Starting phenix.real_space_refine on Sat Sep 12 21:58:50 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7afd_11761/09_2026/7afd_11761_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/7afd_11761/09_2026/7afd_11761.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7afd_11761/09_2026/7afd_11761.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7afd_11761/09_2026/7afd_11761.map" model { file = "/net/cci-nas-00/data/ceres_data/7afd_11761/09_2026/7afd_11761_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7afd_11761/09_2026/7afd_11761_neut.cif" } resolution = 3.44 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= 0.003 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 22 5.21 5 S 28 5.16 5 C 9845 2.51 5 N 3449 2.21 5 O 4730 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 18531 Number of models: 1 Model: "" Number of chains: 12 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: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} 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: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Unusual residues: {' MG': 21} Classifications: {'undetermined': 21} Link IDs: {None: 20} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.83, per 1000 atoms: 0.21 Number of scatterers: 18531 At special positions: 0 Unit cell: (116.095, 116.095, 160.58, 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 22 11.99 O 4730 8.00 N 3449 7.00 C 9845 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: 1.97 Conformation dependent library (CDL) restraints added in 478.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 9 sheets defined 49.5% alpha, 15.7% beta 131 base pairs and 218 stacking pairs defined. Time for finding SS restraints: 2.85 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: 3.511A pdb=" N VAL B 107 " --> pdb=" O ASN B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 148 Processing helix chain 'B' and resid 169 through 180 Processing helix chain 'B' and resid 192 through 196 removed outlier: 4.227A 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: 3.932A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 47 Processing helix chain 'C' and resid 48 through 50 No H-bonds generated for 'chain 'C' and resid 48 through 50' Processing helix chain 'C' and resid 72 through 78 Processing helix chain 'C' and resid 81 through 95 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 15 through 19 Processing helix chain 'G' and resid 21 through 31 Processing helix chain 'G' and resid 35 through 54 removed outlier: 4.209A pdb=" N THR G 49 " --> pdb=" O SER G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 70 removed outlier: 4.141A pdb=" N GLU G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 110 Processing helix chain 'G' and resid 115 through 129 Processing helix chain 'G' and resid 133 through 145 removed outlier: 3.585A pdb=" N LYS G 137 " --> pdb=" O THR G 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 39 Processing helix chain 'I' and resid 41 through 55 removed outlier: 3.932A pdb=" N ARG I 45 " --> pdb=" O ARG I 41 " (cutoff:3.500A) Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 57 through 59 No H-bonds generated for 'chain 'I' and resid 57 through 59' Processing helix chain 'I' and resid 71 through 92 Processing helix chain 'I' and resid 94 through 102 Processing helix chain 'J' and resid 14 through 32 Processing helix chain 'J' and resid 80 through 88 removed outlier: 4.524A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 21 removed outlier: 3.519A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 26 through 38 Processing helix chain 'M' and resid 49 through 62 removed outlier: 4.503A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 83 Processing helix chain 'M' and resid 85 through 93 Processing helix chain 'M' and resid 106 through 111 Processing helix chain 'N' and resid 3 through 20 removed outlier: 3.506A pdb=" N LYS N 7 " --> pdb=" O LYS N 3 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 33 Processing helix chain 'N' and resid 39 through 51 removed outlier: 3.732A pdb=" N LEU N 51 " --> pdb=" O LYS N 47 " (cutoff:3.500A) 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 removed outlier: 3.679A pdb=" N GLU N 86 " --> pdb=" O ILE N 82 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 25 Processing helix chain 'S' and resid 70 through 75 removed outlier: 3.541A pdb=" N GLU S 73 " --> pdb=" O LYS S 70 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 31 through 35 removed outlier: 3.567A pdb=" N GLY B 33 " --> pdb=" O ILE B 40 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 92 removed outlier: 5.721A pdb=" N ILE B 67 " --> pdb=" O PHE B 90 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL B 92 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 6.453A 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: 6.492A pdb=" N HIS C 69 " --> pdb=" O SER C 53 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE C 55 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N THR C 67 " --> pdb=" O ILE C 55 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ILE C 57 " --> pdb=" O ARG C 65 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ARG C 65 " --> pdb=" O ILE C 57 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ILE C 64 " --> pdb=" O GLN C 100 " (cutoff:3.500A) removed outlier: 8.034A pdb=" N ASN C 102 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N VAL C 66 " --> pdb=" O ASN C 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 166 through 171 removed outlier: 6.413A pdb=" N ASP C 181 " --> pdb=" O LYS C 204 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 73 through 75 Processing sheet with id=AA6, first strand: chain 'I' and resid 6 through 9 removed outlier: 3.591A pdb=" N TYR I 6 " --> pdb=" O ILE I 21 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N