Starting phenix.real_space_refine on Sun Aug 24 00:25:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8evh_28629/08_2025/8evh_28629.cif Found real_map, /net/cci-nas-00/data/ceres_data/8evh_28629/08_2025/8evh_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_2025/8evh_28629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8evh_28629/08_2025/8evh_28629.map" model { file = "/net/cci-nas-00/data/ceres_data/8evh_28629/08_2025/8evh_28629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8evh_28629/08_2025/8evh_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-2.0-5787/lib/python3.9/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: 3.41, per 1000 atoms: 0.21 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: 0.84 Conformation dependent library (CDL) restraints added in 403.4 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 2.44 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: 2.93 Time building geometry restraints manager: 1.14 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=" 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 bond pdb=" C ARG B 92 " pdb=" N GLN B 93 " ideal model delta sigma weight residual 1.334 1.276 0.058 1.30e-02 5.92e+03 1.98e+01 ... (remaining 16953 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.25: 24092 7.25 - 14.50: 8 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=" O3' DC J 15 " pdb=" C3' DC J 15 " pdb=" C2' DC J 15 " ideal model delta sigma weight residual 111.50 97.89 13.61 1.50e+00 4.44e-01 8.24e+01 angle pdb=" C2' DC J 15 " pdb=" C1' DC J 15 " pdb=" N1 DC J 15 " ideal model delta sigma weight residual 113.50 100.09 13.41 1.50e+00 4.44e-01 8.00e+01 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=" C2' DG J 72 " pdb=" C1' DG J 72 " pdb=" N9 DG J 72 " ideal model delta sigma weight residual 113.50 122.09 -8.59 1.50e+00 4.44e-01 3.28e+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 2.42 2.08 0.34 2.00e-01 2.50e+01 2.87e+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: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.120 Find NCS groups from input model: 0.140 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:9.850 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 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 : 0.005 0.079 16962 Z= 0.256 Angle : 0.718 36.245 24109 Z= 0.442 Chirality : 0.047 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 aren 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 covalent geometry : bond 0.00524 (16958) covalent geometry : angle 0.71809 (24101) SS BOND : bond 0.00226 ( 4) SS BOND : angle 1.23512 ( 8) hydrogen bonds : bond 0.14513 ( 890) hydrogen bonds : angle 5.08782 ( 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 : 0.356 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: E 90 MET cc_start: 0.8647 (mmp) cc_final: 0.8424 (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 180 THR cc_start: 0.8640 (m) cc_final: 0.8440 (p) 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: -0.3850 (tmm) outliers start: 1 outliers final: 0 residues processed: 291 average time/residue: 0.7171 time to fit residues: 223.9810 Evaluate side-chains 210 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 0.428 ------------------------------------------------------------------------------- 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: 8.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 60 ASN E 125 GLN F 93 GLN M 61 GLN N 28 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 253 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.169160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.102347 restraints weight = 20609.445| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.03 r_work: 0.2952 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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 : 0.005 0.042 16962 Z= 0.209 Angle : 0.635 8.988 24109 Z= 0.361 Chirality : 0.039 0.195 2706 Planarity : 0.004 0.039 2058 Dihedral : 28.496 164.992 4560 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.88 % Allowed : 23.58 % Favored : 72.54 % 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 aren not related in a simple way. whole: 1.38 (0.24), residues: 1275 helix: 2.28 (0.21), residues: 576 sheet: 0.22 (0.35), residues: 232 loop : -0.42 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 42 TYR 0.018 0.002 TYR G 50 PHE 0.011 0.002 PHE M 256 TRP 0.015 0.001 TRP O 193 HIS 0.004 0.001 HIS N 249 Details of bonding type rmsd covalent geometry : bond 0.00482 (16958) covalent geometry : angle 0.63533 (24101) SS BOND : bond 0.00559 ( 4) SS BOND : angle 0.96162 ( 8) hydrogen bonds : bond 0.04660 ( 890) hydrogen bonds : angle 3.60028 ( 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 259 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 216 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.7433 (tpp80) REVERT: C 92 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8927 (mt-10) REVERT: D 32 GLU cc_start: 0.8510 (tm-30) cc_final: 