pdb=" O PHE J 49 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS N 97 " --> pdb=" O GLU J 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 31 through 33 436 hydrogen bonds defined for protein. 1239 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 556 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 249 stacking parallelities Total time for adding SS restraints: 4.34 Time building geometry restraints manager: 1.94 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: 3389 1.33 - 1.45: 7054 1.45 - 1.57: 8363 1.57 - 1.69: 911 1.69 - 1.81: 53 Bond restraints: 19770 Sorted by residual: bond pdb=" C5 2MG 1 966 " pdb=" C4 2MG 1 966 " ideal model delta sigma weight residual 1.382 1.464 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C5 2MG 11207 " pdb=" C4 2MG 11207 " ideal model delta sigma weight residual 1.382 1.455 -0.073 2.00e-02 2.50e+03 1.35e+01 bond pdb=" N VAL J 57 " pdb=" CA VAL J 57 " ideal model delta sigma weight residual 1.459 1.504 -0.045 1.25e-02 6.40e+03 1.28e+01 bond pdb=" N ILE J 40 " pdb=" CA ILE J 40 " ideal model delta sigma weight residual 1.461 1.492 -0.031 9.10e-03 1.21e+04 1.18e+01 bond pdb=" C6 2MG 11207 " pdb=" N1 2MG 11207 " ideal model delta sigma weight residual 1.399 1.331 0.068 2.00e-02 2.50e+03 1.16e+01 ... (remaining 19765 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.05: 28161 2.05 - 4.11: 659 4.11 - 6.16: 70 6.16 - 8.21: 13 8.21 - 10.27: 5 Bond angle restraints: 28908 Sorted by residual: angle pdb=" C THR B 125 " pdb=" CA THR B 125 " pdb=" CB THR B 125 " ideal model delta sigma weight residual 109.83 117.28 -7.45 9.90e-01 1.02e+00 5.67e+01 angle pdb=" C4' U 11211 " pdb=" C3' U 11211 " pdb=" O3' U 11211 " ideal model delta sigma weight residual 109.40 117.38 -7.98 1.50e+00 4.44e-01 2.83e+01 angle pdb=" C GLU M 66 " pdb=" CA GLU M 66 " pdb=" CB GLU M 66 " ideal model delta sigma weight residual 116.63 110.87 5.76 1.16e+00 7.43e-01 2.47e+01 angle pdb=" O3' U 11211 " pdb=" C3' U 11211 " pdb=" C2' U 11211 " ideal model delta sigma weight residual 109.50 116.71 -7.21 1.50e+00 4.44e-01 2.31e+01 angle pdb=" CA GLY B 124 " pdb=" C GLY B 124 " pdb=" O GLY B 124 " ideal model delta sigma weight residual 121.30 116.88 4.42 9.80e-01 1.04e+00 2.04e+01 ... (remaining 28903 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.26: 11372 34.26 - 68.51: 1113 68.51 - 102.77: 140 102.77 - 137.02: 4 137.02 - 171.28: 4 Dihedral angle restraints: 12633 sinusoidal: 9475 harmonic: 3158 Sorted by residual: dihedral pdb=" C5' U 11211 " pdb=" C4' U 11211 " pdb=" C3' U 11211 " pdb=" O3' U 11211 " ideal model delta sinusoidal sigma weight residual 147.00 77.29 69.71 1 8.00e+00 1.56e-02 9.80e+01 dihedral pdb=" C4' U 11211 " pdb=" C3' U 11211 " pdb=" C2' U 11211 " pdb=" C1' U 11211 " ideal model delta sinusoidal sigma weight residual -35.00 30.40 -65.40 1 8.00e+00 1.56e-02 8.76e+01 dihedral pdb=" O4' U 11008 " pdb=" C1' U 11008 " pdb=" N1 U 11008 " pdb=" C2 U 11008 " ideal model delta sinusoidal sigma weight residual 200.00 29.46 170.54 1 1.50e+01 4.44e-03 8.48e+01 ... (remaining 12630 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 3466 0.103 - 0.206: 126 0.206 - 0.310: 11 0.310 - 0.413: 0 0.413 - 0.516: 2 Chirality restraints: 3605 Sorted by residual: chirality pdb=" C3' U 11211 " pdb=" C4' U 11211 " pdb=" O3' U 11211 " pdb=" C2' U 11211 " both_signs ideal model delta sigma weight residual False -2.74 -2.23 -0.52 2.00e-01 2.50e+01 6.66e+00 chirality pdb=" CA VAL J 57 " pdb=" N VAL J 57 " pdb=" C VAL J 57 " pdb=" CB VAL J 57 " both_signs ideal model delta sigma weight residual False 2.44 2.02 0.43 2.00e-01 2.50e+01 4.53e+00 chirality pdb=" CB VAL J 57 " pdb=" CA VAL J 57 " pdb=" CG1 VAL J 57 " pdb=" CG2 VAL J 57 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 3602 not shown) Planarity restraints: 1990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 2MG 1 966 " 0.028 2.00e-02 2.50e+03 4.63e-02 6.96e+01 pdb=" N9 2MG 1 966 " -0.003 2.00e-02 2.50e+03 pdb=" C8 2MG 1 966 " -0.021 2.00e-02 2.50e+03 pdb=" N7 2MG 1 966 " -0.032 2.00e-02 2.50e+03 pdb=" C5 2MG 1 966 " -0.011 2.00e-02 2.50e+03 pdb=" C6 2MG 1 966 " -0.005 2.00e-02 2.50e+03 pdb=" O6 2MG 1 966 " -0.024 2.00e-02 2.50e+03 pdb=" N1 2MG 1 966 " 0.023 2.00e-02 2.50e+03 pdb=" C2 2MG 1 966 " 0.045 2.00e-02 2.50e+03 pdb=" N2 2MG 1 966 " 0.066 2.00e-02 2.50e+03 pdb=" N3 2MG 1 