VAL I 29 " --> pdb=" O ILE I 65 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N VAL I 67 " --> pdb=" O VAL I 29 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 36 through 52 removed outlier: 5.925A pdb=" N GLY J 38 " --> pdb=" O ASP J 75 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP J 75 " --> pdb=" O GLY J 38 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR J 44 " --> pdb=" O THR J 69 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N THR J 69 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS J 46 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE J 67 " --> pdb=" O LYS J 46 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ARG J 48 " --> pdb=" O TYR J 65 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR J 65 " --> pdb=" O ARG J 48 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR J 50 " --> pdb=" O ASP J 63 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASP J 63 " --> pdb=" O THR J 50 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'J' and resid 36 through 52 removed outlier: 5.925A pdb=" N GLY J 38 " --> pdb=" O ASP J 75 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ASP J 75 " --> pdb=" O GLY J 38 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N THR J 44 " --> pdb=" O THR J 69 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N THR J 69 " --> pdb=" O THR J 44 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LYS J 46 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ILE J 67 " --> pdb=" O LYS J 46 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ARG J 48 " --> pdb=" O TYR J 65 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR J 65 " --> pdb=" O ARG J 48 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N THR J 50 " --> pdb=" O ASP J 63 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASP J 63 " --> pdb=" O THR J 50 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N LYS N 97 " --> pdb=" O GLU J 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 31 through 33 removed outlier: 6.311A pdb=" N LEU S 31 " --> pdb=" O ALA S 50 " (cutoff:3.500A) removed outlier: 7.822A pdb=" N HIS S 52 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N THR S 33 " --> pdb=" O HIS S 52 " (cutoff:3.500A) 427 hydrogen bonds defined for protein. 1221 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 304 hydrogen bonds 398 hydrogen bond angles 0 basepair planarities 131 basepair parallelities 218 stacking parallelities Total time for adding SS restraints: 4.30 Time building geometry restraints manager: 2.52 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: 3361 1.33 - 1.45: 7036 1.45 - 1.57: 8440 1.57 - 1.69: 911 1.69 - 1.81: 53 Bond restraints: 19801 Sorted by residual: bond pdb=" N9 A 11363 " pdb=" C4 A 11363 " ideal model delta sigma weight residual 1.374 1.344 0.030 6.00e-03 2.78e+04 2.53e+01 bond pdb=" N VAL S 58 " pdb=" CA VAL S 58 " ideal model delta sigma weight residual 1.456 1.496 -0.040 8.70e-03 1.32e+04 2.08e+01 bond pdb=" N9 A 11227 " pdb=" C4 A 11227 " ideal model delta sigma weight residual 1.374 1.348 0.026 6.00e-03 2.78e+04 1.85e+01 bond pdb=" N9 A 11110 " pdb=" C4 A 11110 " ideal model delta sigma weight residual 1.374 1.350 0.024 6.00e-03 2.78e+04 1.63e+01 bond pdb=" C5 2MG 1 966 " pdb=" C4 2MG 1 966 " ideal model delta sigma weight residual 1.382 1.460 -0.078 2.00e-02 2.50e+03 1.52e+01 ... (remaining 19796 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 27124 2.13 - 4.26: 1730 4.26 - 6.38: 71 6.38 - 8.51: 19 8.51 - 10.64: 5 Bond angle restraints: 28949 Sorted by residual: angle pdb=" N ASN S 53 " pdb=" CA ASN S 53 " pdb=" C ASN S 53 " ideal model delta sigma weight residual 110.53 101.70 8.83 1.32e+00 5.74e-01 4.48e+01 angle pdb=" C1' C 11158 " pdb=" N1 C 11158 " pdb=" C2 C 11158 " ideal model delta sigma weight residual 118.80 125.43 -6.63 1.10e+00 8.26e-01 3.63e+01 angle pdb=" N3 C 11226 " pdb=" C4 C 11226 " pdb=" N4 C 11226 " ideal model delta sigma weight residual 118.00 114.40 3.60 7.00e-01 2.04e+00 2.65e+01 angle pdb=" C3' A 1 983 " pdb=" O3' A 1 983 " pdb=" P C 1 984 " ideal model delta sigma weight residual 119.70 125.83 -6.13 1.20e+00 6.94e-01 2.61e+01 angle pdb=" N1 C 11158 " pdb=" C2 C 11158 " pdb=" O2 C 11158 " ideal model delta sigma weight residual 118.90 121.77 -2.87 6.00e-01 2.78e+00 2.30e+01 ... (remaining 28944 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.20: 11296 35.20 - 70.40: 1196 70.40 - 105.60: 151 105.60 - 140.81: 5 140.81 - 176.01: 3 Dihedral angle restraints: 12651 sinusoidal: 9481 harmonic: 3170 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 25.69 174.31 1 1.50e+01 4.44e-03 8.51e+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 73.83 126.17 1 1.50e+01 4.44e-03 6.79e+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 55.99 176.01 1 1.70e+01 3.46e-03 6.64e+01 ... (remaining 12648 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 2797 0.075 - 0.151: 731 0.151 - 0.226: 66 0.226 - 0.301: 12 0.301 - 0.376: 3 Chirality restraints: 3609 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 2.06 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA PHE I 20 " pdb=" N PHE I 20 " pdb=" C PHE I 20 " pdb=" CB PHE I 20 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.54e+00 chirality pdb=" CA ARG J 37 " pdb=" N ARG J 37 " pdb=" C ARG J 37 " pdb=" CB ARG J 37 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.46e+00 ... (remaining 3606 not shown) Planarity restraints: 1995 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' 2MG 1 966 " -0.036 2.00e-02 2.50e+03 6.33e-02 1.30e+02 pdb=" N9 2MG 1 966 " -0.007 2.00e-02 2.50e+03 pdb=" C8 2MG 1 966 " 0.029 2.00e-02 2.50e+03 pdb=" N7 2MG 1 966 " 0.042 2.00e-02 2.50e+03 pdb=" C5 2MG 1 966 " 0.013 2.00e-02 2.50e+03 pdb=" C6 2MG 1 966 " 0.008 2.00e-02 2.50e+03 pdb=" O6 2MG 1 