Starting phenix.real_space_refine on Sat Sep 12 21:37:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7af5_11753/09_2026/7af5_11753_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7af5_11753/09_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_11753/09_2026/7af5_11753_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7af5_11753/09_2026/7af5_11753_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7af5_11753/09_2026/7af5_11753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7af5_11753/09_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-2.2.1-6174/lib/python3.11/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: 4.04, per 1000 atoms: 0.22 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: 1.60 Conformation dependent library (CDL) restraints added in 435.9 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: 2.62 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: 4.52 Time building geometry restraints manager: 2.16 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: 27277 2.05 - 4.11: 1542 4.11 - 6.16: 70 6.16 - 8.21: 14 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=" N9 G 11279 " pdb=" C8 G 11279 " pdb=" N7 G 11279 " ideal model delta sigma weight residual 113.10 116.03 -2.93 5.00e-01 4.00e+00 3.43e+01 angle pdb=" C1' C 11158 " pdb=" N1 C 11158 " pdb=" C2 C 11158 " ideal model delta sigma weight residual 118.80 124.79 -5.99 1.10e+00 8.26e-01 2.96e+01 angle pdb=" C3' A 1 983 " pdb=" O3' A 1 983 " pdb=" P C 1 984 " ideal model delta sigma weight residual 119.70 126.06 -6.36 1.20e+00 6.94e-01 2.81e+01 angle pdb=" C8 G 11279 " pdb=" N7 G 11279 " pdb=" C5 G 11279 " ideal model delta sigma weight residual 104.30 101.76 2.54 5.00e-01 4.00e+00 2.58e+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: 3115 0.103 - 0.206: 478 0.206 - 0.310: 10 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: 4.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 22.530 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 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= 0.640 Angle : 0.894 10.266 28908 Z= 0.665 Chirality : 0.062 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/Z covalent geometry : bond 0.00730 / 0.64 (19770) covalent geometry : angle 0.89367 / 0.66 (28908) hydrogen bonds : bond 0.18276 / 19.10 ( 782) hydrogen bonds : angle 6.52302 / 8.30 ( 1795) metal coordination : bond 0.15127 / 7.56 ( 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 : 0.477 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: B 9 MET cc_start: 0.1663 (mtt) cc_final: 0.1053 (pmm) REVERT: B 113 ARG cc_start: 0.7326 (tpt170) cc_final: 0.6977 (ttm170) 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: 0.7439 (mm-30) REVERT: B 152 LYS cc_start: 0.7512 (pttt) cc_final: 0.7140 (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: 0.8095 (t0) REVERT: J 87 LEU cc_start: 0.9069 (pp) cc_final: 0.8799 (mt) REVERT: M 69 LEU cc_start: 0.8912 (tp) cc_final: 0.8146 (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: 0.7466 time to fit residues: 231.7406 Evaluate side-chains 194 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 194 time to evaluate : 0.424 ------------------------------------------------------------------------------- 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: 20.0000 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: 6.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.6104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 122 GLN C 8 ASN C 25 ASN C 102 ASN C 140 ASN G 28 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 = 0.3325 r_free = 0.3325 target = 0.076343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.052269 restraints weight = 52581.081| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 2.25 r_work: 0.2632 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2533 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 19771 Z= 0.244 Angle : 0.653 9.419 28908 Z= 0.366 Chirality : 0.045 0.338 3605 Planarity : 0.006 0.099 1990 Dihedral : 22.450 179.046 8370 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.35 % Allowed : 20.46 % Favored : 75.19 % 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: -1.04 (0.25), residues: 1088 helix: 0.17 (0.23), residues: 498 sheet: -1.49 (0.38), residues: 171 loop : -1.25 (0.28), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 53 TYR 0.012 0.001 TYR C 42 PHE 0.017 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/Z covalent geometry : bond 0.00462 / 0.24 (19770) covalent geometry : angle 0.65254 / 0.37 (28908) hydrogen bonds : bond 0.07375 / 8.03 ( 782) hydrogen bonds : angle 4.34415 / 5.73 ( 1795) metal coordination : bond 0.01009 / 0.50 ( 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 253 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 213 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: B 6 MET cc_start: 0.3864 (mpt) cc_final: 0.3454 (ppp) REVERT: B 94 HIS cc_start: 0.7474 (OUTLIER) cc_final: 0.7104 (m90) REVERT: B 117 LEU cc_start: 0.6879 (OUTLIER) cc_final: 0.6357 (mm) REVERT: B 118 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6730 (mp0) REVERT: B 130 THR cc_start: 0.6973 (m) cc_final: 0.6727 (p) REVERT: B 136 MET cc_start: 0.6302 (ttp) cc_final: 0.5971 (mtp) REVERT: M 13 LYS cc_start: 0.8005 (mmtt) cc_final: 0.7276 (ptpt) REVERT: M 41 GLU cc_start: 0.8347 (tp30) cc_final: 0.8083 (tp30) REVERT: M 82 ASP cc_start: 0.8688 (m-30) cc_final: 0.8429 (m-30) REVERT: S 21 LYS cc_start: 0.9147 (ttmm) cc_final: 0.8946 (ttmm) outliers start: 40 outliers final: 21 residues processed: 233 average time/residue: 0.6503 time to fit residues: 169.0006 Evaluate side-chains 209 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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 C residue 52 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 134 MET Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 21 ILE Chi-restraints excluded: chain I residue 65 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 77 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 42 ASP Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 12 ASP 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: 0.8980 chunk 63 optimal weight: 20.0000 chunk 73 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 81 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 46 optimal weight: 8.9990 chunk 121 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 140 ASN G 97 ASN I 126 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.076131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.051867 restraints weight = 52936.741| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 2.38 r_work: 0.2631 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2532 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9019 moved from start: 0.2011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 19771 Z= 0.244 Angle : 0.655 10.557 28908 Z= 0.360 Chirality : 0.045 0.401 3605 Planarity : 0.006 0.099 1990 Dihedral : 22.334 179.217 8370 Min Nonbonded Distance : 1.833 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.66 % Allowed : 22.31 % Favored : 72.03 % 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: -0.61 (0.25), residues: 1088 helix: 0.52 (0.23), residues: 489 sheet: -1.23 (0.39), residues: 167 loop : -1.02 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 95 TYR 0.012 0.002 TYR C 42 PHE 0.016 0.001 PHE B 90 TRP 0.010 0.001 TRP C 201 HIS 0.009 0.001 HIS N 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.24 (19770) covalent geometry : angle 0.65456 / 0.36 (28908) hydrogen bonds : bond 0.06505 / 7.04 ( 782) hydrogen bonds : angle 4.23300 / 5.63 ( 1795) metal coordination : bond 0.00007 / 0.00 ( 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 249 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 197 time to evaluate : 0.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 VAL cc_start: 0.5372 (t) cc_final: 0.4994 (p) REVERT: B 94 HIS cc_start: 0.7548 (OUTLIER) cc_final: 0.7146 (m90) REVERT: B 118 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6392 (mp0) REVERT: C 142 MET cc_start: 0.9232 (mmt) cc_final: 0.9022 (mmt) REVERT: C 170 GLU cc_start: 0.8860 (OUTLIER) cc_final: 0.8658 (tt0) REVERT: I 60 LYS cc_start: 0.9013 (mppt) cc_final: 0.8744 (mmtm) REVERT: M 13 LYS cc_start: 0.7906 (mmtt) cc_final: 0.7117 (ptpt) REVERT: M 81 MET cc_start: 0.9249 (ttm) cc_final: 0.8897 (ttt) REVERT: S 6 LYS cc_start: 0.9230 (OUTLIER) cc_final: 0.8929 (ptmm) outliers start: 52 outliers final: 21 residues processed: 225 average time/residue: 0.6141 time to