966 " 0.041 2.00e-02 2.50e+03 pdb=" C4 2MG 1 966 " 0.018 2.00e-02 2.50e+03 pdb=" CM2 2MG 1 966 " -0.127 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' 2MG 11207 " -0.002 2.00e-02 2.50e+03 1.48e-02 7.08e+00 pdb=" N9 2MG 11207 " 0.009 2.00e-02 2.50e+03 pdb=" C8 2MG 11207 " -0.004 2.00e-02 2.50e+03 pdb=" N7 2MG 11207 " -0.010 2.00e-02 2.50e+03 pdb=" C5 2MG 11207 " -0.004 2.00e-02 2.50e+03 pdb=" C6 2MG 11207 " -0.002 2.00e-02 2.50e+03 pdb=" O6 2MG 11207 " -0.010 2.00e-02 2.50e+03 pdb=" N1 2MG 11207 " 0.004 2.00e-02 2.50e+03 pdb=" C2 2MG 11207 " 0.014 2.00e-02 2.50e+03 pdb=" N2 2MG 11207 " 0.022 2.00e-02 2.50e+03 pdb=" N3 2MG 11207 " 0.014 2.00e-02 2.50e+03 pdb=" C4 2MG 11207 " 0.007 2.00e-02 2.50e+03 pdb=" CM2 2MG 11207 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR C 168 " 0.009 2.00e-02 2.50e+03 1.89e-02 3.56e+00 pdb=" C TYR C 168 " -0.033 2.00e-02 2.50e+03 pdb=" O TYR C 168 " 0.012 2.00e-02 2.50e+03 pdb=" N ARG C 169 " 0.011 2.00e-02 2.50e+03 ... (remaining 1987 not shown) Histogram of nonbonded interaction distances: 1.88 - 2.48: 146 2.48 - 3.09: 12535 3.09 - 3.69: 34106 3.69 - 4.30: 51629 4.30 - 4.90: 71551 Nonbonded interactions: 169967 Sorted by model distance: nonbonded pdb=" OP2 C 11054 " pdb="MG MG 11622 " model vdw 1.876 2.170 nonbonded pdb=" O6 G 11178 " pdb="MG MG 11608 " model vdw 1.940 2.170 nonbonded pdb=" OP1 A 11197 " pdb="MG MG 11616 " model vdw 1.948 2.170 nonbonded pdb=" OP2 U 11095 " pdb="MG MG 11628 " model vdw 1.953 2.170 nonbonded pdb=" OP1 C 11303 " pdb="MG MG 11639 " model vdw 1.981 2.170 ... (remaining 169962 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.340 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 20.920 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 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 : 0.007 0.151 19771 Z= 0.398 Angle : 0.749 10.266 28908 Z= 0.464 Chirality : 0.046 0.516 3605 Planarity : 0.004 0.046 1990 Dihedral : 21.745 171.281 10589 Min Nonbonded Distance : 1.876 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 0.00 % Allowed : 5.98 % Favored : 94.02 % Cbeta Deviations : 0.20 % 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: -1.98 (0.24), residues: 1088 helix: -0.55 (0.23), residues: 481 sheet: -1.83 (0.37), residues: 163 loop : -1.85 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 11 TYR 0.011 0.002 TYR C 42 PHE 0.009 0.002 PHE B 90 TRP 0.011 0.001 TRP C 201 HIS 0.007 0.001 HIS N 71 Details of bonding type rmsd covalent geometry : bond 0.00712 (19770) covalent geometry : angle 0.74941 (28908) hydrogen bonds : bond 0.18276 ( 782) hydrogen bonds : angle 6.52302 ( 1795) metal coordination : bond 0.15127 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.433 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: B 9 MET cc_start: 0.1663 (mtt) cc_final: 0.1053 (pmm) REVERT: B 113 ARG cc_start: 0.7326 (tpt170) cc_final: 0.6984 (ttp-110) REVERT: B 138 THR cc_start: 0.8670 (m) cc_final: 0.8413 (p) REVERT: B 140 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7431 (mm-30) REVERT: B 152 LYS cc_start: 0.7512 (pttt) cc_final: 0.7139 (ptmt) REVERT: G 64 VAL cc_start: 0.8105 (t) cc_final: 0.7687 (t) REVERT: I 47 VAL cc_start: 0.9427 (p) cc_final: 0.9126 (p) REVERT: I 56 ASP cc_start: 0.8302 (t70) cc_final: 0.8096 (t0) REVERT: J 87 LEU cc_start: 0.9069 (pp) cc_final: 0.8799 (mt) REVERT: M 13 LYS cc_start: 0.7832 (mmtt) cc_final: 0.7325 (ptpt) REVERT: M 69 LEU cc_start: 0.8912 (tp) cc_final: 0.8147 (tp) REVERT: M 82 ASP cc_start: 0.8466 (m-30) cc_final: 0.8219 (m-30) REVERT: S 16 LEU cc_start: 0.9325 (mt) cc_final: 0.9118 (mt) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.7030 time to fit residues: 217.3970 Evaluate side-chains 196 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.0570 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN B 227 GLN C 8 ASN C 25 ASN C 102 ASN C 140 ASN G 148 ASN I 32 GLN I 126 GLN J 70 HIS N 49 GLN N 66 GLN S 57 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.076501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.052383 restraints weight = 52541.852| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 2.57 r_work: 0.2646 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work: 0.2549 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 19771 Z= 0.256 Angle : 0.655 8.258 28908 Z= 0.344 Chirality : 0.040 0.272 3605 