Starting phenix.real_space_refine on Sat Jun 14 04:45:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8evi_28630/06_2025/8evi_28630.cif Found real_map, /net/cci-nas-00/data/ceres_data/8evi_28630/06_2025/8evi_28630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8evi_28630/06_2025/8evi_28630.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8evi_28630/06_2025/8evi_28630.map" model { file = "/net/cci-nas-00/data/ceres_data/8evi_28630/06_2025/8evi_28630.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8evi_28630/06_2025/8evi_28630.cif" } resolution = 2.64 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= 0.004 sd= 0.120 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 285 5.49 5 S 37 5.16 5 C 9296 2.51 5 N 2927 2.21 5 O 3612 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-5710/modules/chem_data/mon_lib" Total number of atoms: 16157 Number of models: 1 Model: "" Number of chains: 13 Chain: "J" Number of atoms: 2931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2931 Classifications: {'DNA': 143} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 142} Chain: "I" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2929 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain breaks: 1 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: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 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: "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: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 748 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Time building chain proxies: 9.10, per 1000 atoms: 0.56 Number of scatterers: 16157 At special positions: 0 Unit cell: (140.448, 130.944, 141.504, 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 37 16.00 P 285 15.00 O 3612 8.00 N 2927 7.00 C 9296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS O 220 " distance=2.03 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: 3.91 Conformation dependent library (CDL) restraints added in 1.2 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: 2422 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 24 sheets defined 47.6% alpha, 19.2% beta 138 base pairs and 264 stacking pairs defined. Time for finding SS restraints: 7.25 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.035A 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: 3.748A 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: 4.513A 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: 3.518A 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: 4.422A 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: 3.658A pdb=" N ARG O 235 " --> pdb=" O ALA O 231 " (cutoff:3.500A) removed outlier: 4.158A 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: 7.182A 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: 3.608A 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: 5.137A 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: 3.608A 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: 6.515A 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: 6.515A pdb=" N MET M 169 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 3.606A 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: 4.497A 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: 7.253A 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: 6.307A 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: 4.831A pdb=" N TYR N 207 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 6.819A 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: 4.150A 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: 3.887A 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: 342 hydrogen bonds 684 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 264 stacking parallelities Total time for adding SS restraints: 6.22 Time building geometry restraints manager: 4.65 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: 1917 1.30 - 1.43: 5964 1.43 - 1.56: 8539 1.56 - 1.69: 568 1.69 - 1.82: 60 Bond restraints: 17048 Sorted by residual: bond pdb=" C HIS D 46 " pdb=" O HIS D 46 " ideal model delta sigma weight residual 1.238 1.174 0.064 1.08e-02 8.57e+03 3.53e+01 bond pdb=" C GLN E 125 " pdb=" O GLN E 125 " ideal model delta sigma weight residual 1.237 1.169 0.068 1.19e-02 7.06e+03 3.26e+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 2.69e+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 2.14e+01 bond pdb=" C ARG B 92 " pdb=" N GLN B 93 " ideal model delta sigma weight residual 1.334 1.275 0.058 1.30e-02 5.92e+03 2.00e+01 ... (remaining 17043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.24: 24234 7.24 - 14.49: 5 14.49 - 21.73: 0 21.73 - 28.98: 0 28.98 - 36.22: 1 Bond angle restraints: 24240 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 73.58 36.22 1.23e+00 6.61e-01 8.67e+02 angle pdb=" N LEU O 250 " pdb=" CA LEU O 250 " pdb=" C LEU O 250 " ideal model delta sigma weight residual 111.74 122.51 -10.77 1.35e+00 5.49e-01 6.37e+01 angle pdb=" N LEU O 250 " pdb=" CA LEU O 250 " pdb=" CB LEU O 250 " ideal model delta sigma weight residual 112.13 120.06 -7.93 1.51e+00 4.39e-01 2.75e+01 angle