Starting phenix.real_space_refine on Thu Oct 29 23:36:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7bgd_12178/10_2026/7bgd_12178.cif Found real_map, /net/cci-nas-00/data/ceres_data/7bgd_12178/10_2026/7bgd_12178.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7bgd_12178/10_2026/7bgd_12178.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7bgd_12178/10_2026/7bgd_12178.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7bgd_12178/10_2026/7bgd_12178.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7bgd_12178/10_2026/7bgd_12178.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7bgd_12178/10_2026/7bgd_12178.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7bgd_12178/10_2026/7bgd_12178.map" } resolution = 3.2 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= 0.001 sd= 0.008 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: 5 Type Number sf(0) Gaussians P 1128 5.49 5 S 30 5.16 5 C 17806 2.51 5 N 6522 2.21 5 O 9878 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 35364 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 693 Classifications: {'RNAv2': 32} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 4, 'rna3p_pur': 13, 'rna3p_pyr': 5} Link IDs: {'rna2p': 14, 'rna3p': 17} Chain: "a" Number of atoms: 23497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1096, 23497 Classifications: {'RNAv2': 1096} Modifications used: {'rna2p_pur': 81, 'rna2p_pyr': 59, 'rna3p_pur': 542, 'rna3p_pyr': 414} Link IDs: {'rna2p': 140, 'rna3p': 955} Chain breaks: 1 Chain: "b" Number of atoms: 1299 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1299 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 6, 'TRANS': 156} Chain breaks: 2 Chain: "d" Number of atoms: 1595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1595 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 187} Chain breaks: 1 Chain: "e" Number of atoms: 1169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1169 Classifications: {'peptide': 157} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 149} Chain: "f" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 798 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 1, 'TRANS': 94} Chain: "h" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 1032 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 126} Chain: "k" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 880 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 7, 'TRANS': 110} Chain: "l" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1058 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 8, 'TRANS': 126} Chain: "o" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 738 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "p" Number of atoms: 712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 712 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 84} Chain: "q" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 707 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "r" Number of atoms: 580 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 580 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "t" Number of atoms: 606 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 606 Classifications: {'peptide': 80} Link IDs: {'TRANS': 79} Time building chain proxies: 6.39, per 1000 atoms: 0.18 Number of scatterers: 35364 At special positions: 0 Unit cell: (145.18, 183.26, 172.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 1128 15.00 O 9878 8.00 N 6522 7.00 C 17806 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: 2.78 Conformation dependent library (CDL) restraints added in 560.1 milliseconds 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2616 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 14 sheets defined 34.7% alpha, 17.7% beta 359 base pairs and 687 stacking pairs defined. Time for finding SS restraints: 5.09 Creating SS restraints... Processing helix chain 'b' and resid 27 through 29 No H-bonds generated for 'chain 'b' and resid 27 through 29' Processing helix chain 'b' and resid 43 through 60 Processing helix chain 'b' and resid 61 through 63 No H-bonds generated for 'chain 'b' and resid 61 through 63' Processing helix chain 'b' and resid 77 through 82 Processing helix chain 'b' and resid 206 through 223 removed outlier: 3.631A pdb=" N VAL b 210 " --> pdb=" O ALA b 206 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU b 213 " --> pdb=" O ALA b 209 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA b 218 " --> pdb=" O THR b 214 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 14 removed outlier: 3.633A pdb=" N ARG d 14 " --> pdb=" O LYS d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 45 through 62 removed outlier: 3.597A pdb=" N LEU d 60 " --> pdb=" O LYS d 56 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR d 61 " --> pdb=" O LEU d 57 " (cutoff:3.500A) Processing helix chain 'd' and resid 64 through 74 Processing helix chain 'd' and resid 81 through 91 removed outlier: 3.604A pdb=" N ALA d 91 " --> pdb=" O MET d 87 " (cutoff:3.500A) Processing helix chain 'd' and resid 93 through 101 Processing helix chain 'd' and resid 106 through 116 Processing helix chain 'd' and resid 142 through 146 removed outlier: 4.203A pdb=" N GLN d 146 " --> pdb=" O GLU d 143 " (cutoff:3.500A) Processing helix chain 'd' and resid 148 through 157 removed outlier: 3.751A pdb=" N GLU d 156 " --> pdb=" O VAL d 152 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ILE d 157 " --> pdb=" O GLU d 153 " (cutoff:3.500A) Processing helix chain 'd' and resid 191 through 196 removed outlier: 3.575A pdb=" N VAL d 195 " --> pdb=" O GLU d 191 " (cutoff:3.500A) Processing helix chain 'e' and resid 55 through 68 Processing helix chain 'e' and resid 109 through 116 removed outlier: 3.668A pdb=" N ALA e 113 " --> pdb=" O GLY e 109 " (cutoff:3.500A) Processing helix chain 'e' and resid 132 through 146 Processing helix chain 'e' and resid 149 through 157 Processing helix chain 'f' and resid 15 through 30 removed outlier: 3.512A pdb=" N LYS f 20 " --> pdb=" O GLU f 16 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N ALA f 21 " --> pdb=" O ASP f 17 " (cutoff:3.500A) Processing helix chain 'f' and resid 72 through 83 removed outlier: 3.785A pdb=" N LYS f 81 " --> pdb=" O GLN f 77 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE f 82 " --> pdb=" O ARG f 78 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 20 removed outlier: 3.811A pdb=" N VAL h 20 " --> pdb=" O ASN h 16 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 43 Processing helix chain 'h' and resid 96 through 101 Processing helix chain 'h' and resid 114 through 121 removed outlier: 3.766A pdb=" N ARG h 121 " --> pdb=" O GLU h 117 " (cutoff:3.500A) Processing helix chain 'k' and resid 46 through 51 removed outlier: 3.792A pdb=" N LEU k 50 " --> pdb=" O ALA k 47 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLY k 51 " --> pdb=" O GLY k 48 " (cutoff:3.500A) Processing helix chain 'k' and resid 53 through 57 removed outlier: 3.667A pdb=" N LYS k 57 " --> pdb=" O GLY k 54 " (cutoff:3.500A) Processing helix chain 'k' and resid 59 through 78 removed outlier: 3.771A pdb=" N ALA k 63 " --> pdb=" O THR k 59 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N SER k 73 " --> pdb=" O THR k 69 " (cutoff:3.500A) Processing helix chain 'k' and resid 92 through 103 removed outlier: 3.812A pdb=" N ALA k 96 " --> pdb=" O GLY k 92 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE k 97 " --> pdb=" O ARG k 93 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG k 98 " --> pdb=" O GLU k 94 " (cutoff:3.500A) Processing helix chain 'l' and resid 3 through 8 Processing helix chain 'o' and resid 4 through 12 Processing helix chain 'o' and resid 24 through 46 removed outlier: 3.621A pdb=" N ARG o 44 " --> pdb=" O ASN o 40 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N THR