Starting phenix.real_space_refine on Mon Jun 16 11:56:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7af5_11753/06_2025/7af5_11753_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7af5_11753/06_2025/7af5_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7af5_11753/06_2025/7af5_11753.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7af5_11753/06_2025/7af5_11753.map" model { file = "/net/cci-nas-00/data/ceres_data/7af5_11753/06_2025/7af5_11753_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7af5_11753/06_2025/7af5_11753_neut.cif" } resolution = 2.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 11.14, per 1000 atoms: 0.60 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: 4.33 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 8.45 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: 8.88 Time building geometry restraints manager: 5.27 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: 4.650 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: 0.680 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 52.400 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 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:14.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.720 ------------------------------------------------------------------------------- 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 : 10.26 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.011 0.001 TRP C 201 HIS 0.007 0.001 HIS N 71 PHE 0.009 0.002 PHE B 90 TYR 0.011 0.002 TYR C 42 ARG 0.007 0.001 ARG C 11 Details of bonding type rmsd hydrogen bonds : bond 0.18276 ( 782) hydrogen bonds : angle 6.52302 ( 1795) metal coordination : bond 0.15127 ( 1) covalent geometry : bond 0.00712 (19770) covalent geometry : angle 0.74941 (28908) *********************** 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 : 1.305 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: 0.0749 (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: 0.8458 (p) REVERT: B 140 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7432 (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: 0.8792 (mt) REVERT: J 90 LEU cc_start: 0.7902 (tp) cc_final: 0.7670 (tt) 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: 0.8153 (tp) REVERT: M 82 ASP cc_start: 0.8466 (m-30) cc_final: 0.8220 (m-30) REVERT: S 16 LEU cc_start: 0.9325 (mt) cc_final: 0.9118 (mt) outliers start: 0 outliers final: 1 residues processed: 281 average time/residue: 1.4738 time to fit residues: 458.3336 Evaluate side-chains 198 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 197 time to evaluate : 1.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 30 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 2.9990 chunk 115 optimal weight: 0.8980 chunk 63 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 61 optimal weight: 7.9990 chunk 119 optimal weight: 0.9990 chunk 46 optimal weight: 0.0970 chunk 72 optimal weight: 0.9980 chunk 88 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.078285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.054451 restraints weight = 52383.917| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.40 r_work: 0.2700 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2599 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8904 moved from start: 0.1991 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= 0.147 Angle : 0.608 7.834 28908 Z= 0.320 Chirality : 0.037 0.275 3605 Planarity : 0.005 0.095 1990 Dihedral : 22.461 178.785 8372 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.70 % Allowed : 19.59 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.24), residues: 1088 helix: 0.48 (0.23), residues: 485 sheet: -1.52 (0.39), residues: 166 loop : -1.18 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 201 HIS 0.002 0.001 HIS S 14 PHE 0.016 0.001 PHE B 90 TYR 0.013 0.001 TYR C 42 ARG 0.006 0.001 ARG G 53 Details of bonding type rmsd hydrogen bonds : bond 0.05514 ( 782) hydrogen bonds : angle 4.05422 ( 1795) metal coordination : bond 0.00121 ( 1) covalent geometry : bond 0.00289 (19770) covalent geometry : angle 0.60823 (28908) *********************** 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 262 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 228 time to evaluate : 1.