Planarity : 0.005 0.098 1990 Dihedral : 22.437 178.451 8370 Min Nonbonded Distance : 1.857 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.79 % Allowed : 20.13 % Favored : 75.08 % 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: -0.83 (0.25), residues: 1088 helix: 0.41 (0.23), residues: 488 sheet: -1.47 (0.39), residues: 167 loop : -1.17 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG N 90 TYR 0.012 0.001 TYR C 42 PHE 0.016 0.001 PHE B 90 TRP 0.011 0.001 TRP C 201 HIS 0.006 0.001 HIS N 71 Details of bonding type rmsd covalent geometry : bond 0.00512 (19770) covalent geometry : angle 0.65491 (28908) hydrogen bonds : bond 0.05400 ( 782) hydrogen bonds : angle 4.10574 ( 1795) metal coordination : bond 0.00180 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 221 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.3889 (mpt) cc_final: 0.3190 (ppp) REVERT: B 94 HIS cc_start: 0.7457 (OUTLIER) cc_final: 0.7088 (m90) REVERT: B 117 LEU cc_start: 0.6771 (OUTLIER) cc_final: 0.6346 (mm) REVERT: B 130 THR cc_start: 0.7008 (m) cc_final: 0.6741 (p) REVERT: B 140 GLU cc_start: 0.6931 (mm-30) cc_final: 0.6688 (mm-30) REVERT: G 6 VAL cc_start: 0.6022 (OUTLIER) cc_final: 0.5720 (t) REVERT: G 144 MET cc_start: 0.6081 (tpp) cc_final: 0.5832 (tmt) REVERT: M 13 LYS cc_start: 0.8208 (mmtt) cc_final: 0.7495 (ptpt) REVERT: M 27 LYS cc_start: 0.8853 (ttpt) cc_final: 0.8524 (ttpm) REVERT: M 69 LEU cc_start: 0.9250 (tp) cc_final: 0.8903 (tp) REVERT: M 81 MET cc_start: 0.9243 (ttm) cc_final: 0.8903 (ttt) REVERT: M 82 ASP cc_start: 0.8684 (m-30) cc_final: 0.8460 (m-30) REVERT: S 21 LYS cc_start: 0.9125 (ttmm) cc_final: 0.8889 (ttmm) outliers start: 44 outliers final: 19 residues processed: 240 average time/residue: 0.5921 time to fit residues: 158.8306 Evaluate side-chains 207 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain G residue 6 VAL Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 chunk 73 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 81 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN C 102 ASN C 140 ASN G 28 ASN G 97 ASN I 126 GLN N 66 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.075028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.051102 restraints weight = 53415.555| |-----------------------------------------------------------------------------| r_work (start): 0.2721 rms_B_bonded: 2.40 r_work: 0.2588 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2485 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8982 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 19771 Z= 0.398 Angle : 0.724 10.982 28908 Z= 0.373 Chirality : 0.044 0.274 3605 Planarity : 0.006 0.100 1990 Dihedral : 22.323 178.483 8370 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer: Outliers : 5.33 % Allowed : 23.18 % Favored : 71.49 % 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: -0.57 (0.25), residues: 1088 helix: 0.59 (0.23), residues: 493 sheet: -1.29 (0.39), residues: 167 loop : -1.01 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 143 TYR 0.010 0.002 TYR C 42 PHE 0.014 0.002 PHE B 90 TRP 0.010 0.002 TRP C 201 HIS 0.009 0.002 HIS N 71 Details of bonding type rmsd covalent geometry : bond 0.00796 (19770) covalent geometry : angle 0.72400 (28908) hydrogen bonds : bond 0.05808 ( 782) hydrogen bonds : angle 4.07190 ( 1795) metal coordination : bond 0.00084 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 195 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.3655 (mpt) cc_final: 0.2795 (ppp) REVERT: B 70 VAL cc_start: 0.5522 (t) cc_final: 0.5113 (m) REVERT: B 94 HIS cc_start: 0.7528 (OUTLIER) cc_final: 0.7110 (m90) REVERT: B 118 GLU cc_start: 0.6794 (OUTLIER) cc_final: 0.6370 (mp0) REVERT: B 139 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6700 (mtt180) REVERT: C 170 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.8580 (tt0) REVERT: I 37 GLN cc_start: 0.8670 (pt0) cc_final: 0.8413 (pt0) REVERT: M 13 LYS cc_start: 0.8157 (mmtt) cc_final: 0.7680 (mmpt) REVERT: M 27 LYS cc_start: 0.8866 (ttpt) cc_final: 0.8630 (ttmm) REVERT: M 78 LYS cc_start: 0.9189 (tmtm) cc_final: 0.8971 (tttm) REVERT: M 81 MET cc_start: 0.9265 (ttm) cc_final: 0.8947 (ttt) REVERT: M 82 ASP cc_start: 0.8742 (m-30) cc_final: 0.8421 (m-30) REVERT: S 6 LYS cc_start: 0.9234 (OUTLIER) cc_final: 0.8908 (ptmm) outliers start: 49 outliers final: 25 