0.8272 (tt0) REVERT: D 73 GLU cc_start: 0.8964 (tp30) cc_final: 0.8599 (tp30) REVERT: D 90 GLU cc_start: 0.9239 (OUTLIER) cc_final: 0.8299 (mt-10) REVERT: E 115 LYS cc_start: 0.9055 (mttt) cc_final: 0.8777 (mttp) REVERT: F 35 ARG cc_start: 0.8343 (mtm110) cc_final: 0.7804 (mtp85) REVERT: H 34 TYR cc_start: 0.9182 (m-80) cc_final: 0.8858 (m-80) REVERT: H 68 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8038 (tp30) REVERT: H 90 GLU cc_start: 0.9183 (OUTLIER) cc_final: 0.7884 (mp0) REVERT: M 104 GLU cc_start: 0.8726 (tt0) cc_final: 0.8331 (tt0) REVERT: M 130 ASP cc_start: 0.8803 (p0) cc_final: 0.8579 (p0) REVERT: M 163 THR cc_start: 0.8387 (m) cc_final: 0.7932 (p) REVERT: M 219 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8071 (ttp80) REVERT: M 237 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7804 (mm-30) REVERT: N 23 GLU cc_start: 0.6460 (tp30) cc_final: 0.6205 (tt0) REVERT: N 103 MET cc_start: 0.8993 (OUTLIER) cc_final: 0.8625 (ttm) REVERT: N 111 GLU cc_start: 0.8989 (OUTLIER) cc_final: 0.8506 (pp20) REVERT: N 112 ASP cc_start: 0.8451 (m-30) cc_final: 0.7839 (m-30) REVERT: N 261 LYS cc_start: 0.9017 (mtpm) cc_final: 0.8720 (mtpp) REVERT: O 198 LYS cc_start: -0.0913 (OUTLIER) cc_final: -0.1309 (ptmt) REVERT: O 225 MET cc_start: -0.0603 (ptm) cc_final: -0.2228 (tmm) outliers start: 43 outliers final: 13 residues processed: 241 average time/residue: 0.7245 time to fit residues: 188.5952 Evaluate side-chains 227 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 206 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL 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 G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU 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 218 SER Chi-restraints excluded: chain M residue 219 ARG 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 216 VAL 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: 5.9990 chunk 107 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 74 optimal weight: 7.9990 chunk 20 optimal weight: 0.6980 chunk 99 optimal weight: 10.0000 chunk 77 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** 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 = 0.4049 r_free = 0.4049 target = 0.169166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.103563 restraints weight = 20837.265| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 2.01 r_work: 0.2970 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16962 Z= 0.166 Angle : 0.579 8.790 24109 Z= 0.332 Chirality : 0.036 0.198 2706 Planarity : 0.004 0.039 2058 Dihedral : 28.472 165.889 4560 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.16 % Allowed : 24.03 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.56 (0.24), residues: 1275 helix: 2.43 (0.21), residues: 578 sheet: 0.40 (0.35), residues: 232 loop : -0.40 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 214 TYR 0.012 0.001 TYR G 50 PHE 0.010 0.001 PHE A 67 TRP 0.014 0.001 TRP O 193 HIS 0.003 0.001 HIS M 249 Details of bonding type rmsd covalent geometry : bond 0.00373 (16958) covalent geometry : angle 0.57849 (24101) SS BOND : bond 0.00511 ( 4) SS BOND : angle 0.96857 ( 8) hydrogen bonds : bond 0.03871 ( 890) hydrogen bonds : angle 3.35922 ( 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 243 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 0.456 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8773 (pm20) cc_final: 0.8483 (pm20) REVERT: A 129 ARG cc_start: 0.8625 (OUTLIER) cc_final: 0.7715 (ttp80) REVERT: B 25 ASN cc_start: 0.8537 (m-40) cc_final: 0.8105 (m-40) REVERT: C 91 GLU cc_start: 0.8932 (tt0) cc_final: 0.8324 (tt0) REVERT: C 92 GLU cc_start: 0.9155 (mt-10) cc_final: 0.8940 (mt-10) REVERT: D 44 GLN cc_start: 0.8594 (tt0) cc_final: 0.8351 (tt0) REVERT: D 68 GLU cc_start: 0.8231 (mt-10) cc_final: 0.8022 (mt-10) REVERT: D 73 GLU cc_start: 0.8912 (tp30) cc_final: 0.8606 (tp30) REVERT: D 90 GLU cc_start: 0.9212 (OUTLIER) cc_final: 0.8276 (mt-10) REVERT: E 54 TYR cc_start: 0.9282 (m-80) cc_final: 0.8982 (m-80) REVERT: E 97 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8337 (mt-10) REVERT: E 115 LYS cc_start: 0.9040 (mttt) cc_final: 0.8765 (mttp) REVERT: F 35 ARG cc_start: 0.8495 (mtm110) cc_final: 0.8245 (ttm-80) REVERT: G 64 GLU cc_start: 0.9047 (tt0) cc_final: 0.8765 (tt0) REVERT: G 95 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8719 (ttpt) REVERT: H 34 TYR cc_start: 0.9181 (m-80) cc_final: 0.8869 (m-80) REVERT: H 68 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8043 (tp30) REVERT: H 90 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.7939 (mp0) REVERT: M 104 GLU cc_start: 0.8831 (tt0) cc_final: 0.8426 (tt0) REVERT: M 163 THR cc_start: 0.8498 (m) cc_final: 0.8045 (p) REVERT: M 219 ARG cc_start: 0.8991 (mtp180) cc_final: 0.8212 (ttp80) REVERT: M 237 GLU cc_start: 0.8079 (mm-30) cc_final: 0.7866 (mm-30) REVERT: N 32 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7754 (mm-30) REVERT: N 103 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8670 (ttm) REVERT: N 111 GLU cc_start: 0.9039 (OUTLIER) cc_final: 0.8573 (pp20) REVERT: N 112 ASP cc_start: 0.8311 (m-30) cc_final: 0.7651 (m-30) REVERT: N 261 LYS cc_start: 0.9017 (mtpm) cc_final: 0.8626 (mtpp) REVERT: O 198 LYS cc_start: -0.0887 (OUTLIER) cc_final: -0.1225 (ptmt) REVERT: O 225 MET cc_start: -0.0189 (ptm) cc_final: -0.1809 (tmm) outliers start: 35 outliers final: 11 residues processed: 229 average time/residue: 0.6996 time to fit residues: 172.6779 Evaluate side-chains 222 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 203 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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 90 ASP Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 90 GLU 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 N residue 103 MET Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 140 VAL 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 13 optimal weight: 0.9980 chunk 10 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 113 optimal weight: 0.0970 chunk 129 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 17 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 140 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 overall best weight: 0.5378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4072 r_free = 0.4072 target = 0.171732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.105805 restraints weight = 20847.666| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.07 r_work: 0.2987 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.2694 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= 0.136 Angle : 0.564 9.403 24109 Z= 0.324 Chirality : 0.035 0.192 2706 Planarity : 0.004 0.041 2058 Dihedral : 28.372 167.345 4560 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.07 % Allowed : 24.66 % 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 aren not related in a simple way. whole: 1.67 (0.24), residues: 1275 helix: 2.57 (0.21), residues: 578 sheet: 0.48 (0.37), residues: 208 loop : -0.39 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 42 TYR 0.009 0.001 TYR G 57 PHE 0.010 0.001 PHE O 254 TRP 0.011 0.001 TRP O 193 HIS 0.007 0.001 HIS M 170 Details of bonding type rmsd covalent geometry : bond 0.00295 (16958) covalent geometry : angle 0.56408 (24101) SS BOND : bond 0.00348 ( 4) SS BOND : angle 0.77271 ( 8) hydrogen bonds : bond 0.03557 ( 890) hydrogen bonds : angle 3.25047 ( 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 253 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 219 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8778 (pm20) cc_final: 0.8385 (pm20) REVERT: B 25 ASN cc_start: 0.8509 (m-40) cc_final: 0.8097 (m-40) REVERT: C 20 ARG cc_start: 0.8762 (mtt-85) cc_final: 0.8552 (mtt-85) REVERT: C 91 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8343 (tt0) REVERT: C 92 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8954 (mt-10) REVERT: D 44 GLN cc_start: 0.8612 (tt0) cc_final: 0.8353 (tt0) REVERT: D 73 GLU cc_start: 0.8865 (tp30) cc_final: 0.8639 (tp30) REVERT: D 90 GLU cc_start: 0.9197 (OUTLIER) cc_final: 0.8510 (mt-10) REVERT: E 54 TYR cc_start: 0.9268 (m-80) cc_final: 0.9058 (m-80) REVERT: E 97 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8304 (mt-10) REVERT: E 123 ASP cc_start: 0.9219 (m-30) cc_final: 0.9007 (m-30) REVERT: F 35 ARG cc_start: 0.8479 (mtm110) cc_final: 0.8242 (ttm-80) REVERT: G 64 GLU cc_start: 0.9047 (tt0) cc_final: 0.8763 (tt0) REVERT: H 34 TYR cc_start: 0.9149 (m-80) cc_final: 0.8801 (m-80) REVERT: H 68 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8024 (tp30) REVERT: H 90 GLU cc_start: 0.9208 (OUTLIER) cc_final: 0.7946 (mp0) REVERT: M 104 GLU cc_start: 0.8846 (tt0) cc_final: 0.8461 (tt0) REVERT: M 163 THR cc_start: 0.8470 (m) cc_final: 0.8092 (p) REVERT: M 175 GLU cc_start: 0.8056 (pt0) cc_final: 0.7299 (pm20) REVERT: M 219 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8032 (ttp80) REVERT: N 32 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7710 (mm-30) REVERT: N 103 MET cc_start: 0.8865 (OUTLIER) cc_final: 0.8494 (ttm) REVERT: N 111 GLU cc_start: 0.8969 (OUTLIER) cc_final: 0.8625 (pp20) REVERT: N 112 ASP cc_start: 0.8181 (m-30) cc_final: 0.7647 (m-30) REVERT: N 261 LYS cc_start: 0.9000 (mtpm) cc_final: 0.8727 (mtpp) REVERT: O 225 MET cc_start: -0.0066 (ptm) cc_final: -0.1790 (tmm) outliers start: 34 outliers final: 13 residues processed: 233 average time/residue: 0.6649 time to fit residues: 167.2919 Evaluate side-chains 216 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 196 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER 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 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 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 139 THR Chi-restraints excluded: chain M residue 219 ARG Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 103 MET 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 68 optimal weight: 0.0470 chunk 17 optimal weight: 8.9990 