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.3886 (mpt) cc_final: 0.3315 (ppp) REVERT: B 94 HIS cc_start: 0.7304 (OUTLIER) cc_final: 0.6929 (m90) REVERT: B 108 ARG cc_start: 0.8797 (mtp-110) cc_final: 0.8448 (tpp80) REVERT: B 117 LEU cc_start: 0.6730 (OUTLIER) cc_final: 0.6194 (mm) REVERT: B 118 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6594 (mp0) REVERT: B 130 THR cc_start: 0.6779 (m) cc_final: 0.6544 (p) REVERT: B 175 GLU cc_start: 0.7661 (mt-10) cc_final: 0.7419 (mt-10) REVERT: G 6 VAL cc_start: 0.5925 (OUTLIER) cc_final: 0.5666 (t) REVERT: G 144 MET cc_start: 0.6071 (tpp) cc_final: 0.5866 (tmt) REVERT: I 37 GLN cc_start: 0.8756 (tt0) cc_final: 0.8538 (pt0) REVERT: J 31 ARG cc_start: 0.8501 (mtm-85) cc_final: 0.8247 (ttp80) REVERT: J 47 GLU cc_start: 0.8841 (OUTLIER) cc_final: 0.8640 (tt0) REVERT: M 13 LYS cc_start: 0.8169 (mmtt) cc_final: 0.7519 (ptpt) REVERT: M 82 ASP cc_start: 0.8648 (m-30) cc_final: 0.8421 (m-30) REVERT: S 21 LYS cc_start: 0.9094 (ttmm) cc_final: 0.8866 (ttmm) outliers start: 34 outliers final: 9 residues processed: 244 average time/residue: 1.3335 time to fit residues: 364.4202 Evaluate side-chains 202 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 188 time to evaluate : 1.449 ------------------------------------------------------------------------------- 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 83 ASP Chi-restraints excluded: chain C residue 134 MET 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 47 GLU Chi-restraints excluded: chain J residue 99 GLN Chi-restraints excluded: chain M residue 20 THR Chi-restraints excluded: chain M residue 48 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 145 optimal weight: 0.6980 chunk 146 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 chunk 125 optimal weight: 0.9990 chunk 149 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 52 optimal weight: 0.9980 chunk 47 optimal weight: 10.0000 chunk 78 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 HIS C 140 ASN G 28 ASN G 97 ASN I 126 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.078086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.053979 restraints weight = 52483.432| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 2.17 r_work: 0.2687 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2585 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8909 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 19771 Z= 0.172 Angle : 0.592 10.832 28908 Z= 0.307 Chirality : 0.037 0.244 3605 Planarity : 0.005 0.097 1990 Dihedral : 22.279 176.945 8370 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 4.68 % Allowed : 21.98 % Favored : 73.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.25), residues: 1088 helix: 0.83 (0.23), residues: 496 sheet: -1.36 (0.40), residues: 160 loop : -0.81 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 103 HIS 0.004 0.001 HIS N 71 PHE 0.012 0.001 PHE B 90 TYR 0.011 0.001 TYR C 42 ARG 0.005 0.001 ARG G 53 Details of bonding type rmsd hydrogen bonds : bond 0.04820 ( 782) hydrogen bonds : angle 3.80497 ( 1795) metal coordination : bond 0.00026 ( 1) covalent geometry : bond 0.00342 (19770) covalent geometry : angle 0.59194 (28908) *********************** 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 241 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 1.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.3672 (mpt) cc_final: 0.2829 (ppp) REVERT: B 70 VAL cc_start: 0.5372 (t) cc_final: 0.4943 (m) REVERT: B 118 GLU cc_start: 0.7009 (OUTLIER) cc_final: 0.6526 (mp0) REVERT: G 144 MET cc_start: 0.6766 (tpp) cc_final: 0.6187 (tmt) REVERT: I 59 GLU cc_start: 0.8676 (mp0) cc_final: 0.8310 (pm20) REVERT: I 60 LYS cc_start: 0.8880 (mppt) cc_final: 0.8559 (mmtp) REVERT: M 13 LYS cc_start: 0.8192 (mmtt) cc_final: 0.7491 (ptpt) REVERT: M 27 LYS cc_start: 0.8767 (ttpt) cc_final: 0.8520 (ttmm) REVERT: M 81 MET cc_start: 0.9237 (ttm) cc_final: 0.8828 (ttt) REVERT: S 6 LYS cc_start: 0.9154 (OUTLIER) cc_final: 0.8852 (ptmm) REVERT: S 18 LYS cc_start: 0.9289 (mtmt) cc_final: 0.9083 (mtmt) REVERT: S 21 LYS cc_start: 0.9094 (ttmm) cc_final: 0.8868 (ttmm) outliers start: 43 outliers final: 24 residues processed: 222 average time/residue: 1.2666 time to fit residues: 316.4069 Evaluate side-chains 209 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 GLU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 227 GLN 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 186 THR 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 111 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 77 VAL 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 48 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 43 ASN 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 54 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 151 optimal weight: 0.0070 chunk 98 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 140 optimal weight: 0.9990 overall best weight: 1.7804 ------------------------------------------------------------------------------- 