o 45 " --> pdb=" O GLU o 41 " (cutoff:3.500A) Processing helix chain 'o' and resid 50 through 74 removed outlier: 4.021A pdb=" N ARG o 54 " --> pdb=" O HIS o 50 " (cutoff:3.500A) Processing helix chain 'o' and resid 74 through 86 removed outlier: 3.571A pdb=" N GLY o 86 " --> pdb=" O ILE o 82 " (cutoff:3.500A) Processing helix chain 'p' and resid 55 through 63 removed outlier: 3.569A pdb=" N ASP p 63 " --> pdb=" O LYS p 59 " (cutoff:3.500A) Processing helix chain 'p' and resid 68 through 78 Processing helix chain 'p' and resid 79 through 89 removed outlier: 3.517A pdb=" N LYS p 83 " --> pdb=" O GLY p 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 30 through 35 removed outlier: 3.644A pdb=" N LEU r 34 " --> pdb=" O ASP r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 46 through 51 Processing helix chain 'r' and resid 53 through 70 Processing helix chain 't' and resid 8 through 38 removed outlier: 3.849A pdb=" N LYS t 12 " --> pdb=" O ILE t 8 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN t 24 " --> pdb=" O ARG t 20 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ALA t 27 " --> pdb=" O SER t 23 " (cutoff:3.500A) Processing helix chain 't' and resid 45 through 63 removed outlier: 3.797A pdb=" N LEU t 49 " --> pdb=" O ASN t 45 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N SER t 51 " --> pdb=" O ASN t 47 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS t 55 " --> pdb=" O SER t 51 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N VAL t 57 " --> pdb=" O ALA t 53 " (cutoff:3.500A) Processing helix chain 't' and resid 74 through 79 Processing sheet with id=AA1, first strand: chain 'b' and resid 31 through 35 removed outlier: 4.087A pdb=" N THR b 33 " --> pdb=" O ILE b 40 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE b 38 " --> pdb=" O ARG b 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'b' and resid 90 through 91 removed outlier: 3.936A pdb=" N PHE b 69 " --> pdb=" O PHE b 90 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LEU b 68 " --> pdb=" O PHE b 162 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N VAL b 163 " --> pdb=" O ILE b 186 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N GLY b 185 " --> pdb=" O ILE b 200 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'd' and resid 124 through 126 removed outlier: 3.946A pdb=" N VAL d 126 " --> pdb=" O ILE d 119 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ILE d 119 " --> pdb=" O VAL d 126 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN d 166 " --> pdb=" O THR d 175 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'e' and resid 14 through 24 removed outlier: 5.017A pdb=" N VAL e 15 " --> pdb=" O VAL e 38 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL e 38 " --> pdb=" O VAL e 15 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'e' and resid 85 through 87 removed outlier: 6.369A pdb=" N ILE e 106 " --> pdb=" O SER e 125 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N SER e 127 " --> pdb=" O ILE e 106 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'f' and resid 36 through 40 removed outlier: 5.653A pdb=" N VAL f 37 " --> pdb=" O LYS f 66 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS f 66 " --> pdb=" O VAL f 37 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'f' and resid 36 through 40 removed outlier: 5.653A pdb=" N VAL f 37 " --> pdb=" O LYS f 66 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LYS f 66 " --> pdb=" O VAL f 37 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG f 88 " --> pdb=" O ILE f 9 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'h' and resid 24 through 26 removed outlier: 3.745A pdb=" N ASN h 48 " --> pdb=" O PHE h 63 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'h' and resid 76 through 79 Processing sheet with id=AB1, first strand: chain 'h' and resid 76 through 79 removed outlier: 6.944A pdb=" N LEU h 105 " --> pdb=" O ILE h 128 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N TYR h 130 " --> pdb=" O ILE h 103 " (cutoff:3.500A) removed outlier: 7.052A pdb=" N ILE h 103 " --> pdb=" O TYR h 130 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'k' and resid 41 through 45 removed outlier: 6.550A pdb=" N GLY k 19 " --> pdb=" O GLU k 83 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N THR k 85 " --> pdb=" O GLY k 19 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N ALA k 21 " --> pdb=" O THR k 85 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N LYS k 87 " --> pdb=" O ALA k 21 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ILE k 23 " --> pdb=" O LYS k 87 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL k 82 " --> pdb=" O VAL k 107 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ALA k 109 " --> pdb=" O VAL k 82 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'l' and resid 92 through 95 removed outlier: 6.864A pdb=" N ARG l 67 " --> pdb=" O THR l 48 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N VAL l 50 " --> pdb=" O TYR l 65 " (cutoff:3.500A) removed outlier: 7.171A pdb=" N TYR l 65 " --> pdb=" O VAL l 50 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TYR l 108 " --> pdb=" O ASN l 77 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'p' and resid 5 through 11 removed outlier: 6.319A pdb=" N ASN p 41 " --> pdb=" O PRO p 16 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N TYR p 18 " --> pdb=" O THR p 39 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N THR p 39 " --> pdb=" O TYR p 18 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N ILE p 20 " --> pdb=" O ILE p 37 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'q' and resid 41 through 48 removed outlier: 3.571A pdb=" N TYR q 42 " --> pdb=" O THR q 29 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N THR q 29 " --> pdb=" O TYR q 42 " (cutoff:3.500A) removed outlier: 5.707A pdb=" N THR q 22 " --> pdb=" O ASP q 17 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N ASP q 17 " --> pdb=" O THR q 22 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N THR q 24 " --> pdb=" O VAL q 15 " (cutoff:3.500A) removed outlier: 5.325A pdb=" N GLU q 28 " --> pdb=" O VAL q 11 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N VAL q 11 " --> pdb=" O GLU q 28 " (cutoff:3.500A) removed outlier: 13.031A pdb=" N TYR q 30 " --> pdb=" O VAL q 9 " (cutoff:3.500A) removed outlier: 16.569A pdb=" N VAL q 9 " --> pdb=" O TYR q 30 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N ILE q 60 " --> pdb=" O ILE q 80 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N ILE q 80 " --> pdb=" O ILE q 60 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N LYS q 62 " --> pdb=" O VAL q 78 " (cutoff:3.500A) 417 hydrogen bonds defined for protein. 1191 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 894 hydrogen bonds 1446 hydrogen bond angles 0 basepair planarities 359 basepair parallelities 687 stacking parallelities Total time for adding SS restraints: 14.21 Time building geometry restraints manager: 3.