chunk 146 optimal weight: 0.0970 chunk 10 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 overall best weight: 0.5676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN F 93 GLN G 104 GLN H 60 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 = 0.4073 r_free = 0.4073 target = 0.171576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.107298 restraints weight = 20826.412| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 1.95 r_work: 0.3011 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.3017 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= 0.136 Angle : 0.555 8.795 24109 Z= 0.319 Chirality : 0.035 0.184 2706 Planarity : 0.004 0.041 2058 Dihedral : 28.252 167.478 4560 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.71 % Allowed : 26.47 % Favored : 70.82 % 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 aren not related in a simple way. whole: 1.87 (0.24), residues: 1275 helix: 2.68 (0.21), residues: 578 sheet: 0.50 (0.35), residues: 232 loop : -0.20 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 42 TYR 0.010 0.001 TYR M 72 PHE 0.009 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 covalent geometry : bond 0.00297 (16958) covalent geometry : angle 0.55471 (24101) SS BOND : bond 0.00314 ( 4) SS BOND : angle 0.86772 ( 8) hydrogen bonds : bond 0.03453 ( 890) hydrogen bonds : angle 3.12497 ( 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 229 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 199 time to evaluate : 0.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7762 (ttp80) REVERT: A 133 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8146 (mt-10) REVERT: B 25 ASN cc_start: 0.8547 (m-40) cc_final: 0.8135 (m-40) REVERT: C 71 ARG cc_start: 0.8323 (ttm170) cc_final: 0.8115 (ttp80) REVERT: C 91 GLU cc_start: 0.8929 (tt0) cc_final: 0.8332 (tt0) REVERT: C 92 GLU cc_start: 0.9159 (mt-10) cc_final: 0.8950 (mt-10) REVERT: D 44 GLN cc_start: 0.8583 (tt0) cc_final: 0.7991 (mt0) REVERT: D 90 GLU cc_start: 0.9153 (OUTLIER) cc_final: 0.8468 (mt-10) REVERT: E 54 TYR cc_start: 0.9281 (m-80) cc_final: 0.9066 (m-80) REVERT: E 97 GLU cc_start: 0.8539 (mm-30) cc_final: 0.8304 (mt-10) REVERT: F 35 ARG cc_start: 0.8431 (mtm110) cc_final: 0.8224 (ttm-80) REVERT: G 64 GLU cc_start: 0.9103 (tt0) cc_final: 0.8828 (tt0) REVERT: H 34 TYR cc_start: 0.9115 (m-80) cc_final: 0.8808 (m-80) REVERT: H 68 GLU cc_start: 0.8447 (OUTLIER) cc_final: 0.8002 (tp30) REVERT: M 104 GLU cc_start: 0.8840 (tt0) cc_final: 0.8496 (tt0) REVERT: M 163 THR cc_start: 0.8526 (m) cc_final: 0.8160 (p) REVERT: M 175 GLU cc_start: 0.7850 (pt0) cc_final: 0.6978 (pm20) REVERT: M 219 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8155 (ttp80) REVERT: N 109 THR cc_start: 0.7607 (OUTLIER) cc_final: 0.7340 (m) REVERT: N 111 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8679 (pp20) REVERT: N 261 LYS cc_start: 0.8975 (mtpm) cc_final: 0.8748 (mtpp) REVERT: O 198 LYS cc_start: -0.0737 (OUTLIER) cc_final: -0.1192 (ptmt) REVERT: O 225 MET cc_start: 0.0131 (ptm) cc_final: -0.1457 (tmm) outliers start: 30 outliers final: 13 residues processed: 215 average time/residue: 0.6098 time to fit residues: 142.4338 Evaluate side-chains 216 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 0.274 ------------------------------------------------------------------------------- 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 95 LYS 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 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 139 THR Chi-restraints excluded: chain M residue 219 ARG Chi-restraints excluded: chain N residue 55 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 37 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 44 optimal weight: 0.8980 chunk 97 optimal weight: 5.9990 chunk 115 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 chunk 132 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN G 104 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 = 0.4063 r_free = 0.4063 target = 0.170692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.105389 restraints weight = 20877.431| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 1.97 r_work: 0.2996 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.3234 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= 0.147 Angle : 0.554 8.965 24109 Z= 0.318 Chirality : 0.035 0.181 2706 Planarity : 0.004 0.046 2058 Dihedral : 28.294 166.240 4560 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.98 % Allowed : 25.75 % Favored : 71.27 % 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 aren not related in a simple way. whole: 1.78 (0.24), residues: 1275 helix: 2.63 (0.21), residues: 578 sheet: 0.60 (0.37), residues: 208 loop : -0.34 (0.27), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 42 TYR 0.010 0.001 TYR M 72 PHE 0.010 0.001 PHE A 67 TRP 0.013 0.001 TRP O 193 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00328 (16958) covalent geometry : angle 0.55422 (24101) SS BOND : bond 0.00343 ( 4) SS