pdb=" C4' DT I 149 " pdb=" C3' DT I 149 " pdb=" O3' DT I 149 " ideal model delta sigma weight residual 110.00 103.15 6.85 1.50e+00 4.44e-01 2.09e+01 angle pdb=" O3' DG I 148 " pdb=" C3' DG I 148 " pdb=" C2' DG I 148 " ideal model delta sigma weight residual 111.50 117.57 -6.07 1.50e+00 4.44e-01 1.64e+01 ... (remaining 24235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.16: 7847 33.16 - 66.32: 1678 66.32 - 99.48: 38 99.48 - 132.64: 0 132.64 - 165.81: 2 Dihedral angle restraints: 9565 sinusoidal: 5787 harmonic: 3778 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 -80.24 -42.36 0 2.50e+00 1.60e-01 2.87e+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 122.80 151.21 -28.41 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 -148.65 26.05 0 2.50e+00 1.60e-01 1.09e+02 ... (remaining 9562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.243: 2717 0.243 - 0.486: 3 0.486 - 0.730: 0 0.730 - 0.973: 0 0.973 - 1.216: 1 Chirality restraints: 2721 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 1.29 1.22 2.00e-01 2.50e+01 3.70e+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 3.77e+00 chirality pdb=" CA GLN E 125 " pdb=" N GLN E 125 " pdb=" C GLN E 125 " pdb=" CB GLN E 125 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 2718 not shown) Planarity restraints: 2062 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 147 " -0.033 2.00e-02 2.50e+03 1.65e-02 6.84e+00 pdb=" N1 DT I 147 " 0.022 2.00e-02 2.50e+03 pdb=" C2 DT I 147 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DT I 147 " 0.024 2.00e-02 2.50e+03 pdb=" N3 DT I 147 " -0.016 2.00e-02 2.50e+03 pdb=" C4 DT I 147 " -0.011 2.00e-02 2.50e+03 pdb=" O4 DT I 147 " -0.007 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 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 91 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.81e+00 pdb=" C LYS B 91 " 0.045 2.00e-02 2.50e+03 pdb=" O LYS B 91 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG B 92 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 24 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" CG ASP B 24 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASP B 24 " 0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP B 24 " 0.011 2.00e-02 2.50e+03 ... (remaining 2059 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 180 2.62 - 3.19: 12967 3.19 - 3.76: 28525 3.76 - 4.33: 39717 4.33 - 4.90: 58056 Nonbonded interactions: 139445 Sorted by model distance: nonbonded pdb=" O LYS O 249 " pdb=" CB LYS O 249 " model vdw 2.045 2.752 nonbonded pdb=" N4 DC J 15 " pdb=" O6 DG I 148 " model vdw 2.132 3.120 nonbonded pdb=" OG1 THR O 240 " pdb=" OE1 GLU O 242 " model vdw 2.164 3.040 nonbonded pdb=" NH2 ARG N 120 " pdb=" OD2 ASP N 130 " model vdw 2.199 3.120 nonbonded pdb=" NE2 GLN C 104 " pdb=" OE2 GLU E 94 " model vdw 2.208 3.120 ... (remaining 139440 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' and (resid 12 through 75 or resid 77 through 118)) selection = (chain 'G' and (resid 12 through 75 or resid 77 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: 0.940 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: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 41.910 Find NCS groups from input model: 0.370 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:12.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 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 0.068 17053 Z= 0.247 Angle : 0.685 36.222 24250 Z= 0.419 Chirality : 0.046 1.216 2721 Planarity : 0.004 0.037 2062 Dihedral : 26.592 165.806 7128 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.09 % Allowed : 25.27 % Favored : 74.64 % 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: 2.21 (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 0.13329 ( 892) hydrogen bonds : angle 4.84404 ( 2271) SS BOND : bond 0.00268 ( 5) SS BOND : angle 1.33082 ( 10) covalent geometry : bond 0.00506 (17048) covalent geometry : angle 0.68451 (24240) *********************** 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 206 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 205 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8528 (mtt) cc_final: 0.8185 (mtt) REVERT: C 36 LYS cc_start: 0.8677 (mmmm) cc_final: 0.8405 (mtpp) REVERT: C 42 ARG cc_start: 0.7903 (mtp85) cc_final: 0.7613 (mtp85) REVERT: D 82 LYS cc_start: 0.8566 (mtmm) cc_final: 0.8255 (mtmm) REVERT: D 113 LYS cc_start: 0.7665 (ttmt) cc_final: 0.7311 (ttpt) REVERT: E 64 LYS cc_start: 0.8323 (mttm) cc_final: 0.8115 (mttm) REVERT: G 73 ASN cc_start: 0.8401 (t0) cc_final: 0.7776 (t0) REVERT: G 91 GLU cc_start: 0.7964 (tt0) cc_final: 0.7641 (tt0) REVERT: H 34 TYR cc_start: 0.8495 (m-80) cc_final: 0.8253 (m-80) REVERT: H 60 ASN cc_start: 0.7991 (t0) cc_final: 0.7773 (t0) REVERT: H 68 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6942 (mt-10) REVERT: H 82 LYS cc_start: 0.8270 (mttp) cc_final: 0.8008 (mtmm) REVERT: H 83 ARG cc_start: 0.7614 (mmt90) cc_final: 0.7369 (mmt90) REVERT: M 261 LYS cc_start: 0.8517 (mtpp) cc_final: 0.7384 (tptt) REVERT: M 263 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7155 (mp0) REVERT: N 25 