Starting phenix.real_space_refine on Sat May 17 12:46:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8evh_28629/05_2025/8evh_28629.cif Found real_map, /net/cci-nas-00/data/ceres_data/8evh_28629/05_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_28629/05_2025/8evh_28629.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8evh_28629/05_2025/8evh_28629.map" model { file = "/net/cci-nas-00/data/ceres_data/8evh_28629/05_2025/8evh_28629.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8evh_28629/05_2025/8evh_28629.cif" } resolution = 2.85 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 9.71, per 1000 atoms: 0.60 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: 4.31 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 7.30 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: 6.93 Time building geometry restraints manager: 5.00 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 43.900 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 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:11.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.990 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.015 0.001 TRP O 193 HIS 0.004 0.001 HIS D 46 PHE 0.025 0.002 PHE O 254 TYR 0.028 0.001 TYR O 175 ARG 0.011 0.000 ARG M 176 Details of bonding type rmsd hydrogen bonds : bond 0.14513 ( 890) hydrogen bonds : angle 5.08782 ( 2267) SS BOND : bond 0.00226 ( 4) SS BOND : angle 1.23512 ( 8) covalent geometry : bond 0.00524 (16958) covalent geometry : angle 0.71809 (24101) *********************** 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 : 1.296 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: 1.6970 time to fit residues: 531.4035 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 : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- 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 = 0.4026 r_free = 0.4026 target = 0.167000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.101200 restraints weight = 20638.995| |-----------------------------------------------------------------------------| r_work (start): 0.3152 rms_B_bonded: 1.96 r_work: 0.2931 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 16962 Z= 0.248 Angle : 0.643 9.079 24109 Z= 0.365 Chirality : 0.040 0.200 2706 Planarity : 0.005 0.048 2058 Dihedral : 28.648 164.712 4560 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.61 % Allowed : 23.85 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.24), residues: 1275 helix: 2.21 (0.22), residues: 577 sheet: 0.27 (0.35), residues: 232 loop : -0.48 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP O 193 HIS 0.004 0.001 HIS N 249 PHE 0.013 0.002 PHE O 254 TYR 0.018 0.002 TYR G 50 ARG 0.007 0.001 ARG O 214 Details of bonding type rmsd hydrogen bonds : bond 0.04648 ( 890) hydrogen bonds : angle 3.61516 ( 2267) SS BOND : bond 0.00628 ( 4) SS BOND : angle 1.02462 ( 8) covalent geometry : bond 0.00577 (16958) covalent geometry : angle 0.64252 (24101) *********************** 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 252 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 1.442 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9231 (tttt) cc_final: 0.8990 (ttpp) REVERT: A 129 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.7507 (tpp80) REVERT: B 77 LYS cc_start: 0.8942 (mttt) cc_final: 0.8717 (mttp) REVERT: C 91 GLU cc_start: 0.8921 (tt0) cc_final: 0.8315 (tt0) REVERT: C 92 GLU cc_start: 0.9166 (mt-10) cc_final: 0.8905 (mt-10) REVERT: D 32 GLU cc_start: 0.8560 (tm-30) cc_final: 0.8333 (tt0) REVERT: D 73 GLU cc_start: 0.8973 (tp30) cc_final: 0.8596 (tp30) REVERT: D 90 GLU cc_start: 0.9295 (OUTLIER) cc_final: 0.8242 (mt-10) REVERT: E 115 LYS cc_start: 0.9077 (mttt) cc_final: 0.8812 (mttp) REVERT: F 35 ARG cc_start: 0.8474 (mtm110) cc_final: 0.7873 (mtp85) REVERT: F 91 LYS cc_start: 0.9160 (tttt) cc_final: 0.8603 (ttmm) REVERT: G 64 GLU cc_start: 0.9010 (tt0) cc_final: 0.8691 (tt0) REVERT: H 34 TYR cc_start: 0.9230 (m-80) cc_final: 0.8897 (m-80) REVERT: H 68 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.8066 (tp30) REVERT: H 90 GLU cc_start: 0.9192 (OUTLIER) cc_final: 0.7992 (mp0) REVERT: M 103 MET cc_start: 0.9284 (OUTLIER) cc_final: 0.9022 (ttp) REVERT: M 104 GLU cc_start: 0.8831 (tt0) cc_final: 0.8304 (tt0) REVERT: M 163 THR cc_start: 0.8503 (m) cc_final: 0.8009 (p) REVERT: M 219 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.7918 (ttp80) REVERT: M 235 ASN cc_start: 0.8352 (OUTLIER) cc_final: 0.7131 (t0) REVERT: M 237 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7242 (mm-30) REVERT: N 32 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7738 (mm-30) REVERT: N 103 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8669 (ttm) REVERT: N 111 GLU cc_start: 0.8992 (OUTLIER) cc_final: 0.8474 (pp20) REVERT: N 112 ASP cc_start: 0.8428 (m-30) cc_final: 0.7832 (m-30) REVERT: N 261 LYS cc_start: 0.9074 (mtpm) cc_final: 0.8789 (mtpp) REVERT: O 225 MET cc_start: -0.0317 (ptm) cc_final: -0.2407 (tmm) outliers start: 40 outliers final: 11 residues processed: 235 average time/residue: 1.6775 time to fit residues: 425.4265 Evaluate side-chains 221 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 201 time to evaluate : 1.