BOND : angle 0.90838 ( 8) hydrogen bonds : bond 0.03573 ( 890) hydrogen bonds : angle 3.12649 ( 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 237 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.7743 (ttp80) REVERT: B 25 ASN cc_start: 0.8789 (m-40) cc_final: 0.8355 (m-40) REVERT: C 91 GLU cc_start: 0.8938 (OUTLIER) cc_final: 0.8363 (tt0) REVERT: C 92 GLU cc_start: 0.9129 (mt-10) cc_final: 0.8914 (mt-10) REVERT: D 44 GLN cc_start: 0.8583 (tt0) cc_final: 0.8081 (mt0) REVERT: D 90 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8324 (mt-10) REVERT: E 54 TYR cc_start: 0.9293 (m-80) cc_final: 0.9082 (m-80) REVERT: E 97 GLU cc_start: 0.8531 (mm-30) cc_final: 0.8285 (mt-10) REVERT: G 64 GLU cc_start: 0.9097 (tt0) cc_final: 0.8815 (tt0) REVERT: H 34 TYR cc_start: 0.9138 (m-80) cc_final: 0.8775 (m-80) REVERT: H 68 GLU cc_start: 0.8406 (OUTLIER) cc_final: 0.7966 (tp30) REVERT: M 104 GLU cc_start: 0.8848 (tt0) cc_final: 0.8529 (tt0) REVERT: M 163 THR cc_start: 0.8498 (m) cc_final: 0.8084 (p) REVERT: M 175 GLU cc_start: 0.7809 (pt0) cc_final: 0.7502 (pt0) REVERT: M 219 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8690 (mtm110) REVERT: M 235 ASN cc_start: 0.8136 (OUTLIER) cc_final: 0.7327 (t0) REVERT: M 237 GLU cc_start: 0.7902 (mm-30) cc_final: 0.7259 (mm-30) REVERT: N 32 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7745 (mt-10) REVERT: N 109 THR cc_start: 0.7678 (OUTLIER) cc_final: 0.7231 (t) REVERT: N 111 GLU cc_start: 0.8980 (pp20) cc_final: 0.8526 (pp20) REVERT: N 112 ASP cc_start: 0.7750 (m-30) cc_final: 0.7153 (m-30) REVERT: N 261 LYS cc_start: 0.8937 (mtpm) cc_final: 0.8711 (mtpp) REVERT: O 225 MET cc_start: 0.0139 (ptm) cc_final: -0.0586 (ttm) outliers start: 33 outliers final: 17 residues processed: 220 average time/residue: 0.6318 time to fit residues: 150.1036 Evaluate side-chains 218 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 C residue 95 LYS 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 48 ASP Chi-restraints excluded: chain H residue 68 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 139 THR Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 219 ARG Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 109 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 126 optimal weight: 0.8980 chunk 130 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 74 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 147 optimal weight: 20.0000 chunk 133 optimal weight: 0.5980 chunk 139 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 114 optimal weight: 8.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 38 ASN C 73 ASN D 46 HIS F 93 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.165704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.100676 restraints weight = 20604.995| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.91 r_work: 0.2906 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2771 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.3370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 16962 Z= 0.277 Angle : 0.629 9.133 24109 Z= 0.354 Chirality : 0.039 0.174 2706 Planarity : 0.005 0.056 2058 Dihedral : 28.732 163.802 4560 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.79 % Allowed : 25.11 % Favored : 71.09 % 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 aren not related in a simple way. whole: 1.40 (0.24), residues: 1275 helix: 2.20 (0.21), residues: 577 sheet: 0.58 (0.36), residues: 232 loop : -0.48 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 42 TYR 0.014 0.002 TYR G 50 PHE 0.012 0.002 PHE M 256 TRP 0.012 0.001 TRP O 193 HIS 0.004 0.001 HIS N 249 Details of bonding type rmsd covalent geometry : bond 0.00652 (16958) covalent geometry : angle 0.62841 (24101) SS BOND : bond 0.00650 ( 4) SS BOND : angle 1.10780 ( 8) hydrogen bonds : bond 0.04455 ( 890) hydrogen bonds : angle 3.37144 ( 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 241 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 199 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8812 (mm-30) cc_final: 0.8577 (mt-10) REVERT: A 133 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.7945 (mt-10) REVERT: C 91 GLU cc_start: 0.9027 (OUTLIER) cc_final: 0.8498 (tt0) REVERT: C 92 GLU cc_start: 0.9209 (mt-10) cc_final: 0.8945 (mt-10) REVERT: C 99 LYS cc_start: 0.8524 (mttt) cc_final: 0.8142 (mmmt) REVERT: D 39 TYR cc_start: 0.8580 (t80) cc_final: 0.8316 (t80) REVERT: D 44 GLN cc_start: 0.8567 (tt0) cc_final: 0.8082 (mt0) REVERT: D 90 GLU cc_start: 0.9333 (OUTLIER) cc_final: 0.8294 (mt-10) REVERT: E 97 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8329 (mt-10) REVERT: F 91 LYS cc_start: 0.9177 (tttt) cc_final: 0.8704 (ttmm) REVERT: G 95 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8755 (ttpt) REVERT: H 32 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8116 (tt0) REVERT: H 34 TYR cc_start: 0.9219 (m-80) cc_final: 0.8894 (m-80) REVERT: H 68 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8084 (tp30) REVERT: H 90 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.7996 (mp0) REVERT: M 104 GLU cc_start: 0.8908 (tt0) cc_final: 0.8519 (tt0) REVERT: M 175 GLU cc_start: 0.7965 (pt0) cc_final: 0.7729 (pt0) REVERT: M 235 ASN cc_start: 0.8141 (OUTLIER) cc_final: 0.7294 (t0) REVERT: M 237 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7292 (mm-30) REVERT: N 32 GLU cc_start: 0.8338 (mm-30) cc_final: 0.7795 (mt-10) REVERT: N 111 GLU cc_start: 0.9030 (pp20) cc_final: 0.8603 (pp20) REVERT: N 112 ASP cc_start: 0.8141 (m-30) cc_final: 0.7754 (m-30) REVERT: N 188 ARG cc_start: 0.8066 (mtm110) cc_final: 0.7003 (mtm110) REVERT: N 261 LYS cc_start: 0.8959 (mtpm) cc_final: 0.8753 (mtpp) REVERT: O 198 LYS cc_start: -0.1039 (OUTLIER) cc_final: -0.1519 (ptmt) REVERT: O 225 MET cc_start: -0.0129 (ptm) cc_final: -0.0445 (ttm) outliers start: 42 outliers final: 17 residues processed: 224 average time/residue: 0.6313 time to fit residues: 153.1317 Evaluate side-chains 225 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 199 time to evaluate : 0.465 ------------------------------------------------------------------------------- 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 E residue 87 SER Chi-restraints excluded: chain G residue 95 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 75 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 33 LEU 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 235 ASN Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 169 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 109 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 30 optimal weight: 0.5980 chunk 41 optimal weight: 0.6980 chunk 82 optimal weight: 6.9990 chunk 86 optimal weight: 60.0000 chunk 97 optimal weight: 5.9990 chunk 111 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN D 46 HIS E 108 ASN F 93 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 253 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.169370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.104656 restraints weight = 20822.661| |-----------------------------------------------------------------------------| r_work (start): 0.3175 rms_B_bonded: 2.01 r_work: 0.2961 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.3519 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= 0.148 Angle : 0.569 8.909 24109 Z= 0.325 Chirality : 0.035 0.173 2706 Planarity : 0.004 0.041 2058 Dihedral : 28.370 165.070 4560 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.71 % Allowed : 26.47 % Favored : 70.82 % 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 aren not related in a simple way. whole: 1.64 (0.24), residues: 1275 helix: 2.46 (0.21), residues: 578 sheet: 0.63 (0.36), residues: 232 loop : -0.45 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 42 TYR 0.009 0.001 TYR G 50 PHE 0.010 0.001 PHE A 67 TRP 0.013 0.001 TRP O 193 HIS 0.004 0.001 HIS M 249 Details of bonding type rmsd covalent geometry : bond 0.00330 (16958) covalent geometry : angle 0.56890 (24101) SS BOND : bond 0.00370 ( 4) SS BOND : angle 0.95447 ( 8) hydrogen bonds : bond 0.03549 ( 890) hydrogen bonds : angle 3.16109 ( 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 228 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 198 time to evaluate : 0.401 Fit side-chains revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8787 (m-40) cc_final: 0.8341 (m-40) REVERT: C 20 ARG cc_start: 0.8791 (mtt-85) cc_final: 0.8505 (mtt-85) REVERT: C 91 GLU cc_start: 0.8975 (OUTLIER) cc_final: 0.8427 (tt0) REVERT: C 92 GLU cc_start: 0.9148 (mt-10) cc_final: 0.8919 (mt-10) REVERT: D 44 GLN cc_start: 0.8611 (tt0) cc_final: 0.8103 (mt0) REVERT: D 90 GLU cc_start: 0.9223 (OUTLIER) cc_final: 0.8331 (mt-10) REVERT: E 97 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8312 (mt-10) REVERT: F 91 LYS cc_start: 0.9142 (tttt) cc_final: 0.8639 (ttmm) REVERT: G 15 LYS cc_start: 0.7966 (mtpp) cc_final: 0.7734 (mtmm) REVERT: G 95 LYS cc_start: 0.9110 (OUTLIER) cc_final: 0.8722 (ttpt) REVERT: H 34 TYR cc_start: 0.9121 (m-80) cc_final: 0.8747 (m-80) REVERT: H 68 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8048 (tp30) REVERT: H 90 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8013 (mp0) REVERT: M 32 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8296 (mm-30) REVERT: M 104 GLU cc_start: 0.8863 (tt0) cc_final: 0.8523 (tt0) REVERT: M 175 GLU cc_start: 0.7870 (pt0) cc_final: 0.7636 (pt0) REVERT: M 235 ASN cc_start: 0.8165 (OUTLIER) cc_final: 0.7290 (t0) REVERT: M 237 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7296 (mm-30) REVERT: N 32 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7684 (mt-10) REVERT: N 65 GLN cc_start: 0.8786 (mt0) cc_final: 0.8202 (mp10) REVERT: N 104 GLU cc_start: 0.8119 (tp30) cc_final: 0.7874 (mm-30) REVERT: N 109 THR cc_start: 0.7900 (m) cc_final: 0.7453 (t) REVERT: N 111 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8609 (pp20) REVERT: N 112 ASP cc_start: 0.7875 (m-30) cc_final: 0.7473 (m-30) REVERT: N 169 MET