Starting phenix.real_space_refine on Sun Oct 25 21:58:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7afa_11758/10_2026/7afa_11758_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7afa_11758/10_2026/7afa_11758.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7afa_11758/10_2026/7afa_11758.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7afa_11758/10_2026/7afa_11758.map" model { file = "/net/cci-nas-00/data/ceres_data/7afa_11758/10_2026/7afa_11758_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7afa_11758/10_2026/7afa_11758_neut.cif" } resolution = 2.95 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= 0.004 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 25 5.21 5 S 28 5.16 5 C 9812 2.51 5 N 3440 2.21 5 O 4720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18482 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': 34, 'rna3p': 3, 'rna3p_pur': 212, 'rna3p_pyr': 171} Link IDs: {'rna2p': 70, 'rna3p': 385} 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: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1129 Classifications: {'peptide': 144} Link IDs: {'PTRANS': 5, 'TRANS': 138} 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: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Unusual residues: {' MG': 25} Classifications: {'undetermined': 25} Link IDs: {None: 24} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.76, per 1000 atoms: 0.20 Number of scatterers: 18482 At special positions: 0 Unit cell: (136.71, 113.925, 155.155, 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 25 11.99 O 4720 8.00 N 3440 7.00 C 9812 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: 1.61 Conformation dependent library (CDL) restraints added in 567.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2038 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 10 sheets defined 50.2% alpha, 19.0% beta 139 base pairs and 235 stacking pairs defined. Time for finding SS restraints: 2.67 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: 3.616A pdb=" N GLN B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER B 110 " --> pdb=" O THR B 106 " (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 6 through 11 removed outlier: 3.575A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 47 removed outlier: 3.510A pdb=" N ASN C 32 " --> pdb=" O GLU C 28 " (cutoff:3.500A) Processing helix chain 'C' and resid 72 through 77 Processing helix chain 'C' and resid 81 through 96 Processing helix chain 'C' and resid 108 through 111 Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 129 through 144 Processing helix chain 'C' and resid 156 through 160 Processing helix chain 'G' and resid 20 through 31 Processing helix chain 'G' and resid 35 through 55 Processing helix chain 'G' and resid 57 through 68 Processing helix chain 'G' and resid 92 through 112 removed outlier: 3.566A pdb=" N ALA G 98 " --> pdb=" O VAL G 94 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLY G 112 " --> pdb=" O ALA G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 115 through 129 removed outlier: 3.576A pdb=" N GLU G 129 " --> pdb=" O SER G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 144 Processing helix chain 'I' and resid 34 through 39 Processing helix chain 'I' and resid 41 through 48 Processing helix chain 'I' and resid 49 through 55 Processing helix chain 'I' and resid 71 through 91 Processing helix chain 'I' and resid 94 through 101 Processing helix chain 'J' and resid 14 through 33 Processing helix chain 'J' and resid 83 through 90 Processing helix chain 'M' and resid 14 through 20 removed outlier: 3.836A pdb=" N THR M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 63 removed outlier: 4.162A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N PHE M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 84 removed outlier: 3.697A pdb=" N GLY M 84 " --> pdb=" O LEU M 80 " (cutoff:3.500A) Processing helix chain 'M' and resid 85 through 94 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 33 removed outlier: 3.505A pdb=" N LYS N 7 " --> pdb=" O LYS N 3 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LYS N 19 " --> pdb=" O ALA N 15 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N ALA N 22 " --> pdb=" O ASP N 18 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N LYS N 23 " --> pdb=" O LYS N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 37 through 49 removed outlier: 4.022A pdb=" N GLN N 49 " --> pdb=" O VAL N 45 " (cutoff:3.500A) 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 82 through 90 Processing helix chain 'S' and resid 12 through 26 Processing helix chain 'S' and resid 41 through 45 Processing helix chain 'S' and resid 63 through 67 Processing helix chain 'S' and resid 70 through 75 Processing sheet with id=AA1, first strand: chain 'B' and resid 16 through 19 removed outlier: 5.604A pdb=" N PHE B 16 " --> pdb=" O ILE B 41 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N ILE B 41 " --> pdb=" O PHE B 16 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N HIS B 18 " --> pdb=" O HIS B 39 " (cutoff:3.500A) 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: 5.800A 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: 6.751A pdb=" N HIS C 69 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE C 55 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N THR C 67 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE C 57 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG C 65 " --> pdb=" O ILE C 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 52 through 58 removed outlier: 6.751A pdb=" N HIS C 69 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE C 55 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N THR C 67 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ILE C 57 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ARG C 65 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N ALA C 104 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 5.663A pdb=" N ILE C 68 " --> pdb=" O ALA C 104 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 164 through 171 removed outlier: 6.390A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 73 through 78 Processing sheet with id=AA7, first strand: chain 'I' and resid 6 through 12 removed outlier: 6.250A pdb=" N VAL I 29 " --> pdb=" O ILE I 65 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N VAL I 67 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 