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 75 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 103 MET Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 219 ARG Chi-restraints excluded: chain M residue 235 ASN 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 239 ASP 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 47 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 139 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 145 optimal weight: 20.0000 chunk 108 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 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 = 0.4054 r_free = 0.4054 target = 0.169655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.104740 restraints weight = 20664.575| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 1.95 r_work: 0.2980 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2847 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2738 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= 0.151 Angle : 0.566 8.763 24109 Z= 0.326 Chirality : 0.036 0.194 2706 Planarity : 0.004 0.042 2058 Dihedral : 28.453 166.056 4560 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.43 % Allowed : 24.03 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.24), residues: 1275 helix: 2.48 (0.21), residues: 578 sheet: 0.44 (0.35), residues: 232 loop : -0.39 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 193 HIS 0.004 0.001 HIS B 75 PHE 0.021 0.001 PHE O 254 TYR 0.010 0.001 TYR G 57 ARG 0.006 0.000 ARG O 214 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 890) hydrogen bonds : angle 3.31137 ( 2267) SS BOND : bond 0.00362 ( 4) SS BOND : angle 0.86135 ( 8) covalent geometry : bond 0.00334 (16958) covalent geometry : angle 0.56602 (24101) *********************** 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 249 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 211 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9193 (tttt) cc_final: 0.8937 (ttpp) REVERT: A 129 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.7765 (ttp80) REVERT: A 133 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8177 (mt-10) REVERT: B 25 ASN cc_start: 0.8640 (m-40) cc_final: 0.8220 (m-40) REVERT: C 91 GLU cc_start: 0.8932 (tt0) cc_final: 0.8336 (tt0) REVERT: C 92 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8933 (mt-10) REVERT: D 44 GLN cc_start: 0.8551 (tt0) cc_final: 0.8323 (tt0) REVERT: D 73 GLU cc_start: 0.8909 (tp30) cc_final: 0.8626 (tp30) REVERT: D 90 GLU cc_start: 0.9190 (OUTLIER) cc_final: 0.8508 (mt-10) REVERT: E 97 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8307 (mt-10) REVERT: E 115 LYS cc_start: 0.9019 (mttt) cc_final: 0.8758 (mttp) REVERT: E 123 ASP cc_start: 0.9201 (m-30) cc_final: 0.8975 (m-30) REVERT: F 35 ARG cc_start: 0.8487 (mtm110) cc_final: 0.8249 (ttm-80) REVERT: F 91 LYS cc_start: 0.9132 (tttt) cc_final: 0.8607 (ttmm) REVERT: H 34 TYR cc_start: 0.9161 (m-80) cc_final: 0.8791 (m-80) REVERT: H 68 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.8031 (tp30) REVERT: H 90 GLU cc_start: 0.9220 (OUTLIER) cc_final: 0.7970 (mp0) REVERT: M 103 MET cc_start: 0.9290 (OUTLIER) cc_final: 0.9030 (ttp) REVERT: M 104 GLU cc_start: 0.8827 (tt0) cc_final: 0.8499 (tt0) REVERT: M 163 THR cc_start: 0.8509 (m) cc_final: 0.8057 (p) REVERT: M 219 ARG cc_start: 0.8997 (OUTLIER) cc_final: 0.8211 (ttp80) REVERT: M 235 ASN cc_start: 0.8252 (OUTLIER) cc_final: 0.7261 (t0) REVERT: M 237 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7401 (mm-30) REVERT: N 32 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7802 (mm-30) REVERT: N 103 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8648 (ttm) REVERT: N 111 GLU cc_start: 0.9042 (OUTLIER) cc_final: 0.8580 (pp20) REVERT: N 112 ASP cc_start: 0.8276 (m-30) cc_final: 0.7755 (m-30) REVERT: N 180 THR cc_start: 0.8809 (m) cc_final: 0.8328 (p) REVERT: N 261 LYS cc_start: 0.8993 (mtpm) cc_final: 0.8747 (mtpp) REVERT: O 198 LYS cc_start: -0.0895 (OUTLIER) cc_final: -0.1297 (ptmt) REVERT: O 225 MET cc_start: -0.0088 (ptm) cc_final: -0.2107 (tmm) outliers start: 38 outliers final: 15 residues processed: 236 average time/residue: 1.5328 time to fit residues: 393.2179 Evaluate side-chains 228 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR 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 A residue 133 GLU 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 H residue 53 SER 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 32 GLU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 103 MET Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 219 ARG Chi-restraints excluded: chain M residue 235 ASN 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 9 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 81 optimal weight: 6.9990 chunk 115 optimal weight: 0.8980 chunk 148 optimal weight: 8.9990 chunk 119 optimal weight: 1.9990 chunk 144 optimal weight: 7.9990 chunk 147 optimal weight: 8.9990 chunk 17 optimal weight: 8.9990 chunk 87 optimal weight: 20.0000 chunk 120 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 108 ASN B 27 GLN G 104 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 253 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 = 0.4033 r_free = 0.4033 target = 0.167875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.102603 restraints