Starting phenix.real_space_refine on Thu Aug 6 14:22:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8evh_28629/08_2026/8evh_28629.cif Found real_map, /net/cci-nas-00/data/ceres_data/8evh_28629/08_2026/8evh_28629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8evh_28629/08_2026/8evh_28629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8evh_28629/08_2026/8evh_28629.map" model { file = "/net/cci-nas-00/data/ceres_data/8evh_28629/08_2026/8evh_28629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8evh_28629/08_2026/8evh_28629.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 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 282 5.49 5 S 35 5.16 5 C 9256 2.51 5 N 2913 2.21 5 O 3591 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16077 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2889 Classifications: {'DNA': 141} Link IDs: {'rna3p': 140} Chain breaks: 1 Chain: "J" Number of atoms: 2892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2892 Classifications: {'DNA': 141} Link IDs: {'rna3p': 140} Chain: "M" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "N" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "O" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 746 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Time building chain proxies: 2.66, per 1000 atoms: 0.17 Number of scatterers: 16077 At special positions: 0 Unit cell: (139.392, 128.832, 127.776, 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 35 16.00 P 282 15.00 O 3591 8.00 N 2913 7.00 C 9256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS M 44 " - pdb=" SG CYS M 118 " distance=2.03 Simple disulfide: pdb=" SG CYS M 181 " - pdb=" SG CYS M 246 " distance=2.03 Simple disulfide: pdb=" SG CYS N 44 " - pdb=" SG CYS N 118 " distance=2.03 Simple disulfide: pdb=" SG CYS N 181 " - pdb=" SG CYS N 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 523.7 milliseconds 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2420 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 24 sheets defined 47.6% alpha, 19.2% beta 137 base pairs and 261 stacking pairs defined. Time for finding SS restraints: 1.70 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.036A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.747A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.514A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.742A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.519A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.780A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.421A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.775A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 52 No H-bonds generated for 'chain 'M' and resid 50 through 52' Processing helix chain 'M' and resid 84 through 87 Processing helix chain 'M' and resid 109 through 113 removed outlier: 3.868A pdb=" N SER M 113 " --> pdb=" O SER M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 237 through 241 removed outlier: 3.539A pdb=" N THR M 241 " --> pdb=" O SER M 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 52 No H-bonds generated for 'chain 'N' and resid 50 through 52' Processing helix chain 'N' and resid 109 through 113 removed outlier: 3.751A pdb=" N SER N 113 " --> pdb=" O SER N 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 237 through 241 removed outlier: 4.008A pdb=" N THR N 241 " --> pdb=" O SER N 238 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 185 removed outlier: 4.062A pdb=" N GLN O 176 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU O 182 " --> pdb=" O LEU O 178 " (cutoff:3.500A) Processing helix chain 'O' and resid 207 through 220 Processing helix chain 'O' and resid 226 through 241 removed outlier: 3.783A pdb=" N ALA O 233 " --> pdb=" O LYS O 229 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU O 234 " --> pdb=" O MET O 230 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG O 235 " --> pdb=" O ALA O 231 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASN O 236 " --> pdb=" O ARG O 232 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR O 237 " --> pdb=" O ALA O 233 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY O 238 " --> pdb=" O LEU O 234 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS O 239 " --> pdb=" O ARG O 235 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR O 240 " --> pdb=" O ASN O 236 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.064A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.625A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.160A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.183A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'M' and resid 25 through 26 Processing sheet with id=AB2, first strand: chain 'M' and resid 32 through 34 removed outlier: 3.607A pdb=" N GLU M 32 " --> pdb=" O SER M 137 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LYS M 60 " --> pdb=" O TRP M 69 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N TRP M 69 " --> pdb=" O LYS M 60 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR M 62 " --> pdb=" O LEU M 67 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LEU M 67 " --> pdb=" O THR M 62 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 32 through 34 removed outlier: 3.607A pdb=" N GLU M 32 " --> pdb=" O SER M 137 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR M 131 " --> pdb=" O ARG M 120 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N SER M 122 " --> pdb=" O LEU M 129 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU M 129 " --> pdb=" O SER M 122 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 40 through 43 Processing sheet with id=AB5, first strand: chain 'M' and resid 168 through 171 removed outlier: 6.516A pdb=" N MET M 169 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU M 191 " --> pdb=" O TYR M 207 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TYR M 207 " --> pdb=" O LEU M 191 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TRP M 193 " --> pdb=" O LEU M 205 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 168 through 171 removed outlier: 6.516A pdb=" N MET M 169 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR M 255 " --> pdb=" O GLN M 248 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 177 through 180 removed outlier: 3.795A pdb=" N ASP M 228 " --> pdb=" O SER M 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 25 through 26 Processing sheet with id=AB9, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.500A pdb=" N ILE N 56 " --> pdb=" O TYR N 72 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N TYR N 72 " --> pdb=" O ILE N 56 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TRP N 58 " --> pdb=" O ILE N 70 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 