35 through 52 removed outlier: 7.225A pdb=" N GLN J 35 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASP J 75 " --> pdb=" O ARG J 37 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU J 73 " --> pdb=" O PRO J 39 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU J 71 " --> pdb=" O PRO J 41 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N THR J 69 " --> pdb=" O PRO J 43 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ARG J 45 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE J 67 " --> pdb=" O ARG J 45 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU J 47 " --> pdb=" O TYR J 65 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR J 65 " --> pdb=" O GLU J 47 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N PHE J 49 " --> pdb=" O ASP J 63 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASP J 63 " --> pdb=" O PHE J 49 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 35 through 52 removed outlier: 7.225A pdb=" N GLN J 35 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASP J 75 " --> pdb=" O ARG J 37 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N LEU J 73 " --> pdb=" O PRO J 39 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU J 71 " --> pdb=" O PRO J 41 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N THR J 69 " --> pdb=" O PRO J 43 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ARG J 45 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE J 67 " --> pdb=" O ARG J 45 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU J 47 " --> pdb=" O TYR J 65 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N TYR J 65 " --> pdb=" O GLU J 47 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N PHE J 49 " --> pdb=" O ASP J 63 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ASP J 63 " --> pdb=" O PHE J 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 31 through 33 removed outlier: 5.887A pdb=" N LEU S 31 " --> pdb=" O ALA S 50 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N HIS S 52 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N THR S 33 " --> pdb=" O HIS S 52 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1263 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 346 hydrogen bonds 538 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 235 stacking parallelities Total time for adding SS restraints: 4.73 Time building geometry restraints manager: 2.17 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: 3196 1.33 - 1.45: 7085 1.45 - 1.57: 8503 1.57 - 1.69: 911 1.69 - 1.81: 53 Bond restraints: 19748 Sorted by residual: bond pdb=" C5 2MG 1 966 " pdb=" C4 2MG 1 966 " ideal model delta sigma weight residual 1.382 1.459 -0.077 2.00e-02 2.50e+03 1.49e+01 bond pdb=" C5 2MG 11207 " pdb=" C4 2MG 11207 " ideal model delta sigma weight residual 1.382 1.457 -0.075 2.00e-02 2.50e+03 1.42e+01 bond pdb=" N LYS I 22 " pdb=" CA LYS I 22 " ideal model delta sigma weight residual 1.453 1.488 -0.034 9.20e-03 1.18e+04 1.39e+01 bond pdb=" N ILE J 40 " pdb=" CA ILE J 40 " ideal model delta sigma weight residual 1.460 1.492 -0.032 9.30e-03 1.16e+04 1.18e+01 bond pdb=" N VAL G 73 " pdb=" CA VAL G 73 " ideal model delta sigma weight residual 1.458 1.496 -0.039 1.14e-02 7.69e+03 1.15e+01 ... (remaining 19743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.71: 28097 2.71 - 5.42: 745 5.42 - 8.14: 27 8.14 - 10.85: 8 10.85 - 13.56: 1 Bond angle restraints: 28878 Sorted by residual: angle pdb=" N VAL J 57 " pdb=" CA VAL J 57 " pdb=" C VAL J 57 " ideal model delta sigma weight residual 109.34 122.90 -13.56 2.08e+00 2.31e-01 4.25e+01 angle pdb=" N LYS G 114 " pdb=" CA LYS G 114 " pdb=" C LYS G 114 " ideal model delta sigma weight residual 113.51 123.15 -9.64 1.52e+00 4.33e-01 4.02e+01 angle pdb=" N1 C 11158 " pdb=" C2 C 11158 " pdb=" O2 C 11158 " ideal model delta sigma weight residual 118.90 122.12 -3.22 6.00e-01 2.78e+00 2.87e+01 angle pdb=" C1' C 11158 " pdb=" N1 C 11158 " pdb=" C2 C 11158 " ideal model delta sigma weight residual 118.80 124.66 -5.86 1.10e+00 8.26e-01 2.84e+01 angle pdb=" N SER G 57 " pdb=" CA SER G 57 " pdb=" C SER G 57 " ideal model delta sigma weight residual 111.28 118.14 -6.86 1.35e+00 5.49e-01 2.58e+01 ... (remaining 28873 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.30: 11378 35.30 - 70.60: 1100 70.60 - 105.90: 137 105.90 - 141.20: 1 141.20 - 176.50: 3 Dihedral angle restraints: 12619 sinusoidal: 9470 harmonic: 3149 Sorted by residual: 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 23.50 176.50 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C 11158 " pdb=" C1' C 11158 " pdb=" N1 C 11158 " pdb=" C2 C 11158 " ideal model delta sinusoidal sigma weight residual 200.00 72.86 127.14 1 1.50e+01 4.44e-03 6.84e+01 dihedral pdb=" O4' U 1 960 " pdb=" C1' U 1 960 " pdb=" N1 U 1 960 " pdb=" C2 U 1 960 " ideal model delta sinusoidal sigma weight residual 232.00 59.36 172.64 1 1.70e+01 3.46e-03 6.62e+01 ... (remaining 12616 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 3040 0.107 - 0.214: 540 0.214 - 0.321: 18 0.321 - 0.428: 2 0.428 - 0.535: 2 Chirality restraints: 3602 Sorted by residual: 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 1.91 0.53 2.00e-01 2.50e+01 7.15e+00 chirality pdb=" CA LYS G 114 " pdb=" N LYS G 114 " pdb=" C LYS G 114 " pdb=" CB LYS G 114 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.49e+00 chirality pdb=" CA ASN G 130 " pdb=" N ASN G 130 " pdb=" C ASN G 130 " pdb=" CB ASN G 130 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.67e+00 ... (remaining 3599 not shown) Planarity restraints: 1985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 2MG 11207 " -0.013 2.00e-02 2.50e+03 2.67e-02 2.32e+01 pdb=" N9 2MG 11207 " -0.006 2.00e-02 2.50e+03 pdb=" C8 2MG 11207 " 0.015 2.00e-02 2.50e+03 pdb=" N7 2MG 11207 " 0.019 2.00e-02 2.50e+03 pdb=" C5 2MG 11207 " 0.005 2.00e-02 2.50e+03 pdb=" C6 2MG 11207 " 0.004 2.00e-02 2.50e+03 pdb=" O6 2MG 11207 " 0.013 2.00e-02 2.50e+03 pdb=" N1 2MG 11207 " -0.012 2.00e-02 2.50e+03 pdb=" C2 2MG 11207 " -0.027 2.00e-02 2.50e+03 pdb=" N2 2MG 11207 " -0.038 2.00e-02 2.50e+03 pdb=" N3 2MG 11207 " -0.022 2.00e-02 2.50e+03 pdb=" C4 2MG 11207 " -0.011 2.00e-02 2.50e+03 pdb=" CM2 2MG 11207 " 0.073 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA I 121 " -0.016 2.00e-02 2.50e+03 3.38e-02 1.14e+01 pdb=" C ALA I 121 " 0.058 2.00e-02 2.50e+03 pdb=" O ALA I 121 " -0.022 2.00e-02 2.50e+03 pdb=" N ARG I 122 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG C 59 " -0.053 5.00e-02 4.00e+02 8.13e-02 1.06e+01 pdb=" N PRO C 60 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " -0.045 5.00e-02 4.00e+02 ... (remaining 1982 not shown) Histogram of nonbonded interaction distances: 1.46 - 2.14: 26 2.14 - 2.83: 5712 2.83 - 3.52: 28444 3.52 - 4.21: 57706 4.21 - 4.90: 79797 Nonbonded interactions: 171685 Sorted by model distance: nonbonded pdb=" OP1 G 11094 " pdb="MG MG 11607 " model vdw 1.456 2.170 nonbonded pdb=" OP1 G 11068 " pdb="MG MG 11607 " model vdw 1.822 2.170 nonbonded pdb=" OP2 C 11054 " pdb="MG MG 11617 " model vdw 1.898 2.170 nonbonded pdb=" OP1 C 11303 " pdb="MG MG 11620 " model vdw 1.907 2.170 nonbonded pdb=" OP1 U 11224 " pdb="MG MG 11611 " model vdw 1.930 2.170 ... (remaining 171680 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: 5.