966 " 0.033 2.00e-02 2.50e+03 pdb=" N1 2MG 1 966 " -0.030 2.00e-02 2.50e+03 pdb=" C2 2MG 1 966 " -0.062 2.00e-02 2.50e+03 pdb=" N2 2MG 1 966 " -0.092 2.00e-02 2.50e+03 pdb=" N3 2MG 1 966 " -0.055 2.00e-02 2.50e+03 pdb=" C4 2MG 1 966 " -0.017 2.00e-02 2.50e+03 pdb=" CM2 2MG 1 966 " 0.174 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' 2MG 11207 " 0.023 2.00e-02 2.50e+03 3.02e-02 2.97e+01 pdb=" N9 2MG 11207 " -0.008 2.00e-02 2.50e+03 pdb=" C8 2MG 11207 " -0.014 2.00e-02 2.50e+03 pdb=" N7 2MG 11207 " -0.017 2.00e-02 2.50e+03 pdb=" C5 2MG 11207 " -0.002 2.00e-02 2.50e+03 pdb=" C6 2MG 11207 " -0.007 2.00e-02 2.50e+03 pdb=" O6 2MG 11207 " -0.016 2.00e-02 2.50e+03 pdb=" N1 2MG 11207 " 0.015 2.00e-02 2.50e+03 pdb=" C2 2MG 11207 " 0.030 2.00e-02 2.50e+03 pdb=" N2 2MG 11207 " 0.043 2.00e-02 2.50e+03 pdb=" N3 2MG 11207 " 0.025 2.00e-02 2.50e+03 pdb=" C4 2MG 11207 " 0.009 2.00e-02 2.50e+03 pdb=" CM2 2MG 11207 " -0.082 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS I 60 " -0.022 2.00e-02 2.50e+03 4.49e-02 2.02e+01 pdb=" C LYS I 60 " 0.078 2.00e-02 2.50e+03 pdb=" O LYS I 60 " -0.029 2.00e-02 2.50e+03 pdb=" N LEU I 61 " -0.027 2.00e-02 2.50e+03 ... (remaining 1992 not shown) Histogram of nonbonded interaction distances: 1.85 - 2.46: 293 2.46 - 3.07: 13717 3.07 - 3.68: 38280 3.68 - 4.29: 52570 4.29 - 4.90: 72519 Nonbonded interactions: 177379 Sorted by model distance: nonbonded pdb=" O6 G 11370 " pdb="MG MG 11603 " model vdw 1.850 2.170 nonbonded pdb=" OP1 C 1 972 " pdb="MG MG 11610 " model vdw 1.907 2.170 nonbonded pdb=" OP1 C 1 980 " pdb="MG MG 11602 " model vdw 1.930 2.170 nonbonded pdb=" OP1 A 11197 " pdb="MG MG 11613 " model vdw 2.002 2.170 nonbonded pdb=" OD1 ASN S 53 " pdb=" O GLN S 56 " model vdw 2.047 3.040 ... (remaining 177374 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: 3.610 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 22.800 Find NCS groups from input model: 0.090 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 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 : 0.009 0.151 19802 Z= 0.810 Angle : 1.013 10.638 28949 Z= 0.808 Chirality : 0.066 0.376 3609 Planarity : 0.005 0.063 1995 Dihedral : 22.742 176.008 10599 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 29.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.23 % Favored : 93.77 % Rotamer: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.70 (0.23), residues: 1092 helix: -1.32 (0.21), residues: 484 sheet: -2.19 (0.37), residues: 158 loop : -1.99 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG I 124 TYR 0.017 0.003 TYR I 90 PHE 0.013 0.002 PHE I 20 TRP 0.012 0.002 TRP C 201 HIS 0.010 0.001 HIS S 14 Details of bonding type rmsd/Z covalent geometry : bond 0.00882 / 0.81 (19801) covalent geometry : angle 1.01314 / 0.81 (28949) hydrogen bonds : bond 0.24922 / 27.24 ( 728) hydrogen bonds : angle 9.09304 / 11.90 ( 1619) metal coordination : bond 0.15050 / 7.53 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 0.469 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 115 LYS cc_start: 0.8855 (mttt) cc_final: 0.8550 (mmtm) REVERT: B 192 ASP cc_start: 0.8210 (t0) cc_final: 0.7340 (t0) REVERT: B 213 TYR cc_start: 0.7637 (m-80) cc_final: 0.7333 (m-80) REVERT: C 129 MET cc_start: 0.9126 (mmm) cc_final: 0.8880 (mmm) REVERT: C 181 ASP cc_start: 0.8994 (t70) cc_final: 0.8634 (p0) REVERT: G 7 ILE cc_start: 0.8150 (mt) cc_final: 0.7943 (mp) REVERT: G 103 TRP cc_start: 0.9254 (m-10) cc_final: 0.8963 (m-10) REVERT: G 116 MET cc_start: 0.8064 (pmm) cc_final: 0.7415 (tpt) REVERT: I 11 ARG cc_start: 0.4104 (pmt170) cc_final: 0.3653 (pmt170) REVERT: J 17 LEU cc_start: 0.9636 (mp) cc_final: 0.9424 (mm) REVERT: J 63 ASP cc_start: 0.8109 (t0) cc_final: 0.7828 (t70) REVERT: J 66 GLU cc_start: 0.7907 (tm-30) cc_final: 0.7541 (tm-30) REVERT: M 16 VAL cc_start: 0.9353 (p) cc_final: 0.9102 (p) REVERT: N 89 MET cc_start: 0.9512 (mmt) cc_final: 0.9244 (mmm) REVERT: S 66 MET cc_start: 0.8865 (mtp) cc_final: 0.8548 (mtp) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.1891 time to fit residues: 65.4632 Evaluate side-chains 142 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.4980 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 8.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 5.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 109 GLN B 168 HIS B 177 ASN C 140 ASN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 HIS ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.035915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.028318 restraints weight = 166211.303| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 4.07 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 19802 Z= 0.171 Angle : 0.700 11.124 28949 Z= 0.383 Chirality : 0.044 0.291 3609 Planarity : 0.006 0.057 1995 Dihedral : 23.661 177.959 8374 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.15 % Allowed : 17.70 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.24), residues: 1092 helix: -0.61 (0.21), residues: 507 sheet: -1.78 (0.38), residues: 154 loop : -1.49 (0.28), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 10 TYR 0.015 0.002 TYR I 90 PHE 0.019 0.002 PHE B 184 TRP 0.012 0.002 TRP C 201 HIS 0.013 0.002 HIS S 57 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.17 (19801) covalent geometry : angle 0.70048 / 0.38 (28949) hydrogen bonds : bond 0.13393 / 14.53 ( 728) hydrogen bonds : angle 5.37261 / 6.99 ( 1619) metal coordination : bond 0.02737 / 1.37 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 178 time to evaluate : 0.