cc_start: 0.8551 (ptp) cc_final: 0.8219 (ptm) REVERT: N 172 SER cc_start: 0.8297 (m) cc_final: 0.7839 (p) REVERT: N 261 LYS cc_start: 0.8921 (mtpm) cc_final: 0.8721 (mtpp) outliers start: 30 outliers final: 14 residues processed: 215 average time/residue: 0.6673 time to fit residues: 154.8427 Evaluate side-chains 211 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 190 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 C residue 95 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 95 LYS 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 33 LEU 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 235 ASN 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 253 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 102 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 132 optimal weight: 0.5980 chunk 129 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 142 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 139 optimal weight: 0.9990 chunk 117 optimal weight: 0.0770 chunk 64 optimal weight: 0.8980 chunk 130 optimal weight: 2.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN D 46 HIS F 93 GLN H 46 HIS ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.169860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.105188 restraints weight = 20750.619| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.01 r_work: 0.2980 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16962 Z= 0.142 Angle : 0.567 9.159 24109 Z= 0.324 Chirality : 0.035 0.172 2706 Planarity : 0.004 0.047 2058 Dihedral : 28.307 165.086 4560 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.26 % Allowed : 27.19 % 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 aren not related in a simple way. whole: 1.68 (0.24), residues: 1275 helix: 2.57 (0.21), residues: 577 sheet: 0.59 (0.37), residues: 208 loop : -0.44 (0.27), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG A 42 TYR 0.013 0.001 TYR O 252 PHE 0.012 0.001 PHE O 254 TRP 0.013 0.001 TRP O 193 HIS 0.004 0.001 HIS M 249 Details of bonding type rmsd covalent geometry : bond 0.00313 (16958) covalent geometry : angle 0.56644 (24101) SS BOND : bond 0.00315 ( 4) SS BOND : angle 0.73986 ( 8) hydrogen bonds : bond 0.03423 ( 890) hydrogen bonds : angle 3.11197 ( 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 216 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 191 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8650 (OUTLIER) cc_final: 0.7780 (ttp80) REVERT: B 25 ASN cc_start: 0.8748 (m-40) cc_final: 0.8316 (m-40) REVERT: C 71 ARG cc_start: 0.8095 (ttp80) cc_final: 0.7783 (ttp80) REVERT: C 91 GLU cc_start: 0.8954 (OUTLIER) cc_final: 0.8396 (tt0) REVERT: C 92 GLU cc_start: 0.9131 (mt-10) cc_final: 0.8909 (mt-10) REVERT: D 44 GLN cc_start: 0.8589 (tt0) cc_final: 0.8094 (mt0) REVERT: D 90 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8484 (mt-10) REVERT: E 97 GLU cc_start: 0.8574 (mm-30) cc_final: 0.8313 (mt-10) REVERT: F 91 LYS cc_start: 0.9098 (tttt) cc_final: 0.8607 (ttmm) REVERT: G 95 LYS cc_start: 0.9099 (OUTLIER) cc_final: 0.8700 (ttpt) REVERT: H 34 TYR cc_start: 0.9104 (m-80) cc_final: 0.8744 (m-80) REVERT: H 68 GLU cc_start: 0.8405 (OUTLIER) cc_final: 0.7971 (tp30) REVERT: H 90 GLU cc_start: 0.9140 (OUTLIER) cc_final: 0.7987 (mp0) REVERT: M 32 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8308 (mm-30) REVERT: M 104 GLU cc_start: 0.8862 (tt0) cc_final: 0.8532 (tt0) REVERT: M 219 ARG cc_start: 0.8769 (mtm110) cc_final: 0.8056 (ttp80) REVERT: N 32 GLU cc_start: 0.8234 (mm-30) cc_final: 0.7673 (mt-10) REVERT: N 109 THR cc_start: 0.7880 (m) cc_final: 0.7370 (t) REVERT: N 111 GLU cc_start: 0.9062 (pp20) cc_final: 0.8609 (pp20) REVERT: N 112 ASP cc_start: 0.7877 (m-30) cc_final: 0.7404 (m-30) REVERT: N 169 MET cc_start: 0.8560 (ptp) cc_final: 0.8249 (ptm) REVERT: N 240 ASP cc_start: 0.8623 (m-30) cc_final: 0.8150 (m-30) REVERT: O 198 LYS cc_start: -0.1037 (OUTLIER) cc_final: -0.1496 (ptmt) outliers start: 25 outliers final: 14 residues processed: 207 average time/residue: 0.6916 time to fit residues: 154.4791 Evaluate side-chains 204 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 C residue 95 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 95 LYS 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 139 THR Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 165 SER 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 211 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.0770 chunk 47 optimal weight: 0.6980 chunk 146 optimal weight: 7.9990 chunk 108 optimal weight: 8.9990 chunk 112 optimal weight: 6.9990 chunk 120 optimal weight: 0.9990 chunk 134 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 138 optimal weight: 0.7980 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 253 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.169666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.105036 restraints weight = 20677.326| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.07 r_work: 0.2970 