residues processed: 223 average time/residue: 0.6280 time to fit residues: 156.3998 Evaluate side-chains 213 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 139 ARG Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 95 ARG Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain N residue 66 GLN Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 25 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 65 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 119 optimal weight: 0.1980 chunk 120 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 89 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 HIS G 97 ASN I 32 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.077425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.052896 restraints weight = 53038.192| |-----------------------------------------------------------------------------| r_work (start): 0.2792 rms_B_bonded: 2.59 r_work: 0.2665 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2563 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8936 moved from start: 0.2571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 19771 Z= 0.180 Angle : 0.611 10.345 28908 Z= 0.317 Chirality : 0.037 0.234 3605 Planarity : 0.005 0.102 1990 Dihedral : 22.268 176.478 8370 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 4.90 % Allowed : 25.35 % Favored : 69.75 % 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: -0.16 (0.25), residues: 1088 helix: 0.92 (0.24), residues: 488 sheet: -1.10 (0.40), residues: 162 loop : -0.79 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG J 89 TYR 0.012 0.001 TYR C 42 PHE 0.022 0.001 PHE I 127 TRP 0.012 0.001 TRP C 201 HIS 0.003 0.001 HIS N 71 Details of bonding type rmsd covalent geometry : bond 0.00359 (19770) covalent geometry : angle 0.61100 (28908) hydrogen bonds : bond 0.04841 ( 782) hydrogen bonds : angle 3.89342 ( 1795) metal coordination : bond 0.00037 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.3645 (mpt) cc_final: 0.2983 (ppp) REVERT: B 9 MET cc_start: -0.0546 (pmm) cc_final: -0.0856 (pmm) REVERT: B 70 VAL cc_start: 0.5510 (t) cc_final: 0.5134 (m) REVERT: B 118 GLU cc_start: 0.6812 (OUTLIER) cc_final: 0.6362 (mp0) REVERT: B 137 ARG cc_start: 0.6566 (mtt180) cc_final: 0.6332 (mmm-85) REVERT: I 5 GLN cc_start: 0.8399 (tp-100) cc_final: 0.8185 (tp40) REVERT: I 60 LYS cc_start: 0.8920 (mppt) cc_final: 0.8636 (mmtm) REVERT: I 124 ARG cc_start: 0.9107 (mmm-85) cc_final: 0.8899 (mtp85) REVERT: M 13 LYS cc_start: 0.8166 (mmtt) cc_final: 0.7413 (ptpt) REVERT: M 27 LYS cc_start: 0.8746 (ttpt) cc_final: 0.8506 (ttmm) REVERT: M 59 GLU cc_start: 0.8955 (mt-10) cc_final: 0.8741 (tt0) REVERT: M 81 MET cc_start: 0.9216 (ttm) cc_final: 0.8887 (mtm) REVERT: S 6 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8809 (ptmm) REVERT: S 20 GLU cc_start: 0.8568 (pt0) cc_final: 0.8255 (pt0) outliers start: 45 outliers final: 18 residues processed: 216 average time/residue: 0.6286 time to fit residues: 151.5022 Evaluate side-chains 202 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 182 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain G residue 11 LYS Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 99 GLN Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 69 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 98 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 142 optimal weight: 0.8980 chunk 55 optimal weight: 10.0000 chunk 38 optimal weight: 4.9990 chunk 107 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 140 ASN G 28 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.077172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.053521 restraints weight = 52629.211| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 2.50 r_work: 0.2652 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2550 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8943 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 19771 Z= 0.210 Angle : 0.611 9.347 28908 Z= 0.318 Chirality : 0.037 0.237 3605 Planarity : 0.005 0.101 1990 Dihedral : 22.203 176.565 8370 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.46 % Allowed : 25.68 % Favored : 69.86 % 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: -0.10 (0.25), residues: 1088 helix: 0.94 (0.23), residues: 504 sheet: -0.88 (0.40), residues: 166 loop : -0.87 (0.30), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 138 TYR 0.011 0.001 TYR C 42 PHE 0.012 0.001 PHE B 90 TRP 0.010 0.001 TRP C 201 HIS 0.003 0.001 HIS N 71 Details of bonding type rmsd covalent geometry : bond 0.00420 (19770) covalent geometry : angle 0.61072 (28908) hydrogen bonds : bond 0.04816 ( 782) hydrogen bonds : angle 3.84107 ( 1795) metal coordination : bond 0.00051 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 191 time to evaluate : 0.