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** C 140 ASN G 28 ASN G 97 ASN I 32 GLN I 126 GLN S 57 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.077507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.053974 restraints weight = 52434.846| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 2.32 r_work: 0.2674 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8925 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19771 Z= 0.209 Angle : 0.602 10.934 28908 Z= 0.311 Chirality : 0.037 0.235 3605 Planarity : 0.005 0.097 1990 Dihedral : 22.199 176.312 8370 Min Nonbonded Distance : 1.872 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.90 % Allowed : 23.07 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.25), residues: 1088 helix: 1.03 (0.23), residues: 495 sheet: -1.12 (0.39), residues: 165 loop : -0.68 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 201 HIS 0.005 0.001 HIS N 71 PHE 0.011 0.001 PHE B 90 TYR 0.010 0.001 TYR C 42 ARG 0.006 0.001 ARG I 124 Details of bonding type rmsd hydrogen bonds : bond 0.04758 ( 782) hydrogen bonds : angle 3.74886 ( 1795) metal coordination : bond 0.00032 ( 1) covalent geometry : bond 0.00419 (19770) covalent geometry : angle 0.60244 (28908) *********************** 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 240 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 195 time to evaluate : 1.197 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.3273 (mpt) cc_final: 0.2446 (ppp) REVERT: B 70 VAL cc_start: 0.5327 (t) cc_final: 0.4913 (m) REVERT: B 94 HIS cc_start: 0.7423 (OUTLIER) cc_final: 0.6995 (m90) REVERT: B 118 GLU cc_start: 0.7039 (OUTLIER) cc_final: 0.6470 (mp0) REVERT: C 142 MET cc_start: 0.9126 (mmm) cc_final: 0.8926 (mmt) REVERT: I 5 GLN cc_start: 0.8379 (tp-100) cc_final: 0.8165 (tp40) REVERT: I 37 GLN cc_start: 0.8642 (pt0) cc_final: 0.8332 (pt0) REVERT: I 124 ARG cc_start: 0.9033 (mmm-85) cc_final: 0.8755 (mtp85) REVERT: M 13 LYS cc_start: 0.8172 (mmtt) cc_final: 0.7427 (ptpt) REVERT: M 27 LYS cc_start: 0.8749 (ttpt) cc_final: 0.8530 (ttmm) REVERT: M 82 ASP cc_start: 0.8766 (m-30) cc_final: 0.8404 (m-30) REVERT: S 6 LYS cc_start: 0.9165 (OUTLIER) cc_final: 0.8826 (ptmm) outliers start: 45 outliers final: 27 residues processed: 219 average time/residue: 1.3092 time to fit residues: 322.9938 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 : 1.300 ------------------------------------------------------------------------------- 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 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 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 6 VAL Chi-restraints excluded: chain I residue 7 TYR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 77 VAL 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 30 SER 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 75 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 42 optimal weight: 3.9990 chunk 127 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 150 optimal weight: 1.9990 chunk 61 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 124 optimal weight: 0.6980 chunk 115 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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** C 140 ASN G 28 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 = 0.3356 r_free = 0.3356 target = 0.077671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.053170 restraints weight = 53043.236| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.66 r_work: 0.2672 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work: 0.2571 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 19771 Z= 0.186 Angle : 0.595 9.836 28908 Z= 0.308 Chirality : 0.037 0.237 3605 Planarity : 0.005 0.096 1990 Dihedral : 22.171 175.964 8370 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.79 % Allowed : 25.14 % Favored : 70.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.25), residues: 1088 helix: 1.16 (0.23), residues: 494 sheet: -0.97 (0.39), residues: 164 loop : -0.60 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 201 HIS 0.004 0.001 HIS N 71 PHE 0.026 0.001 PHE I 127 TYR 0.010 0.001 TYR M 86 ARG 0.006 0.000 ARG B 113 Details of bonding type rmsd hydrogen bonds : bond 0.04638 ( 782) hydrogen bonds : angle 3.71734 ( 1795) metal coordination : bond 0.00030 ( 1) covalent geometry : bond 0.00371 (19770) covalent geometry : angle 0.59478 (28908) *********************** 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 233 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 189 time to evaluate : 1.