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 49 MET cc_start: 0.8481 (tpp) cc_final: 0.8193 (tpt) REVERT: B 213 TYR cc_start: 0.8720 (m-80) cc_final: 0.7876 (m-80) REVERT: C 129 MET cc_start: 0.9299 (mmm) cc_final: 0.8917 (mmm) REVERT: G 15 ASP cc_start: 0.6963 (t0) cc_final: 0.6754 (t0) REVERT: G 103 TRP cc_start: 0.9054 (m-10) cc_final: 0.8635 (m-10) REVERT: G 116 MET cc_start: 0.8081 (pmm) cc_final: 0.7301 (tpt) REVERT: I 11 ARG cc_start: 0.3758 (pmt170) cc_final: 0.3379 (pmt170) REVERT: I 59 GLU cc_start: 0.8424 (pm20) cc_final: 0.8118 (pm20) REVERT: I 60 LYS cc_start: 0.9227 (mmmt) cc_final: 0.8827 (mmmt) REVERT: I 118 LEU cc_start: 0.9174 (mt) cc_final: 0.8737 (mt) REVERT: J 17 LEU cc_start: 0.9692 (mp) cc_final: 0.9469 (mm) REVERT: J 19 ASP cc_start: 0.9106 (m-30) cc_final: 0.8729 (m-30) REVERT: J 63 ASP cc_start: 0.8459 (t0) cc_final: 0.7953 (t70) REVERT: J 66 GLU cc_start: 0.7628 (tm-30) cc_final: 0.6794 (tm-30) REVERT: J 88 MET cc_start: 0.9504 (mmm) cc_final: 0.9281 (mmm) REVERT: J 99 GLN cc_start: 0.8776 (mm-40) cc_final: 0.8503 (tm-30) REVERT: M 56 LEU cc_start: 0.9615 (mt) cc_final: 0.9170 (pp) REVERT: M 75 MET cc_start: 0.8978 (mmm) cc_final: 0.8760 (mmp) REVERT: N 89 MET cc_start: 0.9537 (mmt) cc_final: 0.9304 (mmm) REVERT: S 6 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8669 (ptpp) REVERT: S 66 MET cc_start: 0.8959 (mtp) cc_final: 0.8721 (mtp) REVERT: S 71 LEU cc_start: 0.9497 (mt) cc_final: 0.9234 (mt) outliers start: 29 outliers final: 9 residues processed: 195 average time/residue: 0.1431 time to fit residues: 42.4289 Evaluate side-chains 149 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 139 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain G residue 38 THR Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain M residue 19 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain S residue 6 LYS Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 136 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 16 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 81 optimal weight: 0.0270 chunk 59 optimal weight: 9.9990 chunk 7 optimal weight: 30.0000 chunk 46 optimal weight: 20.0000 chunk 121 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 overall best weight: 6.0046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS B 227 GLN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 31 ASN J 64 GLN ** M 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.034717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.027326 restraints weight = 170670.851| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 3.93 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 19802 Z= 0.327 Angle : 0.745 8.973 28949 Z= 0.399 Chirality : 0.048 0.289 3609 Planarity : 0.006 0.055 1995 Dihedral : 23.565 177.557 8374 Min Nonbonded Distance : 1.790 Molprobity Statistics. All-atom Clashscore : 25.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.58 % Allowed : 20.96 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.79 (0.24), residues: 1092 helix: -0.63 (0.21), residues: 508 sheet: -1.68 (0.38), residues: 163 loop : -1.47 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 123 TYR 0.014 0.003 TYR I 90 PHE 0.018 0.002 PHE B 198 TRP 0.012 0.002 TRP G 103 HIS 0.010 0.002 HIS M 91 Details of bonding type rmsd/Z covalent geometry : bond 0.00588 / 0.33 (19801) covalent geometry : angle 0.74530 / 0.40 (28949) hydrogen bonds : bond 0.12468 / 13.58 ( 728) hydrogen bonds : angle 5.45335 / 7.07 ( 1619) metal coordination : bond 0.00120 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 TYR cc_start: 0.8613 (m-80) cc_final: 0.7869 (m-80) REVERT: C 129 MET cc_start: 0.9353 (mmm) cc_final: 0.8940 (mmm) REVERT: G 103 TRP cc_start: 0.8977 (m-10) cc_final: 0.8433 (m-10) REVERT: G 116 MET cc_start: 0.8143 (pmm) cc_final: 0.7380 (tpt) REVERT: G 137 LYS cc_start: 0.8728 (ttpp) cc_final: 0.8200 (tmmt) REVERT: I 60 LYS cc_start: 0.9274 (mmmt) cc_final: 0.9073 (mmmt) REVERT: I 118 LEU cc_start: 0.9282 (mt) cc_final: 0.8864 (mt) REVERT: J 17 LEU cc_start: 0.9723 (mp) cc_final: 0.9492 (mm) REVERT: J 19 ASP cc_start: 0.9152 (m-30) cc_final: 0.8718 (m-30) REVERT: J 63 ASP cc_start: 0.8478 (t0) cc_final: 0.7973 (t70) REVERT: J 66 GLU cc_start: 0.7653 (tm-30) cc_final: 0.7090 (tm-30) REVERT: M 27 LYS cc_start: 0.8985 (mmtt) cc_final: 0.8756 (tppt) REVERT: M 75 MET cc_start: 0.9060 (mmm) cc_final: 0.8768 (mmp) REVERT: N 89 MET cc_start: 0.9554 (mmt) cc_final: 0.9332 (mmm) REVERT: S 66 MET cc_start: 0.9036 (mtp) cc_final: 0.8835 (mtp) outliers start: 33 outliers final: 18 residues processed: 166 average time/residue: 0.1361 time to fit residues: 34.9023 Evaluate side-chains 143 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain B residue 227 GLN Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain J residue 35 GLN Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 38 ASP Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 25 optimal weight: 20.0000 chunk 43 optimal weight: 20.0000 chunk 65 optimal weight: 9.9990 chunk 7 optimal weight: 30.0000 chunk 5 optimal weight: 20.0000 chunk 72 optimal weight: 0.9990 chunk 119 optimal weight: 6.9990 chunk 120 optimal weight: 0.4980 chunk 13 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 overall best weight: 4.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN B 168 HIS ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 142 HIS I 31 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.034540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.026919 restraints weight = 167317.920| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 3.99 r_work (final): 0.2737 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 19802 Z= 0.269 Angle : 0.675 7.602 28949 Z= 0.369 Chirality : 0.044 0.292 3609 Planarity : 0.006 0.049 1995 Dihedral : 23.573 178.284 8374 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 23.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.02 % Allowed : 21.39 % Favored : 74.