weight = 20536.242| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.02 r_work: 0.2936 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.3007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16962 Z= 0.179 Angle : 0.582 8.617 24109 Z= 0.332 Chirality : 0.036 0.190 2706 Planarity : 0.004 0.047 2058 Dihedral : 28.537 165.279 4560 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.88 % Allowed : 24.39 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.24), residues: 1275 helix: 2.39 (0.21), residues: 577 sheet: 0.55 (0.36), residues: 230 loop : -0.44 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 193 HIS 0.004 0.001 HIS N 249 PHE 0.011 0.001 PHE A 67 TYR 0.013 0.001 TYR G 50 ARG 0.005 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03970 ( 890) hydrogen bonds : angle 3.29121 ( 2267) SS BOND : bond 0.00539 ( 4) SS BOND : angle 0.92512 ( 8) covalent geometry : bond 0.00410 (16958) covalent geometry : angle 0.58142 (24101) *********************** 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 256 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 1.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9249 (tttt) cc_final: 0.8988 (ttpp) REVERT: A 129 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.7628 (tpp80) REVERT: A 133 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7915 (mt-10) REVERT: B 25 ASN cc_start: 0.8850 (m-40) cc_final: 0.8359 (m-40) REVERT: B 92 ARG cc_start: 0.8819 (OUTLIER) cc_final: 0.8290 (ttp80) REVERT: C 20 ARG cc_start: 0.8834 (mtt-85) cc_final: 0.8552 (mtt-85) REVERT: C 71 ARG cc_start: 0.8315 (OUTLIER) cc_final: 0.8085 (ttp80) REVERT: C 74 LYS cc_start: 0.9028 (mttt) cc_final: 0.8827 (mppt) REVERT: C 91 GLU cc_start: 0.8960 (tt0) cc_final: 0.8384 (tt0) REVERT: C 92 GLU cc_start: 0.9128 (mt-10) cc_final: 0.8907 (mt-10) REVERT: D 44 GLN cc_start: 0.8495 (tt0) cc_final: 0.7949 (mt0) REVERT: D 73 GLU cc_start: 0.8925 (tp30) cc_final: 0.8695 (tp30) REVERT: D 90 GLU cc_start: 0.9245 (OUTLIER) cc_final: 0.8206 (mt-10) REVERT: E 97 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8297 (mt-10) REVERT: E 115 LYS cc_start: 0.9055 (mttt) cc_final: 0.8789 (mttp) REVERT: E 123 ASP cc_start: 0.9249 (m-30) cc_final: 0.9036 (m-30) REVERT: F 91 LYS cc_start: 0.9141 (tttt) cc_final: 0.8579 (ttmm) REVERT: H 34 TYR cc_start: 0.9202 (m-80) cc_final: 0.8830 (m-80) REVERT: H 68 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8039 (tp30) REVERT: H 90 GLU cc_start: 0.9197 (OUTLIER) cc_final: 0.7932 (mp0) REVERT: M 103 MET cc_start: 0.9325 (OUTLIER) cc_final: 0.9053 (ttp) REVERT: M 104 GLU cc_start: 0.8888 (tt0) cc_final: 0.8533 (tt0) REVERT: M 219 ARG cc_start: 0.8946 (OUTLIER) cc_final: 0.8012 (ttp80) REVERT: M 235 ASN cc_start: 0.8211 (OUTLIER) cc_final: 0.7040 (t0) REVERT: M 237 GLU cc_start: 0.8090 (mm-30) cc_final: 0.7339 (mm-30) REVERT: N 23 GLU cc_start: 0.6100 (OUTLIER) cc_final: 0.5409 (tp30) REVERT: N 32 GLU cc_start: 0.8294 (mm-30) cc_final: 0.7744 (mm-30) REVERT: N 42 MET cc_start: 0.9189 (ptp) cc_final: 0.8813 (mpp) REVERT: N 103 MET cc_start: 0.8935 (ttp) cc_final: 0.8723 (ttm) REVERT: N 111 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8532 (pp20) REVERT: N 112 ASP cc_start: 0.8173 (m-30) cc_final: 0.7701 (m-30) REVERT: N 240 ASP cc_start: 0.8865 (m-30) cc_final: 0.8276 (m-30) REVERT: N 261 LYS cc_start: 0.8955 (mtpm) cc_final: 0.8745 (mtpp) REVERT: O 198 LYS cc_start: -0.0964 (OUTLIER) cc_final: -0.1414 (ptmt) REVERT: O 225 MET cc_start: -0.0018 (ptm) cc_final: -0.1767 (tmm) outliers start: 43 outliers final: 17 residues processed: 234 average time/residue: 1.5980 time to fit residues: 404.2398 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 : 1.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 71 ARG 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 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 62 THR Chi-restraints excluded: chain M residue 103 MET Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 219 ARG Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 239 ASP Chi-restraints excluded: chain O residue 174 LEU Chi-restraints excluded: chain O residue 198 LYS Chi-restraints excluded: chain O residue 211 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 134 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 131 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 96 optimal weight: 5.9990 chunk 123 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 F 93 GLN G 104 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 253 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.163394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.097890 restraints weight = 20746.193| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.96 r_work: 0.2862 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2726 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 16962 Z= 0.330 Angle : 0.664 8.947 24109 Z= 0.375 Chirality : 0.042 0.179 2706 Planarity : 0.005 0.040 2058 Dihedral : 29.104 162.808 4560 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.61 % Allowed : 23.22 % Favored : 72.