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.3492 (mpt) cc_final: 0.2901 (ppp) REVERT: B 9 MET cc_start: -0.0615 (OUTLIER) cc_final: -0.0893 (pmm) REVERT: B 70 VAL cc_start: 0.5568 (t) cc_final: 0.5226 (m) REVERT: B 94 HIS cc_start: 0.7535 (OUTLIER) cc_final: 0.7106 (m90) REVERT: B 118 GLU cc_start: 0.6931 (OUTLIER) cc_final: 0.6393 (mp0) REVERT: B 137 ARG cc_start: 0.6700 (mtt180) cc_final: 0.6436 (mmm-85) REVERT: C 36 ASP cc_start: 0.9085 (t0) cc_final: 0.8865 (m-30) REVERT: G 59 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7122 (tt) REVERT: I 5 GLN cc_start: 0.8357 (tp-100) cc_final: 0.8152 (tp40) REVERT: I 60 LYS cc_start: 0.8992 (mppt) cc_final: 0.8777 (mppt) REVERT: J 20 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8176 (tm-30) REVERT: M 27 LYS cc_start: 0.8770 (ttpt) cc_final: 0.8517 (ttmm) REVERT: M 59 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8718 (tt0) REVERT: M 81 MET cc_start: 0.9238 (ttm) cc_final: 0.8925 (mtm) REVERT: M 82 ASP cc_start: 0.8737 (m-30) cc_final: 0.8473 (m-30) REVERT: S 6 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8821 (ptmm) REVERT: S 20 GLU cc_start: 0.8586 (pt0) cc_final: 0.8235 (pt0) outliers start: 41 outliers final: 22 residues processed: 215 average time/residue: 0.6406 time to fit residues: 153.6414 Evaluate side-chains 208 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 20 GLN Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 44 LYS Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 35 optimal weight: 5.9990 chunk 144 optimal weight: 0.0270 chunk 87 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 149 optimal weight: 2.9990 chunk 110 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 61 optimal weight: 9.9990 chunk 78 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 89 optimal weight: 0.0980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 140 ASN I 32 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.079739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.055660 restraints weight = 52757.114| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 2.54 r_work: 0.2742 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 19771 Z= 0.122 Angle : 0.579 10.329 28908 Z= 0.301 Chirality : 0.035 0.217 3605 Planarity : 0.005 0.096 1990 Dihedral : 22.157 175.381 8370 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 3.37 % Allowed : 28.07 % Favored : 68.55 % 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: 0.05 (0.25), residues: 1088 helix: 1.02 (0.23), residues: 507 sheet: -0.77 (0.40), residues: 165 loop : -0.75 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG J 89 TYR 0.011 0.001 TYR C 42 PHE 0.011 0.001 PHE B 90 TRP 0.014 0.002 TRP B 96 HIS 0.002 0.000 HIS B 170 Details of bonding type rmsd covalent geometry : bond 0.00242 (19770) covalent geometry : angle 0.57862 (28908) hydrogen bonds : bond 0.04417 ( 782) hydrogen bonds : angle 3.74031 ( 1795) metal coordination : bond 0.00009 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 199 time to evaluate : 0.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.3567 (mpt) cc_final: 0.3114 (ppp) REVERT: B 9 MET cc_start: -0.0508 (OUTLIER) cc_final: -0.0740 (pmm) REVERT: B 70 VAL cc_start: 0.5711 (t) cc_final: 0.5325 (m) REVERT: B 94 HIS cc_start: 0.7416 (OUTLIER) cc_final: 0.7015 (m90) REVERT: B 118 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6287 (mp0) REVERT: B 137 ARG cc_start: 0.6619 (mtt180) cc_final: 0.6361 (mmm-85) REVERT: G 119 ARG cc_start: 0.7930 (mtt90) cc_final: 0.7431 (mtt90) REVERT: J 99 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.8268 (mm110) REVERT: M 27 LYS cc_start: 0.8633 (ttpt) cc_final: 0.8205 (ttmm) REVERT: M 81 MET cc_start: 0.9225 (ttm) cc_final: 0.8901 (mtm) REVERT: S 20 GLU cc_start: 0.8526 (pt0) cc_final: 0.8241 (pt0) outliers start: 31 outliers final: 16 residues processed: 216 average time/residue: 0.6523 time to fit