32 through 34 removed outlier: 3.854A pdb=" N TYR N 131 " --> pdb=" O ARG N 120 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N SER N 122 " --> pdb=" O LEU N 129 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU N 129 " --> pdb=" O SER N 122 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 40 through 43 Processing sheet with id=AC3, first strand: chain 'N' and resid 162 through 164 removed outlier: 3.829A pdb=" N VAL N 177 " --> pdb=" O ILE N 233 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE N 229 " --> pdb=" O CYS N 181 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP N 228 " --> pdb=" O SER N 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 168 through 171 removed outlier: 6.308A pdb=" N MET N 169 " --> pdb=" O GLU N 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'N' and resid 211 through 212 removed outlier: 6.454A pdb=" N TRP N 193 " --> pdb=" O LEU N 205 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N TYR N 207 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU N 191 " --> pdb=" O TYR N 207 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 191 through 195 removed outlier: 4.149A pdb=" N VAL O 194 " --> pdb=" O THR O 200 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N THR O 200 " --> pdb=" O VAL O 194 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN O 253 " --> pdb=" O LYS O 244 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS O 244 " --> pdb=" O GLN O 253 " (cutoff:3.500A) 567 hydrogen bonds defined for protein. 1587 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 340 hydrogen bonds 680 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 261 stacking parallelities Total time for adding SS restraints: 2.83 Time building geometry restraints manager: 1.59 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1913 1.30 - 1.43: 5900 1.43 - 1.56: 8525 1.56 - 1.69: 562 1.69 - 1.82: 58 Bond restraints: 16958 Sorted by residual: bond pdb=" C2' DC J 15 " pdb=" C1' DC J 15 " ideal model delta sigma weight residual 1.518 1.446 0.072 1.00e-02 1.00e+04 5.24e+01 bond pdb=" C HIS D 46 " pdb=" O HIS D 46 " ideal model delta sigma weight residual 1.238 1.173 0.064 1.08e-02 8.57e+03 3.56e+01 bond pdb=" C GLN E 125 " pdb=" O GLN E 125 " ideal model delta sigma weight residual 1.237 1.169 0.067 1.19e-02 7.06e+03 3.21e+01 bond pdb=" C ARG B 92 " pdb=" O ARG B 92 " ideal model delta sigma weight residual 1.236 1.169 0.067 1.29e-02 6.01e+03 2.67e+01 bond pdb=" CA ARG B 92 " pdb=" C ARG B 92 " ideal model delta sigma weight residual 1.522 1.458 0.065 1.40e-02 5.10e+03 2.13e+01 ... (remaining 16953 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.25: 24091 7.25 - 14.50: 9 14.50 - 21.75: 0 21.75 - 29.00: 0 29.00 - 36.24: 1 Bond angle restraints: 24101 Sorted by residual: angle pdb=" C LYS O 249 " pdb=" CA LYS O 249 " pdb=" CB LYS O 249 " ideal model delta sigma weight residual 109.80 73.56 36.24 1.23e+00 6.61e-01 8.68e+02 angle pdb=" C2' DC J 15 " pdb=" C1' DC J 15 " pdb=" N1 DC J 15 " ideal model delta sigma weight residual 114.30 100.09 14.21 1.40e+00 5.10e-01 1.03e+02 angle pdb=" N LEU O 250 " pdb=" CA LEU O 250 " pdb=" C LEU O 250 " ideal model delta sigma weight residual 111.74 122.51 -10.77 1.35e+00 5.49e-01 6.36e+01 angle pdb=" C3' DG J 72 " pdb=" C2' DG J 72 " pdb=" C1' DG J 72 " ideal model delta sigma weight residual 102.50 95.45 7.05 1.20e+00 6.94e-01 3.45e+01 angle pdb=" C2' DG J 72 " pdb=" C1' DG J 72 " pdb=" N9 DG J 72 " ideal model delta sigma weight residual 114.30 122.09 -7.79 1.40e+00 5.10e-01 3.10e+01 ... (remaining 24096 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.17: 7821 33.17 - 66.34: 1654 66.34 - 99.52: 37 99.52 - 132.69: 0 132.69 - 165.86: 2 Dihedral angle restraints: 9514 sinusoidal: 5738 harmonic: 3776 Sorted by residual: dihedral pdb=" C LYS O 249 " pdb=" N LYS O 249 " pdb=" CA LYS O 249 " pdb=" CB LYS O 249 " ideal model delta harmonic sigma weight residual -122.60 -80.21 -42.39 0 2.50e+00 1.60e-01 2.88e+02 dihedral pdb=" N LEU O 250 " pdb=" C LEU O 250 " pdb=" CA LEU O 250 " pdb=" CB LEU O 250 " ideal model delta harmonic sigma weight residual 122.80 151.15 -28.35 0 2.50e+00 1.60e-01 1.29e+02 dihedral pdb=" C LEU O 250 " pdb=" N LEU O 250 " pdb=" CA LEU O 250 " pdb=" CB LEU O 250 " ideal model delta harmonic sigma weight residual -122.60 -148.59 25.99 0 2.50e+00 1.60e-01 1.08e+02 ... (remaining 9511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.243: 2701 0.243 - 0.485: 4 0.485 - 0.728: 0 0.728 - 0.971: 0 0.971 - 1.213: 1 Chirality restraints: 2706 Sorted by residual: chirality pdb=" CA LEU O 250 " pdb=" N LEU O 250 " pdb=" C LEU O 250 " pdb=" CB LEU O 250 " both_signs ideal model delta sigma weight residual False 2.51 1.30 1.21 2.00e-01 2.50e+01 3.68e+01 chirality pdb=" CA LYS O 249 " pdb=" N LYS O 249 " pdb=" C LYS O 249 " pdb=" CB LYS O 249 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" C1' DG J 72 " pdb=" O4' DG J 72 " pdb=" C2' DG J 72 " pdb=" N9 DG J 72 " both_signs ideal model delta sigma weight residual False 2.43 2.08 0.35 2.00e-01 2.50e+01 3.08e+00 ... (remaining 2703 not shown) Planarity restraints: 2058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC J 15 " -0.032 2.00e-02 2.50e+03 4.52e-02 4.60e+01 pdb=" N1 DC J 15 " -0.080 2.00e-02 2.50e+03 pdb=" C2 DC J 15 " 0.055 2.00e-02 2.50e+03 pdb=" O2 DC J 15 " 0.008 2.00e-02 2.50e+03 pdb=" N3 DC J 15 " 0.010 2.00e-02 2.50e+03 pdb=" C4 DC J 15 " -0.007 2.00e-02 2.50e+03 pdb=" N4 DC J 15 " -0.033 2.00e-02 2.50e+03 pdb=" C5 DC J 15 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DC J 15 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 147 " -0.034 2.00e-02 2.50e+03 1.88e-02 8.85e+00 pdb=" N1 DT I 147 " 0.027 2.00e-02 2.50e+03 pdb=" C2 DT I 147 " -0.005 2.00e-02 2.50e+03 pdb=" O2 DT I 147 " 0.029 2.00e-02 2.50e+03 pdb=" N3 DT I 147 " -0.023 2.00e-02 2.50e+03 pdb=" C4 DT I 147 " -0.011 2.00e-02 2.50e+03 pdb=" O4 DT I 147 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DT I 147 " 0.006 2.00e-02 2.50e+03 pdb=" C7 DT I 147 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DT I 147 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 72 " -0.009 2.00e-02 2.50e+03 1.70e-02 8.62e+00 pdb=" N9 DG J 72 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DG J 72 " 0.009 2.00e-02 2.50e+03 pdb=" N7 DG J 72 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG J 72 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DG J 72 " 0.001 2.00e-02 2.50e+03 pdb=" O6 DG J 72 " -0.000 2.00e-02 2.50e+03 pdb=" N1 DG J 72 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG J 72 " -0.026 2.00e-02 2.50e+03 pdb=" N2 DG J 72 " 0.031 2.00e-02 2.50e+03 pdb=" N3 DG J 72 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DG J 72 " -0.030 2.00e-02 2.50e+03 ... (remaining 2055 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 174 2.62 - 3.19: 12862 3.19 - 3.76: 28342 3.76 - 4.33: 39525 4.33 - 4.90: 57867 Nonbonded interactions: 138770 Sorted by model distance: nonbonded pdb=" O LYS O 249 " pdb=" CB LYS O 249 " model vdw 2.044 2.752 nonbonded pdb=" OG1 THR O 240 " pdb=" OE1 GLU O 242 " model vdw 2.165 3.040 nonbonded pdb=" NH2 ARG N 120 " pdb=" OD2 ASP N 130 " model vdw 2.200 3.120 nonbonded pdb=" NE2 GLN C 104 " pdb=" OE2 GLU E 94 " model vdw 2.208 3.120 nonbonded pdb=" N GLU B 52 " pdb=" OE1 GLU B 52 " model vdw 2.235 3.120 ... (remaining 138765 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 12 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.340 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 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 : 0.006 0.072 16962 Z= 0.503 Angle : 0.820 36.245 24109 Z= 0.656 Chirality : 0.053 1.213 2706 Planarity : 0.004 0.045 2058 Dihedral : 26.463 165.860 7082 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.09 % Allowed : 25.20 % Favored : 74.71 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.24), residues: 1275 helix: 2.22 (0.22), residues: 570 sheet: 0.25 (0.35), residues: 236 loop : -0.40 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG M 176 TYR 0.028 0.001 TYR O 175 PHE 0.025 0.002 PHE O 254 TRP 0.015 0.001 TRP O 193 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00627 / 0.50 (16958) covalent geometry : angle 0.82011 / 0.66 (24101) SS BOND : bond 0.00226 / 0.11 ( 4) SS BOND : angle 1.23512 / 0.59 ( 8) hydrogen bonds : bond 0.14513 / 9.47 ( 890) hydrogen bonds : angle 5.08782 / 3.70 ( 2267) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 290 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8578 (mt-10) REVERT: D 32 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8097 (tt0) REVERT: D 65 ASP cc_start: 0.8642 (t0) cc_final: 0.8350 (t0) REVERT: D 73 GLU cc_start: 0.8638 (tp30) cc_final: 0.8224 (tp30) REVERT: D 83 ARG cc_start: 0.7775 (mmt90) cc_final: 0.7549 (mmt90) REVERT: E 90 MET cc_start: 0.8647 (mmp) cc_final: 0.8425 (mmm) REVERT: E 115 LYS cc_start: 0.8778 (mttt) cc_final: 0.8538 (mttm) REVERT: F 59 LYS cc_start: 0.8729 (tttt) cc_final: 0.8497 (tptp) REVERT: G 59 THR cc_start: 0.9347 (t) cc_final: 0.9025 (m) REVERT: H 34 TYR cc_start: 0.9017 (m-80) cc_final: 0.8677 (m-80) REVERT: M 104 GLU cc_start: 0.8192 (tt0) cc_final: 0.7977 (tt0) REVERT: N 103 MET cc_start: 0.8796 (ttp) cc_final: 0.8476 (ttm) REVERT: N 111 GLU cc_start: 0.8766 (pp20) cc_final: 0.8362 (pp20) REVERT: N 112 ASP cc_start: 0.8407 (m-30) cc_final: 0.7980 (m-30) REVERT: N 261 LYS cc_start: 0.8993 (mtpm) cc_final: 0.8723 (mtpp) REVERT: O 225 MET cc_start: -0.2950 (ptm) cc_final: -0.3849 (tmm) outliers start: 1 outliers final: 0 residues processed: 291 average time/residue: 0.7175 time to fit residues: 225.0406 Evaluate side-chains 209 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 209 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 30.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.0570 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 3.9990 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 104 GLN D 60 ASN E 125 GLN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 61 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 253 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.171700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.105315 restraints weight = 20717.696| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.03 r_work: 0.3014 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2884 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2884 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16962 Z= 0.153 Angle : 0.670 10.599 24109 Z= 0.376 Chirality : 0.045 0.262 2706 Planarity : 0.004 0.041 2058 Dihedral : 28.695 169.649 4560 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.98 % Allowed : 24.57 % Favored : 72.45 % 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: 1.52 (0.24), residues: 1275 helix: 2.39 (0.22), residues: 577 sheet: 0.36 (0.35), residues: 230 loop : -0.38 (0.29), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG O 214 TYR 0.012 0.001 TYR O 175 PHE 0.008 0.001 PHE E 67 TRP 0.011 0.001 TRP O 215 HIS 0.003 0.001 HIS N 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.15 (16958) covalent geometry : angle 0.66979 / 0.38 (24101) SS BOND : bond 0.00508 / 0.26 ( 4) SS BOND : angle 0.81185 / 0.38 ( 8) hydrogen bonds : bond 0.04793 / 3.25 ( 890) hydrogen bonds : angle 3.77785 / 2.73 ( 2267) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 224 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8118 (m-40) cc_final: 0.7760 (m-40) REVERT: C 20 ARG cc_start: 0.8777 (mtt90) cc_final: 0.8520 (mtt-85) REVERT: C 92 GLU cc_start: 0.9156 (mt-10) cc_final: 0.8903 (mt-10) REVERT: D 73 GLU cc_start: 0.8962 (tp30) cc_final: 0.8532 (tp30) REVERT: D 83 ARG cc_start: 0.8131 (mmt90) cc_final: 0.7895 (mmt90) REVERT: D 90 GLU cc_start: 0.9136 (OUTLIER) cc_final: 0.8122 (mt-10) REVERT: D 116 THR cc_start: 0.9082 (m) cc_final: 0.8825 (m) REVERT: E 115 LYS cc_start: 0.9098 (mttt) cc_final: 0.8831 (mttm) REVERT: F 35 ARG cc_start: 0.8290 (mtm110) cc_final: 0.7753 (mtp85) REVERT: F 59 LYS cc_start: 0.8816 (tttt) cc_final: 0.8525 (tptp) REVERT: G 51 MET cc_start: 0.8868 (tpt) cc_final: 0.8605 (tpt) REVERT: G 64 GLU cc_start: 0.9029 (tt0) cc_final: 0.8699 (tt0) REVERT: G 99 LYS cc_start: 0.8776 (mmtp) cc_final: 0.8523 (mmmt) REVERT: H 34 TYR cc_start: 0.9098 (m-80) cc_final: 0.8774 (m-80) REVERT: H 68 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8157 (mt-10) REVERT: H 90 GLU cc_start: 0.9127 (OUTLIER) cc_final: 0.7881 (mp0) REVERT: M 104 GLU cc_start: 0.8762 (tt0) cc_final: 0.8296 (tt0) REVERT: M 130 ASP cc_start: 0.8626 (p0) cc_final: 0.8421 (p0) REVERT: M 219 ARG cc_start: 0.8890 (OUTLIER) cc_final: 0.7878 (ttp80) REVERT: M 251 GLU cc_start: 0.8341 (mm-30) cc_final: 0.8058 (mm-30) REVERT: N 95 ASP cc_start: 0.8694 (t70) cc_final: 0.8431 (t70) REVERT: N 103 MET cc_start: 0.8938 (OUTLIER) cc_final: 0.8557 (ttm) REVERT: N 111 GLU cc_start: 0.8994 (pp20) cc_final: 0.8502 (pp20) REVERT: N 112 ASP cc_start: 0.8388 (m-30) cc_final: 0.7759 (m-30) REVERT: N 261 LYS cc_start: 0.9017 (mtpm) cc_final: 0.8688 (mtpp) REVERT: O 198 LYS cc_start: -0.1229 (OUTLIER) cc_final: -0.1633 (ptmt) REVERT: O 225 MET cc_start: -0.1591 (ptm) cc_final: -0.2719 (tmm) outliers start: 33 outliers final: 9 residues processed: 240 average time/residue: 0.6739 time to fit residues: 175.2803 Evaluate side-chains 230 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 215 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain M residue 219 