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.960 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: 0.000 Load rotamer database and sin/cos tables:8.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 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 : 0.008 0.219 19749 Z= 0.678 Angle : 0.940 13.558 28878 Z= 0.710 Chirality : 0.067 0.535 3602 Planarity : 0.004 0.081 1985 Dihedral : 21.501 176.502 10581 Min Nonbonded Distance : 1.456 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 7.42 % Favored : 92.58 % Cbeta Deviations : 0.59 % 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: -1.10 (0.24), residues: 1085 helix: -0.23 (0.22), residues: 492 sheet: -0.52 (0.37), residues: 183 loop : -1.27 (0.28), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 111 TYR 0.009 0.001 TYR I 64 PHE 0.028 0.002 PHE B 90 TRP 0.008 0.002 TRP N 42 HIS 0.005 0.001 HIS S 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00766 / 0.68 (19748) covalent geometry : angle 0.93992 / 0.71 (28878) hydrogen bonds : bond 0.20965 / 21.78 ( 789) hydrogen bonds : angle 6.74709 / 9.10 ( 1801) metal coordination : bond 0.21871 / 10.94 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.456 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 129 LEU cc_start: 0.8698 (mt) cc_final: 0.8210 (mp) REVERT: C 112 ASP cc_start: 0.8233 (m-30) cc_final: 0.7911 (m-30) REVERT: C 123 GLN cc_start: 0.9196 (mt0) cc_final: 0.8994 (mt0) REVERT: C 168 TYR cc_start: 0.8444 (t80) cc_final: 0.8209 (t80) REVERT: G 17 LYS cc_start: 0.9374 (tttt) cc_final: 0.9146 (tttt) REVERT: I 60 LYS cc_start: 0.8918 (mppt) cc_final: 0.8622 (mmtm) REVERT: J 20 GLN cc_start: 0.8429 (tp-100) cc_final: 0.7658 (tm-30) REVERT: J 24 GLU cc_start: 0.8474 (mm-30) cc_final: 0.8156 (mm-30) REVERT: J 46 LYS cc_start: 0.9266 (mttm) cc_final: 0.8954 (mtpp) REVERT: J 71 LEU cc_start: 0.9382 (tp) cc_final: 0.9165 (tm) REVERT: J 96 VAL cc_start: 0.9615 (t) cc_final: 0.9350 (m) REVERT: N 26 GLU cc_start: 0.8339 (tm-30) cc_final: 0.8101 (tm-30) REVERT: N 30 ILE cc_start: 0.9432 (mm) cc_final: 0.9225 (mp) REVERT: N 82 ILE cc_start: 0.9713 (mm) cc_final: 0.9447 (mp) REVERT: S 17 LYS cc_start: 0.9384 (mttm) cc_final: 0.9108 (mmmm) REVERT: S 21 LYS cc_start: 0.9214 (mtmm) cc_final: 0.8662 (mmtm) REVERT: S 65 GLU cc_start: 0.8658 (tp30) cc_final: 0.8036 (tp30) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.6399 time to fit residues: 220.7984 Evaluate side-chains 186 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 30.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN C 102 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 ASN ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 ASN J 70 HIS ** J 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 12 HIS ** M 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 GLN S 56 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.044534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.032985 restraints weight = 107183.736| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 3.16 r_work: 0.2562 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9030 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19749 Z= 0.164 Angle : 0.625 10.792 28878 Z= 0.354 Chirality : 0.041 0.234 3602 Planarity : 0.006 0.097 1985 Dihedral : 22.353 175.859 8367 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.49 % Allowed : 21.37 % Favored : 75.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.24), residues: 1085 helix: 0.32 (0.22), residues: 491 sheet: -0.24 (0.38), residues: 176 loop : -0.80 (0.28), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 7 TYR 0.026 0.002 TYR B 213 PHE 0.020 0.002 PHE B 184 TRP 0.012 0.002 TRP N 42 HIS 0.018 0.002 HIS B 94 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.16 (19748) covalent geometry : angle 0.62451 / 0.35 (28878) hydrogen bonds : bond 0.09026 / 9.46 ( 789) hydrogen bonds : angle 4.36636 / 5.90 ( 1801) metal coordination : bond 0.01899 / 0.95 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 225 time to evaluate : 0.290 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 32 PHE cc_start: 0.7826 (t80) cc_final: 0.7522 (m-80) REVERT: B 50 PHE cc_start: 0.6475 (t80) cc_final: 0.5912 (t80) REVERT: B 59 LYS cc_start: 0.6393 (OUTLIER) cc_final: 0.5814 (ptpt) REVERT: B 90 PHE cc_start: 0.6755 (m-80) cc_final: 0.6531 (m-80) REVERT: B 100 MET cc_start: 0.8269 (mtp) cc_final: 0.7947 (mpp) REVERT: B 120 GLN cc_start: 0.7171 (OUTLIER) cc_final: 0.6475 (tm-30) REVERT: B 140 GLU cc_start: 0.9357 (tt0) cc_final: 0.9082 (tp30) REVERT: B 154 MET cc_start: 0.8973 (tpp) cc_final: 0.8758 (tpp) REVERT: C 123 GLN cc_start: 0.9450 (mt0) cc_final: 0.9227 (mt0) REVERT: C 168 TYR cc_start: 0.8883 (t80) cc_final: 0.8601 (t80) REVERT: C 181 ASP cc_start: 0.9142 (t70) cc_final: 0.8214 (p0) REVERT: G 29 ILE cc_start: 0.9403 (mm) cc_final: 0.9200 (mp) REVERT: I 25 ASN cc_start: 0.8790 (p0) cc_final: 0.8524 (p0) REVERT: I 27 LYS cc_start: 0.9118 (ptpp) cc_final: 0.8748 (ptpp) REVERT: J 20 GLN cc_start: 0.8867 (tp-100) cc_final: 0.7942 (tm-30) REVERT: J 24 GLU cc_start: 0.8997 (mm-30) cc_final: 0.8529 (mm-30) REVERT: J 46 LYS cc_start: 0.9421 (mttm) cc_final: 0.8991 (mtpp) REVERT: N 26 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8565 (tm-30) REVERT: N 38 ASP cc_start: 0.9140 (p0) cc_final: 0.8779 (p0) REVERT: N 82 ILE cc_start: 0.9469 (mm) cc_final: 0.9192 (mp) REVERT: S 17 LYS cc_start: 0.9489 (mttm) cc_final: 0.9022 (mtpp) REVERT: S 21 LYS cc_start: 0.9227 (mtmm) cc_final: 0.8762 (mttt) REVERT: S 