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7496 (mm-40) REVERT: N 102 TYR cc_start: 0.8262 (m-80) cc_final: 0.7988 (m-80) REVERT: N 111 GLU cc_start: 0.8429 (pp20) cc_final: 0.8081 (pp20) REVERT: N 112 ASP cc_start: 0.8336 (m-30) cc_final: 0.7761 (m-30) REVERT: N 169 MET cc_start: 0.7898 (ptp) cc_final: 0.7598 (pmm) REVERT: N 180 THR cc_start: 0.8952 (m) cc_final: 0.8696 (p) REVERT: N 219 ARG cc_start: 0.8173 (mtm110) cc_final: 0.7532 (ptm160) REVERT: N 261 LYS cc_start: 0.8461 (mtpm) cc_final: 0.8253 (ttmt) REVERT: N 263 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7288 (tm-30) REVERT: O 187 MET cc_start: 0.3326 (ttt) cc_final: 0.3030 (ttp) REVERT: O 225 MET cc_start: 0.4728 (ptm) cc_final: 0.3896 (ppp) outliers start: 1 outliers final: 0 residues processed: 206 average time/residue: 1.7233 time to fit residues: 382.5731 Evaluate side-chains 166 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 166 time to evaluate : 1.288 ------------------------------------------------------------------------------- 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: 3.9990 chunk 115 optimal weight: 4.9990 chunk 63 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 138 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN E 76 GLN E 125 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 64 ASN M 27 GLN N 61 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 253 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.165255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.115169 restraints weight = 16570.109| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 1.54 r_work: 0.3291 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3133 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17053 Z= 0.162 Angle : 0.587 10.645 24250 Z= 0.339 Chirality : 0.037 0.243 2721 Planarity : 0.004 0.036 2062 Dihedral : 28.646 165.731 4605 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.97 % Allowed : 23.47 % Favored : 72.56 % 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: 1.48 (0.24), residues: 1275 helix: 2.41 (0.22), residues: 575 sheet: 0.46 (0.35), residues: 220 loop : -0.54 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 193 HIS 0.003 0.001 HIS B 75 PHE 0.016 0.001 PHE O 254 TYR 0.012 0.001 TYR N 72 ARG 0.006 0.000 ARG O 214 Details of bonding type rmsd hydrogen bonds : bond 0.04148 ( 892) hydrogen bonds : angle 3.59877 ( 2271) SS BOND : bond 0.00239 ( 5) SS BOND : angle 1.12430 ( 10) covalent geometry : bond 0.00357 (17048) covalent geometry : angle 0.58671 (24240) *********************** 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 202 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 158 time to evaluate : 1.462 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7898 (tp30) cc_final: 0.7644 (mm-30) REVERT: C 36 LYS cc_start: 0.8786 (mmmm) cc_final: 0.8539 (mmmt) REVERT: C 42 ARG cc_start: 0.7890 (mtp85) cc_final: 0.7421 (mtp85) REVERT: D 60 ASN cc_start: 0.7976 (OUTLIER) cc_final: 0.7502 (m-40) REVERT: D 90 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.8007 (mp0) REVERT: D 113 LYS cc_start: 0.7471 (ttmt) cc_final: 0.7045 (ttpt) REVERT: F 91 LYS cc_start: 0.8378 (tttm) cc_final: 0.8068 (tptt) REVERT: G 73 ASN cc_start: 0.7994 (t0) cc_final: 0.7441 (t0) REVERT: G 89 ASN cc_start: 0.8785 (m-40) cc_final: 0.8575 (m110) REVERT: G 91 GLU cc_start: 0.7926 (tt0) cc_final: 0.7686 (tt0) REVERT: H 34 TYR cc_start: 0.8567 (m-80) cc_final: 0.8333 (m-80) REVERT: H 39 TYR cc_start: 0.8060 (t80) cc_final: 0.7376 (t80) REVERT: H 68 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7156 (mt-10) REVERT: M 38 THR cc_start: 0.7710 (p) cc_final: 0.7487 (t) REVERT: M 235 ASN cc_start: 0.7884 (OUTLIER) cc_final: 0.6978 (m110) REVERT: M 261 LYS cc_start: 0.8578 (mtpp) cc_final: 0.7249 (tptt) REVERT: M 263 GLU cc_start: 0.8031 (mm-30) cc_final: 0.7445 (mp0) REVERT: N 25 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7377 (mm-40) REVERT: N 95 ASP cc_start: 0.7875 (t70) cc_final: 0.7650 (t70) REVERT: N 103 MET cc_start: 0.8245 (OUTLIER) cc_final: 0.8031 (ttp) REVERT: N 162 MET cc_start: 0.8884 (mmp) cc_final: 0.8451 (mmp) REVERT: N 261 LYS cc_start: 0.8416 (mtpm) cc_final: 0.8057 (ttmt) REVERT: O 225 MET cc_start: 0.5524 (ptm) cc_final: 0.4587 (ppp) outliers start: 44 outliers final: 11 residues processed: 187 average time/residue: 1.7336 time to fit residues: 350.0928 Evaluate side-chains 167 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 151 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 130 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 81 optimal weight: 4.9990 chunk 116 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 44 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 135 optimal weight: 0.1980 chunk 55 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.8386 ------------------------------------------------------------------------------- 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 ** E 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 60 ASN M 27 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4040 r_free = 0.4040 target = 