fit residues: 154.6050 Evaluate side-chains 208 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 144 LEU 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 170 GLU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 65 ILE Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain M residue 16 VAL 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 M residue 97 VAL Chi-restraints excluded: chain N residue 30 ILE 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 25 optimal weight: 10.0000 chunk 43 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 7 optimal weight: 20.0000 chunk 5 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 119 optimal weight: 0.6980 chunk 120 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 89 optimal weight: 5.9990 chunk 2 optimal weight: 9.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 ASN C 3 GLN C 140 ASN G 28 ASN G 97 ASN I 32 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 = 0.3303 r_free = 0.3303 target = 0.075356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.051367 restraints weight = 53078.330| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 2.44 r_work: 0.2601 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2499 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.2167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 19771 Z= 0.338 Angle : 0.722 8.644 28908 Z= 0.386 Chirality : 0.050 0.387 3605 Planarity : 0.006 0.100 1990 Dihedral : 22.259 179.636 8370 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 6.09 % Allowed : 24.59 % Favored : 69.31 % 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: -0.53 (0.25), residues: 1088 helix: 0.55 (0.23), residues: 490 sheet: -1.07 (0.39), residues: 167 loop : -1.00 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 124 TYR 0.011 0.002 TYR C 42 PHE 0.015 0.002 PHE B 90 TRP 0.011 0.002 TRP C 201 HIS 0.006 0.001 HIS N 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.34 (19770) covalent geometry : angle 0.72167 / 0.39 (28908) hydrogen bonds : bond 0.06575 / 7.09 ( 782) hydrogen bonds : angle 4.22095 / 5.60 ( 1795) metal coordination : bond 0.00104 / 0.05 ( 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 248 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 192 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.1798 (mmp) cc_final: 0.0993 (ppp) REVERT: B 70 VAL cc_start: 0.5218 (t) cc_final: 0.4875 (p) REVERT: B 118 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6257 (mp0) REVERT: B 139 ARG cc_start: 0.7180 (OUTLIER) cc_final: 0.6721 (mtt180) REVERT: I 37 GLN cc_start: 0.8660 (pt0) cc_final: 0.8372 (pt0) REVERT: M 27 LYS cc_start: 0.8844 (ttmt) cc_final: 0.8638 (ttmm) REVERT: M 78 LYS cc_start: 0.9192 (tttm) cc_final: 0.8959 (tttm) REVERT: M 81 MET cc_start: 0.9274 (OUTLIER) cc_final: 0.8954 (ttt) REVERT: M 82 ASP cc_start: 0.8792 (m-30) cc_final: 0.8474 (m-30) REVERT: S 6 LYS cc_start: 0.9232 (OUTLIER) cc_final: 0.8893 (ptmm) outliers start: 56 outliers final: 25 residues processed: 223 average time/residue: 0.6360 time to fit residues: 158.7531 Evaluate side-chains 214 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 185 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 122 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 65 ILE Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 83 THR Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain M residue 16 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 81 MET Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 30 ILE Chi-restraints excluded: chain N residue 45 VAL Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 11 ILE Chi-restraints excluded: chain S residue 12 ASP 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: 0.5980 chunk 53 optimal weight: 9.9990 chunk 98 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 142 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 107 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 140 optimal weight: 0.7980 chunk 115 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 39 HIS C 140 ASN G 97 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.077610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.053982 restraints weight = 52653.212| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 2.63 r_work: 0.2679 