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4586 1.32 - 1.45: 16148 1.45 - 1.57: 15375 1.57 - 1.69: 2254 1.69 - 1.81: 56 Bond restraints: 38419 Sorted by residual: bond pdb=" C SER l 118 " pdb=" N GLY l 119 " ideal model delta sigma weight residual 1.330 1.440 -0.110 8.80e-03 1.29e+04 1.55e+02 bond pdb=" C THR l 117 " pdb=" N SER l 118 " ideal model delta sigma weight residual 1.330 1.487 -0.157 1.45e-02 4.76e+03 1.17e+02 bond pdb=" C PHE b 90 " pdb=" N TYR b 91 " ideal model delta sigma weight residual 1.330 1.455 -0.125 1.47e-02 4.63e+03 7.18e+01 bond pdb=" C TYR b 91 " pdb=" N ILE b 92 " ideal model delta sigma weight residual 1.332 1.420 -0.088 1.36e-02 5.41e+03 4.18e+01 bond pdb=" CG1 ILE d 128 " pdb=" CD1 ILE d 128 " ideal model delta sigma weight residual 1.513 1.365 0.148 3.90e-02 6.57e+02 1.45e+01 ... (remaining 38414 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.08: 56045 4.08 - 8.15: 1323 8.15 - 12.23: 79 12.23 - 16.30: 3 16.30 - 20.38: 1 Bond angle restraints: 57451 Sorted by residual: angle pdb=" C SER l 118 " pdb=" N GLY l 119 " pdb=" CA GLY l 119 " ideal model delta sigma weight residual 119.92 129.97 -10.05 9.60e-01 1.09e+00 1.10e+02 angle pdb=" C3' A a 540 " pdb=" O3' A a 540 " pdb=" P A a 541 " ideal model delta sigma weight residual 119.70 130.72 -11.02 1.20e+00 6.94e-01 8.43e+01 angle pdb=" C3' G A 17 " pdb=" O3' G A 17 " pdb=" P G A 18 " ideal model delta sigma weight residual 119.70 129.51 -9.81 1.20e+00 6.94e-01 6.68e+01 angle pdb=" CA PHE b 90 " pdb=" C PHE b 90 " pdb=" N TYR b 91 " ideal model delta sigma weight residual 116.45 106.52 9.93 1.23e+00 6.61e-01 6.52e+01 angle pdb=" N SER l 128 " pdb=" CA SER l 128 " pdb=" C SER l 128 " ideal model delta sigma weight residual 111.14 102.70 8.44 1.08e+00 8.57e-01 6.10e+01 ... (remaining 57446 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.20: 18163 34.20 - 68.40: 2259 68.40 - 102.60: 150 102.60 - 136.79: 2 136.79 - 170.99: 3 Dihedral angle restraints: 20577 sinusoidal: 16523 harmonic: 4054 Sorted by residual: dihedral pdb=" C4' C a1551 " pdb=" C3' C a1551 " pdb=" C2' C a1551 " pdb=" C1' C a1551 " ideal model delta sinusoidal sigma weight residual 36.34 -44.10 80.44 1 3.10e+00 1.04e-01 8.33e+02 dihedral pdb=" C4' U a 437 " pdb=" C3' U a 437 " pdb=" C2' U a 437 " pdb=" C1' U a 437 " ideal model delta sinusoidal sigma weight residual 36.34 -42.28 78.63 1 3.10e+00 1.04e-01 8.02e+02 dihedral pdb=" C4' U a1549 " pdb=" C3' U a1549 " pdb=" C2' U a1549 " pdb=" C1' U a1549 " ideal model delta sinusoidal sigma weight residual 36.34 -41.79 78.13 1 3.10e+00 1.04e-01 7.94e+02 ... (remaining 20574 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 5362 0.108 - 0.216: 1193 0.216 - 0.324: 736 0.324 - 0.432: 45 0.432 - 0.540: 9 Chirality restraints: 7345 Sorted by residual: chirality pdb=" P A A 23 " pdb=" OP1 A A 23 " pdb=" OP2 A A 23 " pdb=" O5' A A 23 " both_signs ideal model delta sigma weight residual True 2.17 -2.71 -0.54 2.00e-01 2.50e+01 7.28e+00 chirality pdb=" P U a 155 " pdb=" OP1 U a 155 " pdb=" OP2 U a 155 " pdb=" O5' U a 155 " both_signs ideal model delta sigma weight residual True 2.17 -2.69 -0.52 2.00e-01 2.50e+01 6.64e+00 chirality pdb=" P G A 18 " pdb=" OP1 G A 18 " pdb=" OP2 G A 18 " pdb=" O5' G A 18 " both_signs ideal model delta sigma weight residual True 2.17 -2.68 -0.50 2.00e-01 2.50e+01 6.33e+00 ... (remaining 7342 not shown) Planarity restraints: 3085 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR b 91 " 0.030 2.00e-02 2.50e+03 6.39e-02 4.08e+01 pdb=" C TYR b 91 " -0.110 2.00e-02 2.50e+03 pdb=" O TYR b 91 " 0.045 2.00e-02 2.50e+03 pdb=" N ILE b 92 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE b 90 " 0.028 2.00e-02 2.50e+03 6.07e-02 3.68e+01 pdb=" C PHE b 90 " -0.105 2.00e-02 2.50e+03 pdb=" O PHE b 90 " 0.044 2.00e-02 2.50e+03 pdb=" N TYR b 91 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY l 119 " 0.027 2.00e-02 2.50e+03 5.83e-02 3.40e+01 pdb=" C GLY l 119 " -0.101 2.00e-02 2.50e+03 pdb=" O GLY l 119 " 0.040 2.00e-02 2.50e+03 pdb=" N VAL l 120 " 0.033 2.00e-02 2.50e+03 ... (remaining 3082 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 10539 2.84 - 3.36: 26884 3.36 - 3.87: 80066 3.87 - 4.39: 89718 4.39 - 4.90: 119146 Nonbonded interactions: 326353 Sorted by model distance: nonbonded pdb=" OP1 A a 212 " pdb=" O2' C a 229 " model vdw 2.327 3.040 nonbonded pdb=" O2' G a 262 " pdb=" O ASP q 20 " model vdw 2.329 3.040 nonbonded pdb=" O2' G a 900 " pdb=" O6 G a 916 " model vdw 2.331 3.040 nonbonded pdb=" OP1 U a 383 " pdb=" OG1 THR p 70 " model vdw 2.334 3.040 nonbonded pdb=" O ILE o 29 " pdb=" OG1 THR o 33 " model vdw 2.336 3.040 ... (remaining 326348 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=0.00 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: 1.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.030 Extract box with map and model: 0.520 Check model and map are aligned: 0.120 Set scattering table: 0.090 Process input model: 39.640 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.157 38419 Z= 0.412 Angle : 1.504 20.379 57451 Z= 0.640 Chirality : 0.119 0.540 7345 Planarity : 0.009 0.102 3085 Dihedral : 21.355 170.993 17961 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.29 % Allowed : 7.97 % Favored : 91.74 % Rotamer: Outliers : 2.16 % Allowed : 10.70 % Favored : 87.15 % 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: -5.26 (0.16), residues: 1380 helix: -4.32 (0.10), residues: 475 sheet: -2.84 (0.30), residues: 229 loop : -3.02 (0.19), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG l 127 TYR 0.032 0.004 TYR q 30 PHE 0.025 0.003 PHE e 31 TRP 0.047 0.005 TRP b 96 HIS 0.048 0.004 HIS k 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00828 / 0.41 (38419) covalent geometry : angle 1.50389 / 0.64 (57451) hydrogen bonds : bond 0.12081 / 6.38 ( 1305) hydrogen bonds : angle 5.69283 / 2.35 ( 2637) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 409 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 24 ASN cc_start: 0.8124 (t0) cc_final: 0.7921 (t0) REVERT: b 27 MET cc_start: 0.7285 (mmm) cc_final: 0.6707 (mmm) REVERT: b 59 GLN cc_start: 0.7837 (tp40) cc_final: 0.7536 (mm-40) REVERT: b 73 LYS cc_start: 0.7724 (tptt) cc_final: 0.7523 (tptm) REVERT: b 77 GLN cc_start: 0.7228 (pt0) cc_final: 0.6675 (pm20) REVERT: b 188 ASP cc_start: 0.5682 (m-30) cc_final: 0.4688 (t0) REVERT: e 32 ARG cc_start: 0.7392 (mtm180) cc_final: 0.7169 (mtm-85) REVERT: e 88 ARG cc_start: 0.8005 (mtt-85) cc_final: 0.7596 (mtt180) REVERT: f 5 GLU cc_start: 0.7090 (tt0) cc_final: 0.6744 (tt0) REVERT: f 70 ASN cc_start: 0.7400 (p0) cc_final: 0.7093 (p0) REVERT: f 74 ASP cc_start: 0.8072 (p0) cc_final: 0.7859 (p0) REVERT: f 79 LEU cc_start: 0.8108 (mm) cc_final: 0.7880 (mt) REVERT: h 21 ARG cc_start: 0.7846 (mmt-90) cc_final: 0.7592 (mpt180) REVERT: h 105 LEU cc_start: 0.9115 (OUTLIER) cc_final: 0.8817 (pp) REVERT: l 25 ASN cc_start: 0.8907 (p0) cc_final: 0.8623 (p0) REVERT: l 53 MET cc_start: 0.8684 (ptm) cc_final: 0.8447 (ptm) REVERT: l 60 SER cc_start: 0.7870 (t) cc_final: 0.7361 (t) REVERT: o 59 MET cc_start: 0.8020 (mtt) cc_final: 0.7783 (mtt) REVERT: p 62 ASN cc_start: 0.8065 (m-40) cc_final: 0.7736 (m110) REVERT: p 77 LYS cc_start: 0.8602 (mtmt) cc_final: 0.8371 (mtmt) REVERT: q 70 SER cc_start: 0.8910 (t) cc_final: 0.8507 (t) outliers start: 26 outliers final: 8 residues processed: 424 average time/residue: 0.2527 time to fit residues: 166.5871 Evaluate side-chains 330 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 321 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain r residue 76 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: [216, 98, 194, 227, 107, 10, 66, 247, 130, 124, 103] chunk 216 optimal weight: 4.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 9.9990 chunk 227 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 5.9990 chunk 247 optimal weight: 0.8980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 9.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 44 GLN b 66 GLN ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 159 GLN b 190 ASN ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 118 HIS ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 18 ASN h 22 HIS k 18 ASN k 77 HIS l 5 ASN l 6 GLN ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS p 46 ASN p 87 GLN t 42 ASN t 64 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.106991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.082509 restraints weight = 75127.793| |-----------------------------------------------------------------------------| r_work (start): 0.3137 rms_B_bonded: 0.89 r_work: 0.2970 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.072 38419 Z= 0.365 Angle : 1.492 24.973 57451 Z= 0.597 Chirality : 0.131 1.882 7345 Planarity : 0.006 0.074 3085 Dihedral : 18.888 178.691 15101 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 11.