0.162471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.112227 restraints weight = 16594.300| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.55 r_work: 0.3248 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 moved from start: 0.1314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17053 Z= 0.202 Angle : 0.598 10.006 24250 Z= 0.346 Chirality : 0.038 0.231 2721 Planarity : 0.004 0.038 2062 Dihedral : 28.755 165.503 4605 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.06 % Allowed : 22.74 % Favored : 73.19 % 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: 1.36 (0.24), residues: 1275 helix: 2.21 (0.22), residues: 575 sheet: 0.53 (0.35), residues: 220 loop : -0.51 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 193 HIS 0.004 0.001 HIS C 31 PHE 0.016 0.002 PHE O 254 TYR 0.013 0.001 TYR N 72 ARG 0.005 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.04398 ( 892) hydrogen bonds : angle 3.52837 ( 2271) SS BOND : bond 0.00309 ( 5) SS BOND : angle 1.09962 ( 10) covalent geometry : bond 0.00462 (17048) covalent geometry : angle 0.59782 (24240) *********************** 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 203 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 158 time to evaluate : 1.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 74 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7679 (mt-10) REVERT: C 36 LYS cc_start: 0.8796 (mmmm) cc_final: 0.8515 (mmmt) REVERT: C 42 ARG cc_start: 0.7844 (mtp85) cc_final: 0.7345 (mtp85) REVERT: D 60 ASN cc_start: 0.8058 (OUTLIER) cc_final: 0.7626 (m-40) REVERT: D 82 LYS cc_start: 0.8295 (OUTLIER) cc_final: 0.7966 (mttm) REVERT: D 90 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.8021 (mp0) REVERT: D 113 LYS cc_start: 0.7737 (ttmt) cc_final: 0.7254 (ttpt) REVERT: E 40 ARG cc_start: 0.7558 (OUTLIER) cc_final: 0.6976 (ttt-90) REVERT: E 90 MET cc_start: 0.7931 (OUTLIER) cc_final: 0.6948 (mtp) REVERT: G 73 ASN cc_start: 0.7968 (t0) cc_final: 0.7525 (t0) REVERT: G 95 LYS cc_start: 0.8347 (tttp) cc_final: 0.7929 (ttmt) REVERT: H 68 GLU cc_start: 0.7352 (OUTLIER) cc_final: 0.7138 (mt-10) REVERT: M 38 THR cc_start: 0.7593 (p) cc_final: 0.7324 (t) REVERT: M 111 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.7961 (pp20) REVERT: M 235 ASN cc_start: 0.7850 (OUTLIER) cc_final: 0.6991 (m110) REVERT: M 261 LYS cc_start: 0.8544 (mtpp) cc_final: 0.7676 (mtpp) REVERT: M 263 GLU cc_start: 0.7929 (mm-30) cc_final: 0.7428 (mp0) REVERT: N 95 ASP cc_start: 0.7882 (t70) cc_final: 0.7580 (t70) REVERT: N 103 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7947 (ttp) REVERT: N 162 MET cc_start: 0.8893 (mmp) cc_final: 0.8618 (mmp) REVERT: N 261 LYS cc_start: 0.8400 (mtpm) cc_final: 0.8100 (ttmt) REVERT: O 211 LEU cc_start: 0.4394 (OUTLIER) cc_final: 0.4180 (tm) REVERT: O 225 MET cc_start: 0.6001 (ptm) cc_final: 0.4923 (ppp) REVERT: O 250 LEU cc_start: 0.5106 (OUTLIER) cc_final: 0.4906 (tp) REVERT: O 253 GLN cc_start: 0.5345 (OUTLIER) cc_final: 0.4001 (mp10) outliers start: 45 outliers final: 13 residues processed: 187 average time/residue: 1.6762 time to fit residues: 338.6684 Evaluate side-chains 181 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 156 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET 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 M residue 39 SER Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain O residue 211 LEU Chi-restraints excluded: chain O residue 226 THR Chi-restraints excluded: chain O residue 250 LEU Chi-restraints excluded: chain O residue 253 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 18 optimal weight: 4.9990 chunk 80 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 109 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 chunk 105 optimal weight: 0.9990 chunk 93 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN E 76 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 60 ASN M 27 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.162278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.112078 restraints weight = 16622.749| |-----------------------------------------------------------------------------| r_work (start): 0.3447 rms_B_bonded: 1.55 r_work: 0.3246 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17053 Z= 0.200 Angle : 0.594 9.812 24250 Z= 0.343 Chirality : 0.038 0.215 2721 Planarity : 0.004 0.053 2062 Dihedral : 28.738 165.838 4605 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.06 % Allowed : 23.47 % Favored : 72.47 % 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: 1.33 (0.24), residues: 1275 helix: 2.15 (0.22), residues: 575 sheet: 0.59 (0.35), residues: 220 loop : -0.53 (0.28), residues: 480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 193 HIS 0.004 0.001 HIS M 249 PHE 0.009 0.001 PHE F 61 TYR 0.018 0.001 TYR O 252 ARG 0.006 0.000 ARG N 176 Details of bonding type rmsd hydrogen bonds : bond 0.04295 ( 892) hydrogen bonds : angle 3.46388 ( 2271) SS BOND : bond 0.00305 ( 5) SS BOND : angle 1.11897 ( 10) covalent geometry : bond 0.00458 (17048) covalent geometry : angle 0.59355 (24240) *********************** 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 