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.63 (0.24), residues: 1092 helix: -0.49 (0.21), residues: 508 sheet: -1.65 (0.39), residues: 159 loop : -1.41 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 95 TYR 0.012 0.002 TYR I 90 PHE 0.017 0.002 PHE B 198 TRP 0.011 0.002 TRP C 201 HIS 0.011 0.002 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00492 / 0.27 (19801) covalent geometry : angle 0.67465 / 0.37 (28949) hydrogen bonds : bond 0.11548 / 12.54 ( 728) hydrogen bonds : angle 5.27600 / 6.86 ( 1619) metal coordination : bond 0.00168 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 137 time to evaluate : 0.465 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: B 194 ASP cc_start: 0.8861 (t0) cc_final: 0.8422 (p0) REVERT: B 213 TYR cc_start: 0.8586 (m-80) cc_final: 0.7862 (m-80) REVERT: C 129 MET cc_start: 0.9377 (mmm) cc_final: 0.8950 (mmm) REVERT: G 10 ARG cc_start: 0.5716 (OUTLIER) cc_final: 0.5489 (mtp85) REVERT: G 103 TRP cc_start: 0.8852 (m-10) cc_final: 0.8370 (m-10) REVERT: G 116 MET cc_start: 0.8113 (pmm) cc_final: 0.7313 (tpt) REVERT: G 137 LYS cc_start: 0.8782 (ttpp) cc_final: 0.8299 (tmmt) REVERT: I 60 LYS cc_start: 0.9330 (mmmt) cc_final: 0.9128 (mmmt) REVERT: I 118 LEU cc_start: 0.9349 (mt) cc_final: 0.8956 (mt) REVERT: J 17 LEU cc_start: 0.9719 (mp) cc_final: 0.9485 (mm) REVERT: J 19 ASP cc_start: 0.9156 (m-30) cc_final: 0.8695 (m-30) REVERT: J 63 ASP cc_start: 0.8492 (t0) cc_final: 0.8016 (t70) REVERT: J 66 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7354 (tm-30) REVERT: J 88 MET cc_start: 0.9445 (mmm) cc_final: 0.9210 (mmm) REVERT: J 99 GLN cc_start: 0.8808 (mm-40) cc_final: 0.8501 (tm-30) REVERT: M 27 LYS cc_start: 0.8934 (mmtt) cc_final: 0.8726 (tppt) REVERT: M 75 MET cc_start: 0.9042 (mmm) cc_final: 0.8746 (mmp) REVERT: N 86 GLU cc_start: 0.9342 (pm20) cc_final: 0.9120 (pm20) REVERT: N 89 MET cc_start: 0.9563 (mmt) cc_final: 0.9338 (mmm) REVERT: S 66 MET cc_start: 0.9088 (mtp) cc_final: 0.8880 (mtp) outliers start: 37 outliers final: 22 residues processed: 163 average time/residue: 0.1341 time to fit residues: 34.2260 Evaluate side-chains 152 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 9 MET Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 56 ASP Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 33 THR Chi-restraints excluded: chain S residue 48 THR Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 69 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 98 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 chunk 142 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 38 optimal weight: 10.0000 chunk 107 optimal weight: 0.9980 chunk 74 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 39 HIS B 109 GLN B 168 HIS ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.035697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.028041 restraints weight = 163230.200| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 4.18 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.3232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 19802 Z= 0.140 Angle : 0.596 9.651 28949 Z= 0.331 Chirality : 0.039 0.302 3609 Planarity : 0.005 0.044 1995 Dihedral : 23.495 179.183 8374 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 4.67 % Allowed : 21.72 % Favored : 73.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.24), residues: 1092 helix: -0.30 (0.22), residues: 509 sheet: -1.35 (0.40), residues: 157 loop : -1.27 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 11 TYR 0.015 0.002 TYR I 90 PHE 0.015 0.002 PHE B 126 TRP 0.014 0.001 TRP C 201 HIS 0.013 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 (19801) covalent geometry : angle 0.59636 / 0.33 (28949) hydrogen bonds : bond 0.10869 / 11.68 ( 728) hydrogen bonds : angle 4.90661 / 6.41 ( 1619) metal coordination : bond 0.00029 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 149 time to evaluate : 0.464 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: B 213 TYR cc_start: 0.8500 (m-80) cc_final: 0.7799 (m-80) REVERT: C 129 MET cc_start: 0.9364 (mmm) cc_final: 0.8892 (mmm) REVERT: G 103 TRP cc_start: 0.8849 (m-10) cc_final: 0.8365 (m-10) REVERT: G 106 GLU cc_start: 0.9131 (pp20) cc_final: 0.8905 (pp20) REVERT: G 116 MET cc_start: 0.8075 (pmm) cc_final: 0.7163 (tpt) REVERT: G 137 LYS cc_start: 0.8780 (ttpp) cc_final: 0.8307 (tmmt) REVERT: I 118 LEU cc_start: 0.9236 (mt) cc_final: 0.8806 (mt) REVERT: J 17 LEU cc_start: 0.9711 (mp) cc_final: 0.9487 (mm) REVERT: J 19 ASP cc_start: 0.9170 (m-30) cc_final: 0.8708 (p0) REVERT: J 63 ASP cc_start: 0.8517 (t0) cc_final: 0.8027 (t70) REVERT: J 66 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7430 (tp30) REVERT: J 99 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8510 (tm-30) REVERT: M 75 MET cc_start: 0.9151 (mmm) cc_final: 0.8862 (mmp) REVERT: N 89 MET cc_start: 0.9560 (mmt) cc_final: 0.9350 (mmm) REVERT: S 66 MET cc_start: 0.9089 (mtp) cc_final: 0.8835 (mtp) REVERT: S 71 LEU cc_start: 0.9534 (mt) cc_final: 0.9316 (mt) outliers start: 43 outliers final: 20 residues processed: 182 average time/residue: 0.1429 time to fit residues: 39.9140 Evaluate side-chains 144 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain I residue 11 ARG Chi-restraints excluded: chain I residue 34 SER Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 35 optimal weight: 20.0000 chunk 144 optimal weight: 7.9990 chunk 87 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 149 optimal weight: 7.9990 chunk 110 optimal weight: 8.9990 chunk 76 optimal weight: 0.6980 chunk 61 optimal weight: 5.9990 chunk 78 optimal weight: 1.9990 chunk 38 optimal weight: 20.0000 chunk 89 optimal weight: 5.