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 5.06 % Allowed : 18.74 % Favored : 76.20 % 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: -3.65 (0.19), residues: 1380 helix: -2.09 (0.19), residues: 483 sheet: -2.72 (0.30), residues: 240 loop : -2.47 (0.21), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG d 5 TYR 0.019 0.002 TYR p 40 PHE 0.034 0.002 PHE k 61 TRP 0.020 0.003 TRP k 44 HIS 0.013 0.002 HIS k 118 Details of bonding type rmsd/Z covalent geometry : bond 0.00731 / 0.37 (38419) covalent geometry : angle 1.49238 / 0.60 (57451) hydrogen bonds : bond 0.06881 / 3.64 ( 1305) hydrogen bonds : angle 3.92460 / 1.65 ( 2637) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 335 time to evaluate : 0.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 59 GLN cc_start: 0.7767 (tp40) cc_final: 0.7566 (mm-40) REVERT: b 77 GLN cc_start: 0.7140 (pt0) cc_final: 0.6588 (pm20) REVERT: b 151 ILE cc_start: 0.6788 (OUTLIER) cc_final: 0.6516 (pp) REVERT: d 47 TYR cc_start: 0.9146 (t80) cc_final: 0.8897 (t80) REVERT: d 119 ILE cc_start: 0.8491 (OUTLIER) cc_final: 0.8194 (pt) REVERT: d 149 ASN cc_start: 0.7219 (t0) cc_final: 0.6463 (t0) REVERT: f 5 GLU cc_start: 0.7859 (tt0) cc_final: 0.7586 (tt0) REVERT: f 74 ASP cc_start: 0.8213 (p0) cc_final: 0.7785 (p0) REVERT: f 79 LEU cc_start: 0.8319 (mm) cc_final: 0.7974 (mt) REVERT: h 22 HIS cc_start: 0.8832 (OUTLIER) cc_final: 0.8143 (m-70) REVERT: h 39 ILE cc_start: 0.9285 (mm) cc_final: 0.9051 (mt) REVERT: h 98 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8600 (mp) REVERT: k 24 ARG cc_start: 0.8136 (tpt-90) cc_final: 0.7837 (tpt-90) REVERT: k 65 MET cc_start: 0.7959 (OUTLIER) cc_final: 0.7560 (mmp) REVERT: k 125 LYS cc_start: 0.8242 (tmmt) cc_final: 0.7682 (tptm) REVERT: l 60 SER cc_start: 0.8299 (t) cc_final: 0.7971 (p) REVERT: o 64 ARG cc_start: 0.8190 (tpm170) cc_final: 0.7927 (tpm170) REVERT: p 21 VAL cc_start: 0.9398 (OUTLIER) cc_final: 0.9165 (m) REVERT: p 62 ASN cc_start: 0.8340 (m-40) cc_final: 0.8006 (m110) REVERT: q 70 SER cc_start: 0.9194 (t) cc_final: 0.8985 (t) REVERT: r 27 ASP cc_start: 0.8448 (OUTLIER) cc_final: 0.7743 (t0) outliers start: 61 outliers final: 43 residues processed: 370 average time/residue: 0.2313 time to fit residues: 135.6888 Evaluate side-chains 370 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 320 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 61 LYS Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 12 THR Chi-restraints excluded: chain h residue 22 HIS Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 90 HIS Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain l residue 132 THR Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 76 SER Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 26 ILE Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 40 SER Chi-restraints excluded: chain t residue 57 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: [142, 216, 26, 4, 37, 127, 81, 154, 96, 48, 208] chunk 142 optimal weight: 6.9990 chunk 216 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 127 optimal weight: 0.9980 chunk 81 optimal weight: 5.9990 chunk 154 optimal weight: 0.8980 chunk 96 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 208 optimal weight: 3.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 67 GLN d 109 GLN ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 37 ASN p 87 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.109178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.085182 restraints weight = 74987.757| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 0.90 r_work: 0.3023 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 38419 Z= 0.248 Angle : 1.194 18.761 57451 Z= 0.486 Chirality : 0.102 1.588 7345 Planarity : 0.005 0.078 3085 Dihedral : 18.986 174.493 15101 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 5.97 % Allowed : 19.65 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.74 (0.21), residues: 1380 helix: -0.94 (0.22), residues: 486 sheet: -2.53 (0.30), residues: 237 loop : -2.17 (0.22), residues: 657 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG q 39 TYR 0.018 0.002 TYR q 30 PHE 0.025 0.002 PHE k 61 TRP 0.015 0.002 TRP k 44 HIS 0.023 0.002 HIS h 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00502 / 0.25 (38419) covalent geometry : angle 1.19417 / 0.49 (57451) hydrogen bonds : bond 0.06013 / 3.21 ( 1305) hydrogen bonds : angle 3.59878 / 1.52 ( 2637) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 327 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 59 GLN cc_start: 0.7989 (tp40) cc_final: 0.7682 (mm-40) REVERT: b 73 LYS cc_start: 0.7478 (tptt) cc_final: 0.7247 (ttpt) REVERT: b 77 GLN cc_start: 0.7106 (pt0) cc_final: 0.6645 (pm20) REVERT: b 151 ILE cc_start: 0.6867 (OUTLIER) cc_final: 0.6651 (pp) REVERT: d 47 TYR cc_start: 0.9116 (t80) cc_final: 0.8895 (t80) REVERT: d 119 ILE cc_start: 0.8606 (OUTLIER) cc_final: 0.8319 (pt) REVERT: f 2 ARG cc_start: 0.8076 (mtt-85) cc_final: 0.7807 (mtt-85) REVERT: f 60 TYR cc_start: 0.8606 (m-80) cc_final: 0.8238 (m-80) REVERT: f 78 ARG cc_start: 0.8610 (tmm-80) cc_final: 0.8279 (tmm-80) REVERT: f 79 LEU cc_start: 0.8411 (mm) cc_final: 0.8136 (mt) REVERT: h 39 ILE cc_start: 0.9229 (mm) cc_final: 0.8977 (mt) REVERT: h 61 ARG cc_start: 0.8542 (ttm110) cc_final: 0.8255 (ttm170) REVERT: k 24 ARG cc_start: 0.8154 (tpt-90) cc_final: 0.7802 (tpt-90) REVERT: k 65 MET cc_start: 0.7958 (OUTLIER) cc_final: 0.7562 (mmt) REVERT: k 125 LYS cc_start: 0.8203 (tmmt) cc_final: 0.7659 (tptm) REVERT: l 60 SER cc_start: 0.8136 (t) cc_final: 0.7645 (p) REVERT: o 26 GLU cc_start: 0.8642 (mp0) cc_final: 0.8374 (mp0) REVERT: p 21 VAL cc_start: 0.9410 (OUTLIER) cc_final: 0.9191 (m) REVERT: p 50 ILE cc_start: 0.8802 (OUTLIER) cc_final: 0.8546 (pt) REVERT: p 62 ASN cc_start: 0.8239 (m-40) cc_final: 0.7900 (m110) REVERT: p 88 LYS cc_start: 0.8286 (ttmm) cc_final: 0.7923 (ttpp) REVERT: q 70 SER cc_start: 0.9110 (t) cc_final: 0.8762 (t) REVERT: r 27 ASP cc_start: 0.8270 (OUTLIER) cc_final: 0.7564 (t70) REVERT: r 70 MET cc_start: 0.8091 (mmp) cc_final: 0.7882 (mmp) outliers start: 72 outliers final: 48 residues processed: 373 average time/residue: 0.2298 time to fit residues: 135.9510 Evaluate side-chains 374 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 320 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 50 ILE Chi-restraints excluded: chain p residue 53 ASP Chi-restraints excluded: chain p residue 76 SER Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 39 ARG Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 32 VAL Chi-restraints excluded: chain t residue 57 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: [31, 38, 129, 138, 180, 18, 173, 88, 106, 14, 4] chunk 31 optimal weight: 6.9990 chunk 38 optimal weight: 5.9990 chunk 129 optimal weight: 0.7980 chunk 138 optimal weight: 3.9990 chunk 180 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 173 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 149 ASN ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 87 GLN t 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.108348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.083860 restraints weight = 74829.136| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 0.96 r_work: 0.3013 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2910 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2910 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 38419 Z= 0.275 Angle : 1.175 17.525 57451 Z= 0.479 Chirality : 0.099 1.580 7345 Planarity : 0.005 0.060 3085 Dihedral : 18.874 175.859 15101 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.62 % Favored : 91.38 % Rotamer: Outliers : 6.22 % Allowed : 20.81 % Favored : 72.97 % 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: -2.37 (0.22), residues: 1380 helix: -0.48 (0.23), residues: 484 sheet: -2.41 (0.30), residues: 250 loop : -2.03 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG d 5 TYR 0.018 0.002 TYR f 60 PHE 0.028 0.002 PHE r 18 TRP 0.010 0.002 TRP k 44 HIS 0.013 0.002 HIS o 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00561 / 0.28 (38419) covalent geometry : angle 1.17484 / 0.48 (57451) hydrogen bonds : bond 0.06028 / 3.23 ( 1305) hydrogen bonds : angle 3.50085 / 1.48 ( 2637) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 321 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 59 GLN cc_start: 0.7908 (tp40) cc_final: 0.7629 (mm-40) REVERT: b 77 GLN cc_start: 0.7088 (pt0) cc_final: 0.6737 (pm20) REVERT: b 151 ILE cc_start: 0.6742 (OUTLIER) cc_final: 0.6474 (pp) REVERT: d 47 TYR cc_start: 0.9122 (t80) cc_final: 0.8886 (t80) REVERT: d 119 ILE cc_start: 0.8653 (OUTLIER) cc_final: 0.8360 (pt) REVERT: f 74 ASP cc_start: 0.8394 (p0) cc_final: 0.7860 (p0) REVERT: f 79 LEU cc_start: 0.8419 (mm) cc_final: 0.8137 (mt) REVERT: h 39 ILE cc_start: 0.9239 (mm) cc_final: 0.9001 (mt) REVERT: h 98 LEU cc_start: 0.8969 (OUTLIER) cc_final: 0.8565 (mp) REVERT: k 24 ARG cc_start: 0.8149 (tpt-90) cc_final: 0.7921 (tpt-90) REVERT: k 65 MET cc_start: 0.7952 (OUTLIER) cc_final: 0.7534 (mmt) REVERT: k 125 LYS cc_start: 0.8400 (tmmt) cc_final: 0.7810 (tptm) REVERT: l 60 SER cc_start: 0.8225 (t) cc_final: 0.7715 (p) REVERT: o 26 GLU cc_start: 0.8586 (mp0) cc_final: 0.8305 (mp0) REVERT: o 64 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7680 (tmm-80) REVERT: p 50 ILE cc_start: 0.8710 (OUTLIER) cc_final: 0.8387 (pt) REVERT: p 62 ASN cc_start: 0.8101 (m-40) cc_final: 0.7621 (m110) REVERT: q 70 SER cc_start: 0.9116 (t) cc_final: 0.8727 (t) REVERT: r 27 ASP cc_start: 0.8190 (OUTLIER) cc_final: 0.7551 (t70) REVERT: r 73 LEU cc_start: 0.9145 (mt) cc_final: 0.8933 (mt) outliers start: 75 outliers final: 58 residues processed: 365 average time/residue: 0.2267 time to fit residues: 131.6006 Evaluate side-chains 375 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 310 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain d residue 31 TYR Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 74 ILE Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain o residue 64 ARG Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 50 ILE Chi-restraints excluded: chain p residue 76 SER Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 25 HIS Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 38 ILE Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 32 VAL Chi-restraints excluded: chain t residue 40 SER Chi-restraints excluded: chain t residue 56 LEU Chi-restraints excluded: chain t residue 57 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: [223, 228, 166, 176, 36, 192, 77, 86, 246, 149, 208] chunk 223 optimal weight: 0.9980 chunk 228 optimal weight: 0.8980 chunk 166 optimal weight: 5.9990 chunk 176 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 192 optimal weight: 0.0570 chunk 77 optimal weight: 5.9990 chunk 86 optimal weight: 4.9990 chunk 246 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 208 optimal weight: 0.6980 overall best weight: 1.1300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 146 GLN ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 87 GLN t 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.110280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.085597 restraints weight = 74630.456| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 0.87 r_work: 0.3054 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 38419 Z= 0.186 Angle : 1.127 16.824 57451 Z= 0.459 Chirality : 0.094 1.374 7345 Planarity : 0.005 0.057 3085 Dihedral : 18.924 177.232 15101 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 5.97 % Allowed : 21.97 % Favored : 72.06 % 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: -2.12 (0.22), residues: 1380 helix: -0.19 (0.23), residues: 485 sheet: -2.40 (0.31), residues: 237 loop : -1.92 (0.23), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG r 47 TYR 0.027 0.002 TYR d 197 PHE 0.032 0.002 PHE r 18 TRP 0.011 0.002 TRP d 9 HIS 0.012 0.001 HIS o 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.19 (38419) covalent geometry : angle 1.12679 / 0.46 (57451) hydrogen bonds : bond 0.05890 / 3.16 ( 1305) hydrogen bonds : angle 3.45921 / 1.46 ( 2637) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 395 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 323 time to evaluate : 0.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 28 LYS cc_start: 0.8033 (ptmt) cc_final: 0.7547 (tptm) REVERT: b 59 GLN cc_start: 0.7891 (tp40) cc_final: 0.7608 (mm-40) REVERT: b 73 LYS cc_start: 0.7148 (ttpt) cc_final: 0.6503 (tptm) REVERT: b 77 GLN cc_start: 0.7044 (pt0) cc_final: 0.6683 (pm20) REVERT: b 151 ILE cc_start: 0.6859 (OUTLIER) cc_final: 0.6630 (pp) REVERT: d 119 ILE cc_start: 0.8630 (OUTLIER) cc_final: 0.8356 (pt) REVERT: d 198 TYR cc_start: 0.8966 (m-80) cc_final: 0.8681 (m-80) REVERT: e 41 ASP cc_start: 0.8162 (p0) cc_final: 0.7931 (p0) REVERT: f 1 MET cc_start: 0.6941 (tpp) cc_final: 0.6686 (tpt) REVERT: f 74 ASP cc_start: 0.8261 (p0) cc_final: 0.7891 (p0) REVERT: f 79 LEU cc_start: 0.8430 (OUTLIER) cc_final: 0.8224 (mt) REVERT: h 39 ILE cc_start: 0.9207 (mm) cc_final: 0.8976 (mt) REVERT: h 98 LEU cc_start: 0.8942 (OUTLIER) cc_final: 0.8547 (mp) REVERT: k 24 ARG cc_start: 0.8113 (tpt-90) cc_final: 0.7875 (tpt-90) REVERT: k 65 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7495 (mmt) REVERT: k 125 LYS cc_start: 0.8369 (tmmt) cc_final: 0.7787 (tptm) REVERT: l 60 SER cc_start: 0.8214 (t) cc_final: 0.7724 (p) REVERT: l 103 LEU cc_start: 0.9034 (mp) cc_final: 0.8823 (mp) REVERT: p 21 VAL cc_start: 0.9399 (OUTLIER) cc_final: 0.9160 (m) REVERT: p 50 ILE cc_start: 0.8704 (OUTLIER) cc_final: 0.8424 (pt) REVERT: p 62 ASN cc_start: 0.8180 (m-40) cc_final: 0.7711 (m110) REVERT: p 89 LYS cc_start: 0.8323 (mtmm) cc_final: 0.8104 (ttpp) REVERT: q 70 SER cc_start: 0.9069 (t) cc_final: 0.8639 (t) REVERT: r 27 ASP cc_start: 0.8097 (OUTLIER) cc_final: 0.7475 (t70) REVERT: r 73 LEU cc_start: 0.9120 (mt) cc_final: 0.8906 (mt) outliers start: 72 outliers final: 44 residues processed: 368 average time/residue: 0.2316 time to fit residues: 135.2448 Evaluate side-chains 357 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 305 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 146 GLN Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 109 HIS Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 50 ILE Chi-restraints excluded: chain p residue 76 SER Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 25 HIS Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 57 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: [97, 243, 167, 106, 15, 17, 10, 148, 44, 56, 110] chunk 97 optimal weight: 7.9990 chunk 243 optimal weight: 4.9990 chunk 167 optimal weight: 3.9990 chunk 106 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 10 optimal weight: 20.0000 chunk 148 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 110 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 35 GLN ** d 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 112 GLN h 122 ASN k 40 ASN ** k 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS p 73 ASN p 87 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.103693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.086852 restraints weight = 75208.830| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 1.43 r_work: 0.2805 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.067 38419 Z= 0.503 Angle : 1.385 20.350 57451 Z= 0.564 Chirality : 0.117 1.967 7345 Planarity : 0.006 0.069 3085 Dihedral : 18.925 176.255 15101 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 12.