residues: 157.3347 Evaluate side-chains 199 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 99 GLN Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain N residue 43 ASN Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 129 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 119 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 149 optimal weight: 8.9990 chunk 94 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.078642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.054684 restraints weight = 53013.737| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.17 r_work: 0.2705 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.2607 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.3138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19771 Z= 0.158 Angle : 0.589 10.706 28908 Z= 0.304 Chirality : 0.035 0.233 3605 Planarity : 0.005 0.093 1990 Dihedral : 22.089 175.574 8370 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.48 % Allowed : 30.14 % Favored : 66.38 % 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: 0.16 (0.25), residues: 1088 helix: 1.09 (0.23), residues: 507 sheet: -0.69 (0.40), residues: 166 loop : -0.69 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 89 TYR 0.010 0.001 TYR C 42 PHE 0.013 0.001 PHE B 90 TRP 0.014 0.001 TRP B 96 HIS 0.003 0.001 HIS N 71 Details of bonding type rmsd covalent geometry : bond 0.00320 (19770) covalent geometry : angle 0.58865 (28908) hydrogen bonds : bond 0.04416 ( 782) hydrogen bonds : angle 3.71275 ( 1795) metal coordination : bond 0.00029 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 185 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.3650 (mpt) cc_final: 0.3105 (ppp) REVERT: B 9 MET cc_start: -0.0175 (OUTLIER) cc_final: -0.0403 (pmm) REVERT: B 70 VAL cc_start: 0.5746 (t) cc_final: 0.5352 (m) REVERT: B 94 HIS cc_start: 0.7631 (OUTLIER) cc_final: 0.7176 (m90) REVERT: B 118 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6505 (mp0) REVERT: B 137 ARG cc_start: 0.6664 (mtt180) cc_final: 0.6384 (mmm-85) REVERT: G 119 ARG cc_start: 0.7968 (mtt90) cc_final: 0.7460 (mtt90) REVERT: I 59 GLU cc_start: 0.8781 (mp0) cc_final: 0.8450 (pm20) REVERT: I 60 LYS cc_start: 0.8787 (mppt) cc_final: 0.8553 (mmtm) REVERT: I 105 THR cc_start: 0.8545 (t) cc_final: 0.8318 (m) REVERT: J 99 GLN cc_start: 0.8527 (OUTLIER) cc_final: 0.8167 (mm110) REVERT: M 13 LYS cc_start: 0.8257 (mmtt) cc_final: 0.7614 (ptpt) REVERT: M 27 LYS cc_start: 0.8587 (ttpt) cc_final: 0.8326 (ttmm) REVERT: M 81 MET cc_start: 0.9190 (ttm) cc_final: 0.8961 (mtp) REVERT: S 17 LYS cc_start: 0.9251 (mmmm) cc_final: 0.8972 (mmmm) REVERT: S 20 GLU cc_start: 0.8590 (pt0) cc_final: 0.8227 (pt0) outliers start: 32 outliers final: 25 residues processed: 203 average time/residue: 0.6550 time to fit residues: 148.0842 Evaluate side-chains 209 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 144 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 99 GLN Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 96 optimal weight: 0.0170 chunk 6 optimal weight: 6.9990 chunk 137 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 136 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 101 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 7 optimal weight: 8.9990 chunk 87 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 overall best weight: 3.0024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN C 140 ASN I 5 GLN I 32 GLN I 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.075862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.052698 restraints weight = 52344.405| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.10 r_work: 0.2618 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.2812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 19771 Z= 0.321 Angle : 0.684 11.753 28908 Z= 0.352 Chirality : 0.041 0.265 3605 Planarity : 0.006 0.091 1990 Dihedral : 22.096 176.459 8370 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.03 % Allowed : 29.92 % Favored : 66.05 % 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: 0.15 (0.26), residues: 1088 helix: 1.11 (0.23), residues: 503 sheet: -0.67 (0.39), residues: 166 loop : -0.72 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 89 TYR 0.013 0.002 TYR M 86 PHE 0.022 0.002 PHE S 74 TRP 0.018 0.002 TRP B 96 HIS 0.006 0.001 HIS N 71 Details of bonding