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 HIS ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN B 168 HIS ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN ** M 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.035428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.027742 restraints weight = 164365.084| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 4.19 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.734 19802 Z= 0.250 Angle : 0.611 11.159 28949 Z= 0.335 Chirality : 0.040 0.288 3609 Planarity : 0.005 0.041 1995 Dihedral : 23.406 178.576 8374 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 19.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.15 % Allowed : 23.67 % Favored : 73.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.36 (0.24), residues: 1092 helix: -0.35 (0.22), residues: 514 sheet: -1.29 (0.41), residues: 155 loop : -1.27 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 33 TYR 0.015 0.002 TYR G 44 PHE 0.016 0.002 PHE B 184 TRP 0.010 0.001 TRP C 201 HIS 0.011 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.18 (19801) covalent geometry : angle 0.61080 / 0.33 (28949) hydrogen bonds : bond 0.10580 / 11.43 ( 728) hydrogen bonds : angle 4.91738 / 6.48 ( 1619) metal coordination : bond 0.73421 / 36.71 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 213 TYR cc_start: 0.8519 (m-80) cc_final: 0.7795 (m-80) REVERT: C 129 MET cc_start: 0.9352 (mmm) cc_final: 0.8925 (mmm) REVERT: C 211 MET cc_start: 0.7540 (OUTLIER) cc_final: 0.7212 (mmm) REVERT: G 10 ARG cc_start: 0.5992 (OUTLIER) cc_final: 0.5372 (ptp90) REVERT: G 103 TRP cc_start: 0.8846 (m-10) cc_final: 0.8449 (m-10) REVERT: G 106 GLU cc_start: 0.9141 (pp20) cc_final: 0.8928 (pp20) REVERT: G 116 MET cc_start: 0.8002 (pmm) cc_final: 0.7055 (tpt) REVERT: G 137 LYS cc_start: 0.8803 (ttpp) cc_final: 0.8390 (pptt) REVERT: I 37 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8376 (pp30) REVERT: I 59 GLU cc_start: 0.8542 (pm20) cc_final: 0.8242 (pm20) REVERT: I 118 LEU cc_start: 0.9305 (mt) cc_final: 0.8904 (mt) REVERT: J 19 ASP cc_start: 0.9198 (m-30) cc_final: 0.8725 (p0) REVERT: J 47 GLU cc_start: 0.8305 (tp30) cc_final: 0.7948 (mp0) REVERT: J 63 ASP cc_start: 0.8492 (t0) cc_final: 0.7978 (t70) REVERT: J 99 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8540 (tm-30) REVERT: M 27 LYS cc_start: 0.9285 (tppt) cc_final: 0.8963 (tppt) REVERT: M 75 MET cc_start: 0.9153 (mmm) cc_final: 0.8856 (mmp) REVERT: N 89 MET cc_start: 0.9580 (mmt) cc_final: 0.9369 (mmm) REVERT: S 13 LEU cc_start: 0.9481 (OUTLIER) cc_final: 0.9279 (pt) REVERT: S 66 MET cc_start: 0.9117 (mtp) cc_final: 0.8796 (mtp) REVERT: S 71 LEU cc_start: 0.9574 (mt) cc_final: 0.9356 (mt) outliers start: 29 outliers final: 18 residues processed: 148 average time/residue: 0.1279 time to fit residues: 29.9133 Evaluate side-chains 145 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain C residue 211 MET Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain I residue 37 GLN Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain S residue 13 LEU Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 3.9990 chunk 112 optimal weight: 0.5980 chunk 119 optimal weight: 4.9990 chunk 74 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 149 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN B 168 HIS B 177 ASN ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.036035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.028387 restraints weight = 165838.679| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 4.16 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 19802 Z= 0.132 Angle : 0.577 11.575 28949 Z= 0.320 Chirality : 0.037 0.284 3609 Planarity : 0.004 0.042 1995 Dihedral : 23.380 179.461 8374 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 3.37 % Allowed : 24.21 % Favored : 72.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.18 (0.24), residues: 1092 helix: -0.25 (0.22), residues: 509 sheet: -1.09 (0.41), residues: 154 loop : -1.15 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 10 TYR 0.014 0.002 TYR I 38 PHE 0.016 0.001 PHE B 184 TRP 0.012 0.001 TRP C 201 HIS 0.011 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.13 (19801) covalent geometry : angle 0.57716 / 0.32 (28949) hydrogen bonds : bond 0.10391 / 11.19 ( 728) hydrogen bonds : angle 4.79544 / 6.32 ( 1619) metal coordination : bond 0.01295 / 0.65 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 141 time to evaluate : 0.458 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: B 213 TYR cc_start: 0.8523 (m-80) cc_final: 0.7815 (m-80) REVERT: C 129 MET cc_start: 0.9316 (mmm) cc_final: 0.8881 (mmm) REVERT: G 10 ARG cc_start: 0.6096 (OUTLIER) cc_final: 0.5556 (ptp90) REVERT: G 103 TRP cc_start: 0.8886 (m-10) cc_final: 0.8404 (m-10) REVERT: G 106 GLU cc_start: 0.9153 (pp20) cc_final: 0.8916 (pp20) REVERT: G 116 MET cc_start: 0.8013 (pmm) cc_final: 0.7046 (tpt) REVERT: G 137 LYS cc_start: 0.8801 (ttpp) cc_final: 0.8317 (tmmt) REVERT: I 59 GLU cc_start: 0.8421 (pm20) cc_final: 0.8015 (pm20) REVERT: I 98 LEU cc_start: 0.9497 (mt) cc_final: 0.9176 (mt) REVERT: I 118 LEU cc_start: 0.9293 (mt) cc_final: 0.8876 (mt) REVERT: J 19 ASP cc_start: 0.9187 (m-30) cc_final: 0.8739 (p0) REVERT: J 63 ASP cc_start: 0.8519 (t0) cc_final: 0.8009 (t70) REVERT: J 99 GLN cc_start: 0.8786 (mm-40) cc_final: 0.8558 (tm-30) REVERT: M 75 MET cc_start: 0.9208 (mmm) cc_final: 0.8900 (mmp) REVERT: N 86 GLU cc_start: 0.9428 (pm20) cc_final: 0.9186 (pm20) REVERT: N 89 MET cc_start: 0.9543 (mmt) cc_final: 0.9334 (mmm) REVERT: S 66 MET cc_start: 0.9105 (mtp) cc_final: 0.8728 (mtp) REVERT: S 71 LEU cc_start: 0.9567 (mt) cc_final: 0.9358 (mt) outliers start: 31 outliers final: 19 residues processed: 166 average time/residue: 0.1376 time to fit residues: 35.3737 Evaluate side-chains 146 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 126 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 69 THR Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 96 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 137 optimal