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.3465 (mpt) cc_final: 0.2767 (ppp) REVERT: B 70 VAL cc_start: 0.5290 (t) cc_final: 0.4909 (m) REVERT: B 94 HIS cc_start: 0.7309 (OUTLIER) cc_final: 0.6914 (m90) REVERT: B 118 GLU cc_start: 0.7099 (OUTLIER) cc_final: 0.6533 (mp0) REVERT: I 37 GLN cc_start: 0.8663 (pt0) cc_final: 0.8380 (pt0) REVERT: I 124 ARG cc_start: 0.9028 (mmm-85) cc_final: 0.8772 (mtp85) REVERT: M 13 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7414 (ptpt) REVERT: M 27 LYS cc_start: 0.8752 (ttpt) cc_final: 0.8512 (ttmm) REVERT: N 39 GLU cc_start: 0.9057 (OUTLIER) cc_final: 0.8712 (tm-30) REVERT: S 6 LYS cc_start: 0.9149 (OUTLIER) cc_final: 0.8796 (ptmm) REVERT: S 17 LYS cc_start: 0.9287 (mmmm) cc_final: 0.9075 (mmmm) outliers start: 44 outliers final: 28 residues processed: 216 average time/residue: 1.6648 time to fit residues: 405.8246 Evaluate side-chains 216 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 1.361 ------------------------------------------------------------------------------- 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 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 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 7 TYR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 46 LYS Chi-restraints excluded: chain J residue 76 ILE Chi-restraints excluded: chain J residue 77 VAL 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 30 SER Chi-restraints excluded: chain M residue 48 LEU Chi-restraints excluded: chain M residue 97 VAL Chi-restraints excluded: chain N residue 39 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 142 optimal weight: 1.9990 chunk 62 optimal weight: 6.9990 chunk 49 optimal weight: 10.0000 chunk 129 optimal weight: 0.6980 chunk 145 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 115 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 146 optimal weight: 6.9990 chunk 23 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 140 ASN G 28 ASN I 32 GLN I 126 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.076842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.052480 restraints weight = 53290.296| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 2.30 r_work: 0.2644 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2539 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8946 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19771 Z= 0.237 Angle : 0.622 10.252 28908 Z= 0.322 Chirality : 0.038 0.248 3605 Planarity : 0.005 0.093 1990 Dihedral : 22.131 176.058 8370 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.90 % Allowed : 26.33 % Favored : 68.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.26), residues: 1088 helix: 1.12 (0.23), residues: 501 sheet: -0.92 (0.39), residues: 165 loop : -0.60 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 201 HIS 0.006 0.001 HIS N 71 PHE 0.030 0.002 PHE I 127 TYR 0.011 0.002 TYR M 86 ARG 0.005 0.001 ARG B 113 Details of bonding type rmsd hydrogen bonds : bond 0.04796 ( 782) hydrogen bonds : angle 3.75520 ( 1795) metal coordination : bond 0.00040 ( 1) covalent geometry : bond 0.00474 (19770) covalent geometry : angle 0.62229 (28908) *********************** 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 232 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 187 time to evaluate : 1.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 VAL cc_start: 0.5345 (t) cc_final: 0.4944 (m) REVERT: B 94 HIS cc_start: 0.7382 (OUTLIER) cc_final: 0.6950 (m90) REVERT: B 118 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6589 (mp0) REVERT: I 37 GLN cc_start: 0.8647 (pt0) cc_final: 0.8401 (pt0) REVERT: I 59 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8471 (pm20) REVERT: I 60 LYS cc_start: 0.8883 (mmtm) cc_final: 0.8669 (mmtm) REVERT: I 124 ARG cc_start: 0.9074 (mmm-85) cc_final: 0.8834 (mtp85) REVERT: M 13 LYS cc_start: 0.8166 (mmtt) cc_final: 0.7385 (ptpt) REVERT: M 27 LYS cc_start: 0.8766 (ttpt) cc_final: 0.8525 (ttmm) REVERT: S 6 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8797 (ptmm) REVERT: S 66 MET cc_start: 0.9130 (ttm) cc_final: 0.8831 (ttp) outliers start: 45 outliers final: 24 residues processed: 212 average time/residue: 1.3269 time to fit residues: 315.2224 Evaluate side-chains 209 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 181 time to evaluate : 1.302 ------------------------------------------------------------------------------- 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 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 59 GLU Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 77 VAL 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 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 6 LYS Chi-restraints excluded: chain S residue 12 ASP 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 