ARG Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 239 ASP Chi-restraints excluded: chain O residue 198 LYS Chi-restraints excluded: chain O residue 253 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 75 optimal weight: 10.0000 chunk 107 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 chunk 74 optimal weight: 20.0000 chunk 20 optimal weight: 3.9990 chunk 99 optimal weight: 40.0000 chunk 77 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 13 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN C 104 GLN F 25 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 28 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.169921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.104217 restraints weight = 20866.908| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 1.96 r_work: 0.2982 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16962 Z= 0.163 Angle : 0.641 9.020 24109 Z= 0.361 Chirality : 0.044 0.282 2706 Planarity : 0.004 0.038 2058 Dihedral : 28.777 169.143 4560 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.16 % Allowed : 24.57 % Favored : 72.27 % 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: 1.55 (0.24), residues: 1275 helix: 2.43 (0.21), residues: 578 sheet: 0.36 (0.35), residues: 230 loop : -0.40 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 42 TYR 0.013 0.001 TYR G 50 PHE 0.021 0.002 PHE O 254 TRP 0.013 0.001 TRP O 193 HIS 0.005 0.001 HIS M 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00336 / 0.16 (16958) covalent geometry : angle 0.64052 / 0.36 (24101) SS BOND : bond 0.00434 / 0.22 ( 4) SS BOND : angle 0.92632 / 0.44 ( 8) hydrogen bonds : bond 0.04537 / 3.07 ( 890) hydrogen bonds : angle 3.55034 / 2.57 ( 2267) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 212 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7953 (ttp-170) REVERT: B 25 ASN cc_start: 0.8282 (m-40) cc_final: 0.7902 (m-40) REVERT: C 20 ARG cc_start: 0.8819 (mtt90) cc_final: 0.8553 (mtt-85) REVERT: C 75 LYS cc_start: 0.8617 (mmtt) cc_final: 0.8364 (mmtt) REVERT: C 92 GLU cc_start: 0.9161 (mt-10) cc_final: 0.8928 (mt-10) REVERT: D 68 GLU cc_start: 0.8279 (mt-10) cc_final: 0.8020 (mt-10) REVERT: D 73 GLU cc_start: 0.8948 (tp30) cc_final: 0.8611 (tp30) REVERT: D 83 ARG cc_start: 0.8316 (mmt90) cc_final: 0.8046 (mmt90) REVERT: D 90 GLU cc_start: 0.9167 (OUTLIER) cc_final: 0.8168 (mt-10) REVERT: E 76 GLN cc_start: 0.8618 (tt0) cc_final: 0.8377 (mt0) REVERT: E 115 LYS cc_start: 0.9044 (mttt) cc_final: 0.8759 (mttp) REVERT: F 35 ARG cc_start: 0.8359 (mtm110) cc_final: 0.7818 (mtp85) REVERT: F 59 LYS cc_start: 0.8824 (tttt) cc_final: 0.8531 (tptp) REVERT: G 64 GLU cc_start: 0.9016 (tt0) cc_final: 0.8743 (tt0) REVERT: G 99 LYS cc_start: 0.8862 (mmtp) cc_final: 0.8574 (mmmt) REVERT: H 34 TYR cc_start: 0.9158 (m-80) cc_final: 0.8807 (m-80) REVERT: H 68 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8008 (tp30) REVERT: H 90 GLU cc_start: 0.9176 (OUTLIER) cc_final: 0.7912 (mp0) REVERT: H 113 LYS cc_start: 0.9205 (ttpp) cc_final: 0.8926 (ttpt) REVERT: M 81 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8104 (ttpp) REVERT: M 104 GLU cc_start: 0.8716 (tt0) cc_final: 0.8233 (tt0) REVERT: M 163 THR cc_start: 0.8363 (m) cc_final: 0.7957 (p) REVERT: M 175 GLU cc_start: 0.7751 (pt0) cc_final: 0.7098 (pm20) REVERT: M 219 ARG cc_start: 0.8968 (mtp180) cc_final: 0.8120 (ttp80) REVERT: N 103 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8609 (ttm) REVERT: N 111 GLU cc_start: 0.9029 (OUTLIER) cc_final: 0.8507 (pp20) REVERT: N 112 ASP cc_start: 0.8374 (m-30) cc_final: 0.7813 (m-30) REVERT: N 261 LYS cc_start: 0.9035 (mtpm) cc_final: 0.8730 (mtpp) REVERT: O 225 MET cc_start: -0.0817 (ptm) cc_final: -0.2273 (tmm) outliers start: 35 outliers final: 14 residues processed: 232 average time/residue: 0.7037 time to fit residues: 177.3711 Evaluate side-chains 228 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 207 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 81 LYS Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 239 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 113 optimal weight: 0.4980 chunk 129 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 140 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.170864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.105485 restraints weight = 20816.241| |-----------------------------------------------------------------------------| r_work (start): 0.3213 rms_B_bonded: 1.92 r_work: 0.3003 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16962 Z= 0.134 Angle : 0.618 9.857 24109 Z= 0.347 Chirality : 0.043 0.286 2706 Planarity : 0.004 0.045 2058 Dihedral : 28.822 169.929 4560 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.07 % Allowed : 25.47 % Favored : 71.45 % 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: 1.68 (0.24), residues: 1275 helix: 2.55 (0.21), residues: 578 sheet: 0.42 (0.35), residues: 230 loop : -0.35 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 42 TYR 0.011 0.001 TYR E 54 PHE 0.014 0.001 PHE O 254 TRP 0.012 0.001 TRP O 193 HIS 0.005 0.001 HIS M 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.13 (16958) covalent geometry : angle 0.61836 / 0.35 (24101) SS BOND : bond 0.00387 / 0.19 ( 4) SS BOND : angle 0.75438 / 0.36 ( 8) hydrogen bonds : bond 0.04188 / 2.84 ( 890) hydrogen bonds : angle 3.39725 / 2.46 ( 2267) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 210 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8835 (pm20) cc_final: 0.8531 (pm20) REVERT: B 25 ASN cc_start: 0.8311 (m-40) cc_final: 0.7923 (m-40) REVERT: C 20 ARG cc_start: 0.8831 (mtt90) cc_final: 0.8561 (mtt-85) REVERT: C 91 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8352 (tt0) REVERT: C 92 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8918 (mt-10) REVERT: D 68 GLU cc_start: 0.8264 (mt-10) cc_final: 0.8018 (mt-10) REVERT: D 73 GLU cc_start: 0.8913 (tp30) cc_final: 0.8604 (tp30) REVERT: D 83 ARG cc_start: 0.8276 (mmt90) cc_final: 0.8015 (mmt90) REVERT: D 90 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8210 (mt-10) REVERT: E 97 GLU cc_start: 0.8669 (mm-30) cc_final: 0.8309 (mt-10) REVERT: E 115 LYS cc_start: 0.8999 (mttt) cc_final: 0.8710 (mttp) REVERT: F 35 ARG cc_start: 0.8316 (mtm110) cc_final: 0.7783 (mtp85) REVERT: G 64 GLU cc_start: 0.9018 (tt0) cc_final: 0.8736 (tt0) REVERT: H 34 TYR cc_start: 0.9125 (m-80) cc_final: 0.8790 (m-80) REVERT: H 68 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8013 (tp30) REVERT: H 113 LYS cc_start: 0.9199 (ttpp) cc_final: 0.8924 (ttpt) REVERT: M 81 LYS cc_start: 0.8686 (OUTLIER) cc_final: 0.8060 (ttpp) REVERT: M 104 GLU cc_start: 0.8735 (tt0) cc_final: 0.8264 (tt0) REVERT: M 163 THR cc_start: 0.8428 (m) cc_final: 0.8059 (p) REVERT: M 175 GLU cc_start: 0.7664 (pt0) cc_final: 0.6978 (pm20) REVERT: M 219 ARG cc_start: 0.8984 (mtp180) cc_final: 0.8117 (ttp80) REVERT: M 247 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8778 (tp) REVERT: N 32 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7775 (mm-30) REVERT: N 42 MET cc_start: 0.9232 (ptp) cc_final: 0.8927 (mpp) REVERT: N 103 MET cc_start: 0.8981 (ttp) cc_final: 0.8629 (ttm) REVERT: N 111 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8567 (pp20) REVERT: N 112 ASP cc_start: 0.8413 (m-30) cc_final: 0.7699 (m-30) REVERT: N 186 ASP cc_start: 0.9070 (OUTLIER) cc_final: 0.8794 (t70) REVERT: N 261 LYS cc_start: 0.9022 (mtpm) cc_final: 0.8715 (mtpp) REVERT: O 198 LYS cc_start: -0.0899 (OUTLIER) cc_final: -0.1283 (ptmt) REVERT: O 225 MET cc_start: -0.0532 (ptm) cc_final: -0.2093 (tmm) outliers start: 34 outliers final: 14 residues processed: 230 average time/residue: 0.8024 time to fit residues: 199.8507 Evaluate side-chains 227 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 205 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 81 LYS Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 186 ASP Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 239 ASP Chi-restraints excluded: chain O residue 198 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 68 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 146 optimal weight: 50.0000 chunk 10 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 72 optimal weight: 50.0000 chunk 55 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 130 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 93 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.168341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.102782 restraints weight = 20682.787| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 1.95 r_work: 0.2955 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16962 Z= 0.172 Angle : 0.636 10.633 24109 Z= 0.352 Chirality : 0.044 0.289 2706 Planarity : 0.004 0.052 2058 Dihedral : 28.960 168.981 4560 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.61 % Allowed : 25.20 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.55 (0.24), residues: 1275 helix: 2.39 (0.21), residues: 577 sheet: 0.42 (0.35), residues: 232 loop : -0.38 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 42 TYR 0.014 0.001 TYR E 54 PHE 0.010 0.002 PHE O 254 TRP 0.012 0.001 TRP O 193 HIS 0.012 0.001 HIS M 170 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.17 (16958) covalent geometry : angle 0.63542 / 0.35 (24101) SS BOND : bond 0.00474 / 0.24 ( 4) SS BOND : angle 0.92377 / 0.42 ( 8) hydrogen bonds : bond 0.04515 / 3.06 ( 890) hydrogen bonds : angle 3.38540 / 2.47 ( 2267) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 195 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8802 (pm20) cc_final: 0.8452 (pm20) REVERT: A 129 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7714 (ttp80) REVERT: A 133 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8075 (mt-10) REVERT: B 25 ASN cc_start: 0.8560 (m-40) cc_final: 0.8084 (m-40) REVERT: C 20 ARG cc_start: 0.8842 (mtt90) cc_final: 0.8549 (mtt-85) REVERT: C 91 GLU cc_start: 0.8957 (OUTLIER) cc_final: 0.8529 (tt0) REVERT: C 92 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8931 (mt-10) REVERT: D 68 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7904 (mt-10) REVERT: D 73 GLU cc_start: 0.8958 (tp30) cc_final: 0.8673 (tp30) REVERT: D 83 ARG cc_start: 0.8307 (mmt90) cc_final: 0.8081 (mmm-85) REVERT: D 90 GLU cc_start: 0.9228 (OUTLIER) cc_final: 0.8221 (mt-10) REVERT: E 97 GLU cc_start: 0.8643 (mm-30) cc_final: 0.8337 (mt-10) REVERT: E 115 LYS cc_start: 0.9047 (mttt) cc_final: 0.8754 (mttp) REVERT: F 35 ARG cc_start: 0.8431 (mtm110) cc_final: 0.8222 (ttm-80) REVERT: G 95 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8696 (ttpt) REVERT: H 32 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.8205 (tt0) REVERT: H 34 TYR cc_start: 0.9184 (m-80) cc_final: 0.8841 (m-80) REVERT: H 68 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8047 (tp30) REVERT: H 113 LYS cc_start: 0.9217 (ttpp) cc_final: 0.8942 (ttpt) REVERT: M 81 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8085 (ttpp) REVERT: M 104 GLU cc_start: 0.8787 (tt0) cc_final: 0.8355 (tt0) REVERT: M 163 THR cc_start: 0.8459 (m) cc_final: 0.7980 (p) REVERT: M 169 MET cc_start: 0.8646 (OUTLIER) cc_final: 0.8330 (ptm) REVERT: M 175 GLU cc_start: 0.7644 (pt0) cc_final: 0.6910 (pm20) REVERT: M 219 ARG cc_start: 0.8975 (OUTLIER) cc_final: 0.7978 (ttp80) REVERT: N 42 MET cc_start: 0.9097 (ptp) cc_final: 0.8809 (mpp) REVERT: N 103 MET cc_start: 0.8996 (ttp) cc_final: 0.8668 (ttm) REVERT: N 111 GLU cc_start: 0.8993 (OUTLIER) cc_final: 0.8574 (pp20) REVERT: N 112 ASP cc_start: 0.8365 (m-30) cc_final: 0.7835 (m-30) REVERT: N 261 LYS cc_start: 0.8998 (mtpm) cc_final: 0.8700 (mtpp) REVERT: O 198 LYS cc_start: -0.0813 (OUTLIER) cc_final: -0.1205 (ptmt) REVERT: O 225 MET cc_start: 0.0032 (ptm) cc_final: -0.1815 (tmm) outliers start: 40 outliers final: 15 residues processed: 219 average time/residue: 0.7512 time to fit residues: 178.6528 Evaluate side-chains 222 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 195 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 81 LYS Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 169 MET Chi-restraints excluded: chain M residue 219 ARG Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 239 ASP Chi-restraints excluded: chain O residue 174 LEU Chi-restraints excluded: chain O residue 198 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 37 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 44 optimal weight: 0.9990 chunk 97 optimal weight: 10.0000 chunk 115 optimal weight: 0.5980 chunk 91 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 104 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 43 optimal weight: 0.2980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.170043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.104762 restraints weight = 20793.793| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.92 r_work: 0.2995 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 16962 Z= 0.131 Angle : 0.607 9.715 24109 Z= 0.340 Chirality : 0.042 0.293 2706 Planarity : 0.004 0.048 2058 Dihedral : 28.907 170.230 4560 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.07 % Allowed : 25.38 % Favored : 71.54 % 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: 1.68 (0.24), residues: 1275 helix: 2.56 (0.21), residues: 577 sheet: 0.54 (0.37), residues: 206 loop : -0.40 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 42 TYR 0.025 0.001 TYR O 237 PHE 0.010 0.001 PHE A 67 TRP 0.012 0.001 TRP O 193 HIS 0.003 0.001 HIS M 