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.07 % Favored : 89.93 % Rotamer: Outliers : 7.46 % Allowed : 21.48 % Favored : 71.06 % 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: -2.31 (0.22), residues: 1380 helix: -0.41 (0.22), residues: 489 sheet: -2.26 (0.31), residues: 245 loop : -2.09 (0.23), residues: 646 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG d 5 TYR 0.028 0.003 TYR d 47 PHE 0.020 0.003 PHE l 28 TRP 0.013 0.003 TRP d 9 HIS 0.014 0.002 HIS o 51 Details of bonding type rmsd/Z covalent geometry : bond 0.01029 / 0.50 (38419) covalent geometry : angle 1.38517 / 0.56 (57451) hydrogen bonds : bond 0.07187 / 3.88 ( 1305) hydrogen bonds : angle 3.70736 / 1.56 ( 2637) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 386 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 296 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: b 28 LYS cc_start: 0.8051 (ptmt) cc_final: 0.7546 (tptm) REVERT: b 59 GLN cc_start: 0.7989 (tp40) cc_final: 0.7693 (mm-40) REVERT: b 77 GLN cc_start: 0.7067 (pt0) cc_final: 0.6467 (pm20) REVERT: b 151 ILE cc_start: 0.6890 (OUTLIER) cc_final: 0.6642 (pp) REVERT: d 119 ILE cc_start: 0.8736 (OUTLIER) cc_final: 0.8413 (pt) REVERT: d 120 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8627 (mt) REVERT: d 198 TYR cc_start: 0.9066 (m-80) cc_final: 0.8841 (m-80) REVERT: f 1 MET cc_start: 0.6934 (tpp) cc_final: 0.6720 (tpt) REVERT: f 74 ASP cc_start: 0.8563 (p0) cc_final: 0.7987 (p0) REVERT: f 79 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8262 (mt) REVERT: h 39 ILE cc_start: 0.9310 (mm) cc_final: 0.9060 (mt) REVERT: h 72 ARG cc_start: 0.8992 (OUTLIER) cc_final: 0.8652 (mtt90) REVERT: h 98 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8552 (mp) REVERT: k 24 ARG cc_start: 0.8184 (tpt-90) cc_final: 0.7881 (tpt-90) REVERT: k 65 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.7563 (mmt) REVERT: k 76 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.7726 (pp20) REVERT: k 77 HIS cc_start: 0.7573 (m-70) cc_final: 0.7201 (m-70) REVERT: k 125 LYS cc_start: 0.8503 (tmmt) cc_final: 0.7827 (tptm) REVERT: l 60 SER cc_start: 0.8316 (t) cc_final: 0.7981 (t) REVERT: l 75 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.8065 (mp0) REVERT: p 62 ASN cc_start: 0.8284 (m-40) cc_final: 0.7772 (m110) REVERT: q 4 ARG cc_start: 0.6963 (tpm170) cc_final: 0.6750 (tpm170) REVERT: r 27 ASP cc_start: 0.8332 (OUTLIER) cc_final: 0.7681 (t70) outliers start: 90 outliers final: 69 residues processed: 351 average time/residue: 0.2337 time to fit residues: 129.6433 Evaluate side-chains 374 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 295 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 6 MET Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 31 TYR Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 112 GLN Chi-restraints excluded: chain d residue 119 ILE Chi-restraints excluded: chain d residue 120 LEU Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 168 ASP Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 61 ASN Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain f residue 86 ILE Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 27 LEU Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 72 ARG Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 76 GLU Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 74 ILE Chi-restraints excluded: chain l residue 75 GLU Chi-restraints excluded: chain l residue 90 HIS Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain o residue 12 ILE Chi-restraints excluded: chain o residue 13 LYS Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain p residue 12 SER Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 39 THR Chi-restraints excluded: chain p residue 76 SER Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 25 HIS Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 31 THR Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 39 VAL Chi-restraints excluded: chain t residue 40 SER Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 56 LEU Chi-restraints excluded: chain t residue 57 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: [100, 221, 120, 165, 207, 155, 9, 87, 123, 131, 133] chunk 100 optimal weight: 10.0000 chunk 221 optimal weight: 5.9990 chunk 120 optimal weight: 4.9990 chunk 165 optimal weight: 5.9990 chunk 207 optimal weight: 0.2980 chunk 155 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 123 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 chunk 133 optimal weight: 0.9980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 73 ASN p 87 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.110919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.087911 restraints weight = 74798.105| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 0.79 r_work: 0.3075 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 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 : 0.004 0.052 38419 Z= 0.190 Angle : 1.107 15.975 57451 Z= 0.450 Chirality : 0.091 1.264 7345 Planarity : 0.004 0.069 3085 Dihedral : 19.039 179.527 15101 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.39 % Favored : 92.61 % Rotamer: Outliers : 5.14 % Allowed : 24.63 % Favored : 70.23 % 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: -1.86 (0.22), residues: 1380 helix: 0.08 (0.23), residues: 484 sheet: -2.27 (0.32), residues: 230 loop : -1.82 (0.23), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG d 111 TYR 0.021 0.002 TYR d 47 PHE 0.021 0.002 PHE f 59 TRP 0.012 0.002 TRP d 9 HIS 0.013 0.002 HIS o 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.19 (38419) covalent geometry : angle 1.10652 / 0.45 (57451) hydrogen bonds : bond 0.05843 / 3.13 ( 1305) hydrogen bonds : angle 3.44163 / 1.46 ( 2637) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 334 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 28 LYS cc_start: 0.8046 (ptmt) cc_final: 0.7564 (tptm) REVERT: b 59 GLN cc_start: 0.8101 (tp40) cc_final: 0.7818 (mm-40) REVERT: b 77 GLN cc_start: 0.6844 (pt0) cc_final: 0.6518 (pm20) REVERT: b 151 ILE cc_start: 0.6870 (OUTLIER) cc_final: 0.6648 (pp) REVERT: f 74 ASP cc_start: 0.8390 (p0) cc_final: 0.7607 (p0) REVERT: f 78 ARG cc_start: 0.8569 (tmm-80) cc_final: 0.8332 (tmm-80) REVERT: f 79 LEU cc_start: 0.8411 (OUTLIER) cc_final: 0.8106 (mt) REVERT: h 39 ILE cc_start: 0.9226 (mm) cc_final: 0.8994 (mt) REVERT: h 61 ARG cc_start: 0.8554 (ttm110) cc_final: 0.8197 (ttm170) REVERT: h 98 LEU cc_start: 0.8894 (OUTLIER) cc_final: 0.8559 (mp) REVERT: k 65 MET cc_start: 0.7747 (OUTLIER) cc_final: 0.7325 (mmt) REVERT: k 76 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7669 (pp20) REVERT: k 77 HIS cc_start: 0.7702 (m-70) cc_final: 0.7336 (m-70) REVERT: k 125 LYS cc_start: 0.8425 (tmmt) cc_final: 0.7810 (tptm) REVERT: p 21 VAL cc_start: 0.9370 (OUTLIER) cc_final: 0.9170 (m) REVERT: p 62 ASN cc_start: 0.8096 (m-40) cc_final: 0.7657 (m110) REVERT: p 89 LYS cc_start: 0.8580 (ttpp) cc_final: 0.8306 (ttpp) REVERT: q 4 ARG cc_start: 0.6811 (tpm170) cc_final: 0.6595 (tpm170) REVERT: q 70 SER cc_start: 0.9048 (t) cc_final: 0.8603 (t) REVERT: r 27 ASP cc_start: 0.7968 (OUTLIER) cc_final: 0.7447 (t70) REVERT: r 73 LEU cc_start: 0.9169 (mt) cc_final: 0.8924 (mt) REVERT: t 15 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7608 (tm-30) outliers start: 62 outliers final: 47 residues processed: 372 average time/residue: 0.2321 time to fit residues: 136.8275 Evaluate side-chains 365 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 311 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 160 THR Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 76 GLU Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 76 SER Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 56 LEU Chi-restraints excluded: chain t residue 57 