type rmsd covalent geometry : bond 0.00643 (19770) covalent geometry : angle 0.68355 (28908) hydrogen bonds : bond 0.05192 ( 782) hydrogen bonds : angle 3.80377 ( 1795) metal coordination : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 178 time to evaluate : 0.468 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.3466 (mpt) cc_final: 0.2891 (ppp) REVERT: B 70 VAL cc_start: 0.5808 (t) cc_final: 0.5454 (m) REVERT: B 94 HIS cc_start: 0.7584 (OUTLIER) cc_final: 0.7123 (m90) REVERT: B 118 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6598 (mp0) REVERT: G 29 ILE cc_start: 0.8909 (mm) cc_final: 0.8641 (mp) REVERT: G 119 ARG cc_start: 0.8037 (mtt90) cc_final: 0.7834 (mtt90) REVERT: I 60 LYS cc_start: 0.8924 (mppt) cc_final: 0.8714 (mmtm) REVERT: M 13 LYS cc_start: 0.8198 (mmtt) cc_final: 0.7444 (mttt) REVERT: M 27 LYS cc_start: 0.8651 (ttpt) cc_final: 0.8418 (ttmm) REVERT: M 81 MET cc_start: 0.9248 (ttm) cc_final: 0.9037 (mtp) REVERT: S 17 LYS cc_start: 0.9263 (mmmm) cc_final: 0.8947 (mmmm) REVERT: S 20 GLU cc_start: 0.8598 (pt0) cc_final: 0.8252 (pt0) outliers start: 37 outliers final: 26 residues processed: 200 average time/residue: 0.6321 time to fit residues: 141.4444 Evaluate side-chains 203 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 175 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 44 LYS Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain S residue 12 ASP Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 85 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 124 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 chunk 132 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 95 optimal weight: 1.9990 chunk 96 optimal weight: 20.0000 chunk 80 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.077334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.053491 restraints weight = 52033.550| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.44 r_work: 0.2668 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2566 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 19771 Z= 0.163 Angle : 0.630 10.729 28908 Z= 0.327 Chirality : 0.037 0.234 3605 Planarity : 0.005 0.095 1990 Dihedral : 22.151 175.946 8370 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 3.48 % Allowed : 30.14 % Favored : 66.38 % 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: 0.14 (0.26), residues: 1088 helix: 1.13 (0.23), residues: 507 sheet: -0.68 (0.40), residues: 165 loop : -0.78 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG J 89 TYR 0.014 0.001 TYR M 86 PHE 0.018 0.001 PHE S 74 TRP 0.014 0.001 TRP B 96 HIS 0.002 0.001 HIS N 71 Details of bonding type rmsd covalent geometry : bond 0.00333 (19770) covalent geometry : angle 0.62965 (28908) hydrogen bonds : bond 0.04857 ( 782) hydrogen bonds : angle 3.81959 ( 1795) metal coordination : bond 0.00043 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.3781 (mpt) cc_final: 0.3231 (ppp) REVERT: B 9 MET cc_start: -0.0669 (pmm) cc_final: -0.0915 (pmm) REVERT: B 70 VAL cc_start: 0.5736 (t) cc_final: 0.5443 (m) REVERT: B 94 HIS cc_start: 0.7687 (OUTLIER) cc_final: 0.7242 (m90) REVERT: B 118 GLU cc_start: 0.7010 (OUTLIER) cc_final: 0.6562 (mp0) REVERT: B 137 ARG cc_start: 0.6693 (mtt180) cc_final: 0.6418 (mmm-85) REVERT: G 29 ILE cc_start: 0.8855 (mm) cc_final: 0.8577 (mp) REVERT: M 13 LYS cc_start: 0.8192 (mmtt) cc_final: 0.7478 (mttt) REVERT: M 27 LYS cc_start: 0.8590 (ttpt) cc_final: 0.8352 (ttmm) REVERT: M 81 MET cc_start: 0.9239 (ttm) cc_final: 0.8914 (mtm) REVERT: S 17 LYS cc_start: 0.9215 (mmmm) cc_final: 0.8896 (mmmm) REVERT: S 20 GLU cc_start: 0.8563 (pt0) cc_final: 0.8189 (pt0) outliers start: 32 outliers final: 25 residues processed: 207 average time/residue: 0.6113 time to fit residues: 141.4524 Evaluate side-chains 206 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 93 ASP Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 99 GLN Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 112 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 143 optimal weight: 0.8980 chunk 54 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 20 optimal weight: 7.9990 chunk 61 optimal weight: 6.9990 chunk 116 optimal weight: 0.0980 chunk 42 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 overall best weight: 3.