65 GLU cc_start: 0.9032 (tp30) cc_final: 0.8381 (tp30) REVERT: S 66 MET cc_start: 0.9174 (mtp) cc_final: 0.8934 (mtm) outliers start: 32 outliers final: 10 residues processed: 245 average time/residue: 0.5363 time to fit residues: 148.2515 Evaluate side-chains 199 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain I residue 128 SER Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 25 VAL Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 83 LYS Chi-restraints excluded: chain S residue 31 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [62, 39, 119, 120, 0, 142, 70, 13, 6, 76, 141] chunk 62 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 119 optimal weight: 0.4980 chunk 120 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 142 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 76 optimal weight: 2.9990 chunk 141 optimal weight: 0.7980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 58 ASN B 227 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 ASN ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN ** M 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.044458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.033099 restraints weight = 108141.011| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 3.07 r_work: 0.2564 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9026 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19749 Z= 0.155 Angle : 0.580 9.903 28878 Z= 0.329 Chirality : 0.039 0.212 3602 Planarity : 0.005 0.061 1985 Dihedral : 22.227 176.106 8367 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 14.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.71 % Allowed : 25.08 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.06 (0.24), residues: 1085 helix: 0.46 (0.22), residues: 498 sheet: 0.01 (0.39), residues: 170 loop : -0.51 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG J 7 TYR 0.020 0.002 TYR B 213 PHE 0.017 0.002 PHE B 126 TRP 0.008 0.001 TRP N 42 HIS 0.010 0.001 HIS B 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.15 (19748) covalent geometry : angle 0.57967 / 0.33 (28878) hydrogen bonds : bond 0.07828 / 8.20 ( 789) hydrogen bonds : angle 4.22887 / 5.72 ( 1801) metal coordination : bond 0.00367 / 0.18 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 217 time to evaluate : 0.454 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 PHE cc_start: 0.6575 (t80) cc_final: 0.6211 (t80) REVERT: B 90 PHE cc_start: 0.6903 (m-80) cc_final: 0.5913 (m-80) REVERT: B 100 MET cc_start: 0.8350 (mtp) cc_final: 0.8037 (mpp) REVERT: B 120 GLN cc_start: 0.6936 (OUTLIER) cc_final: 0.6733 (tm-30) REVERT: B 140 GLU cc_start: 0.9303 (tt0) cc_final: 0.9003 (tp30) REVERT: B 147 SER cc_start: 0.9357 (t) cc_final: 0.9113 (p) REVERT: B 154 MET cc_start: 0.8920 (tpp) cc_final: 0.8031 (mmm) REVERT: B 181 ILE cc_start: 0.4361 (OUTLIER) cc_final: 0.4117 (tp) REVERT: C 36 ASP cc_start: 0.9261 (p0) cc_final: 0.9025 (p0) REVERT: C 123 GLN cc_start: 0.9444 (mt0) cc_final: 0.9204 (mt0) REVERT: C 168 TYR cc_start: 0.8900 (t80) cc_final: 0.8670 (t80) REVERT: C 181 ASP cc_start: 0.9195 (t70) cc_final: 0.8249 (p0) REVERT: J 20 GLN cc_start: 0.8854 (tp-100) cc_final: 0.7910 (tm-30) REVERT: J 24 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8509 (mm-30) REVERT: J 46 LYS cc_start: 0.9468 (mttm) cc_final: 0.8965 (mtpp) REVERT: J 66 GLU cc_start: 0.8292 (tm-30) cc_final: 0.7939 (tm-30) REVERT: S 21 LYS cc_start: 0.9219 (mtmm) cc_final: 0.8830 (mtmt) REVERT: S 65 GLU cc_start: 0.8964 (tp30) cc_final: 0.8713 (tp30) outliers start: 34 outliers final: 11 residues processed: 230 average time/residue: 0.5370 time to fit residues: 139.0786 Evaluate side-chains 204 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 120 GLN Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 63 LEU Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain S residue 13 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [7, 146, 79, 21, 135, 24, 69, 66, 108, 96, 87] chunk 7 optimal weight: 30.0000 chunk 146 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 21 optimal weight: 20.0000 chunk 135 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 69 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 108 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 87 optimal weight: 3.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 178 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 97 ASN ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN ** M 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.043468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.032358 restraints weight = 108265.023| |-----------------------------------------------------------------------------| r_work (start): 0.2641 rms_B_bonded: 3.00 r_work: 0.2519 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9052 moved from start: 0.2641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 19749 Z= 0.264 Angle : 0.644 10.749 28878 Z= 0.355 Chirality : 0.043 0.226 3602 Planarity : 0.005 0.056 1985 Dihedral : 22.122 174.540 8367 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.69 % Allowed : 25.74 % Favored : 69.57 % 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: -0.07 (0.24), residues: 1085 helix: 0.45 (0.22), residues: 498 sheet: -0.07 (0.38), residues: 167 loop : -0.46 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 107 TYR 0.027 0.002 TYR M 86 PHE 0.017 0.002 PHE N 21 TRP 0.017 0.002 TRP N 42 HIS 0.006 0.002 HIS B 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00500 / 0.26 (19748) covalent geometry : angle 0.64443 / 0.36 (28878) hydrogen bonds : bond 0.07660 / 7.99 ( 789) hydrogen bonds : angle 4.24127 / 5.64 ( 1801) metal coordination : bond 0.00642 / 0.32 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 198 time to evaluate : 0.421 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 50 PHE cc_start: 0.6775 (t80) cc_final: 0.6140 (t80) REVERT: B 90 PHE cc_start: 0.7267 (m-80) cc_final: 0.5816 (m-80) REVERT: B 100 MET cc_start: 0.8603 (mtp) cc_final: 0.8303 (mpp) REVERT: B 130 THR cc_start: 0.8783 (OUTLIER) cc_final: 0.8556 (p) REVERT: B 136 MET cc_start: 0.9501 (mtm) cc_final: 0.9025 (mtm) REVERT: B 140 GLU cc_start: 0.9371 (tt0) cc_final: 0.9170 (tp30) REVERT: B 147 SER cc_start: 0.9318 (t) cc_final: 0.9014 (p) REVERT: B 154 MET cc_start: 0.8806 (tpp) cc_final: 0.7870 (mmm) REVERT: B 162 PHE cc_start: 0.8124 (t80) cc_final: 0.7729 (t80) REVERT: B 181 ILE cc_start: 0.5185 (OUTLIER) cc_final: 0.4893 (tp) REVERT: C 36 ASP cc_start: 0.9280 (p0) cc_final: 0.9014 (p0) REVERT: C 58 GLU cc_start: 0.8773 (OUTLIER) cc_final: 0.8244 (pm20) REVERT: C 123 GLN cc_start: 0.9468 (mt0) cc_final: 0.9234 (mt0) REVERT: C 168 TYR cc_start: 0.8926 (t80) cc_final: 0.8691 (t80) REVERT: C 181 ASP cc_start: 0.9211 (t70) cc_final: 0.8266 (p0) REVERT: J 20 GLN cc_start: 0.8911 (tp-100) cc_final: 0.7993 (tm-30) REVERT: J 24 GLU cc_start: 0.9071 (mm-30) cc_final: 0.8550 (mm-30) REVERT: J 46 LYS cc_start: 0.9475 (mttm) cc_final: 0.9023 (mtpp) REVERT: J 66 GLU cc_start: 0.8329 (tm-30) cc_final: 0.8099 (tm-30) REVERT: S 21 LYS cc_start: 0.9270 (mtmm) cc_final: 0.9029 (mttt) outliers start: 43 outliers final: 16 residues processed: 223 average time/residue: 0.5099 time to fit residues: 128.8130 Evaluate side-chains 199 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain S residue 13 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [32, 91, 64, 125, 45, 92, 117, 120, 115, 17, 53] chunk 32 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 125 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 117 optimal weight: 6.9990 chunk 120 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 17 optimal weight: 10.0000 chunk 53 optimal weight: 8.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 GLN C 185 ASN G 97 ASN ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN ** M 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.043771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.032560 restraints weight = 107643.866| |-----------------------------------------------------------------------------| r_work (start): 0.2665 rms_B_bonded: 3.07 r_work: 0.2545 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9041 moved from start: 0.2870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19749 Z= 0.167 Angle : 0.597 11.148 28878 Z= 0.337 Chirality : 0.039 0.191 3602 Planarity : 0.005 0.058 1985 Dihedral : 22.178 175.105 8367 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 4.47 % Allowed : 26.17 % Favored : 69.36 % 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: -0.07 (0.24), residues: 1085 helix: 0.36 (0.22), residues: 504 sheet: 0.03 (0.39), residues: 162 loop : -0.40 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 139 TYR 0.015 0.002 TYR B 213 PHE 0.026 0.002 PHE N 21 TRP 0.021 0.001 TRP N 42 HIS 0.007 0.001 HIS B 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.17 (19748) covalent geometry : angle 0.59722 / 0.34 (28878) hydrogen bonds : bond 0.07294 / 7.60 ( 789) hydrogen bonds : angle 4.16681 / 5.55 ( 1801) metal coordination : bond 0.00406 / 0.20 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 200 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 MET cc_start: 0.3474 (pmm) cc_final: 0.3272 (pmm) REVERT: B 90 PHE cc_start: 0.7360 (m-80) cc_final: 0.5941 (m-80) REVERT: B 94 HIS cc_start: 0.6891 (OUTLIER) cc_final: 0.6426 (p-80) REVERT: B 100 MET cc_start: 0.8644 (mtp) cc_final: 0.8192 (mtt) REVERT: B 113 ARG cc_start: 0.8191 (mtm-85) cc_final: 0.7863 (ptp90) REVERT: B 130 THR cc_start: 0.8839 (OUTLIER) cc_final: 0.8602 (p) REVERT: B 147 SER cc_start: 0.9333 (t) cc_final: 0.9031 (p) REVERT: B 154 MET cc_start: 0.8754 (OUTLIER) cc_final: 0.7908 (mmm) REVERT: B 181 ILE cc_start: 0.5394 (OUTLIER) cc_final: 0.5111 (tp) REVERT: C 36 ASP cc_start: 0.9247 (p0) cc_final: 0.8971 (p0) REVERT: C 123 GLN cc_start: 0.9438 (mt0) cc_final: 0.9197 (mt0) REVERT: C 168 TYR cc_start: 0.8902 (t80) cc_final: 0.8649 (t80) REVERT: C 181 ASP cc_start: 0.9178 (t70) cc_final: 0.8242 (p0) REVERT: C 211 MET cc_start: 0.8077 (tpt) cc_final: 0.7875 (mmm) REVERT: J 20 GLN cc_start: 0.8859 (tp-100) cc_final: 0.7880 (tm-30) REVERT: J 24 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8509 (mm-30) REVERT: J 46 LYS cc_start: 0.9443 (mttm) cc_final: 0.9050 (mtpp) REVERT: J 66 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7981 (tm-30) REVERT: J 96 VAL cc_start: 0.9702 (OUTLIER) cc_final: 0.9443 (m) REVERT: M 47 GLU cc_start: 0.8349 (pp20) cc_final: 0.8121 (pm20) REVERT: S 21 LYS cc_start: 0.9300 (mtmm) cc_final: 0.9066 (mttt) REVERT: S 65 GLU cc_start: 0.8982 (tp30) cc_final: 0.8780 (tp30) outliers start: 41 outliers final: 19 residues processed: 223 average time/residue: 0.5344 time to fit residues: 134.9917 Evaluate side-chains 204 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain B residue 181 ILE Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 51 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [92, 8, 11, 149, 18, 4, 31, 44, 21, 132, 124] chunk 92 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 11 optimal weight: 20.0000 chunk 149 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 132 optimal weight: 4.9990 chunk 124 optimal weight: 10.0000 overall best weight: 5.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 120 GLN G 52 GLN G 97 ASN J 64 GLN ** M 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.042169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.031288 restraints weight = 109027.438| |-----------------------------------------------------------------------------| r_work (start): 0.2605 rms_B_bonded: 2.93 r_work: 0.2480 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2480 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.2899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 19749 Z= 0.352 Angle : 0.734 9.652 28878 Z= 0.397 Chirality : 0.049 0.269 3602 Planarity : 0.006 0.064 1985 Dihedral : 22.082 173.865 8367 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 6.11 % Allowed : 27.15 % Favored : 66.74 % 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: -0.25 (0.25), residues: 1085 helix: 0.26 (0.22), residues: 504 sheet: -0.11 (0.39), residues: 162 loop : -0.54 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 119 TYR 0.018 0.002 TYR C 193 PHE 0.023 0.002 PHE N 21 TRP 0.020 0.002 TRP N 42 HIS 0.010 0.002 HIS S 69 Details of bonding type rmsd/Z covalent geometry : bond 0.00653 / 0.35 (19748) covalent geometry : angle 0.73399 / 0.40 (28878) hydrogen bonds : bond 0.08050 / 8.32 ( 789) hydrogen bonds : angle 4.35773 / 5.78 ( 1801) metal coordination : bond 0.01218 / 0.61 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 183 time to evaluate : 0.