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.24), residues: 1275 helix: 1.93 (0.21), residues: 574 sheet: 0.48 (0.36), residues: 232 loop : -0.66 (0.28), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 193 HIS 0.004 0.001 HIS N 249 PHE 0.013 0.002 PHE E 78 TYR 0.015 0.002 TYR G 50 ARG 0.010 0.001 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.04972 ( 890) hydrogen bonds : angle 3.55620 ( 2267) SS BOND : bond 0.00784 ( 4) SS BOND : angle 1.14404 ( 8) covalent geometry : bond 0.00777 (16958) covalent geometry : angle 0.66397 (24101) *********************** 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 243 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 192 time to evaluate : 1.374 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9313 (tttt) cc_final: 0.9019 (ttpp) REVERT: A 97 GLU cc_start: 0.8861 (mm-30) cc_final: 0.8613 (mt-10) REVERT: A 115 LYS cc_start: 0.8988 (OUTLIER) cc_final: 0.8606 (mmtp) REVERT: A 129 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7710 (tpp80) REVERT: C 71 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7999 (ttp80) REVERT: C 91 GLU cc_start: 0.9046 (tt0) cc_final: 0.8519 (tt0) REVERT: C 92 GLU cc_start: 0.9252 (mt-10) cc_final: 0.8992 (mt-10) REVERT: C 99 LYS cc_start: 0.8546 (mttt) cc_final: 0.8144 (mmmt) REVERT: D 39 TYR cc_start: 0.8607 (t80) cc_final: 0.8275 (t80) REVERT: D 44 GLN cc_start: 0.8535 (tt0) cc_final: 0.8024 (mt0) REVERT: D 59 MET cc_start: 0.9508 (mmm) cc_final: 0.9233 (mmp) REVERT: D 90 GLU cc_start: 0.9329 (OUTLIER) cc_final: 0.8263 (mp0) REVERT: E 97 GLU cc_start: 0.8656 (mm-30) cc_final: 0.8363 (mt-10) REVERT: E 115 LYS cc_start: 0.9098 (mttt) cc_final: 0.8843 (mttp) REVERT: F 77 LYS cc_start: 0.9131 (OUTLIER) cc_final: 0.8850 (mttt) REVERT: F 91 LYS cc_start: 0.9171 (tttt) cc_final: 0.8651 (ttmm) REVERT: G 51 MET cc_start: 0.8977 (OUTLIER) cc_final: 0.8529 (tpt) REVERT: H 32 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8134 (tt0) REVERT: H 34 TYR cc_start: 0.9246 (m-80) cc_final: 0.8935 (m-80) REVERT: H 68 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8086 (tp30) REVERT: H 90 GLU cc_start: 0.9245 (OUTLIER) cc_final: 0.8150 (mp0) REVERT: M 32 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8299 (mm-30) REVERT: M 103 MET cc_start: 0.9354 (OUTLIER) cc_final: 0.8983 (ttp) REVERT: M 104 GLU cc_start: 0.8914 (tt0) cc_final: 0.8525 (tt0) REVERT: M 235 ASN cc_start: 0.8212 (OUTLIER) cc_final: 0.7600 (t0) REVERT: M 237 GLU cc_start: 0.8121 (mm-30) cc_final: 0.7528 (mm-30) REVERT: N 23 GLU cc_start: 0.6265 (OUTLIER) cc_final: 0.5447 (tp30) REVERT: N 42 MET cc_start: 0.9142 (ptp) cc_final: 0.8773 (mpp) REVERT: N 103 MET cc_start: 0.9017 (ttp) cc_final: 0.8767 (ttm) REVERT: N 111 GLU cc_start: 0.9028 (OUTLIER) cc_final: 0.8482 (pp20) REVERT: N 112 ASP cc_start: 0.8450 (m-30) cc_final: 0.7965 (m-30) REVERT: O 198 LYS cc_start: -0.0936 (OUTLIER) cc_final: -0.1327 (ptmt) REVERT: O 225 MET cc_start: 0.0721 (ptm) cc_final: -0.1534 (tmm) outliers start: 51 outliers final: 22 residues processed: 218 average time/residue: 1.6519 time to fit residues: 389.3493 Evaluate side-chains 233 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 196 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 103 MET 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 235 ASN Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 138 VAL 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 174 LEU Chi-restraints excluded: chain O residue 198 LYS Chi-restraints excluded: chain O residue 253 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 144 optimal weight: 6.9990 chunk 93 optimal weight: 3.9990 chunk 143 optimal weight: 0.9990 chunk 26 optimal weight: 0.5980 chunk 119 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 136 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 135 optimal weight: 3.9990 chunk 87 optimal weight: 20.0000 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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 G 104 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 253 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.167505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.102963 restraints weight = 20654.941| |-----------------------------------------------------------------------------| r_work (start): 0.3157 rms_B_bonded: 1.88 r_work: 0.2938 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.3520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16962 Z= 0.164 Angle : 0.573 8.709 24109 Z= 0.330 Chirality : 0.036 0.173 2706 Planarity : 0.004 0.039 2058 Dihedral : 28.623 164.281 4560 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.52 % Allowed : 23.85 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.24), residues: 1275 helix: 2.32 (0.21), residues: 577 sheet: 0.59 (0.36), residues: 232 loop : -0.56 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 193 HIS 0.004 0.001 HIS B 75 PHE 0.011 0.001 PHE A 67 TYR 0.014 0.001 TYR O 252 ARG 0.011 0.001 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03695 ( 890) hydrogen bonds : angle 3.25790 ( 2267) SS BOND : bond 0.00451 ( 4) SS BOND : angle 0.95268 ( 8) covalent geometry : bond 0.00367 (16958) covalent geometry : angle 0.57275 (24101) *********************** 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 241 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 202 time to evaluate : 1.500 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9281 (tttt) cc_final: 0.9036 (ttpp) REVERT: A 133 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7963 (mt-10) REVERT: B 25 ASN cc_start: 0.8884 (m-40) cc_final: 0.8399 (m-40) REVERT: C 71 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.8047 (ttp80) REVERT: C 91 GLU cc_start: 0.9006 (tt0) cc_final: 0.8518 (tt0) REVERT: C 92 GLU cc_start: 0.9154 (mt-10) cc_final: 0.8926 (mt-10) REVERT: D 44 GLN cc_start: 0.8507 (tt0) cc_final: 0.8002 (mt0) REVERT: D 59 MET cc_start: 0.9435 (mmm) cc_final: 0.9153 (mmp) REVERT: D 90 GLU cc_start: 0.9271 (OUTLIER) cc_final: 0.8374 (mt-10) REVERT: E 97 GLU cc_start: 0.8627 (mm-30) cc_final: 0.8343 (mt-10) REVERT: F 77 LYS cc_start: 0.9076 (OUTLIER) cc_final: 0.8842 (mttt) REVERT: F 91 LYS cc_start: 0.9148 (tttt) cc_final: 0.8643 (ttmm) REVERT: G 51 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8341 (tpt) REVERT: H 34 TYR cc_start: 0.9141 (m-80) cc_final: 0.8775 (m-80) REVERT: H 68 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8037 (tp30) REVERT: H 90 GLU cc_start: 0.9239 (OUTLIER) cc_final: 0.7998 (mp0) REVERT: M 32 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.8275 (mm-30) REVERT: M 103 MET cc_start: 0.9329 (OUTLIER) cc_final: 0.8980 (ttp) REVERT: M 104 GLU cc_start: 0.8901 (tt0) cc_final: 0.8521 (tt0) REVERT: M 175 GLU cc_start: 0.8021 (pt0) cc_final: 0.7323 (pm20) REVERT: M 235 ASN cc_start: 0.8189 (OUTLIER) cc_final: 0.7318 (t0) REVERT: M 237 GLU cc_start: 0.8169 (mm-30) cc_final: 0.7409 (mm-30) REVERT: N 32 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7820 (mt-10) REVERT: N 42 MET cc_start: 0.9065 (ptp) cc_final: 0.8781 (mpp) REVERT: N 111 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8501 (pp20) REVERT: N 112 ASP cc_start: 0.8345 (m-30) cc_final: 0.7927 (m-30) REVERT: N 240 ASP cc_start: 0.8720 (m-30) cc_final: 0.8119 (m-30) REVERT: O 198 LYS cc_start: -0.1266 (OUTLIER) cc_final: -0.1703 (ptmt) REVERT: O 225 MET cc_start: 0.0303 (ptm) cc_final: -0.1216 (tmm) outliers start: 39 outliers final: 18 residues processed: 226 average time/residue: 1.5143 time to fit residues: 371.3038 Evaluate side-chains 227 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 197 time to evaluate : 1.504 ------------------------------------------------------------------------------- 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 71 ARG Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 51 MET 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 32 GLU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 103 MET 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 55 THR Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 140 VAL Chi-restraints excluded: chain N residue 192 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 129 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 70 optimal weight: 0.9980 chunk 149 optimal weight: 6.9990 chunk 68 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 76 GLN C 104 GLN G 104 GLN H 46 HIS ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 253 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 = 0.4035 r_free = 0.4035 target = 0.168207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.103142 restraints weight = 20773.151| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.01 r_work: 0.2955 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3606 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= 0.150 Angle : 0.566 8.932 24109 Z= 0.326 Chirality : 0.035 0.171 2706 Planarity : 0.004 0.040 2058 Dihedral : 28.505 164.790 4560 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.98 % Allowed : 25.02 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.24), residues: 1275 helix: 2.47 (0.21), residues: 577 sheet: 0.56 (0.36), residues: 232 loop : -0.49 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 193 HIS 0.004 0.001 HIS F 75 PHE 0.010 0.001 PHE A 67 TYR 0.015 0.001 TYR E 54 ARG 0.012 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03548 ( 890) hydrogen bonds : angle 3.18581 ( 2267) SS BOND : bond 0.00408 ( 4) SS BOND : angle 0.84187 ( 8) covalent geometry : bond 0.00334 (16958) covalent geometry : angle 0.56616 (24101) *********************** 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 237 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 204 time to evaluate : 1.369 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9266 (tttt) cc_final: 0.9013 (ttpp) REVERT: A 129 ARG cc_start: 0.8670 (OUTLIER) cc_final: 0.7682 (tpp80) REVERT: B 25 ASN cc_start: 0.8853 (m-40) cc_final: 0.8385 (m-40) REVERT: C 71 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7981 (ttp80) REVERT: C 91 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8553 (tt0) REVERT: C 92 GLU cc_start: 0.9160 (mt-10) cc_final: 0.8941 (mt-10) REVERT: D 44 GLN cc_start: 0.8509 (tt0) cc_final: 0.8003 (mt0) REVERT: D 59 MET cc_start: 0.9428 (mmm) cc_final: 0.9126 (mmp) REVERT: D 90 GLU cc_start: 0.9226 (OUTLIER) cc_final: 0.8331 (mt-10) REVERT: E 97 GLU cc_start: 0.8607 (mm-30) cc_final: 0.8325 (mt-10) REVERT: F 77 LYS cc_start: 0.9062 (OUTLIER) cc_final: 0.8818 (mttt) REVERT: F 91 LYS cc_start: 0.9130 (tttt) cc_final: 0.8589 (ttmm) REVERT: G 51 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8337 (tpt) REVERT: H 34 TYR