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 16962 Z= 0.153 Angle : 0.569 8.962 24109 Z= 0.325 Chirality : 0.035 0.173 2706 Planarity : 0.004 0.058 2058 Dihedral : 28.316 164.377 4560 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.44 % Allowed : 26.92 % 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 aren not related in a simple way. whole: 1.70 (0.24), residues: 1275 helix: 2.54 (0.21), residues: 577 sheet: 0.58 (0.35), residues: 232 loop : -0.39 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG A 42 TYR 0.016 0.001 TYR E 54 PHE 0.010 0.001 PHE O 254 TRP 0.014 0.001 TRP O 193 HIS 0.004 0.001 HIS M 249 Details of bonding type rmsd covalent geometry : bond 0.00343 (16958) covalent geometry : angle 0.56848 (24101) SS BOND : bond 0.00422 ( 4) SS BOND : angle 0.82118 ( 8) hydrogen bonds : bond 0.03559 ( 890) hydrogen bonds : angle 3.12190 ( 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 213 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 186 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8644 (OUTLIER) cc_final: 0.7765 (ttp80) REVERT: B 25 ASN cc_start: 0.8787 (m-40) cc_final: 0.8327 (m-40) REVERT: C 91 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8393 (tt0) REVERT: C 92 GLU cc_start: 0.9135 (mt-10) cc_final: 0.8920 (mt-10) REVERT: D 44 GLN cc_start: 0.8586 (tt0) cc_final: 0.8083 (mt0) REVERT: D 90 GLU cc_start: 0.9222 (OUTLIER) cc_final: 0.8334 (mt-10) REVERT: E 97 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8294 (mt-10) REVERT: F 91 LYS cc_start: 0.9100 (tttt) cc_final: 0.8619 (ttmm) REVERT: G 95 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8692 (ttpt) REVERT: H 34 TYR cc_start: 0.9131 (m-80) cc_final: 0.8768 (m-80) REVERT: H 68 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7975 (tp30) REVERT: H 90 GLU cc_start: 0.9142 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: M 32 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8300 (mm-30) REVERT: M 104 GLU cc_start: 0.8825 (tt0) cc_final: 0.8524 (tt0) REVERT: M 219 ARG cc_start: 0.8814 (mtm110) cc_final: 0.8087 (ttp80) REVERT: M 237 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7926 (mm-30) REVERT: N 109 THR cc_start: 0.7847 (m) cc_final: 0.7407 (t) REVERT: N 112 ASP cc_start: 0.7862 (m-30) cc_final: 0.7581 (m-30) REVERT: N 169 MET cc_start: 0.8516 (ptp) cc_final: 0.8197 (ptm) REVERT: N 240 ASP cc_start: 0.8662 (m-30) cc_final: 0.8180 (m-30) REVERT: O 198 LYS cc_start: -0.1287 (OUTLIER) cc_final: -0.1742 (ptmt) outliers start: 27 outliers final: 16 residues processed: 203 average time/residue: 0.6351 time to fit residues: 139.3437 Evaluate side-chains 213 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 190 time to evaluate : 0.374 ------------------------------------------------------------------------------- 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 C residue 95 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 95 LYS 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 33 LEU 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 N residue 55 THR Chi-restraints excluded: chain N residue 165 SER 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 211 LEU Chi-restraints excluded: chain O residue 253 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 81 optimal weight: 6.9990 chunk 32 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 149 optimal weight: 20.0000 chunk 85 optimal weight: 50.0000 chunk 49 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 144 optimal weight: 1.9990 chunk 151 optimal weight: 40.0000 chunk 42 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 27 GLN C 104 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4046 r_free = 0.4046 target = 0.169200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.104336 restraints weight = 20685.180| |-----------------------------------------------------------------------------| r_work (start): 0.3194 rms_B_bonded: 2.00 r_work: 0.2981 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.167 16962 Z= 0.208 Angle : 0.793 59.132 24109 Z= 0.461 Chirality : 0.037 0.536 2706 Planarity : 0.004 0.050 2058 Dihedral : 28.314 164.385 4560 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 2.26 % Allowed : 26.56 % Favored : 71.18 % Cbeta Deviations : 0.08 % 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 aren not related in a simple way. whole: 1.69 (0.24), residues: 1275 helix: 2.53 (0.21), residues: 577 sheet: 0.57 (0.35), residues: 232 loop : -0.40 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG A 42 TYR 0.015 0.001 TYR E 54 PHE 0.010 0.001 PHE O 254 TRP 0.013 0.001 TRP O 193 HIS 0.004 0.001 HIS M 249 Details of bonding type rmsd covalent geometry : bond 0.00443 (16958) covalent geometry : angle 0.79259 (24101) SS BOND : bond 0.00672 ( 4) SS BOND : angle 0.99745 ( 8) hydrogen bonds : bond 0.03628 ( 890) hydrogen bonds : angle 3.12141 ( 2267) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6120.52 seconds wall clock time: 104 minutes 31.77 seconds (6271.77 seconds total)