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: [225, 42, 106, 2, 17, 216, 215, 213, 111, 160, 238] chunk 225 optimal weight: 8.9990 chunk 42 optimal weight: 4.9990 chunk 106 optimal weight: 10.0000 chunk 2 optimal weight: 30.0000 chunk 17 optimal weight: 8.9990 chunk 216 optimal weight: 4.9990 chunk 215 optimal weight: 0.4980 chunk 213 optimal weight: 3.9990 chunk 111 optimal weight: 9.9990 chunk 160 optimal weight: 2.9990 chunk 238 optimal weight: 0.7980 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 112 GLN ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 77 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 87 GLN r 57 GLN t 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.108211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.084044 restraints weight = 74711.326| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 0.93 r_work: 0.3023 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 38419 Z= 0.278 Angle : 1.150 16.855 57451 Z= 0.468 Chirality : 0.096 1.435 7345 Planarity : 0.005 0.068 3085 Dihedral : 18.953 179.454 15101 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.71 % Favored : 90.29 % Rotamer: Outliers : 5.97 % Allowed : 23.80 % Favored : 70.23 % 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: -1.80 (0.22), residues: 1380 helix: 0.17 (0.24), residues: 482 sheet: -2.24 (0.32), residues: 235 loop : -1.79 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG k 93 TYR 0.023 0.002 TYR d 197 PHE 0.018 0.002 PHE f 59 TRP 0.010 0.002 TRP d 9 HIS 0.013 0.002 HIS o 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00568 / 0.28 (38419) covalent geometry : angle 1.14968 / 0.47 (57451) hydrogen bonds : bond 0.05934 / 3.20 ( 1305) hydrogen bonds : angle 3.49816 / 1.47 ( 2637) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 305 time to evaluate : 0.765 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 151 ILE cc_start: 0.6926 (OUTLIER) cc_final: 0.6694 (pp) REVERT: f 78 ARG cc_start: 0.8575 (tmm-80) cc_final: 0.8373 (tmm-80) REVERT: f 79 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8057 (mt) REVERT: h 39 ILE cc_start: 0.9254 (mm) cc_final: 0.9002 (mt) REVERT: h 61 ARG cc_start: 0.8563 (ttm110) cc_final: 0.8167 (ttm170) REVERT: h 98 LEU cc_start: 0.8935 (OUTLIER) cc_final: 0.8569 (mp) REVERT: k 65 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7392 (mmt) REVERT: k 76 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7650 (pp20) REVERT: k 125 LYS cc_start: 0.8443 (tmmt) cc_final: 0.7790 (tptm) REVERT: p 62 ASN cc_start: 0.8158 (m-40) cc_final: 0.7610 (m110) REVERT: q 70 SER cc_start: 0.9090 (t) cc_final: 0.8698 (t) REVERT: r 27 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7469 (t70) outliers start: 72 outliers final: 58 residues processed: 351 average time/residue: 0.2340 time to fit residues: 130.5812 Evaluate side-chains 361 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 297 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 31 TYR Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 112 GLN Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 34 THR Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 115 LEU Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 160 THR Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain h residue 127 ILE Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 76 GLU Chi-restraints excluded: chain k residue 86 VAL Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 74 ILE Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain o residue 13 LYS Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 76 SER Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 31 THR Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 40 SER Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 56 LEU Chi-restraints excluded: chain t residue 57 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: [234, 119, 231, 139, 4, 143, 163, 146, 237, 186, 111] chunk 234 optimal weight: 7.9990 chunk 119 optimal weight: 5.9990 chunk 231 optimal weight: 0.8980 chunk 139 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 143 optimal weight: 3.9990 chunk 163 optimal weight: 0.6980 chunk 146 optimal weight: 1.9990 chunk 237 optimal weight: 0.9980 chunk 186 optimal weight: 9.9990 chunk 111 optimal weight: 8.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 112 GLN d 146 GLN k 77 HIS ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS p 87 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.109212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.085290 restraints weight = 74622.931| |-----------------------------------------------------------------------------| r_work (start): 0.3198 rms_B_bonded: 0.96 r_work: 0.3040 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2939 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2939 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 38419 Z= 0.219 Angle : 1.124 16.269 57451 Z= 0.458 Chirality : 0.093 1.320 7345 Planarity : 0.005 0.064 3085 Dihedral : 18.988 179.361 15101 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.84 % Favored : 91.16 % Rotamer: Outliers : 5.31 % Allowed : 24.46 % Favored : 70.23 % 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: -1.73 (0.22), residues: 1380 helix: 0.25 (0.24), residues: 482 sheet: -2.22 (0.32), residues: 233 loop : -1.77 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG k 93 TYR 0.023 0.002 TYR r 75 PHE 0.018 0.002 PHE d 79 TRP 0.010 0.002 TRP d 9 HIS 0.013 0.002 HIS o 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.22 (38419) covalent geometry : angle 1.12424 / 0.46 (57451) hydrogen bonds : bond 0.05876 / 3.16 ( 1305) hydrogen bonds : angle 3.48771 / 1.47 ( 2637) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 316 time to evaluate : 0.732 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 151 ILE cc_start: 0.6921 (OUTLIER) cc_final: 0.6701 (pp) REVERT: f 66 LYS cc_start: 0.8263 (tptt) cc_final: 0.8013 (tptt) REVERT: f 74 ASP cc_start: 0.8392 (p0) cc_final: 0.7839 (p0) REVERT: f 79 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8163 (mt) REVERT: h 39 ILE cc_start: 0.9230 (mm) cc_final: 0.8987 (mt) REVERT: h 61 ARG cc_start: 0.8557 (ttm110) cc_final: 0.8170 (ttm170) REVERT: h 98 LEU cc_start: 0.8941 (OUTLIER) cc_final: 0.8564 (mp) REVERT: k 65 MET cc_start: 0.7837 (OUTLIER) cc_final: 0.7390 (mmt) REVERT: k 76 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7628 (pp20) REVERT: k 125 LYS cc_start: 0.8429 (tmmt) cc_final: 0.7784 (tptm) REVERT: l 75 GLU cc_start: 0.8280 (OUTLIER) cc_final: 0.7882 (mp0) REVERT: p 21 VAL cc_start: 0.9413 (OUTLIER) cc_final: 0.9144 (m) REVERT: p 62 ASN cc_start: 0.8170 (m-40) cc_final: 0.7619 (m110) REVERT: q 70 SER cc_start: 0.9048 (t) cc_final: 0.8706 (t) REVERT: r 27 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7393 (t70) REVERT: r 72 LEU cc_start: 0.9310 (mp) cc_final: 0.9099 (mp) outliers start: 64 outliers final: 51 residues processed: 355 average time/residue: 0.2273 time to fit residues: 129.1982 Evaluate side-chains 366 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 307 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 112 GLN Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 146 GLN Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 76 GLU Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 75 GLU Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 50 HIS Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 76 SER Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 40 SER Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 56 LEU Chi-restraints excluded: chain t residue 57 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: [88, 242, 19, 8, 170, 90, 132, 49, 57, 144, 151] chunk 88 optimal weight: 6.9990 chunk 242 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 8 optimal weight: 5.9990 chunk 170 