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work: 0.2578 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 19771 Z= 0.136 Angle : 0.563 8.852 28908 Z= 0.321 Chirality : 0.038 0.325 3605 Planarity : 0.005 0.104 1990 Dihedral : 22.287 179.105 8370 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.46 % Allowed : 26.66 % Favored : 68.88 % 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: -0.26 (0.25), residues: 1088 helix: 0.75 (0.23), residues: 496 sheet: -1.03 (0.40), residues: 165 loop : -0.80 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 95 TYR 0.012 0.001 TYR C 42 PHE 0.019 0.001 PHE I 127 TRP 0.015 0.001 TRP B 104 HIS 0.003 0.001 HIS N 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.14 (19770) covalent geometry : angle 0.56345 / 0.32 (28908) hydrogen bonds : bond 0.05729 / 6.16 ( 782) hydrogen bonds : angle 4.00256 / 5.29 ( 1795) metal coordination : bond 0.00023 / 0.01 ( 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 239 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 198 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.2116 (OUTLIER) cc_final: 0.1346 (ppp) REVERT: B 9 MET cc_start: -0.0095 (pmm) cc_final: -0.0310 (pmm) REVERT: B 70 VAL cc_start: 0.5189 (t) cc_final: 0.4795 (m) REVERT: B 118 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6307 (mp0) REVERT: G 144 MET cc_start: 0.6086 (tpp) cc_final: 0.5748 (tmt) REVERT: I 37 GLN cc_start: 0.8616 (pt0) cc_final: 0.8291 (pt0) REVERT: J 45 ARG cc_start: 0.9127 (OUTLIER) cc_final: 0.8897 (ttt180) REVERT: M 13 LYS cc_start: 0.8098 (mmtt) cc_final: 0.7354 (ptpt) REVERT: M 27 LYS cc_start: 0.8746 (ttmt) cc_final: 0.8510 (ttmm) REVERT: M 82 ASP cc_start: 0.8728 (m-30) cc_final: 0.8454 (m-30) REVERT: S 6 LYS cc_start: 0.9158 (OUTLIER) cc_final: 0.8833 (ptmm) REVERT: S 20 GLU cc_start: 0.8611 (pt0) cc_final: 0.8279 (pt0) outliers start: 41 outliers final: 17 residues processed: 222 average time/residue: 0.6173 time to fit residues: 153.1162 Evaluate side-chains 205 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 184 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain C residue 53 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 122 SER Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain I residue 89 GLU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 45 ARG Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 99 GLN Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain N residue 66 GLN Chi-restraints excluded: chain S residue 6 LYS 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: 10.0000 chunk 144 optimal weight: 0.9980 chunk 87 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 78 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 89 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 GLN C 140 ASN G 28 ASN I 32 GLN N 66 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.077179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.053063 restraints weight = 52288.177| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.37 r_work: 0.2668 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2567 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9003 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 19771 Z= 0.167 Angle : 0.591 13.691 28908 Z= 0.326 Chirality : 0.039 0.336 3605 Planarity : 0.005 0.101 1990 Dihedral : 22.201 179.270 8370 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.90 % Allowed : 27.20 % Favored : 67.90 % 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: 0.88 (0.23), residues: 496 sheet: -0.90 (0.40), residues: 165 loop : -0.73 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 143 TYR 0.011 0.002 TYR C 42 PHE 0.020 0.001 PHE I 127 TRP 0.014 0.001 TRP B 104 HIS 0.003 0.001 HIS N 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.17 (19770) covalent geometry : angle 0.59147 / 0.33 (28908) hydrogen bonds : bond 0.05529 / 5.93 ( 782) hydrogen bonds : angle 3.96089 / 5.23 ( 1795) metal coordination : bond 0.00049 / 0.02 ( 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 236 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.1928 (OUTLIER) cc_final: 0.1132 (ppp) REVERT: B 9 MET cc_start: 0.0171 (OUTLIER) cc_final: -0.0041 (pmm) REVERT: B 70 VAL cc_start: 0.5294 (t) cc_final: 0.4892 (m) REVERT: B 118 