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00250 / 0.13 (16958) covalent geometry : angle 0.60661 / 0.34 (24101) SS BOND : bond 0.00384 / 0.19 ( 4) SS BOND : angle 0.74402 / 0.35 ( 8) hydrogen bonds : bond 0.04077 / 2.78 ( 890) hydrogen bonds : angle 3.27423 / 2.38 ( 2267) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 0.362 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8785 (pm20) cc_final: 0.8444 (pm20) REVERT: B 25 ASN cc_start: 0.8558 (m-40) cc_final: 0.8130 (m-40) REVERT: C 20 ARG cc_start: 0.8828 (mtt90) cc_final: 0.8535 (mtt-85) REVERT: C 91 GLU cc_start: 0.8946 (OUTLIER) cc_final: 0.8377 (tt0) REVERT: C 92 GLU cc_start: 0.9144 (mt-10) cc_final: 0.8925 (mt-10) REVERT: D 73 GLU cc_start: 0.8876 (tp30) cc_final: 0.8633 (tp30) REVERT: D 83 ARG cc_start: 0.8259 (mmt90) cc_final: 0.7977 (mmt90) REVERT: D 90 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8875 (mp0) REVERT: E 76 GLN cc_start: 0.8582 (tt0) cc_final: 0.8295 (mt0) REVERT: E 97 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8302 (mt-10) REVERT: F 35 ARG cc_start: 0.8407 (mtm110) cc_final: 0.8202 (ttm-80) REVERT: G 64 GLU cc_start: 0.9083 (tt0) cc_final: 0.8758 (tt0) REVERT: H 34 TYR cc_start: 0.9152 (m-80) cc_final: 0.8769 (m-80) REVERT: H 68 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7984 (tp30) REVERT: H 90 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.7827 (mp0) REVERT: H 113 LYS cc_start: 0.9203 (ttpp) cc_final: 0.8930 (ttpt) REVERT: M 81 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8049 (ttpp) REVERT: M 104 GLU cc_start: 0.8761 (tt0) cc_final: 0.8307 (tt0) REVERT: M 163 THR cc_start: 0.8469 (m) cc_final: 0.8014 (p) REVERT: M 219 ARG cc_start: 0.8976 (OUTLIER) cc_final: 0.8009 (ttp80) REVERT: N 32 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7792 (mm-30) REVERT: N 42 MET cc_start: 0.9106 (ptp) cc_final: 0.8870 (mpp) REVERT: N 103 MET cc_start: 0.8990 (ttp) cc_final: 0.8660 (ttm) REVERT: N 109 THR cc_start: 0.7823 (OUTLIER) cc_final: 0.7491 (m) REVERT: N 111 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8558 (pp20) REVERT: N 112 ASP cc_start: 0.8356 (m-30) cc_final: 0.7831 (m-30) REVERT: N 261 LYS cc_start: 0.8994 (mtpm) cc_final: 0.8719 (mtpp) REVERT: O 198 LYS cc_start: -0.1109 (OUTLIER) cc_final: -0.1523 (ptmt) REVERT: O 225 MET cc_start: -0.0708 (ptm) cc_final: -0.2054 (tmm) outliers start: 34 outliers final: 15 residues processed: 226 average time/residue: 0.6603 time to fit residues: 161.8837 Evaluate side-chains 213 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 81 LYS Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 219 ARG Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 239 ASP Chi-restraints excluded: chain O residue 174 LEU Chi-restraints excluded: chain O residue 198 LYS Chi-restraints excluded: chain O residue 237 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 126 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 chunk 74 optimal weight: 20.0000 chunk 91 optimal weight: 9.9990 chunk 147 optimal weight: 10.0000 chunk 133 optimal weight: 0.7980 chunk 139 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 145 optimal weight: 7.9990 chunk 114 optimal weight: 6.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN D 92 GLN E 76 GLN F 93 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.165253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.098897 restraints weight = 20491.313| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.03 r_work: 0.2886 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 16962 Z= 0.272 Angle : 0.711 9.067 24109 Z= 0.384 Chirality : 0.048 0.301 2706 Planarity : 0.006 0.063 2058 Dihedral : 29.175 167.430 4560 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 4.25 % Allowed : 25.11 % Favored : 70.64 % 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: 1.15 (0.23), residues: 1275 helix: 2.00 (0.21), residues: 576 sheet: 0.43 (0.35), residues: 230 loop : -0.59 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 42 TYR 0.023 0.002 TYR E 54 PHE 0.013 0.002 PHE A 78 TRP 0.012 0.001 TRP O 193 HIS 0.005 0.001 HIS N 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00616 / 0.27 (16958) covalent geometry : angle 0.71092 / 0.38 (24101) SS BOND : bond 0.00739 / 0.37 ( 4) SS BOND : angle 1.23506 / 0.52 ( 8) hydrogen bonds : bond 0.05403 / 3.66 ( 890) hydrogen bonds : angle 3.55242 / 2.60 ( 2267) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 193 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7800 (ttp80) REVERT: C 91 GLU cc_start: 0.9036 (OUTLIER) cc_final: 0.8501 (tt0) REVERT: C 92 GLU cc_start: 0.9206 (mt-10) cc_final: 0.8958 (mt-10) REVERT: C 99 LYS cc_start: 0.8586 (mttt) cc_final: 0.8307 (mmpt) REVERT: D 73 GLU cc_start: 0.9006 (tp30) cc_final: 0.8764 (tp30) REVERT: D 83 ARG cc_start: 0.8355 (mmt90) cc_final: 0.8047 (mmt90) REVERT: D 90 GLU cc_start: 0.9299 (OUTLIER) cc_final: 0.8213 (mp0) REVERT: E 97 GLU cc_start: 0.8639 (mm-30) cc_final: 0.8358 (mt-10) REVERT: F 91 LYS cc_start: 0.9153 (tttt) cc_final: 0.8651 (ttmm) REVERT: G 95 LYS cc_start: 0.9148 (OUTLIER) cc_final: 0.8735 (ttpt) REVERT: H 32 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8174 (tt0) REVERT: H 34 TYR cc_start: 0.9251 (m-80) cc_final: 0.8907 (m-80) REVERT: H 68 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.8062 (tp30) REVERT: H 90 GLU cc_start: 0.9200 (OUTLIER) cc_final: 0.7967 (mp0) REVERT: H 113 LYS cc_start: 0.9234 (ttpp) cc_final: 0.8819 (ttpt) REVERT: M 104 GLU cc_start: 0.8837 (tt0) cc_final: 0.8419 (tt0) REVERT: M 175 GLU cc_start: 0.7905 (pt0) cc_final: 0.7633 (pt0) REVERT: M 219 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8666 (mtm110) REVERT: M 237 GLU cc_start: 0.8044 (mm-30) cc_final: 0.7836 (mm-30) REVERT: M 247 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8807 (tp) REVERT: N 42 MET cc_start: 0.9091 (ptp) cc_final: 0.8756 (mpp) REVERT: N 103 MET cc_start: 0.8975 (ttp) cc_final: 0.8657 (ttm) REVERT: N 109 THR cc_start: 0.7875 (OUTLIER) cc_final: 0.7615 (m) REVERT: N 111 GLU cc_start: 0.9055 (OUTLIER) cc_final: 0.8625 (pp20) REVERT: N 112 ASP cc_start: 0.8359 (m-30) cc_final: 0.7787 (m-30) REVERT: N 188 ARG cc_start: 0.8041 (mtm110) cc_final: 0.6986 (mtm110) REVERT: N 261 LYS cc_start: 0.8922 (mtpm) cc_final: 0.8693 (mtpp) REVERT: O 198 LYS cc_start: -0.0877 (OUTLIER) cc_final: -0.1275 (ptmt) REVERT: O 225 MET cc_start: -0.0013 (ptm) cc_final: -0.1470 (tmm) outliers start: 47 outliers final: 21 residues processed: 218 average time/residue: 0.7550 time to fit residues: 178.0263 Evaluate side-chains 226 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 95 ASP Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 219 ARG Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 239 ASP Chi-restraints