142 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 109 optimal weight: 3.9990 chunk 122 optimal weight: 10.0000 chunk 22 optimal weight: 4.9990 chunk 127 optimal weight: 5.9990 chunk 118 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 chunk 4 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- 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 ** 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 = 0.3312 r_free = 0.3312 target = 0.075669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.051245 restraints weight = 52789.145| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 2.51 r_work: 0.2611 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2512 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 19771 Z= 0.321 Angle : 0.679 10.674 28908 Z= 0.351 Chirality : 0.041 0.264 3605 Planarity : 0.006 0.093 1990 Dihedral : 22.138 176.655 8370 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.14 % Favored : 95.77 % Rotamer: Outliers : 4.68 % Allowed : 28.51 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.25), residues: 1088 helix: 1.05 (0.23), residues: 508 sheet: -0.76 (0.40), residues: 166 loop : -0.81 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 201 HIS 0.006 0.001 HIS N 71 PHE 0.033 0.002 PHE I 127 TYR 0.015 0.002 TYR M 86 ARG 0.009 0.001 ARG G 138 Details of bonding type rmsd hydrogen bonds : bond 0.05202 ( 782) hydrogen bonds : angle 3.80482 ( 1795) metal coordination : bond 0.00082 ( 1) covalent geometry : bond 0.00641 (19770) covalent geometry : angle 0.67866 (28908) *********************** 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 227 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 184 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.1973 (mmp) cc_final: 0.0914 (ppp) REVERT: B 70 VAL cc_start: 0.5470 (t) cc_final: 0.5098 (m) REVERT: B 94 HIS cc_start: 0.7511 (OUTLIER) cc_final: 0.7103 (m90) REVERT: B 118 GLU cc_start: 0.7184 (OUTLIER) cc_final: 0.6633 (mp0) REVERT: C 181 ASP cc_start: 0.8504 (t0) cc_final: 0.8301 (t0) REVERT: G 29 ILE cc_start: 0.8919 (mm) cc_final: 0.8640 (mp) REVERT: I 105 THR cc_start: 0.8657 (t) cc_final: 0.8453 (m) REVERT: J 20 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8295 (tm-30) REVERT: M 7 ILE cc_start: 0.8812 (mm) cc_final: 0.8591 (mm) REVERT: M 13 LYS cc_start: 0.8179 (mmtt) cc_final: 0.7658 (mmpt) REVERT: M 27 LYS cc_start: 0.8842 (ttpt) cc_final: 0.8610 (ttmm) REVERT: S 6 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8839 (ptmm) REVERT: S 17 LYS cc_start: 0.9301 (mmmm) cc_final: 0.9060 (mmmm) outliers start: 43 outliers final: 27 residues processed: 206 average time/residue: 1.3153 time to fit residues: 304.6972 Evaluate side-chains 208 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 1.310 ------------------------------------------------------------------------------- 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 83 ASP Chi-restraints excluded: chain C residue 94 ILE 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 G residue 59 LEU Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 111 VAL Chi-restraints excluded: chain J residue 8 ILE Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 20 GLN 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 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 6 LYS Chi-restraints excluded: chain S residue 12 ASP 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 38 optimal weight: 3.9990 chunk 144 optimal weight: 0.5980 chunk 91 optimal weight: 7.9990 chunk 94 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 53 optimal weight: 9.9990 chunk 48 optimal weight: 30.0000 chunk 95 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- 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 = 0.3345 r_free = 0.3345 target = 0.077248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.052694 restraints weight = 52775.595| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.58 r_work: 0.2662 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8939 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 19771 Z= 0.187 Angle : 0.623 11.280 28908 Z= 0.324 Chirality : 0.037 0.240 3605 Planarity : 0.005 0.094 1990 Dihedral : 22.169 176.026 8370 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.14 % Favored : 95.77 % Rotamer: Outliers : 3.59 % Allowed : 28.73 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.26), residues: 1088 helix: 1.09 (0.23), residues: 509 sheet: -0.78 (0.40), residues: 165 loop : -0.76 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 201 HIS 0.004 0.001 HIS N 71 PHE 0.032 0.001 PHE I 127 TYR 0.013 0.002 TYR M 86 ARG 0.009 0.000 ARG J 31 Details of bonding type rmsd hydrogen