205 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 160 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 74 GLU cc_start: 0.8072 (mt-10) cc_final: 0.7784 (mt-10) REVERT: C 36 LYS cc_start: 0.8828 (mmmm) cc_final: 0.8568 (mmmt) REVERT: C 42 ARG cc_start: 0.7840 (mtp85) cc_final: 0.7336 (mtp85) REVERT: D 60 ASN cc_start: 0.8053 (OUTLIER) cc_final: 0.7628 (m-40) REVERT: D 82 LYS cc_start: 0.8232 (OUTLIER) cc_final: 0.7907 (mttm) REVERT: D 90 GLU cc_start: 0.8235 (OUTLIER) cc_final: 0.8004 (mp0) REVERT: D 113 LYS cc_start: 0.7729 (ttmt) cc_final: 0.7287 (ttpt) REVERT: E 40 ARG cc_start: 0.7504 (OUTLIER) cc_final: 0.6887 (ttt-90) REVERT: E 90 MET cc_start: 0.7937 (OUTLIER) cc_final: 0.6908 (mtp) REVERT: G 71 ARG cc_start: 0.7577 (ttm110) cc_final: 0.7343 (ttm170) REVERT: G 73 ASN cc_start: 0.7960 (t0) cc_final: 0.7502 (t0) REVERT: H 34 TYR cc_start: 0.8685 (m-80) cc_final: 0.8364 (m-80) REVERT: H 68 GLU cc_start: 0.7347 (OUTLIER) cc_final: 0.7136 (mt-10) REVERT: M 38 THR cc_start: 0.7469 (p) cc_final: 0.7192 (t) REVERT: M 111 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8044 (pp20) REVERT: M 235 ASN cc_start: 0.7805 (OUTLIER) cc_final: 0.6958 (m110) REVERT: M 261 LYS cc_start: 0.8556 (mtpp) cc_final: 0.8291 (mtpp) REVERT: N 65 GLN cc_start: 0.8359 (mt0) cc_final: 0.8158 (mp10) REVERT: N 95 ASP cc_start: 0.7856 (t70) cc_final: 0.7511 (t70) REVERT: N 103 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7765 (ttp) REVERT: N 108 LEU cc_start: 0.8202 (mp) cc_final: 0.7931 (mp) REVERT: N 162 MET cc_start: 0.8872 (mmp) cc_final: 0.8658 (mmp) REVERT: N 261 LYS cc_start: 0.8434 (mtpm) cc_final: 0.8031 (ttpt) outliers start: 45 outliers final: 17 residues processed: 189 average time/residue: 1.7768 time to fit residues: 362.0239 Evaluate side-chains 184 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 158 time to evaluate : 1.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET 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 M residue 39 SER Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 172 SER Chi-restraints excluded: chain N residue 255 THR Chi-restraints excluded: chain O residue 226 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 74 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 146 optimal weight: 20.0000 chunk 136 optimal weight: 0.0670 chunk 78 optimal weight: 0.7980 chunk 103 optimal weight: 0.8980 chunk 2 optimal weight: 5.9990 chunk 124 optimal weight: 0.8980 chunk 6 optimal weight: 4.9990 chunk 118 optimal weight: 8.9990 chunk 34 optimal weight: 2.9990 overall best weight: 0.6718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 60 ASN M 27 GLN N 28 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.163951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.113950 restraints weight = 16760.276| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 1.55 r_work: 0.3270 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3113 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17053 Z= 0.150 Angle : 0.581 10.106 24250 Z= 0.337 Chirality : 0.036 0.193 2721 Planarity : 0.004 0.041 2062 Dihedral : 28.728 166.585 4605 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.15 % Allowed : 23.92 % Favored : 71.93 % 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: 1.39 (0.24), residues: 1275 helix: 2.30 (0.22), residues: 573 sheet: 0.68 (0.37), residues: 196 loop : -0.60 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 193 HIS 0.003 0.001 HIS M 249 PHE 0.011 0.001 PHE O 254 TYR 0.013 0.001 TYR F 51 ARG 0.004 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 892) hydrogen bonds : angle 3.39431 ( 2271) SS BOND : bond 0.00286 ( 5) SS BOND : angle 0.99723 ( 10) covalent geometry : bond 0.00331 (17048) covalent geometry : angle 0.58120 (24240) *********************** 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 205 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 159 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7884 (tp30) cc_final: 0.7606 (mm-30) REVERT: A 133 GLU cc_start: 0.7548 (mt-10) cc_final: 0.7237 (mt-10) REVERT: B 74 GLU cc_start: 0.8051 (mt-10) cc_final: 0.7764 (mt-10) REVERT: C 36 LYS cc_start: 0.8821 (mmmm) cc_final: 0.8516 (mmmt) REVERT: C 42 ARG cc_start: 0.7819 (mtp85) cc_final: 0.7339 (mtp85) REVERT: D 60 ASN cc_start: 0.7976 (OUTLIER) cc_final: 0.7565 (m-40) REVERT: D 82 LYS cc_start: 0.8225 (OUTLIER) cc_final: 0.7895 (mttm) REVERT: D 90 GLU cc_start: 0.8189 (OUTLIER) cc_final: 0.7955 (mp0) REVERT: D 113 LYS cc_start: 0.7705 (ttmt) cc_final: 0.7296 (ttpt) REVERT: E 40 ARG cc_start: 0.7543 (OUTLIER) cc_final: 0.6978 (ttt-90) REVERT: E 90 MET cc_start: 0.7855 (OUTLIER) cc_final: 0.6895 (mtp) REVERT: G 71 ARG cc_start: 0.7576 (ttm110) cc_final: 0.7343 (ttm170) REVERT: G 73 ASN cc_start: 0.7931 (t0) cc_final: 0.7461 (t0) REVERT: G 84 GLN cc_start: 0.8180 (OUTLIER) cc_final: 0.7350 (tm-30) REVERT: H 34 TYR cc_start: 0.8676 (m-80) cc_final: 0.8367 (m-80) REVERT: H 39 TYR cc_start: 0.7897 (t80) cc_final: 0.7262 (t80) REVERT: H 68 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.7100 (mt-10) REVERT: H 82 LYS cc_start: 0.7890 (OUTLIER) cc_final: 