excluded: chain O residue 174 LEU Chi-restraints excluded: chain O residue 198 LYS Chi-restraints excluded: chain O residue 223 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 109 optimal weight: 0.9990 chunk 78 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 41 optimal weight: 0.7980 chunk 82 optimal weight: 10.0000 chunk 86 optimal weight: 50.0000 chunk 97 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 10 optimal weight: 0.8980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4033 r_free = 0.4033 target = 0.167871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.102092 restraints weight = 20668.506| |-----------------------------------------------------------------------------| r_work (start): 0.3155 rms_B_bonded: 2.02 r_work: 0.2941 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16962 Z= 0.139 Angle : 0.635 9.454 24109 Z= 0.351 Chirality : 0.043 0.301 2706 Planarity : 0.004 0.054 2058 Dihedral : 29.067 170.367 4560 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.71 % Allowed : 26.29 % Favored : 71.00 % 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: 1.37 (0.24), residues: 1275 helix: 2.32 (0.21), residues: 575 sheet: 0.39 (0.37), residues: 206 loop : -0.56 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 42 TYR 0.019 0.001 TYR E 54 PHE 0.010 0.001 PHE A 67 TRP 0.012 0.001 TRP O 193 HIS 0.003 0.001 HIS M 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.14 (16958) covalent geometry : angle 0.63478 / 0.35 (24101) SS BOND : bond 0.00515 / 0.26 ( 4) SS BOND : angle 0.85259 / 0.39 ( 8) hydrogen bonds : bond 0.04250 / 2.89 ( 890) hydrogen bonds : angle 3.36466 / 2.45 ( 2267) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 204 time to evaluate : 0.478 Fit side-chains revert: symmetry clash REVERT: A 133 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8157 (mt-10) REVERT: B 25 ASN cc_start: 0.8696 (m-40) cc_final: 0.8178 (m-40) REVERT: C 20 ARG cc_start: 0.8821 (mtt90) cc_final: 0.8495 (mtt-85) REVERT: C 91 GLU cc_start: 0.8983 (tt0) cc_final: 0.8667 (tt0) REVERT: C 92 GLU cc_start: 0.9146 (mt-10) cc_final: 0.8917 (mt-10) REVERT: C 99 LYS cc_start: 0.8523 (mttt) cc_final: 0.8258 (mmpt) REVERT: D 73 GLU cc_start: 0.8917 (tp30) cc_final: 0.8659 (tp30) REVERT: D 83 ARG cc_start: 0.8296 (mmt90) cc_final: 0.8015 (mmt90) REVERT: D 90 GLU cc_start: 0.9261 (OUTLIER) cc_final: 0.8241 (mt-10) REVERT: D 102 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8349 (mp0) REVERT: E 76 GLN cc_start: 0.8552 (mt0) cc_final: 0.8259 (mt0) REVERT: E 97 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8283 (mt-10) REVERT: F 91 LYS cc_start: 0.9123 (tttt) cc_final: 0.8590 (ttmm) REVERT: G 64 GLU cc_start: 0.9107 (tt0) cc_final: 0.8760 (tt0) REVERT: H 34 TYR cc_start: 0.9173 (m-80) cc_final: 0.8842 (m-80) REVERT: H 68 GLU cc_start: 0.8400 (OUTLIER) cc_final: 0.8032 (tp30) REVERT: H 90 GLU cc_start: 0.9189 (OUTLIER) cc_final: 0.7963 (mp0) REVERT: H 113 LYS cc_start: 0.9204 (ttpp) cc_final: 0.8945 (ttpt) REVERT: M 104 GLU cc_start: 0.8771 (tt0) cc_final: 0.8332 (tt0) REVERT: M 175 GLU cc_start: 0.7746 (pt0) cc_final: 0.7271 (pt0) REVERT: M 219 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.7987 (ttp80) REVERT: M 237 GLU cc_start: 0.8039 (mm-30) cc_final: 0.7675 (mm-30) REVERT: N 32 GLU cc_start: 0.8353 (mm-30) cc_final: 0.7843 (mm-30) REVERT: N 103 MET cc_start: 0.8908 (ttp) cc_final: 0.8546 (ttm) REVERT: N 109 THR cc_start: 0.7860 (OUTLIER) cc_final: 0.7589 (m) REVERT: N 111 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8631 (pp20) REVERT: N 112 ASP cc_start: 0.8277 (m-30) cc_final: 0.7710 (m-30) REVERT: N 261 LYS cc_start: 0.8920 (mtpm) cc_final: 0.8711 (mtpp) REVERT: O 198 LYS cc_start: -0.0963 (OUTLIER) cc_final: -0.1362 (ptmt) REVERT: O 225 MET cc_start: -0.0193 (ptm) cc_final: -0.1586 (tmm) outliers start: 30 outliers final: 16 residues processed: 222 average time/residue: 0.8107 time to fit residues: 194.5634 Evaluate side-chains 225 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 219 ARG Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 239 ASP Chi-restraints excluded: chain O residue 174 LEU Chi-restraints excluded: chain O residue 198 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 102 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 132 optimal weight: 0.5980 chunk 129 optimal weight: 0.8980 chunk 98 optimal weight: 30.0000 chunk 142 optimal weight: 2.9990 chunk 99 optimal weight: 40.0000 chunk 139 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 64 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN E 76 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.167941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.102234 restraints weight = 20606.935| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.91 r_work: 0.2949 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16962 Z= 0.154 Angle : 0.629 9.593 24109 Z= 0.350 Chirality : 0.043 0.294 2706 Planarity : 0.004 0.057 2058 Dihedral : 28.966 170.078 4560 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.71 % Allowed : 26.74 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.24), residues: 1275 helix: 2.36 (0.21), residues: 577 sheet: 0.30 (0.37), residues: 206 loop : -0.54 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 42 TYR 0.019 0.001 TYR E 54 PHE 0.011 0.001 PHE A 67 TRP 0.012 0.001 TRP O 193 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.15 (16958) covalent geometry : angle 0.62928 / 0.35 (24101) SS BOND : bond 0.00381 / 0.19 ( 4) SS BOND : angle 1.04259 / 0.44 ( 8) hydrogen bonds : bond 0.04211 / 2.87 ( 890) hydrogen bonds : angle 3.33466 / 2.43 ( 2267) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8768 (m-40) cc_final: 0.8263 (m-40) REVERT: C 20 ARG cc_start: 0.8828 (mtt90) cc_final: 0.8506 (mtt-85) REVERT: C 91 GLU cc_start: 0.8968 (tt0) cc_final: 0.8382 (tt0) REVERT: C 92 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8905 (mt-10) REVERT: D 73 GLU cc_start: 0.8917 (tp30) cc_final: 0.8688 (tp30) REVERT: D 83 ARG cc_start: 0.8286 (mmt90) cc_final: 0.8005 (mmt90) REVERT: D 90 GLU cc_start: 0.9249 (OUTLIER) cc_final: 0.8227 (mt-10) REVERT: E 76 GLN cc_start: 0.8517 (OUTLIER) cc_final: 0.8303 (mt0) REVERT: E 97 GLU cc_start: 0.8580 (mm-30) cc_final: 0.8314 (mt-10) REVERT: F 91 LYS cc_start: 0.9103 (tttt) cc_final: 0.8585 (ttmm) REVERT: G 64 GLU cc_start: 0.9047 (tt0) cc_final: 0.8737 (tt0) REVERT: H 34 TYR cc_start: 0.9169 (m-80) cc_final: 0.8839 (m-80) REVERT: H 68 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.8008 (tp30) REVERT: H 90 GLU cc_start: 0.9178 (OUTLIER) cc_final: 0.7899 (mp0) REVERT: H 113 LYS cc_start: 0.9208 (ttpp) cc_final: 0.8797 (ttpt) REVERT: M 104 GLU cc_start: 0.8765 (tt0) cc_final: 0.8352 (tt0) REVERT: M 219 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8703 (mtm110) REVERT: M 237 GLU cc_start: 0.8082 (mm-30) cc_final: 0.7875 (mm-30) REVERT: N 32 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7788 (mm-30) REVERT: N 103 MET cc_start: 0.8815 (ttp) cc_final: 0.8521 (ttm) REVERT: N 109 THR cc_start: 0.7870 (OUTLIER) cc_final: 0.7616 (m) REVERT: N 111 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8577 (pp20) REVERT: N 112 ASP cc_start: 0.8274 (m-30) cc_final: 0.7745 (m-30) REVERT: N 261 LYS cc_start: 0.8924 (mtpm) cc_final: 0.8716 (mtpp) REVERT: O 198 LYS cc_start: -0.0692 (OUTLIER) cc_final: -0.1077 (ptmt) REVERT: O 225 MET cc_start: 0.0131 (ptm) cc_final: -0.0463 (ttm) outliers start: 30 outliers final: 18 residues processed: 215 average time/residue: 0.7911 time to fit residues: 183.8325 Evaluate side-chains 209 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 183 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 219 ARG Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 239 ASP Chi-restraints excluded: chain O residue 174 LEU Chi-restraints excluded: chain O residue 198 LYS Chi-restraints excluded: chain O residue 223 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.0970 chunk 47 optimal weight: 0.9980 chunk 146 optimal weight: 9.9990 chunk 108 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 chunk 120 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 96 optimal weight: 10.0000 chunk 60 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 chunk 138 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 104 GLN E 76 GLN E 108 ASN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.168750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.102943 restraints weight = 20559.296| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 1.94 r_work: 0.2968 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 16962 Z= 0.131 Angle : 0.616 9.396 24109 Z= 0.345 Chirality : 0.042 0.295 2706 Planarity : 0.004 0.058 2058 Dihedral : 28.905 170.838 4560 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.53 % Allowed : 27.01 % Favored : 70.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.24), residues: 1275 helix: 2.47 (0.21), residues: 577 sheet: 0.29 (0.37), residues: 206 loop : -0.51 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 42 TYR 0.017 0.001 TYR E 54 PHE 0.010 0.001 PHE A 67 TRP 0.013 0.001 TRP O 193 HIS 0.003 0.001 HIS M 249 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.13 (16958) covalent geometry : angle 0.61594 / 0.34 (24101) SS BOND : bond 0.00410 / 0.21 ( 4) SS BOND : angle 0.90018 / 0.38 ( 8) hydrogen bonds : bond 0.04013 / 2.74 ( 890) hydrogen bonds : angle 3.28744 / 2.39 ( 2267) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8794 (pm20) cc_final: 0.8429 (pm20) REVERT: B 25 ASN cc_start: 0.8724 (m-40) cc_final: 0.8297 (m-40) REVERT: C 20 ARG cc_start: 0.8828 (mtt90) cc_final: 0.8508 (mtt-85) REVERT: C 91 GLU cc_start: 0.8965 (tt0) cc_final: 0.8635 (tt0) REVERT: C 92 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8923 (mt-10) REVERT: D 73 GLU cc_start: 0.8890 (tp30) cc_final: 0.8678 (tp30) REVERT: D 83 ARG cc_start: 0.8239 (mmt90) cc_final: 0.7963 (mmt90) REVERT: D 90 GLU cc_start: 0.9182 (OUTLIER) cc_final: 0.8253 (mt-10) REVERT: D 102 GLU cc_start: 0.9067 (OUTLIER) cc_final: 0.8351 (mp0) REVERT: E 76 GLN cc_start: 0.8281 (OUTLIER) cc_final: 0.7959 (mt0) REVERT: E 97 GLU cc_start: 0.8569 (mm-30) cc_final: 0.8309 (mt-10) REVERT: E 123 ASP cc_start: 0.9220 (m-30) cc_final: 0.9007 (m-30) REVERT: F 91 LYS cc_start: 0.9088 (tttt) cc_final: 0.8564 (ttmm) REVERT: H 34 TYR cc_start: 0.9145 (m-80) cc_final: 0.8801 (m-80) REVERT: H 68 GLU cc_start: 0.8411 (OUTLIER) cc_final: 0.7990 (tp30) REVERT: H 90 GLU cc_start: 0.9185 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: H 113 LYS cc_start: 0.9202 (ttpp) cc_final: 0.8721 (ttpt) REVERT: M 104 GLU cc_start: 0.8744 (tt0) cc_final: 0.8341 (tt0) REVERT: M 175 GLU cc_start: 0.7756 (pt0) cc_final: 0.7147 (pm20) REVERT: M 219 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8697 (mtm110) REVERT: M 237 GLU cc_start: 0.8065 (mm-30) cc_final: 0.7858 (mm-30) REVERT: N 109 THR cc_start: 0.7767 (OUTLIER) cc_final: 0.7527 (m) REVERT: N 111 GLU cc_start: 0.8968 (OUTLIER) cc_final: 0.8593 (pp20) REVERT: N 169 MET cc_start: 0.8656 (ptp) cc_final: 0.8395 (mtm) REVERT: N 261 LYS cc_start: 0.8903 (mtpm) cc_final: 0.8701 (mtpp) REVERT: O 198 LYS cc_start: -0.1091 (OUTLIER) cc_final: -0.1513 (ptmt) REVERT: O 225 MET cc_start: -0.0545 (ptm) cc_final: -0.0949 (ttm) outliers start: 28 outliers final: 18 residues processed: 206 average time/residue: 0.7074 time to fit residues: 157.8736 Evaluate side-chains 218 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 102 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 219 ARG Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 162 MET Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 239 ASP Chi-restraints excluded: chain O residue 174 LEU Chi-restraints excluded: chain O residue 198 LYS Chi-restraints excluded: chain O residue 223 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 81 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 149 optimal weight: 9.9990 chunk 85 optimal weight: 50.0000 chunk 49 optimal weight: 2.9990 chunk 115 optimal weight: 0.7980 chunk 144 optimal weight: 20.0000 chunk 151 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 76 GLN C 38 ASN E 76 GLN G 104 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.166142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.099691 restraints weight = 20526.655| |-----------------------------------------------------------------------------| r_work (start): 0.3118 rms_B_bonded: 1.93 r_work: 0.2914 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16962 Z= 0.248 Angle : 0.675 8.875 24109 Z= 0.370 Chirality : 0.046 0.298 2706 Planarity : 0.005 0.055 2058 Dihedral : 29.050 168.958 4560 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.71 % Allowed : 27.01 % Favored : 70.28 % 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: 1.13 (0.23), residues: 1275 helix: 2.11 (0.21), residues: 576 sheet: 0.18 (0.37), residues: 206 loop : -0.63 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 42 TYR 0.025 0.002 TYR E 54 PHE 0.018 0.002 PHE E 78 TRP 0.012 0.001 TRP O 193 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00559 / 0.25 (16958) covalent geometry : angle 0.67507 / 0.37 (24101) SS BOND : bond 0.00685 / 0.35 ( 4) SS BOND : angle 1.20780 / 0.51 ( 8) hydrogen bonds : bond 0.04843 / 3.29 ( 890) hydrogen bonds : angle 3.43791 / 2.52 ( 2267) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6699.05 seconds wall clock time: 114 minutes 20.43 seconds (6860.43 seconds total)