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 140 ASN I 5 GLN I 32 GLN I 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.075552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.051518 restraints weight = 52648.893| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 2.44 r_work: 0.2613 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2513 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8969 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.081 19771 Z= 0.343 Angle : 0.710 13.820 28908 Z= 0.365 Chirality : 0.042 0.266 3605 Planarity : 0.006 0.090 1990 Dihedral : 22.105 176.598 8370 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.32 % Favored : 95.59 % Rotamer: Outliers : 3.59 % Allowed : 30.36 % Favored : 66.05 % 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: 0.08 (0.26), residues: 1088 helix: 1.08 (0.23), residues: 501 sheet: -0.71 (0.39), residues: 166 loop : -0.79 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 89 TYR 0.021 0.002 TYR M 86 PHE 0.021 0.002 PHE S 74 TRP 0.021 0.002 TRP B 104 HIS 0.005 0.001 HIS N 71 Details of bonding type rmsd covalent geometry : bond 0.00691 (19770) covalent geometry : angle 0.70975 (28908) hydrogen bonds : bond 0.05284 ( 782) hydrogen bonds : angle 3.94287 ( 1795) metal coordination : bond 0.00046 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2176 Ramachandran restraints generated. 1088 Oldfield, 0 Emsley, 1088 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 VAL cc_start: 0.5689 (t) cc_final: 0.5355 (m) REVERT: B 94 HIS cc_start: 0.7679 (OUTLIER) cc_final: 0.7350 (m90) REVERT: B 118 GLU cc_start: 0.7016 (OUTLIER) cc_final: 0.6565 (mp0) REVERT: B 203 ASN cc_start: 0.2563 (t0) cc_final: 0.2354 (t0) REVERT: M 13 LYS cc_start: 0.8198 (mmtt) cc_final: 0.7412 (mttt) REVERT: M 27 LYS cc_start: 0.8677 (ttpt) cc_final: 0.8457 (ttmm) REVERT: M 81 MET cc_start: 0.9238 (ttm) cc_final: 0.9026 (mtp) REVERT: S 17 LYS cc_start: 0.9253 (mmmm) cc_final: 0.8932 (mmmm) REVERT: S 20 GLU cc_start: 0.8662 (pt0) cc_final: 0.8337 (pt0) outliers start: 33 outliers final: 26 residues processed: 205 average time/residue: 0.6223 time to fit residues: 143.0761 Evaluate side-chains 208 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 180 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 83 ASP Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 195 VAL Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 22 THR Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 101 SER Chi-restraints excluded: chain M residue 7 ILE Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 30 SER Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 62 optimal weight: 9.9990 chunk 149 optimal weight: 0.8980 chunk 142 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 135 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 97 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 118 optimal weight: 0.9980 chunk 95 optimal weight: 10.0000 chunk 150 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN G 142 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.078344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.054750 restraints weight = 52104.676| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 2.36 r_work: 0.2701 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2598 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.3205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19771 Z= 0.146 Angle : 0.639 12.946 28908 Z= 0.329 Chirality : 0.036 0.236 3605 Planarity : 0.005 0.095 1990 Dihedral : 22.175 175.553 8370 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 10.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.86 % Favored : 96.05 % Rotamer: Outliers : 2.72 % Allowed : 31.23 % Favored : 66.05 % 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: 0.15 (0.26), residues: 1088 helix: 1.13 (0.23), residues: 501 sheet: -0.67 (0.39), residues: 165 loop : -0.74 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG J 89 TYR 0.022 0.002 TYR I 38 PHE 0.016 0.001 PHE S 74 TRP 0.013 0.002 TRP B 104 HIS 0.003 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00303 (19770) covalent geometry : angle 0.63876 (28908) hydrogen bonds : bond 0.04786 ( 782) hydrogen bonds : angle 3.90329 ( 1795) metal coordination : bond 0.00051 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7229.81 seconds wall clock time: 123 minutes 58.32 seconds (7438.32 seconds total)