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 132 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 144 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 119 ASN ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 87 GLN q 5 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.109753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.086235 restraints weight = 74906.807| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 0.97 r_work: 0.3050 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2947 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.3454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 38419 Z= 0.219 Angle : 1.111 15.938 57451 Z= 0.453 Chirality : 0.091 1.212 7345 Planarity : 0.005 0.077 3085 Dihedral : 18.985 179.192 15101 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.06 % Favored : 90.94 % Rotamer: Outliers : 5.22 % Allowed : 24.63 % Favored : 70.15 % 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: -1.66 (0.22), residues: 1380 helix: 0.33 (0.24), residues: 482 sheet: -2.21 (0.31), residues: 233 loop : -1.74 (0.24), residues: 665 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG d 200 TYR 0.023 0.002 TYR r 75 PHE 0.018 0.002 PHE d 79 TRP 0.010 0.002 TRP d 9 HIS 0.012 0.002 HIS o 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.22 (38419) covalent geometry : angle 1.11118 / 0.45 (57451) hydrogen bonds : bond 0.05821 / 3.13 ( 1305) hydrogen bonds : angle 3.46832 / 1.46 ( 2637) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2760 Ramachandran restraints generated. 1380 Oldfield, 0 Emsley, 1380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 313 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: b 151 ILE cc_start: 0.6929 (OUTLIER) cc_final: 0.6719 (pp) REVERT: b 154 MET cc_start: 0.5907 (tpt) cc_final: 0.5687 (tpt) REVERT: f 2 ARG cc_start: 0.7679 (mtt-85) cc_final: 0.7153 (mtt180) REVERT: f 74 ASP cc_start: 0.8407 (p0) cc_final: 0.7858 (p0) REVERT: f 79 LEU cc_start: 0.8370 (OUTLIER) cc_final: 0.8101 (mt) REVERT: h 39 ILE cc_start: 0.9236 (mm) cc_final: 0.8992 (mt) REVERT: h 61 ARG cc_start: 0.8558 (ttm110) cc_final: 0.8182 (ttm170) REVERT: h 98 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8580 (mp) REVERT: k 65 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7364 (mmt) REVERT: k 76 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7630 (pp20) REVERT: k 125 LYS cc_start: 0.8415 (tmmt) cc_final: 0.7788 (tptm) REVERT: l 75 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7890 (mp0) REVERT: l 103 LEU cc_start: 0.9154 (mp) cc_final: 0.8933 (mp) REVERT: p 21 VAL cc_start: 0.9410 (OUTLIER) cc_final: 0.9154 (m) REVERT: p 62 ASN cc_start: 0.8140 (m-40) cc_final: 0.7591 (m110) REVERT: p 78 GLU cc_start: 0.8020 (mm-30) cc_final: 0.7809 (mm-30) REVERT: q 70 SER cc_start: 0.9082 (t) cc_final: 0.8736 (t) REVERT: r 27 ASP cc_start: 0.7891 (OUTLIER) cc_final: 0.7272 (t70) outliers start: 63 outliers final: 52 residues processed: 352 average time/residue: 0.2307 time to fit residues: 129.9098 Evaluate side-chains 371 residues out of total 1206 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 311 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain b residue 97 LEU Chi-restraints excluded: chain b residue 151 ILE Chi-restraints excluded: chain b residue 184 VAL Chi-restraints excluded: chain b residue 190 ASN Chi-restraints excluded: chain b residue 221 ILE Chi-restraints excluded: chain d residue 19 LEU Chi-restraints excluded: chain d residue 64 THR Chi-restraints excluded: chain d residue 141 VAL Chi-restraints excluded: chain d residue 155 VAL Chi-restraints excluded: chain e residue 25 VAL Chi-restraints excluded: chain e residue 31 PHE Chi-restraints excluded: chain e residue 39 VAL Chi-restraints excluded: chain e residue 77 VAL Chi-restraints excluded: chain e residue 111 VAL Chi-restraints excluded: chain e residue 117 LEU Chi-restraints excluded: chain e residue 161 VAL Chi-restraints excluded: chain e residue 164 LEU Chi-restraints excluded: chain f residue 6 VAL Chi-restraints excluded: chain f residue 10 VAL Chi-restraints excluded: chain f residue 20 LYS Chi-restraints excluded: chain f residue 79 LEU Chi-restraints excluded: chain h residue 2 THR Chi-restraints excluded: chain h residue 25 LEU Chi-restraints excluded: chain h residue 42 SER Chi-restraints excluded: chain h residue 49 VAL Chi-restraints excluded: chain h residue 59 VAL Chi-restraints excluded: chain h residue 75 THR Chi-restraints excluded: chain h residue 97 VAL Chi-restraints excluded: chain h residue 98 LEU Chi-restraints excluded: chain h residue 105 LEU Chi-restraints excluded: chain k residue 26 THR Chi-restraints excluded: chain k residue 34 ILE Chi-restraints excluded: chain k residue 65 MET Chi-restraints excluded: chain k residue 76 GLU Chi-restraints excluded: chain k residue 85 THR Chi-restraints excluded: chain l residue 30 SER Chi-restraints excluded: chain l residue 50 VAL Chi-restraints excluded: chain l residue 68 VAL Chi-restraints excluded: chain l residue 75 GLU Chi-restraints excluded: chain l residue 92 VAL Chi-restraints excluded: chain l residue 111 VAL Chi-restraints excluded: chain l residue 130 TYR Chi-restraints excluded: chain o residue 45 THR Chi-restraints excluded: chain o residue 74 ASP Chi-restraints excluded: chain p residue 21 VAL Chi-restraints excluded: chain p residue 22 VAL Chi-restraints excluded: chain p residue 76 SER Chi-restraints excluded: chain q residue 30 TYR Chi-restraints excluded: chain q residue 32 THR Chi-restraints excluded: chain q residue 40 VAL Chi-restraints excluded: chain q residue 59 ASP Chi-restraints excluded: chain r residue 15 VAL Chi-restraints excluded: chain r residue 27 ASP Chi-restraints excluded: chain r residue 76 VAL Chi-restraints excluded: chain t residue 4 ILE Chi-restraints excluded: chain t residue 37 THR Chi-restraints excluded: chain t residue 40 SER Chi-restraints excluded: chain t residue 49 LEU Chi-restraints excluded: chain t residue 56 LEU Chi-restraints excluded: chain t residue 57 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 248 random chunks: [61, 29, 27, 127, 47, 207, 13, 63, 84, 185, 96] chunk 61 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 27 optimal weight: 6.9990 chunk 127 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 185 optimal weight: 10.0000 chunk 96 optimal weight: 8.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** b 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 112 GLN d 146 GLN h 122 ASN ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 50 HIS p 73 ASN p 87 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.104460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.086962 restraints weight = 75203.656| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.50 r_work: 0.2828 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.3462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.080 38419 Z= 0.460 Angle : 1.327 19.779 57451 Z= 0.540 Chirality : 0.109 1.448 7345 Planarity : 0.006 0.076 3085 Dihedral : 19.034 179.636 15101 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 6.22 % Allowed : 23.80 % Favored : 69.98 % 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: -2.00 (0.22), residues: 1380 helix: -0.04 (0.23), residues: 486 sheet: -2.30 (0.30), residues: 244 loop : -1.90 (0.24), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG q 39 TYR 0.032 0.003 TYR r 75 PHE 0.019 0.003 PHE e 95 TRP 0.012 0.003 TRP d 9 HIS 0.015 0.002 HIS o 51 Details of bonding type rmsd/Z covalent geometry : bond 0.00943 / 0.46 (38419) covalent geometry : angle 1.32716 / 0.54 (57451) hydrogen bonds : bond 0.06916 / 3.73 ( 1305) hydrogen bonds : angle 3.69662 / 1.55 ( 2637) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8869.94 seconds wall clock time: 152 minutes 35.96 seconds (9155.96 seconds total)