bonds : bond 0.04810 ( 782) hydrogen bonds : angle 3.74419 ( 1795) metal coordination : bond 0.00033 ( 1) covalent geometry : bond 0.00377 (19770) covalent geometry : angle 0.62262 (28908) *********************** 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 224 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 191 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 6 MET cc_start: 0.2008 (mmp) cc_final: 0.1000 (ppp) REVERT: B 70 VAL cc_start: 0.5524 (t) cc_final: 0.5090 (m) REVERT: B 94 HIS cc_start: 0.7346 (OUTLIER) cc_final: 0.6965 (m90) REVERT: B 118 GLU cc_start: 0.7265 (OUTLIER) cc_final: 0.6771 (mp0) REVERT: C 36 ASP cc_start: 0.9077 (t0) cc_final: 0.8872 (m-30) REVERT: G 29 ILE cc_start: 0.8859 (mm) cc_final: 0.8584 (mp) REVERT: I 105 THR cc_start: 0.8581 (t) cc_final: 0.8371 (m) REVERT: I 124 ARG cc_start: 0.9047 (mmm-85) cc_final: 0.8819 (mtp85) REVERT: M 13 LYS cc_start: 0.8139 (mmtt) cc_final: 0.7392 (mttt) REVERT: M 27 LYS cc_start: 0.8783 (ttpt) cc_final: 0.8539 (ttmm) REVERT: S 6 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8769 (ptmm) outliers start: 33 outliers final: 23 residues processed: 212 average time/residue: 1.3591 time to fit residues: 322.9688 Evaluate side-chains 212 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 186 time to evaluate : 1.300 ------------------------------------------------------------------------------- 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 94 ILE 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 8 ILE Chi-restraints excluded: chain J residue 17 LEU Chi-restraints excluded: chain J residue 77 VAL 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 30 SER Chi-restraints excluded: chain M residue 44 LYS Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 11 ILE 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 63 optimal weight: 20.0000 chunk 81 optimal weight: 5.9990 chunk 93 optimal weight: 9.9990 chunk 151 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 33 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 150 optimal weight: 5.9990 chunk 145 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 140 ASN ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.074715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.050677 restraints weight = 53171.369| |-----------------------------------------------------------------------------| r_work (start): 0.2723 rms_B_bonded: 2.45 r_work: 0.2588 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2487 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8985 moved from start: 0.2693 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= 0.414 Angle : 0.753 11.953 28908 Z= 0.386 Chirality : 0.044 0.282 3605 Planarity : 0.006 0.091 1990 Dihedral : 22.165 177.196 8370 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.96 % Favored : 94.94 % Rotamer: Outliers : 4.03 % Allowed : 28.94 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.25), residues: 1088 helix: 0.98 (0.23), residues: 498 sheet: -0.74 (0.40), residues: 165 loop : -0.73 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 96 HIS 0.007 0.001 HIS N 71 PHE 0.033 0.002 PHE I 127 TYR 0.018 0.002 TYR M 86 ARG 0.009 0.001 ARG J 31 Details of bonding type rmsd hydrogen bonds : bond 0.05583 ( 782) hydrogen bonds : angle 3.93150 ( 1795) metal coordination : bond 0.00109 ( 1) covalent geometry : bond 0.00830 (19770) covalent geometry : angle 0.75334 (28908) *********************** 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 232 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 195 time to evaluate : 1.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 VAL cc_start: 0.5510 (t) cc_final: 0.5133 (m) REVERT: B 94 HIS cc_start: 0.7568 (OUTLIER) cc_final: 0.7278 (m90) REVERT: B 118 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6634 (mp0) REVERT: B 139 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6591 (mtt180) REVERT: B 203 ASN cc_start: 0.2501 (t0) cc_final: 0.2298 (t0) REVERT: I 124 ARG cc_start: 0.9140 (mmm-85) cc_final: 0.8869 (mtp85) REVERT: M 13 LYS cc_start: 0.8156 (mmtt) cc_final: 0.7741 (mmpt) REVERT: M 27 LYS cc_start: 0.8883 (ttpt) cc_final: 0.8654 (ttmm) REVERT: S 6 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8842 (ptmm) REVERT: S 17 LYS cc_start: 0.9292 (mmmm) cc_final: 0.9080 (mmmm) outliers start: 37 outliers final: 24 residues processed: 217 average time/residue: 1.3183 time to fit residues: 322.9869 Evaluate side-chains 213 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 185 time to evaluate : 1.295 ------------------------------------------------------------------------------- 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 