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 MET cc_start: 0.3974 (pmm) cc_final: 0.3702 (pmm) REVERT: B 50 PHE cc_start: 0.7887 (t80) cc_final: 0.7621 (m-80) REVERT: B 90 PHE cc_start: 0.7637 (m-80) cc_final: 0.7203 (m-80) REVERT: B 94 HIS cc_start: 0.7310 (OUTLIER) cc_final: 0.6872 (p-80) REVERT: B 100 MET cc_start: 0.8826 (mtp) cc_final: 0.8327 (mtt) REVERT: B 140 GLU cc_start: 0.9360 (tt0) cc_final: 0.8933 (tp30) REVERT: B 147 SER cc_start: 0.9373 (t) cc_final: 0.9072 (p) REVERT: B 154 MET cc_start: 0.8681 (tpp) cc_final: 0.8369 (tpp) REVERT: B 173 ILE cc_start: 0.8907 (OUTLIER) cc_final: 0.8316 (mm) REVERT: C 36 ASP cc_start: 0.9291 (p0) cc_final: 0.9021 (p0) REVERT: C 58 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8515 (pm20) REVERT: C 123 GLN cc_start: 0.9466 (mt0) cc_final: 0.9233 (mt0) REVERT: C 168 TYR cc_start: 0.8889 (t80) cc_final: 0.8656 (t80) REVERT: C 181 ASP cc_start: 0.9217 (t70) cc_final: 0.8277 (p0) REVERT: C 211 MET cc_start: 0.8323 (tpt) cc_final: 0.7977 (mmm) REVERT: I 27 LYS cc_start: 0.8550 (ptpp) cc_final: 0.8312 (ptpp) REVERT: I 57 MET cc_start: 0.8709 (mtm) cc_final: 0.8361 (ptp) REVERT: J 20 GLN cc_start: 0.8917 (tp-100) cc_final: 0.8009 (tm-30) REVERT: J 24 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8510 (mm-30) REVERT: J 46 LYS cc_start: 0.9422 (mttm) cc_final: 0.9015 (mtpp) REVERT: J 67 ILE cc_start: 0.9372 (mm) cc_final: 0.9169 (mm) REVERT: J 96 VAL cc_start: 0.9764 (OUTLIER) cc_final: 0.9516 (m) REVERT: S 12 ASP cc_start: 0.8226 (p0) cc_final: 0.7939 (p0) REVERT: S 21 LYS cc_start: 0.9241 (mtmm) cc_final: 0.9012 (mttt) outliers start: 56 outliers final: 23 residues processed: 219 average time/residue: 0.4895 time to fit residues: 122.4266 Evaluate side-chains 201 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 131 LYS Chi-restraints excluded: chain B residue 173 ILE Chi-restraints excluded: chain C residue 58 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 58 VAL Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 74 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 91 ASP Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 98 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 51 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [101, 55, 117, 88, 63, 125, 100, 34, 39, 150, 11] chunk 101 optimal weight: 6.9990 chunk 55 optimal weight: 4.9990 chunk 117 optimal weight: 0.0570 chunk 88 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 chunk 125 optimal weight: 0.6980 chunk 100 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 39 optimal weight: 10.0000 chunk 150 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 overall best weight: 1.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 GLN G 97 ASN ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 56 HIS J 64 GLN ** M 12 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 52 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.043002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.032081 restraints weight = 107301.985| |-----------------------------------------------------------------------------| r_work (start): 0.2649 rms_B_bonded: 2.97 r_work: 0.2527 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.3136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 19749 Z= 0.160 Angle : 0.624 12.612 28878 Z= 0.347 Chirality : 0.039 0.195 3602 Planarity : 0.005 0.065 1985 Dihedral : 22.198 174.786 8367 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 4.47 % Allowed : 29.33 % Favored : 66.19 % 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: -0.07 (0.25), residues: 1085 helix: 0.44 (0.22), residues: 503 sheet: 0.02 (0.40), residues: 159 loop : -0.50 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 63 TYR 0.019 0.002 TYR C 193 PHE 0.024 0.002 PHE N 21 TRP 0.019 0.001 TRP N 42 HIS 0.005 0.001 HIS B 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.16 (19748) covalent geometry : angle 0.62393 / 0.35 (28878) hydrogen bonds : bond 0.07300 / 7.59 ( 789) hydrogen bonds : angle 4.19774 / 5.56 ( 1801) metal coordination : bond 0.00341 / 0.17 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 187 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 MET cc_start: 0.3606 (pmm) cc_final: 0.3372 (pmm) REVERT: B 32 PHE cc_start: 0.8246 (t80) cc_final: 0.7773 (m-80) REVERT: B 50 PHE cc_start: 0.7820 (t80) cc_final: 0.7584 (m-80) REVERT: B 94 HIS cc_start: 0.7181 (OUTLIER) cc_final: 0.6653 (p-80) REVERT: B 100 MET cc_start: 0.8826 (mtp) cc_final: 0.8317 (mtt) REVERT: B 122 GLN cc_start: 0.8740 (mm-40) cc_final: 0.7889 (mt0) REVERT: B 136 MET cc_start: 0.9544 (mtm) cc_final: 0.8672 (mpp) REVERT: B 139 ARG cc_start: 0.8572 (mpp80) cc_final: 0.7498 (mpp80) REVERT: B 147 SER cc_start: 0.9393 (t) cc_final: 0.9091 (p) REVERT: B 154 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8024 (mmm) REVERT: C 36 ASP cc_start: 0.9234 (p0) cc_final: 0.8958 (p0) REVERT: C 62 LYS cc_start: 0.8780 (mmmt) cc_final: 0.8529 (mmmm) REVERT: C 123 GLN cc_start: 0.9440 (mt0) cc_final: 0.9107 (mt0) REVERT: C 181 ASP cc_start: 0.9189 (t70) cc_final: 0.8238 (p0) REVERT: C 211 MET cc_start: 0.8348 (tpt) cc_final: 0.8069 (mmm) REVERT: G 126 ASP cc_start: 0.8019 (p0) cc_final: 0.7701 (p0) REVERT: J 20 GLN cc_start: 0.8863 (tp-100) cc_final: 0.7879 (tm-30) REVERT: J 24 GLU cc_start: 0.9029 (mm-30) cc_final: 0.8521 (mm-30) REVERT: J 96 VAL cc_start: 0.9733 (OUTLIER) cc_final: 0.9503 (m) REVERT: M 114 LYS cc_start: 0.8938 (ptpp) cc_final: 0.8720 (ptpp) REVERT: S 12 ASP cc_start: 0.8227 (p0) cc_final: 0.7942 (p0) REVERT: S 21 LYS cc_start: 0.9260 (mtmm) cc_final: 0.8953 (mttt) outliers start: 41 outliers final: 19 residues processed: 212 average time/residue: 0.5364 time to fit residues: 128.7158 Evaluate side-chains 194 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain S residue 13 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [102, 53, 97, 36, 129, 2, 26, 105, 52, 31, 67] chunk 102 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 97 optimal weight: 0.0980 chunk 36 optimal weight: 10.0000 chunk 129 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 105 optimal weight: 1.9990 chunk 52 optimal weight: 0.0870 chunk 31 optimal weight: 10.0000 chunk 67 optimal weight: 1.9990 overall best weight: 1.0362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 120 GLN B 168 HIS G 97 ASN J 56 HIS J 64 GLN M 12 HIS M 52 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.043931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.033218 restraints weight = 107407.244| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 2.92 r_work: 0.2561 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9029 moved from start: 0.3421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 19749 Z= 0.143 Angle : 0.625 11.352 28878 Z= 0.347 Chirality : 0.039 0.255 3602 Planarity : 0.005 0.059 1985 Dihedral : 22.161 175.653 8367 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 15.