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6260 (mp0) REVERT: G 119 ARG cc_start: 0.7629 (mtt90) cc_final: 0.7410 (mtt90) REVERT: G 144 MET cc_start: 0.6834 (tpp) cc_final: 0.6261 (tmt) REVERT: I 37 GLN cc_start: 0.8613 (pt0) cc_final: 0.8273 (pt0) REVERT: I 59 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8346 (pm20) REVERT: I 60 LYS cc_start: 0.8831 (mppt) cc_final: 0.8451 (mmtm) REVERT: M 13 LYS cc_start: 0.8146 (mmtt) cc_final: 0.7416 (mttt) REVERT: M 27 LYS cc_start: 0.8750 (ttmt) cc_final: 0.8520 (ttmm) REVERT: S 6 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8811 (ptmm) REVERT: S 20 GLU cc_start: 0.8590 (pt0) cc_final: 0.8267 (pt0) outliers start: 45 outliers final: 24 residues processed: 213 average time/residue: 0.6376 time to fit residues: 152.0946 Evaluate side-chains 215 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 186 time to evaluate : 0.562 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 6 MET Chi-restraints excluded: chain B residue 9 MET 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 122 SER Chi-restraints excluded: chain C residue 186 THR Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain G residue 11 LYS Chi-restraints excluded: chain I residue 59 GLU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 45 ARG 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 20 THR Chi-restraints excluded: chain M residue 28 THR Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain N residue 14 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 129 optimal weight: 0.0980 chunk 112 optimal weight: 2.9990 chunk 119 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 94 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 86 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3366 r_free = 0.3366 target = 0.078356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.054877 restraints weight = 52544.988| |-----------------------------------------------------------------------------| r_work (start): 0.2815 rms_B_bonded: 2.42 r_work: 0.2690 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8986 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19771 Z= 0.132 Angle : 0.566 11.473 28908 Z= 0.316 Chirality : 0.037 0.322 3605 Planarity : 0.005 0.102 1990 Dihedral : 22.200 178.810 8370 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.70 % Allowed : 28.29 % Favored : 68.01 % 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: 0.92 (0.23), residues: 498 sheet: -0.84 (0.39), residues: 165 loop : -0.71 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG J 89 TYR 0.011 0.001 TYR C 42 PHE 0.019 0.001 PHE S 74 TRP 0.018 0.001 TRP B 104 HIS 0.002 0.001 HIS B 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 (19770) covalent geometry : angle 0.56600 / 0.32 (28908) hydrogen bonds : bond 0.05360 / 5.74 ( 782) hydrogen bonds : angle 3.94176 / 5.19 ( 1795) metal coordination : bond 0.00017 / 0.01 ( 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 219 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.2027 (mmp) cc_final: 0.1239 (ppp) REVERT: B 9 MET cc_start: 0.0150 (OUTLIER) cc_final: -0.0066 (pmm) REVERT: B 70 VAL cc_start: 0.5387 (t) cc_final: 0.5026 (m) REVERT: B 94 HIS cc_start: 0.7559 (OUTLIER) cc_final: 0.7144 (m90) REVERT: B 118 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6243 (mp0) REVERT: B 154 MET cc_start: 0.5667 (ttp) cc_final: 0.5464 (tmm) REVERT: G 119 ARG cc_start: 0.7717 (mtt90) cc_final: 0.7360 (mtt90) REVERT: G 144 MET cc_start: 0.6781 (tpp) cc_final: 0.6190 (tmt) REVERT: I 5 GLN cc_start: 0.8334 (tp-100) cc_final: 0.8111 (tp40) REVERT: I 37 GLN cc_start: 0.8611 (pt0) cc_final: 0.8276 (pt0) REVERT: I 59 GLU cc_start: 0.8776 (mp0) cc_final: 0.8426 (pm20) REVERT: I 60 LYS cc_start: 0.8785 (mppt) cc_final: 0.8367 (mmtm) REVERT: I 124 ARG cc_start: 0.9003 (mmm-85) cc_final: 0.8768 (mtp85) REVERT: M 13 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7377 (mttt) REVERT: M 27 LYS cc_start: 0.8705 (ttmt) cc_final: 0.8461 (ttmm) REVERT: M 82 ASP cc_start: 0.8772 (m-30) cc_final: 0.8516 (m-30) REVERT: S 6 LYS cc_start: 0.9116 (OUTLIER) cc_final: 0.8778 (ptmm) REVERT: S 17 LYS cc_start: 0.9221 (mmmm) cc_final: 0.8877 (mmmm) REVERT: S 20 GLU cc_start: 0.8585 (pt0) cc_final: 0.8107 (pt0) outliers start: 34 outliers