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 8 ILE 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 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 44 LYS Chi-restraints excluded: chain M residue 97 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 111 optimal weight: 1.9990 chunk 130 optimal weight: 0.9990 chunk 110 optimal weight: 0.7980 chunk 101 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 98 optimal weight: 7.9990 chunk 89 optimal weight: 0.0770 chunk 64 optimal weight: 9.9990 chunk 82 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN B 146 ASN C 140 ASN 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 = 0.3380 r_free = 0.3380 target = 0.078873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.054940 restraints weight = 52839.400| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.23 r_work: 0.2714 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.3203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 19771 Z= 0.141 Angle : 0.629 13.063 28908 Z= 0.325 Chirality : 0.036 0.234 3605 Planarity : 0.005 0.093 1990 Dihedral : 22.156 175.466 8370 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.58 % Favored : 96.23 % Rotamer: Outliers : 2.61 % Allowed : 31.01 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.25), residues: 1088 helix: 1.04 (0.23), residues: 503 sheet: -0.73 (0.40), residues: 164 loop : -0.64 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 104 HIS 0.004 0.001 HIS M 12 PHE 0.035 0.001 PHE I 127 TYR 0.011 0.002 TYR M 86 ARG 0.008 0.001 ARG J 31 Details of bonding type rmsd hydrogen bonds : bond 0.04686 ( 782) hydrogen bonds : angle 3.86141 ( 1795) metal coordination : bond 0.00014 ( 1) covalent geometry : bond 0.00285 (19770) covalent geometry : angle 0.62937 (28908) ********************** 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 215 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 191 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 70 VAL cc_start: 0.5648 (t) cc_final: 0.5286 (m) REVERT: B 94 HIS cc_start: 0.7695 (OUTLIER) cc_final: 0.7178 (m90) REVERT: B 139 ARG cc_start: 0.7159 (OUTLIER) cc_final: 0.6535 (mtt180) REVERT: B 203 ASN cc_start: 0.2557 (t0) cc_final: 0.2336 (t0) REVERT: I 124 ARG cc_start: 0.9010 (mmm-85) cc_final: 0.8771 (mtp85) REVERT: M 12 HIS cc_start: 0.5982 (p90) cc_final: 0.5782 (p90) REVERT: M 27 LYS cc_start: 0.8683 (ttpt) cc_final: 0.8292 (ttmm) REVERT: S 6 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8749 (ptmm) REVERT: S 17 LYS cc_start: 0.9314 (mmmm) cc_final: 0.9077 (mmmm) REVERT: S 20 GLU cc_start: 0.8531 (pt0) cc_final: 0.8215 (pt0) outliers start: 24 outliers final: 16 residues processed: 207 average time/residue: 1.1957 time to fit residues: 279.3515 Evaluate side-chains 203 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 HIS 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 84 VAL Chi-restraints excluded: chain C residue 93 ASP 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 8 ILE 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 116 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 103 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 98 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 chunk 63 optimal weight: 20.0000 chunk 79 optimal weight: 2.9990 chunk 6 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN C 140 ASN J 4 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.078235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.053891 restraints weight = 52827.184| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.76 r_work: 0.2692 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work: 0.2589 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 19771 Z= 0.172 Angle : 0.628 12.455 28908 Z= 0.324 Chirality : 0.037 0.247 3605 Planarity : 0.005 0.092 1990 Dihedral : 22.115 175.704 8370 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.32 % Favored : 95.59 % Rotamer: Outliers : 2.61 % Allowed : 30.79 % Favored : 66.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.18 (0.25), residues: 1088 helix: 1.07 (0.23), residues: 502 sheet: -0.72 (0.40), residues: 158 loop : -0.57 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 104 HIS 0.003 0.001 HIS N 71 PHE 0.034 0.001 PHE I 127 TYR 0.012 0.001 TYR M 86 ARG 0.011 0.000 ARG G 119 Details of bonding type rmsd hydrogen bonds : bond 0.04569 ( 782) hydrogen bonds : angle 3.85275 ( 1795) metal coordination : bond 0.00078 ( 1) covalent geometry : bond 0.00352 (19770) covalent geometry : angle 0.62790 (28908) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15137.82 seconds wall clock time: 261 minutes 27.59 seconds (15687.59 seconds total)