cc_start: 0.9126 (m-80) cc_final: 0.8756 (m-80) REVERT: H 68 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8004 (tp30) REVERT: H 90 GLU cc_start: 0.9244 (OUTLIER) cc_final: 0.7995 (mp0) REVERT: M 32 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8290 (mm-30) REVERT: M 104 GLU cc_start: 0.8866 (tt0) cc_final: 0.8513 (tt0) REVERT: M 175 GLU cc_start: 0.8027 (pt0) cc_final: 0.7614 (pm20) REVERT: M 235 ASN cc_start: 0.8174 (OUTLIER) cc_final: 0.7541 (t0) REVERT: M 237 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7561 (mm-30) REVERT: N 32 GLU cc_start: 0.8278 (mm-30) cc_final: 0.7799 (mt-10) REVERT: N 109 THR cc_start: 0.7798 (m) cc_final: 0.7335 (t) REVERT: N 111 GLU cc_start: 0.9033 (pp20) cc_final: 0.8505 (pp20) REVERT: N 240 ASP cc_start: 0.8711 (m-30) cc_final: 0.8080 (m-30) REVERT: O 198 LYS cc_start: -0.0908 (OUTLIER) cc_final: -0.1311 (ptmt) REVERT: O 225 MET cc_start: 0.0223 (ptm) cc_final: -0.0095 (ttm) outliers start: 33 outliers final: 13 residues processed: 222 average time/residue: 1.5644 time to fit residues: 376.0333 Evaluate side-chains 222 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 198 time to evaluate : 1.302 ------------------------------------------------------------------------------- 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 71 ARG Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 51 MET 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 32 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 235 ASN Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 192 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 15 optimal weight: 0.6980 chunk 60 optimal weight: 0.5980 chunk 142 optimal weight: 4.9990 chunk 1 optimal weight: 0.4980 chunk 110 optimal weight: 5.9990 chunk 121 optimal weight: 0.6980 chunk 71 optimal weight: 0.9990 chunk 95 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 122 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 73 ASN C 104 GLN G 104 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 253 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.168751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.104027 restraints weight = 20603.985| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 2.07 r_work: 0.2964 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.2830 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.2830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3652 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= 0.143 Angle : 0.569 8.670 24109 Z= 0.326 Chirality : 0.035 0.172 2706 Planarity : 0.004 0.049 2058 Dihedral : 28.466 164.898 4560 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.07 % Allowed : 25.11 % Favored : 71.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.24), residues: 1275 helix: 2.54 (0.21), residues: 577 sheet: 0.61 (0.36), residues: 232 loop : -0.48 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 193 HIS 0.004 0.001 HIS M 249 PHE 0.010 0.001 PHE A 67 TYR 0.016 0.001 TYR E 54 ARG 0.015 0.000 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03487 ( 890) hydrogen bonds : angle 3.15841 ( 2267) SS BOND : bond 0.00349 ( 4) SS BOND : angle 0.79492 ( 8) covalent geometry : bond 0.00316 (16958) covalent geometry : angle 0.56869 (24101) *********************** 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 235 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 1.503 Fit side-chains revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9258 (tttt) cc_final: 0.9011 (ttpp) REVERT: B 25 ASN cc_start: 0.8829 (m-40) cc_final: 0.8351 (m-40) REVERT: C 71 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7977 (ttp80) REVERT: C 91 GLU cc_start: 0.9003 (OUTLIER) cc_final: 0.8544 (tt0) REVERT: C 92 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8929 (mt-10) REVERT: D 44 GLN cc_start: 0.8562 (tt0) cc_final: 0.8050 (mt0) REVERT: D 59 MET cc_start: 0.9413 (mmm) cc_final: 0.9098 (mmp) REVERT: D 90 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.8323 (mt-10) REVERT: E 97 GLU cc_start: 0.8593 (mm-30) cc_final: 0.8318 (mt-10) REVERT: F 77 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8800 (mttt) REVERT: F 91 LYS cc_start: 0.9118 (tttt) cc_final: 0.8580 (ttmm) REVERT: H 34 TYR cc_start: 0.9116 (m-80) cc_final: 0.8739 (m-80) REVERT: H 68 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.7977 (tp30) REVERT: H 90 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.7978 (mp0) REVERT: M 32 GLU cc_start: 0.8607 (OUTLIER) cc_final: 0.8287 (mm-30) REVERT: M 104 GLU cc_start: 0.8868 (tt0) cc_final: 0.8497 (tt0) REVERT: M 175 GLU cc_start: 0.8044 (pt0) cc_final: 0.7626 (pm20) REVERT: M 235 ASN cc_start: 0.8168 (OUTLIER) cc_final: 0.7504 (t0) REVERT: M 237 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7432 (mm-30) REVERT: N 32 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7810 (mt-10) REVERT: N 109 THR cc_start: 0.7740 (m) cc_final: 0.7380 (t) REVERT: N 111 GLU cc_start: 0.9051 (pp20) cc_final: 0.8568 (pp20) REVERT: N 112 ASP cc_start: 0.7624 (m-30) cc_final: 0.7273 (m-30) REVERT: N 240 ASP cc_start: 0.8656 (m-30) cc_final: 0.8038 (m-30) REVERT: O 198 LYS cc_start: -0.0921 (OUTLIER) cc_final: -0.1327 (ptmt) REVERT: O 225 MET cc_start: 0.0182 (ptm) cc_final: -0.0127 (ttm) outliers start: 