weight: 0.9990 chunk 9 optimal weight: 40.0000 chunk 136 optimal weight: 0.9980 chunk 2 optimal weight: 20.0000 chunk 101 optimal weight: 7.9990 chunk 37 optimal weight: 20.0000 chunk 7 optimal weight: 20.0000 chunk 87 optimal weight: 0.9980 chunk 12 optimal weight: 20.0000 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 19 GLN ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN ** M 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.035089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.027401 restraints weight = 166347.695| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 4.04 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8738 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 19802 Z= 0.239 Angle : 0.665 15.778 28949 Z= 0.355 Chirality : 0.042 0.286 3609 Planarity : 0.005 0.061 1995 Dihedral : 23.339 179.208 8374 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 21.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 3.15 % Allowed : 25.41 % Favored : 71.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.30 (0.24), residues: 1092 helix: -0.37 (0.22), residues: 517 sheet: -1.01 (0.42), residues: 152 loop : -1.24 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 10 TYR 0.010 0.002 TYR C 168 PHE 0.014 0.002 PHE B 184 TRP 0.010 0.002 TRP S 34 HIS 0.012 0.002 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00441 / 0.24 (19801) covalent geometry : angle 0.66501 / 0.35 (28949) hydrogen bonds : bond 0.10392 / 11.29 ( 728) hydrogen bonds : angle 4.94141 / 6.50 ( 1619) metal coordination : bond 0.00668 / 0.33 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 128 time to evaluate : 0.451 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: B 213 TYR cc_start: 0.8573 (m-80) cc_final: 0.7831 (m-80) REVERT: C 129 MET cc_start: 0.9301 (mmm) cc_final: 0.8927 (mmm) REVERT: G 10 ARG cc_start: 0.6289 (OUTLIER) cc_final: 0.5818 (ptp90) REVERT: G 103 TRP cc_start: 0.8910 (m-10) cc_final: 0.8417 (m-10) REVERT: G 106 GLU cc_start: 0.9170 (pp20) cc_final: 0.8938 (pp20) REVERT: G 116 MET cc_start: 0.8095 (pmm) cc_final: 0.7180 (tpt) REVERT: G 137 LYS cc_start: 0.8807 (ttpp) cc_final: 0.8295 (tmmt) REVERT: I 118 LEU cc_start: 0.9333 (mt) cc_final: 0.8933 (mt) REVERT: J 19 ASP cc_start: 0.9193 (m-30) cc_final: 0.8725 (p0) REVERT: J 63 ASP cc_start: 0.8555 (t0) cc_final: 0.8039 (t70) REVERT: J 99 GLN cc_start: 0.8781 (mm-40) cc_final: 0.8549 (tm-30) REVERT: M 27 LYS cc_start: 0.9308 (tppt) cc_final: 0.9020 (tppt) REVERT: M 75 MET cc_start: 0.9071 (mmm) cc_final: 0.8741 (mmp) REVERT: N 86 GLU cc_start: 0.9386 (pm20) cc_final: 0.9168 (pm20) REVERT: N 89 MET cc_start: 0.9559 (mmt) cc_final: 0.9359 (mmm) REVERT: S 66 MET cc_start: 0.9068 (mtp) cc_final: 0.8711 (mtp) outliers start: 29 outliers final: 20 residues processed: 151 average time/residue: 0.1396 time to fit residues: 32.7105 Evaluate side-chains 145 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 SER Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 53 ILE Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain M residue 16 VAL Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 85 optimal weight: 3.9990 chunk 86 optimal weight: 2.9990 chunk 124 optimal weight: 0.4980 chunk 45 optimal weight: 20.0000 chunk 132 optimal weight: 0.8980 chunk 4 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 95 optimal weight: 9.9990 chunk 96 optimal weight: 40.0000 chunk 80 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 GLN B 168 HIS ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.035580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2801 r_free = 0.2801 target = 0.027911 restraints weight = 166459.927| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 4.17 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19802 Z= 0.158 Angle : 0.615 12.761 28949 Z= 0.333 Chirality : 0.038 0.284 3609 Planarity : 0.004 0.040 1995 Dihedral : 23.363 179.696 8374 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 18.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 2.93 % Allowed : 25.73 % Favored : 71.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -1.16 (0.24), residues: 1092 helix: -0.28 (0.22), residues: 515 sheet: -0.96 (0.42), residues: 156 loop : -1.13 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 10 TYR 0.012 0.002 TYR B 213 PHE 0.016 0.001 PHE B 184 TRP 0.012 0.001 TRP C 201 HIS 0.012 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 (19801) covalent geometry : angle 0.61498 / 0.33 (28949) hydrogen bonds : bond 0.10209 / 11.01 ( 728) hydrogen bonds : angle 4.88970 / 6.46 ( 1619) metal coordination : bond 0.00096 / 0.05 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.419 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 213 TYR cc_start: 0.8552 (m-80) cc_final: 0.7821 (m-80) REVERT: C 129 MET cc_start: 0.9339 (mmm) cc_final: 0.8920 (mmm) REVERT: G 10 ARG cc_start: 0.6046 (OUTLIER) cc_final: 0.5533 (ptp90) REVERT: G 52 GLN cc_start: 0.9064 (tm-30) cc_final: 0.8750 (pp30) REVERT: G 103 TRP cc_start: 0.8862 (m-10) cc_final: 0.8372 (m-10) REVERT: G 106 GLU cc_start: 0.9167 (pp20) cc_final: 0.8923 (pp20) REVERT: G 116 MET cc_start: 0.8019 (pmm) cc_final: 0.7053 (tpt) REVERT: G 137 LYS cc_start: 0.8785 (ttpp) cc_final: 0.8289 (tmmt) REVERT: I 64 TYR cc_start: 0.7537 (t80) cc_final: 0.7025 (t80) REVERT: I 98 LEU cc_start: 0.9502 (mt) cc_final: 0.9160 (mt) REVERT: I 118 LEU cc_start: 0.9310 (mt) cc_final: 0.8904 (mt) REVERT: J 19 ASP cc_start: 0.9240 (m-30) cc_final: 0.8787 (p0) REVERT: J 63 ASP cc_start: 0.8501 (t0) cc_final: 0.7970 (t70) REVERT: J 99 GLN cc_start: 0.8812 (mm-40) cc_final: 0.8532 (tm-30) REVERT: M 75 MET cc_start: 0.9140 (mmm) cc_final: 0.8865 (mmp) REVERT: N 86 GLU cc_start: 0.9414 (pm20) cc_final: 0.9175 (pm20) REVERT: N 89 MET cc_start: 0.9592 (mmt) cc_final: 0.9331 (mmm) REVERT: S 66 MET cc_start: 0.9089 (mtp) cc_final: 0.8702 (mtp) outliers start: 27 outliers final: 21 residues processed: 153 average time/residue: 0.1372 time to fit residues: 32.7048 Evaluate side-chains 149 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain I residue 104 VAL Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 112 optimal weight: 5.9990 chunk 12 optimal weight: 20.0000 chunk 143 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 37 optimal weight: 20.0000 chunk 10 optimal weight: 20.0000 chunk 20 optimal weight: 20.0000 chunk 61 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 42 optimal weight: 20.0000 chunk 32 optimal weight: 20.0000 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 8 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.034834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.027166 restraints weight = 167358.451| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 4.10 r_work (final): 0.2748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.3673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 19802 Z= 0.263 Angle : 0.692 13.604 28949 Z= 0.369 Chirality : 0.043 0.281 3609 Planarity : 0.005 0.067 1995 Dihedral : 23.346 179.713 8374 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 22.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.93 % Allowed : 25.52 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.33 (0.24), residues: 1092 helix: -0.43 (0.22), residues: 517 sheet: -1.04 (0.42), residues: 153 loop : -1.21 (0.29), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 10 TYR 0.010 0.002 TYR C 168 PHE 0.014 0.002 PHE B 184 TRP 0.010 0.002 TRP S 34 HIS 0.011 0.002 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.26 (19801) covalent geometry : angle 0.69241 / 0.37 (28949) hydrogen bonds : bond 0.10389 / 11.30 ( 728) hydrogen bonds : angle 5.02842 / 6.64 ( 1619) metal coordination : bond 0.00133 / 0.07 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 124 time to evaluate : 0.465 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: B 213 TYR cc_start: 0.8560 (m-80) cc_final: 0.7818 (m-80) REVERT: C 129 MET cc_start: 0.9310 (mmm) cc_final: 0.8964 (mmm) REVERT: G 10 ARG cc_start: 0.6183 (OUTLIER) cc_final: 0.5046 (mtp85) REVERT: G 52 GLN cc_start: 0.9031 (tm-30) cc_final: 0.8702 (pp30) REVERT: G 103 TRP cc_start: 0.8810 (m-10) cc_final: 0.8357 (m-10) REVERT: G 116 MET cc_start: 0.8033 (pmm) cc_final: 0.7094 (tpt) REVERT: I 64 TYR cc_start: 0.7439 (t80) cc_final: 0.6866 (t80) REVERT: I 118 LEU cc_start: 0.9442 (mt) cc_final: 0.9068 (mt) REVERT: J 19 ASP cc_start: 0.9190 (m-30) cc_final: 0.8720 (p0) REVERT: J 63 ASP cc_start: 0.8570 (t0) cc_final: 0.8068 (t70) REVERT: J 99 GLN cc_start: 0.8810 (mm-40) cc_final: 0.8536 (tm-30) REVERT: M 31 LYS cc_start: 0.9635 (mtmm) cc_final: 0.9391 (mtmm) REVERT: M 75 MET cc_start: 0.9049 (mmm) cc_final: 0.8733 (mmp) REVERT: N 89 MET cc_start: 0.9580 (mmt) cc_final: 0.9337 (mmm) REVERT: S 66 MET cc_start: 0.9065 (mtp) cc_final: 0.8699 (mtp) outliers start: 27 outliers final: 21 residues processed: 145 average time/residue: 0.1326 time to fit residues: 30.2994 Evaluate side-chains 143 residues out of total 921 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 VAL Chi-restraints excluded: chain B residue 122 GLN Chi-restraints excluded: chain B residue 123 ASP Chi-restraints excluded: chain B residue 191 SER Chi-restraints excluded: chain C residue 192 THR Chi-restraints excluded: chain C residue 198 VAL Chi-restraints excluded: chain G residue 10 ARG Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain I residue 112 GLU Chi-restraints excluded: chain I residue 116 VAL Chi-restraints excluded: chain J residue 36 VAL Chi-restraints excluded: chain J residue 51 VAL Chi-restraints excluded: chain J residue 80 THR Chi-restraints excluded: chain M residue 53 ILE Chi-restraints excluded: chain N residue 16 LEU Chi-restraints excluded: chain N residue 34 VAL Chi-restraints excluded: chain N residue 74 LEU Chi-restraints excluded: chain S residue 44 MET Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 62 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 chunk 142 optimal weight: 0.6980 chunk 114 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 97 optimal weight: 6.9990 chunk 56 optimal weight: 0.9990 chunk 118 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 150 optimal weight: 3.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 168 HIS ** G 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 130 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.035770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.028132 restraints weight = 163260.096| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 4.13 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8739 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 19802 Z= 0.142 Angle : 0.625 13.633 28949 Z= 0.338 Chirality : 0.037 0.282 3609 Planarity : 0.004 0.040 1995 Dihedral : 23.336 178.682 8374 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 17.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 2.61 % Allowed : 25.84 % Favored : 71.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.25), residues: 1092 helix: -0.27 (0.22), residues: 517 sheet: -0.85 (0.43), residues: 154 loop : -1.01 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 102 TYR 0.010 0.002 TYR M 86 PHE 0.016 0.001 PHE B 184 TRP 0.014 0.002 TRP C 201 HIS 0.013 0.001 HIS B 168 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (19801) covalent geometry : angle 0.62497 / 0.34 (28949) hydrogen bonds : bond 0.10160 / 10.93 ( 728) hydrogen bonds : angle 4.84521 / 6.51 ( 1619) metal coordination : bond 0.00042 / 0.02 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3210.13 seconds wall clock time: 56 minutes 39.91 seconds (3399.91 seconds total)