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.71 % Allowed : 31.41 % Favored : 64.89 % 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: -0.06 (0.25), residues: 1085 helix: 0.34 (0.22), residues: 502 sheet: 0.24 (0.40), residues: 159 loop : -0.45 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 63 TYR 0.016 0.002 TYR C 168 PHE 0.022 0.002 PHE G 62 TRP 0.026 0.002 TRP N 42 HIS 0.005 0.001 HIS J 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 (19748) covalent geometry : angle 0.62488 / 0.35 (28878) hydrogen bonds : bond 0.07020 / 7.28 ( 789) hydrogen bonds : angle 4.19598 / 5.55 ( 1801) metal coordination : bond 0.00168 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 195 time to evaluate : 0.467 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 MET cc_start: 0.3597 (pmm) cc_final: 0.3374 (pmm) REVERT: B 32 PHE cc_start: 0.8363 (t80) cc_final: 0.7845 (m-80) REVERT: B 90 PHE cc_start: 0.7541 (m-80) cc_final: 0.6269 (m-80) REVERT: B 94 HIS cc_start: 0.7299 (OUTLIER) cc_final: 0.6884 (p-80) REVERT: B 100 MET cc_start: 0.8844 (mtp) cc_final: 0.8331 (mtt) REVERT: B 122 GLN cc_start: 0.8702 (mm-40) cc_final: 0.7871 (mt0) REVERT: B 133 GLU cc_start: 0.8446 (tm-30) cc_final: 0.8165 (tm-30) REVERT: B 136 MET cc_start: 0.9533 (mtm) cc_final: 0.8683 (mpp) REVERT: B 139 ARG cc_start: 0.8572 (mpp80) cc_final: 0.7497 (mpp80) REVERT: B 147 SER cc_start: 0.9378 (t) cc_final: 0.9080 (p) REVERT: B 154 MET cc_start: 0.8594 (tpp) cc_final: 0.8003 (mmm) REVERT: C 36 ASP cc_start: 0.9212 (p0) cc_final: 0.8933 (p0) REVERT: C 62 LYS cc_start: 0.8812 (mmmt) cc_final: 0.8572 (mmmm) REVERT: C 123 GLN cc_start: 0.9357 (mt0) cc_final: 0.9105 (mt0) REVERT: C 181 ASP cc_start: 0.9201 (t70) cc_final: 0.8259 (p0) REVERT: C 211 MET cc_start: 0.8422 (tpt) cc_final: 0.8108 (mmm) REVERT: I 115 LYS cc_start: 0.9425 (mmtp) cc_final: 0.9040 (mptt) REVERT: J 20 GLN cc_start: 0.8872 (tp-100) cc_final: 0.8026 (tm-30) REVERT: J 24 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8565 (mm-30) REVERT: J 46 LYS cc_start: 0.9331 (mtpp) cc_final: 0.8991 (mttm) REVERT: M 52 GLN cc_start: 0.9450 (OUTLIER) cc_final: 0.8773 (pm20) REVERT: M 72 GLU cc_start: 0.8766 (tm-30) cc_final: 0.7989 (tm-30) REVERT: M 114 LYS cc_start: 0.8936 (ptpp) cc_final: 0.8715 (ptpp) REVERT: S 12 ASP cc_start: 0.8134 (p0) cc_final: 0.7867 (p0) REVERT: S 21 LYS cc_start: 0.9289 (mtmm) cc_final: 0.9060 (mttt) REVERT: S 44 MET cc_start: 0.9396 (ptp) cc_final: 0.9169 (ptp) outliers start: 34 outliers final: 17 residues processed: 216 average time/residue: 0.5101 time to fit residues: 125.5613 Evaluate side-chains 194 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 52 GLN Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain S residue 51 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [1, 75, 37, 60, 44, 96, 47, 127, 107, 10, 113] chunk 1 optimal weight: 10.0000 chunk 75 optimal weight: 0.7980 chunk 37 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 96 optimal weight: 10.0000 chunk 47 optimal weight: 6.9990 chunk 127 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 30.0000 chunk 113 optimal weight: 0.0060 overall best weight: 1.5000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 168 HIS G 97 ASN ** G 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN M 52 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.043923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.033102 restraints weight = 107167.128| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 3.07 r_work: 0.2563 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9035 moved from start: 0.3512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19749 Z= 0.155 Angle : 0.654 12.458 28878 Z= 0.358 Chirality : 0.039 0.335 3602 Planarity : 0.005 0.064 1985 Dihedral : 22.116 175.699 8367 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 3.60 % Allowed : 33.04 % Favored : 63.36 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.25), residues: 1085 helix: 0.21 (0.22), residues: 500 sheet: 0.41 (0.41), residues: 159 loop : -0.47 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG I 95 TYR 0.021 0.002 TYR B 213 PHE 0.046 0.002 PHE B 50 TRP 0.024 0.002 TRP N 42 HIS 0.009 0.001 HIS M 12 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.16 (19748) covalent geometry : angle 0.65392 / 0.36 (28878) hydrogen bonds : bond 0.06926 / 7.22 ( 789) hydrogen bonds : angle 4.21434 / 5.59 ( 1801) metal coordination : bond 0.00209 / 0.10 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 190 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 9 MET cc_start: 0.3694 (pmm) cc_final: 0.3439 (pmm) REVERT: B 94 HIS cc_start: 0.7290 (OUTLIER) cc_final: 0.6891 (p-80) REVERT: B 100 MET cc_start: 0.8870 (mtp) cc_final: 0.8371 (mtt) REVERT: B 122 GLN cc_start: 0.8743 (mm-40) cc_final: 0.7924 (mt0) REVERT: B 133 GLU cc_start: 0.8519 (tm-30) cc_final: 0.8297 (tm-30) REVERT: B 136 MET cc_start: 0.9546 (mtm) cc_final: 0.8573 (mpp) REVERT: B 139 ARG cc_start: 0.8623 (mpp80) cc_final: 0.7403 (mpp80) REVERT: B 147 SER cc_start: 0.9395 (t) cc_final: 0.9103 (p) REVERT: B 154 MET cc_start: 0.8576 (OUTLIER) cc_final: 0.7991 (mmm) REVERT: C 36 ASP cc_start: 0.9214 (p0) cc_final: 0.8946 (p0) REVERT: C 62 LYS cc_start: 0.8765 (mmmt) cc_final: 0.8547 (mmmm) REVERT: C 123 GLN cc_start: 0.9362 (mt0) cc_final: 0.9108 (mt0) REVERT: C 181 ASP cc_start: 0.9182 (t70) cc_final: 0.8248 (p0) REVERT: C 211 MET cc_start: 0.8442 (tpt) cc_final: 0.8168 (mmm) REVERT: I 112 GLU cc_start: 0.7742 (tm-30) cc_final: 0.7273 (tm-30) REVERT: I 115 LYS cc_start: 0.9299 (mmtp) cc_final: 0.9032 (mptt) REVERT: J 20 GLN cc_start: 0.8894 (tp-100) cc_final: 0.8042 (tm-30) REVERT: J 24 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8696 (mm-30) REVERT: M 52 GLN cc_start: 0.9400 (OUTLIER) cc_final: 0.8987 (pm20) REVERT: M 114 LYS cc_start: 0.8880 (ptpp) cc_final: 0.8664 (ptpp) outliers start: 33 outliers final: 17 residues processed: 211 average time/residue: 0.5063 time to fit residues: 121.7764 Evaluate side-chains 199 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain G residue 33 ASP Chi-restraints excluded: chain G residue 41 SER Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 94 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 52 GLN Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain S residue 51 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [52, 33, 126, 2, 117, 43, 143, 125, 83, 127, 140] chunk 52 optimal weight: 0.0870 chunk 33 optimal weight: 20.0000 chunk 126 optimal weight: 0.0980 chunk 2 optimal weight: 10.0000 chunk 117 optimal weight: 0.0070 chunk 43 optimal weight: 10.0000 chunk 143 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 83 optimal weight: 0.9980 chunk 127 optimal weight: 0.8980 chunk 140 optimal weight: 3.