34 outliers final: 18 residues processed: 220 average time/residue: 1.6031 time to fit residues: 381.4645 Evaluate side-chains 226 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 199 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 114 VAL 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 32 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 235 ASN Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 239 ASP Chi-restraints excluded: chain O residue 174 LEU Chi-restraints excluded: chain O residue 198 LYS Chi-restraints excluded: chain O residue 211 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 20 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 15 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 122 optimal weight: 0.5980 chunk 94 optimal weight: 4.9990 chunk 142 optimal weight: 0.7980 chunk 78 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 G 104 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 253 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.168136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.103282 restraints weight = 20639.689| |-----------------------------------------------------------------------------| r_work (start): 0.3164 rms_B_bonded: 1.97 r_work: 0.2949 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work: 0.2814 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16962 Z= 0.163 Angle : 0.576 8.550 24109 Z= 0.329 Chirality : 0.035 0.172 2706 Planarity : 0.004 0.052 2058 Dihedral : 28.440 164.227 4560 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.07 % Allowed : 25.56 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.24), residues: 1275 helix: 2.47 (0.21), residues: 577 sheet: 0.65 (0.36), residues: 232 loop : -0.47 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 193 HIS 0.003 0.001 HIS F 75 PHE 0.010 0.001 PHE A 67 TYR 0.017 0.001 TYR E 54 ARG 0.014 0.001 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03680 ( 890) hydrogen bonds : angle 3.17823 ( 2267) SS BOND : bond 0.00421 ( 4) SS BOND : angle 0.85499 ( 8) covalent geometry : bond 0.00368 (16958) covalent geometry : angle 0.57549 (24101) *********************** 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 240 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 206 time to evaluate : 1.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9250 (tttt) cc_final: 0.8999 (ttpp) REVERT: A 79 LYS cc_start: 0.8923 (tptp) cc_final: 0.8710 (tmtt) REVERT: A 129 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.7803 (ttp80) REVERT: B 25 ASN cc_start: 0.8854 (m-40) cc_final: 0.8383 (m-40) REVERT: C 71 ARG cc_start: 0.8143 (OUTLIER) cc_final: 0.7880 (ttp80) REVERT: C 91 GLU cc_start: 0.9006 (tt0) cc_final: 0.8558 (tt0) REVERT: C 92 GLU cc_start: 0.9143 (mt-10) cc_final: 0.8911 (mt-10) REVERT: D 44 GLN cc_start: 0.8528 (tt0) cc_final: 0.8046 (mt0) REVERT: D 59 MET cc_start: 0.9458 (mmm) cc_final: 0.9166 (mmp) REVERT: D 90 GLU cc_start: 0.9228 (OUTLIER) cc_final: 0.8275 (mt-10) REVERT: E 97 GLU cc_start: 0.8598 (mm-30) cc_final: 0.8325 (mt-10) REVERT: F 77 LYS cc_start: 0.9078 (OUTLIER) cc_final: 0.8815 (mttt) REVERT: F 91 LYS cc_start: 0.9120 (tttt) cc_final: 0.8601 (ttmm) REVERT: G 51 MET cc_start: 0.8918 (OUTLIER) cc_final: 0.8366 (tpt) REVERT: H 34 TYR cc_start: 0.9156 (m-80) cc_final: 0.8817 (m-80) REVERT: H 68 GLU cc_start: 0.8422 (OUTLIER) cc_final: 0.7992 (tp30) REVERT: H 90 GLU cc_start: 0.9201 (OUTLIER) cc_final: 0.7888 (mp0) REVERT: M 32 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8308 (mm-30) REVERT: M 104 GLU cc_start: 0.8860 (tt0) cc_final: 0.8513 (tt0) REVERT: M 175 GLU cc_start: 0.8006 (pt0) cc_final: 0.7613 (pm20) REVERT: M 235 ASN cc_start: 0.8151 (OUTLIER) cc_final: 0.7529 (t0) REVERT: M 237 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7582 (mm-30) REVERT: N 32 GLU cc_start: 0.8293 (mm-30) cc_final: 0.7753 (mt-10) REVERT: N 65 GLN cc_start: 0.8883 (mt0) cc_final: 0.8322 (mp10) REVERT: N 109 THR cc_start: 0.7980 (m) cc_final: 0.7591 (t) REVERT: N 111 GLU cc_start: 0.9077 (pp20) cc_final: 0.8572 (pp20) REVERT: N 112 ASP cc_start: 0.7895 (m-30) cc_final: 0.7474 (m-30) REVERT: O 198 LYS cc_start: -0.0982 (OUTLIER) cc_final: -0.1404 (ptmt) outliers start: 34 outliers final: 18 residues processed: 225 average time/residue: 1.6504 time to fit residues: 402.6540 Evaluate side-chains 225 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 197 time to evaluate : 1.410 ------------------------------------------------------------------------------- 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 71 ARG Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 51 MET 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 32 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 235 ASN Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 239 ASP Chi-restraints excluded: chain O residue 174 LEU Chi-restraints excluded: chain O residue 198 LYS Chi-restraints excluded: chain O residue 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 56 optimal weight: 0.0170 chunk 77 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 147 optimal weight: 7.9990 chunk 146 optimal weight: 10.0000 chunk 94 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 76 GLN C 104 GLN D 92 GLN G 104 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 = 0.3988 r_free = 0.3988 target = 0.163685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.097683 restraints weight = 20638.782| |-----------------------------------------------------------------------------| r_work (start): 0.3090 rms_B_bonded: 2.02 r_work: 0.2865 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 16962 Z= 0.319 Angle : 0.671 9.822 24109 Z= 0.377 Chirality : 0.041 0.171 2706 Planarity : 0.005 0.063 2058 Dihedral : 28.926 161.025 4560 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.80 % Allowed : 25.75 % Favored : 71.