final: 23 residues processed: 203 average time/residue: 0.6325 time to fit residues: 143.1316 Evaluate side-chains 207 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 180 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 144 LEU 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 186 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 45 ARG 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 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 14 VAL Chi-restraints excluded: chain N residue 26 GLU Chi-restraints excluded: chain S residue 6 LYS 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: 20.0000 chunk 6 optimal weight: 10.0000 chunk 137 optimal weight: 3.9990 chunk 9 optimal weight: 30.0000 chunk 136 optimal weight: 0.5980 chunk 2 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 37 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 87 optimal weight: 0.8980 chunk 12 optimal weight: 10.0000 overall best weight: 3.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN I 32 GLN ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.075944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.051470 restraints weight = 52386.256| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 2.33 r_work: 0.2615 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.093 19771 Z= 0.295 Angle : 0.687 11.647 28908 Z= 0.366 Chirality : 0.047 0.375 3605 Planarity : 0.006 0.096 1990 Dihedral : 22.101 179.433 8370 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.32 % Favored : 95.59 % Rotamer: Outliers : 4.24 % Allowed : 28.51 % Favored : 67.25 % 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 (0.25), residues: 1088 helix: 0.88 (0.23), residues: 502 sheet: -0.76 (0.40), residues: 166 loop : -0.79 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG G 138 TYR 0.015 0.002 TYR M 86 PHE 0.021 0.002 PHE S 74 TRP 0.023 0.002 TRP B 96 HIS 0.005 0.001 HIS N 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.29 (19770) covalent geometry : angle 0.68675 / 0.37 (28908) hydrogen bonds : bond 0.05915 / 6.33 ( 782) hydrogen bonds : angle 3.99757 / 5.22 ( 1795) metal coordination : bond 0.00082 / 0.04 ( 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 222 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 183 time to evaluate : 0.485 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.1699 (mmp) cc_final: 0.0897 (ppp) REVERT: B 9 MET cc_start: 0.0051 (OUTLIER) cc_final: -0.0201 (pmm) REVERT: B 70 VAL cc_start: 0.5427 (t) cc_final: 0.4953 (m) REVERT: B 94 HIS cc_start: 0.7613 (OUTLIER) cc_final: 0.7216 (m90) REVERT: B 113 ARG cc_start: 0.6303 (tpp80) cc_final: 0.5969 (tpp80) REVERT: B 118 GLU cc_start: 0.6894 (OUTLIER) cc_final: 0.6299 (mp0) REVERT: B 139 ARG cc_start: 0.7152 (OUTLIER) cc_final: 0.6645 (mtt180) REVERT: G 144 MET cc_start: 0.6830 (tpp) cc_final: 0.6335 (tmt) REVERT: I 37 GLN cc_start: 0.8686 (pt0) cc_final: 0.8411 (pt0) REVERT: I 59 GLU cc_start: 0.8821 (mp0) cc_final: 0.8379 (pm20) REVERT: I 60 LYS cc_start: 0.8854 (mppt) cc_final: 0.8555 (mmtp) REVERT: M 13 LYS cc_start: 0.8165 (mmtt) cc_final: 0.7384 (mttt) REVERT: M 27 LYS cc_start: 0.8810 (ttmt) cc_final: 0.8576 (ttmm) REVERT: S 6 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8850 (ptmm) REVERT: S 17 LYS cc_start: 0.9242 (mmmm) cc_final: 0.8901 (mmmm) REVERT: S 20 GLU cc_start: 0.8709 (pt0) cc_final: 0.8247 (pt0) outliers start: 39 outliers final: 28 residues processed: 207 average time/residue: 0.6627 time to fit residues: 153.1738 Evaluate side-chains 209 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 176 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 139 ARG 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 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 G residue 11 LYS Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 45 ARG 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 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 14 VAL Chi-restraints excluded: chain N residue 26 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 85 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 45 optimal weight: 9.9990 chunk 132 optimal weight: 4.9990 chunk 4 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 95 optimal weight: 9.9990 chunk 96 