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 168 HIS G 97 ASN J 64 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.044436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2741 r_free = 0.2741 target = 0.033652 restraints weight = 107511.456| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 3.03 r_work: 0.2597 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9018 moved from start: 0.3721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 19749 Z= 0.138 Angle : 0.668 12.638 28878 Z= 0.364 Chirality : 0.038 0.380 3602 Planarity : 0.005 0.085 1985 Dihedral : 22.133 176.461 8367 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 15.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.51 % Allowed : 34.02 % Favored : 63.47 % 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: 1085 helix: 0.08 (0.22), residues: 497 sheet: 0.41 (0.41), residues: 159 loop : -0.54 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG I 95 TYR 0.021 0.002 TYR B 213 PHE 0.050 0.003 PHE B 50 TRP 0.027 0.002 TRP N 42 HIS 0.005 0.001 HIS B 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (19748) covalent geometry : angle 0.66776 / 0.36 (28878) hydrogen bonds : bond 0.06861 / 7.13 ( 789) hydrogen bonds : angle 4.25677 / 5.66 ( 1801) metal coordination : bond 0.00100 / 0.05 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 209 time to evaluate : 0.443 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: B 9 MET cc_start: 0.3612 (pmm) cc_final: 0.3343 (pmm) REVERT: B 90 PHE cc_start: 0.7504 (m-80) cc_final: 0.6216 (m-80) REVERT: B 100 MET cc_start: 0.8845 (mtp) cc_final: 0.8321 (mtt) REVERT: B 122 GLN cc_start: 0.8748 (mm-40) cc_final: 0.7919 (mt0) REVERT: B 133 GLU cc_start: 0.8529 (tm-30) cc_final: 0.8281 (tm-30) REVERT: B 136 MET cc_start: 0.9498 (mtm) cc_final: 0.8903 (mpp) REVERT: B 147 SER cc_start: 0.9379 (t) cc_final: 0.9112 (p) REVERT: B 154 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.7946 (mmm) REVERT: C 36 ASP cc_start: 0.9212 (p0) cc_final: 0.8945 (p0) REVERT: C 41 GLN cc_start: 0.9391 (pp30) cc_final: 0.9145 (pp30) REVERT: C 62 LYS cc_start: 0.8757 (mmmt) cc_final: 0.8538 (mmmm) REVERT: C 123 GLN cc_start: 0.9340 (mt0) cc_final: 0.9068 (mt0) REVERT: C 181 ASP cc_start: 0.9176 (t70) cc_final: 0.8227 (p0) REVERT: C 211 MET cc_start: 0.8434 (tpt) cc_final: 0.8169 (mmm) REVERT: G 110 LYS cc_start: 0.8414 (pptt) cc_final: 0.8206 (pptt) REVERT: I 112 GLU cc_start: 0.7787 (tm-30) cc_final: 0.7313 (tm-30) REVERT: I 115 LYS cc_start: 0.9333 (mmtp) cc_final: 0.9075 (mptt) REVERT: J 20 GLN cc_start: 0.8878 (tp-100) cc_final: 0.8012 (tm-30) REVERT: J 24 GLU cc_start: 0.8970 (mm-30) cc_final: 0.8692 (mm-30) REVERT: N 43 ASN cc_start: 0.9190 (m-40) cc_final: 0.8863 (m110) REVERT: S 73 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8555 (mp0) outliers start: 23 outliers final: 17 residues processed: 223 average time/residue: 0.5191 time to fit residues: 131.9678 Evaluate side-chains 209 residues out of total 917 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 67 ILE Chi-restraints excluded: chain B residue 154 MET Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain G residue 113 ASP Chi-restraints excluded: chain I residue 29 VAL Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 77 VAL Chi-restraints excluded: chain J residue 84 VAL Chi-restraints excluded: chain J residue 85 ASP Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 83 LEU Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain S residue 51 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: [36, 41, 35, 24, 14, 127, 99, 149, 42, 108, 139] chunk 36 optimal weight: 10.0000 chunk 41 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 24 optimal weight: 20.0000 chunk 14 optimal weight: 10.0000 chunk 127 optimal weight: 6.9990 chunk 99 optimal weight: 0.9990 chunk 149 optimal weight: 4.9990 chunk 42 optimal weight: 10.0000 chunk 108 optimal weight: 0.4980 chunk 139 optimal weight: 0.7980 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 168 HIS G 97 ASN I 37 GLN I 110 GLN J 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.044347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2738 r_free = 0.2738 target = 0.033576 restraints weight = 107616.930| |-----------------------------------------------------------------------------| r_work (start): 0.2712 rms_B_bonded: 3.03 r_work: 0.2594 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2594 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.3715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.151 19749 Z= 0.218 Angle : 0.827 61.589 28878 Z= 0.427 Chirality : 0.040 0.381 3602 Planarity : 0.007 0.182 1985 Dihedral : 22.121 176.471 8367 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 17.98 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.41 % Favored : 96.50 % Rotamer: Outliers : 2.40 % Allowed : 34.24 % Favored : 63.36 % Cbeta Deviations : 0.10 % 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: -0.28 (0.24), residues: 1085 helix: 0.08 (0.22), residues: 496 sheet: 0.43 (0.41), residues: 159 loop : -0.57 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 63 TYR 0.019 0.002 TYR B 213 PHE 0.031 0.002 PHE B 50 TRP 0.024 0.002 TRP N 42 HIS 0.007 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00448 / 0.22 (19748) covalent geometry : angle 0.82653 / 0.43 (28878) hydrogen bonds : bond 0.06874 / 7.15 ( 789) hydrogen bonds : angle 4.26532 / 5.66 ( 1801) metal coordination : bond 0.00076 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5304.27 seconds wall clock time: 91 minutes 30.13 seconds (5490.13 seconds total)