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.24), residues: 1275 helix: 1.98 (0.21), residues: 572 sheet: 0.48 (0.35), residues: 232 loop : -0.70 (0.28), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 193 HIS 0.009 0.001 HIS H 46 PHE 0.013 0.002 PHE M 256 TYR 0.026 0.002 TYR E 54 ARG 0.015 0.001 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.04919 ( 890) hydrogen bonds : angle 3.47258 ( 2267) SS BOND : bond 0.00824 ( 4) SS BOND : angle 1.16686 ( 8) covalent geometry : bond 0.00751 (16958) covalent geometry : angle 0.67104 (24101) ********************** 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 232 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 201 time to evaluate : 1.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.9333 (tttt) cc_final: 0.9054 (ttpp) REVERT: A 133 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8003 (mt-10) REVERT: C 71 ARG cc_start: 0.8132 (OUTLIER) cc_final: 0.7902 (ttp80) REVERT: C 91 GLU cc_start: 0.9079 (tt0) cc_final: 0.8638 (tt0) REVERT: C 92 GLU cc_start: 0.9247 (mt-10) cc_final: 0.8984 (mt-10) REVERT: C 99 LYS cc_start: 0.8518 (mttt) cc_final: 0.8205 (mmmt) REVERT: D 39 TYR cc_start: 0.8595 (t80) cc_final: 0.8240 (t80) REVERT: D 44 GLN cc_start: 0.8532 (tt0) cc_final: 0.8044 (mt0) REVERT: D 59 MET cc_start: 0.9537 (mmm) cc_final: 0.9225 (mmp) REVERT: D 90 GLU cc_start: 0.9340 (OUTLIER) cc_final: 0.8260 (mp0) REVERT: E 97 GLU cc_start: 0.8640 (mm-30) cc_final: 0.8346 (mt-10) REVERT: F 77 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8853 (mttt) REVERT: F 91 LYS cc_start: 0.9156 (tttt) cc_final: 0.8670 (ttmm) REVERT: G 51 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8506 (tpt) REVERT: H 34 TYR cc_start: 0.9257 (m-80) cc_final: 0.8903 (m-80) REVERT: H 68 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.8062 (tp30) REVERT: H 90 GLU cc_start: 0.9207 (OUTLIER) cc_final: 0.8076 (mp0) REVERT: M 104 GLU cc_start: 0.8940 (tt0) cc_final: 0.8534 (tt0) REVERT: M 175 GLU cc_start: 0.8078 (pt0) cc_final: 0.7650 (pm20) REVERT: M 235 ASN cc_start: 0.8196 (OUTLIER) cc_final: 0.7670 (t0) REVERT: M 237 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7652 (mm-30) REVERT: N 32 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7799 (mt-10) REVERT: N 109 THR cc_start: 0.8099 (m) cc_final: 0.7592 (t) REVERT: N 111 GLU cc_start: 0.9085 (pp20) cc_final: 0.8614 (pp20) REVERT: N 112 ASP cc_start: 0.8251 (m-30) cc_final: 0.7631 (m-30) REVERT: O 198 LYS cc_start: -0.0681 (OUTLIER) cc_final: -0.1054 (ptmt) outliers start: 31 outliers final: 17 residues processed: 221 average time/residue: 1.7060 time to fit residues: 406.2753 Evaluate side-chains 226 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 1.358 ------------------------------------------------------------------------------- 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 71 ARG Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 51 MET 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 162 MET Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 235 ASN 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 29 optimal weight: 0.2980 chunk 109 optimal weight: 5.9990 chunk 106 optimal weight: 3.9990 chunk 127 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 95 optimal weight: 5.9990 chunk 121 optimal weight: 0.5980 chunk 96 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 76 GLN C 104 GLN G 104 GLN N 65 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 = 0.4023 r_free = 0.4023 target = 0.166985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.102238 restraints weight = 20673.833| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 1.96 r_work: 0.2937 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 16962 Z= 0.166 Angle : 0.592 8.544 24109 Z= 0.337 Chirality : 0.036 0.169 2706 Planarity : 0.004 0.053 2058 Dihedral : 28.625 161.901 4560 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.71 % Allowed : 26.11 % Favored : 71.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.24), residues: 1275 helix: 2.26 (0.21), residues: 576 sheet: 0.56 (0.36), residues: 232 loop : -0.58 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 193 HIS 0.003 0.001 HIS M 249 PHE 0.015 0.001 PHE O 254 TYR 0.020 0.001 TYR E 54 ARG 0.016 0.001 ARG A 42 Details of bonding type rmsd hydrogen bonds : bond 0.03720 ( 890) hydrogen bonds : angle 3.26849 ( 2267) SS BOND : bond 0.00499 ( 4) SS BOND : angle 1.00963 ( 8) covalent geometry : bond 0.00375 (16958) covalent geometry : angle 0.59229 (24101) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14465.81 seconds wall clock time: 248 minutes 40.51 seconds (14920.51 seconds total)