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 140 ASN ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 66 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.076540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.052172 restraints weight = 52729.133| |-----------------------------------------------------------------------------| r_work (start): 0.2768 rms_B_bonded: 2.40 r_work: 0.2634 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2531 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9023 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 19771 Z= 0.213 Angle : 0.631 11.598 28908 Z= 0.345 Chirality : 0.042 0.353 3605 Planarity : 0.006 0.098 1990 Dihedral : 22.134 179.360 8370 Min Nonbonded Distance : 1.848 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.04 % Favored : 95.77 % Rotamer: Outliers : 4.03 % Allowed : 28.62 % Favored : 67.36 % 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: -0.01 (0.26), residues: 1088 helix: 0.93 (0.23), residues: 497 sheet: -0.74 (0.40), residues: 166 loop : -0.73 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 138 TYR 0.017 0.002 TYR M 86 PHE 0.024 0.001 PHE B 90 TRP 0.028 0.002 TRP B 96 HIS 0.004 0.001 HIS N 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.21 (19770) covalent geometry : angle 0.63104 / 0.35 (28908) hydrogen bonds : bond 0.05750 / 6.17 ( 782) hydrogen bonds : angle 3.96231 / 5.17 ( 1795) metal coordination : bond 0.00065 / 0.03 ( 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 220 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 183 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.1740 (mmp) cc_final: 0.0974 (ppp) REVERT: B 9 MET cc_start: -0.0021 (OUTLIER) cc_final: -0.0275 (pmm) REVERT: B 70 VAL cc_start: 0.5390 (t) cc_final: 0.4957 (m) REVERT: B 94 HIS cc_start: 0.7541 (OUTLIER) cc_final: 0.7147 (m90) REVERT: B 113 ARG cc_start: 0.6303 (tpp80) cc_final: 0.5949 (tpp80) REVERT: B 118 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6422 (mp0) REVERT: B 139 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6636 (mtt180) REVERT: I 37 GLN cc_start: 0.8664 (pt0) cc_final: 0.8323 (pt0) REVERT: I 124 ARG cc_start: 0.9049 (mmm-85) cc_final: 0.8826 (mtp85) REVERT: M 13 LYS cc_start: 0.8119 (mmtt) cc_final: 0.7320 (mttt) REVERT: M 27 LYS cc_start: 0.8779 (ttmt) cc_final: 0.8566 (ttmm) REVERT: M 82 ASP cc_start: 0.8833 (m-30) cc_final: 0.8588 (m-30) REVERT: S 6 LYS cc_start: 0.9171 (OUTLIER) cc_final: 0.8824 (ptmm) REVERT: S 17 LYS cc_start: 0.9237 (mmmm) cc_final: 0.8875 (mmmm) REVERT: S 20 GLU cc_start: 0.8609 (pt0) cc_final: 0.8127 (pt0) outliers start: 37 outliers final: 24 residues processed: 206 average time/residue: 0.6363 time to fit residues: 146.9221 Evaluate side-chains 208 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.479 ------------------------------------------------------------------------------- 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 139 ARG Chi-restraints excluded: chain B residue 144 LEU 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 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 I residue 111 VAL Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 45 ARG 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 44 LYS Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 14 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 112 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 143 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 37 optimal weight: 9.9990 chunk 10 optimal weight: 30.0000 chunk 20 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 116 optimal weight: 1.9990 chunk 42 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 140 ASN I 32 GLN I 110 GLN ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 66 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.075501 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.051039 restraints weight = 52777.958| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 2.47 r_work: 0.2601 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2501 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2501 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9040 moved from start: 0.2655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.118 19771 Z= 0.322 Angle : 0.719 12.286 28908 Z= 0.383 