0.7341 (mtmm) REVERT: M 38 THR cc_start: 0.7338 (p) cc_final: 0.7081 (t) REVERT: M 111 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8046 (pp20) REVERT: M 235 ASN cc_start: 0.7824 (OUTLIER) cc_final: 0.6978 (m110) REVERT: M 261 LYS cc_start: 0.8552 (mtpp) cc_final: 0.8245 (mtpp) REVERT: N 65 GLN cc_start: 0.8353 (mt0) cc_final: 0.8142 (mp10) REVERT: N 95 ASP cc_start: 0.7861 (t70) cc_final: 0.7488 (t70) REVERT: N 103 MET cc_start: 0.8052 (OUTLIER) cc_final: 0.7725 (ttp) REVERT: N 108 LEU cc_start: 0.8203 (mp) cc_final: 0.7938 (mp) REVERT: N 162 MET cc_start: 0.8867 (mmp) cc_final: 0.8659 (mmp) REVERT: N 261 LYS cc_start: 0.8454 (mtpm) cc_final: 0.8045 (ttpt) outliers start: 46 outliers final: 16 residues processed: 190 average time/residue: 1.7618 time to fit residues: 360.6625 Evaluate side-chains 186 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 159 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain G residue 84 GLN 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 82 LYS Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 172 SER Chi-restraints excluded: chain O residue 226 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 120 optimal weight: 6.9990 chunk 11 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 102 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 96 optimal weight: 4.9990 chunk 72 optimal weight: 0.9990 chunk 32 optimal weight: 0.3980 chunk 133 optimal weight: 10.0000 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 60 ASN M 27 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3955 r_free = 0.3955 target = 0.158105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.105870 restraints weight = 16682.411| |-----------------------------------------------------------------------------| r_work (start): 0.3324 rms_B_bonded: 1.61 r_work: 0.3122 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.1723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 17053 Z= 0.247 Angle : 0.621 8.996 24250 Z= 0.359 Chirality : 0.040 0.199 2721 Planarity : 0.004 0.037 2062 Dihedral : 28.846 166.368 4605 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.88 % Allowed : 24.19 % Favored : 71.93 % 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: 1.11 (0.24), residues: 1275 helix: 1.99 (0.22), residues: 571 sheet: 0.70 (0.37), residues: 196 loop : -0.70 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 193 HIS 0.005 0.001 HIS M 249 PHE 0.012 0.002 PHE O 254 TYR 0.014 0.002 TYR N 72 ARG 0.006 0.001 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.04709 ( 892) hydrogen bonds : angle 3.51825 ( 2271) SS BOND : bond 0.00353 ( 5) SS BOND : angle 1.15937 ( 10) covalent geometry : bond 0.00572 (17048) covalent geometry : angle 0.62023 (24240) *********************** 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 204 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 161 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 74 GLU cc_start: 0.7894 (mt-10) cc_final: 0.7580 (mt-10) REVERT: C 36 LYS cc_start: 0.8579 (mmmm) cc_final: 0.8252 (mmmt) REVERT: C 42 ARG cc_start: 0.7444 (mtp85) cc_final: 0.6768 (mtp85) REVERT: D 60 ASN cc_start: 0.7804 (OUTLIER) cc_final: 0.7328 (m-40) REVERT: D 82 LYS cc_start: 0.8067 (OUTLIER) cc_final: 0.7767 (mttm) REVERT: D 90 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.6726 (mp0) REVERT: D 113 LYS cc_start: 0.7373 (ttmt) cc_final: 0.6923 (ttpt) REVERT: E 40 ARG cc_start: 0.7302 (OUTLIER) cc_final: 0.6708 (ttt-90) REVERT: E 90 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.6659 (mtp) REVERT: E 131 ARG cc_start: 0.7956 (OUTLIER) cc_final: 0.7028 (mtp85) REVERT: G 71 ARG cc_start: 0.7391 (ttm110) cc_final: 0.7143 (ttm170) REVERT: G 73 ASN cc_start: 0.7748 (t0) cc_final: 0.7146 (t0) REVERT: G 95 LYS cc_start: 0.8091 (tttp) cc_final: 0.7630 (ttmt) REVERT: G 99 LYS cc_start: 0.7979 (mtpt) cc_final: 0.6972 (mtpt) REVERT: H 68 GLU cc_start: 0.7179 (mt-10) cc_final: 0.6947 (mt-10) REVERT: M 38 THR cc_start: 0.7315 (p) cc_final: 0.7047 (t) REVERT: M 111 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8059 (pp20) REVERT: M 235 ASN cc_start: 0.7733 (OUTLIER) cc_final: 0.6841 (m110) REVERT: N 65 GLN cc_start: 0.8313 (mt0) cc_final: 0.8035 (mp10) REVERT: N 95 ASP cc_start: 0.7670 (t70) cc_final: 0.7211 (t70) REVERT: N 103 MET cc_start: 0.8035 (OUTLIER) cc_final: 0.7730 (ttp) REVERT: N 108 LEU cc_start: 0.8067 (mp) cc_final: 0.7807 (mp) REVERT: N 261 LYS cc_start: 0.8253 (mtpm) cc_final: 0.7836 (ttpt) REVERT: O 253 GLN cc_start: 0.5402 (OUTLIER) cc_final: 0.4123 (mp10) outliers start: 43 outliers final: 18 residues processed: 190 average time/residue: 1.7325 time to fit residues: 355.2446 Evaluate side-chains 184 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 1.