Chirality : 0.049 0.383 3605 Planarity : 0.006 0.096 1990 Dihedral : 22.111 179.934 8370 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.78 % Favored : 95.13 % Rotamer: Outliers : 3.48 % Allowed : 29.49 % Favored : 67.03 % 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: -0.19 (0.25), residues: 1088 helix: 0.79 (0.23), residues: 497 sheet: -0.72 (0.40), residues: 166 loop : -0.87 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG G 119 TYR 0.021 0.002 TYR M 86 PHE 0.021 0.002 PHE B 90 TRP 0.026 0.002 TRP B 96 HIS 0.005 0.001 HIS N 71 Details of bonding type rmsd/Z covalent geometry : bond 0.00625 / 0.32 (19770) covalent geometry : angle 0.71880 / 0.38 (28908) hydrogen bonds : bond 0.06150 / 6.61 ( 782) hydrogen bonds : angle 4.04828 / 5.26 ( 1795) metal coordination : bond 0.00118 / 0.06 ( 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 213 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 181 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.1883 (mmp) cc_final: 0.1099 (ppp) REVERT: B 70 VAL cc_start: 0.5461 (t) cc_final: 0.5095 (m) REVERT: B 94 HIS cc_start: 0.7545 (OUTLIER) cc_final: 0.7177 (m90) REVERT: B 95 ARG cc_start: 0.4876 (ttp80) cc_final: 0.4354 (ttt-90) REVERT: B 113 ARG cc_start: 0.6350 (tpp80) cc_final: 0.6130 (tpp80) REVERT: B 118 GLU cc_start: 0.7033 (OUTLIER) cc_final: 0.6450 (mp0) REVERT: B 139 ARG cc_start: 0.7209 (OUTLIER) cc_final: 0.6684 (mtt180) REVERT: I 37 GLN cc_start: 0.8689 (pt0) cc_final: 0.8371 (pt0) REVERT: I 59 GLU cc_start: 0.8852 (mp0) cc_final: 0.8412 (pm20) REVERT: I 105 THR cc_start: 0.8792 (t) cc_final: 0.8587 (m) REVERT: M 13 LYS cc_start: 0.8038 (mmtt) cc_final: 0.7193 (mttt) REVERT: M 78 LYS cc_start: 0.9239 (tmtm) cc_final: 0.9016 (tttm) REVERT: M 82 ASP cc_start: 0.8788 (m-30) cc_final: 0.8445 (m-30) REVERT: S 6 LYS cc_start: 0.9203 (OUTLIER) cc_final: 0.8855 (ptmm) REVERT: S 17 LYS cc_start: 0.9264 (mmmm) cc_final: 0.8914 (mmmm) REVERT: S 20 GLU cc_start: 0.8721 (pt0) cc_final: 0.8270 (pt0) outliers start: 32 outliers final: 21 residues processed: 204 average time/residue: 0.6535 time to fit residues: 148.8452 Evaluate side-chains 204 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 0.670 ------------------------------------------------------------------------------- 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 122 SER Chi-restraints excluded: chain C residue 144 LEU Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 45 ARG 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 44 LYS Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 14 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 62 optimal weight: 8.9990 chunk 149 optimal weight: 0.7980 chunk 142 optimal weight: 0.7980 chunk 114 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 110 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 118 optimal weight: 0.9980 chunk 95 optimal weight: 8.9990 chunk 150 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 140 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.077949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.053631 restraints weight = 52786.845| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.57 r_work: 0.2682 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9004 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 19771 Z= 0.139 Angle : 0.596 12.006 28908 Z= 0.331 Chirality : 0.038 0.319 3605 Planarity : 0.005 0.101 1990 Dihedral : 22.178 178.754 8370 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.95 % Favored : 95.96 % Rotamer: Outliers : 2.50 % Allowed : 30.69 % Favored : 66.81 % 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: -0.13 (0.25), residues: 1088 helix: 0.85 (0.23), residues: 506 sheet: -0.71 (0.40), residues: 165 loop : -0.88 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG G 119 TYR 0.016 0.002 TYR M 86 PHE 0.024 0.001 PHE I 127 TRP 0.021 0.002 TRP B 96 HIS 0.003 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.14 (19770) covalent geometry : angle 0.59550 / 0.33 (28908) hydrogen bonds : bond 0.05542 / 5.92 ( 782) hydrogen bonds : angle 3.95971 / 5.13 ( 1795) metal coordination : bond 0.00059 / 0.03 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7089.24 seconds wall clock time: 121 minutes 29.75 seconds (7289.75 seconds total)