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain M residue 247 LEU Chi-restraints excluded: chain N residue 25 GLN Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 255 THR Chi-restraints excluded: chain O residue 226 THR 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 92 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 30 optimal weight: 0.5980 chunk 54 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 34 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 141 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 60 ASN M 27 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3985 r_free = 0.3985 target = 0.160834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.108970 restraints weight = 16689.989| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 1.59 r_work: 0.3167 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7175 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17053 Z= 0.149 Angle : 0.588 8.605 24250 Z= 0.342 Chirality : 0.037 0.201 2721 Planarity : 0.004 0.043 2062 Dihedral : 28.789 167.236 4605 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.52 % Allowed : 25.09 % Favored : 71.39 % 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: 1.28 (0.24), residues: 1275 helix: 2.17 (0.22), residues: 573 sheet: 0.70 (0.37), residues: 196 loop : -0.63 (0.28), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 193 HIS 0.004 0.001 HIS M 249 PHE 0.024 0.001 PHE O 254 TYR 0.013 0.001 TYR B 51 ARG 0.007 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 892) hydrogen bonds : angle 3.41005 ( 2271) SS BOND : bond 0.00269 ( 5) SS BOND : angle 1.00526 ( 10) covalent geometry : bond 0.00325 (17048) covalent geometry : angle 0.58781 (24240) *********************** 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 194 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 155 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7639 (tp30) cc_final: 0.7359 (mm-30) REVERT: B 74 GLU cc_start: 0.7781 (mt-10) cc_final: 0.7493 (mt-10) REVERT: C 36 LYS cc_start: 0.8661 (mmmm) cc_final: 0.8337 (mmmt) REVERT: C 42 ARG cc_start: 0.7534 (mtp85) cc_final: 0.6969 (mtp85) REVERT: D 60 ASN cc_start: 0.7666 (OUTLIER) cc_final: 0.7223 (m-40) REVERT: D 82 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7733 (mttm) REVERT: D 113 LYS cc_start: 0.7331 (ttmt) cc_final: 0.6935 (ttpt) REVERT: E 40 ARG cc_start: 0.7312 (OUTLIER) cc_final: 0.6736 (ttt-90) REVERT: E 90 MET cc_start: 0.7603 (OUTLIER) cc_final: 0.6636 (mtp) REVERT: G 71 ARG cc_start: 0.7396 (ttm110) cc_final: 0.7154 (ttm170) REVERT: G 73 ASN cc_start: 0.7675 (t0) cc_final: 0.7066 (t0) REVERT: H 68 GLU cc_start: 0.7020 (OUTLIER) cc_final: 0.6796 (mt-10) REVERT: M 38 THR cc_start: 0.7234 (p) cc_final: 0.6951 (t) REVERT: M 111 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.8027 (pp20) REVERT: M 235 ASN cc_start: 0.7731 (OUTLIER) cc_final: 0.6856 (m110) REVERT: N 25 GLN cc_start: 0.7531 (mm-40) cc_final: 0.7225 (mt0) REVERT: N 65 GLN cc_start: 0.8288 (mt0) cc_final: 0.7992 (mp10) REVERT: N 95 ASP cc_start: 0.7585 (t70) cc_final: 0.7106 (t70) REVERT: N 103 MET cc_start: 0.7886 (OUTLIER) cc_final: 0.7577 (ttp) REVERT: N 108 LEU cc_start: 0.8044 (mp) cc_final: 0.7777 (mp) REVERT: N 261 LYS cc_start: 0.8254 (mtpm) cc_final: 0.7815 (ttpt) REVERT: O 253 GLN cc_start: 0.5171 (OUTLIER) cc_final: 0.4791 (pp30) outliers start: 39 outliers final: 16 residues processed: 183 average time/residue: 1.6918 time to fit residues: 334.4049 Evaluate side-chains 178 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 153 time to evaluate : 1.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET 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 M residue 111 GLU Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 228 ASP Chi-restraints excluded: chain O residue 226 THR Chi-restraints excluded: chain O residue 253 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 47 optimal weight: 4.9990 chunk 16 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 93 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 113 optimal weight: 20.0000 chunk 142 optimal weight: 6.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN M 27 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3945 r_free = 0.3945 target = 0.157136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.105479 restraints weight = 16666.931| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 1.58 r_work: 0.3118 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 17053 Z= 0.269 Angle : 0.641 8.414 24250 Z= 0.369 Chirality : 0.041 0.200 2721 Planarity : 0.005 0.037 2062 Dihedral : 28.864 165.960 4605 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.61 % Allowed : 25.27 % Favored : 71.12 % 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: 0.98 (0.24), residues: 1275 helix: 1.86 (0.22), residues: 571 sheet: 0.66 (0.37), residues: 196 loop : -0.76 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 193 HIS 0.005 0.001 HIS M 249 PHE 0.015 0.002 PHE O 254 TYR 0.018 0.002 TYR B 88 ARG 0.006 0.001 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.04867 ( 892) hydrogen bonds : angle 3.55710 ( 2271) SS BOND : bond 0.00362 ( 5) SS BOND : angle 1.21678 ( 10) covalent geometry : bond 0.00627 (17048) covalent geometry : angle 0.64042 (24240) *********************** 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 194 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 154 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 52 GLU cc_start: 0.6990 (mp0) cc_final: 0.6654 (mm-30) REVERT: B 74 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7665 (mt-10) REVERT: B 84 MET cc_start: 0.8113 (mmm) cc_final: 0.7903 (mmm) REVERT: C 36 LYS cc_start: 0.8577 (mmmm) cc_final: 0.8250 (mmmt) REVERT: C 42 ARG cc_start: 0.7412 (mtp85) cc_final: 0.6723 (mtp85) REVERT: D 60 ASN cc_start: 0.7811 (OUTLIER) cc_final: 0.7323 (m-40) REVERT: D 113 LYS cc_start: 0.7326 (ttmt) cc_final: 0.6869 (ttpt) REVERT: E 40 ARG cc_start: 0.7329 (OUTLIER) cc_final: 0.6658 (ttt-90) REVERT: E 90 MET cc_start: 0.7620 (OUTLIER) cc_final: 0.6644 (mtp) REVERT: F 35 ARG cc_start: 0.7990 (mtp-110) cc_final: 0.7702 (mtp85) REVERT: G 71 ARG cc_start: 0.7382 (ttm110) cc_final: 0.7127 (ttm170) REVERT: G 73 ASN cc_start: 0.7758 (t0) cc_final: 0.7159 (t0) REVERT: G 95 LYS cc_start: 0.8099 (tttp) cc_final: 0.7634 (ttmt) REVERT: G 99 LYS cc_start: 0.7965 (mtpt) cc_final: 0.6967 (mtpt) REVERT: H 68 GLU cc_start: 0.7187 (OUTLIER) cc_final: 0.6961 (mt-10) REVERT: H 82 LYS cc_start: 0.7592 (mtmm) cc_final: 0.7167 (mtmm) REVERT: M 38 THR cc_start: 0.7280 (p) cc_final: 0.7003 (t) REVERT: M 111 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7850 (pp20) REVERT: M 235 ASN cc_start: 0.7750 (OUTLIER) cc_final: 0.6857 (m110) REVERT: N 23 GLU cc_start: 0.5305 (OUTLIER) cc_final: 0.4852 (tp30) REVERT: N 65 GLN cc_start: 0.8292 (mt0) cc_final: 0.8036 (mp10) REVERT: N 95 ASP cc_start: 0.7606 (t70) cc_final: 0.7100 (t70) REVERT: N 103 MET cc_start: 0.8040 (OUTLIER) cc_final: 0.7733 (ttp) REVERT: N 108 LEU cc_start: 0.8081 (mp) cc_final: 0.7833 (mp) REVERT: N 261 LYS cc_start: 0.8248 (mtpm) cc_final: 0.7804 (ttpt) REVERT: O 253 GLN cc_start: 0.5188 (OUTLIER) cc_final: 0.4079 (mp10) outliers start: 40 outliers final: 17 residues processed: 182 average time/residue: 1.6839 time to fit residues: 331.2369 Evaluate side-chains 177 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 151 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET 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 M residue 39 SER Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 255 THR Chi-restraints excluded: chain O residue 226 THR 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 15 optimal weight: 10.0000 chunk 106 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 24 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 111 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 130 optimal weight: 9.9990 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 76 GLN C 104 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN M 27 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3970 r_free = 0.3970 target = 0.159541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.107556 restraints weight = 16625.032| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.59 r_work: 0.3146 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2987 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17053 Z= 0.168 Angle : 0.600 8.143 24250 Z= 0.350 Chirality : 0.037 0.205 2721 Planarity : 0.004 0.043 2062 Dihedral : 28.844 166.992 4605 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.80 % Allowed : 25.81 % Favored : 71.39 % 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: 1.13 (0.24), residues: 1275 helix: 2.00 (0.22), residues: 575 sheet: 0.67 (0.37), residues: 196 loop : -0.69 (0.27), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 193 HIS 0.004 0.001 HIS M 249 PHE 0.012 0.001 PHE O 254 TYR 0.017 0.001 TYR D 37 ARG 0.007 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.04250 ( 892) hydrogen bonds : angle 3.46387 ( 2271) SS BOND : bond 0.00331 ( 5) SS BOND : angle 1.08100 ( 10) covalent geometry : bond 0.00375 (17048) covalent geometry : angle 0.59947 (24240) *********************** 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 190 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 159 time to evaluate : 1.333 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7657 (tp30) cc_final: 0.7416 (mm-30) REVERT: B 52 GLU cc_start: 0.6930 (mp0) cc_final: 0.6599 (mm-30) REVERT: B 74 GLU cc_start: 0.7964 (mt-10) cc_final: 0.7658 (mt-10) REVERT: C 36 LYS cc_start: 0.8663 (mmmm) cc_final: 0.8341 (mmmt) REVERT: C 42 ARG cc_start: 0.7406 (mtp85) cc_final: 0.6829 (mtp85) REVERT: D 60 ASN cc_start: 0.7698 (OUTLIER) cc_final: 0.7231 (m-40) REVERT: D 113 LYS cc_start: 0.7292 (ttmt) cc_final: 0.6820 (ttpt) REVERT: E 40 ARG cc_start: 0.7306 (OUTLIER) cc_final: 0.6732 (ttt-90) REVERT: E 90 MET cc_start: 0.7609 (OUTLIER) cc_final: 0.6630 (mtp) REVERT: F 35 ARG cc_start: 0.7965 (mtp-110) cc_final: 0.7659 (mtp85) REVERT: G 71 ARG cc_start: 0.7396 (ttm110) cc_final: 0.7146 (ttm170) REVERT: G 73 ASN cc_start: 0.7705 (t0) cc_final: 0.7098 (t0) REVERT: G 99 LYS cc_start: 0.8020 (mtpt) cc_final: 0.6975 (mtpt) REVERT: H 68 GLU cc_start: 0.7045 (OUTLIER) cc_final: 0.6820 (mt-10) REVERT: H 82 LYS cc_start: 0.7593 (mtmm) cc_final: 0.7103 (mtmm) REVERT: M 38 THR cc_start: 0.7215 (p) cc_final: 0.6919 (t) REVERT: M 111 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7848 (pp20) REVERT: M 235 ASN cc_start: 0.7751 (OUTLIER) cc_final: 0.6884 (m110) REVERT: N 23 GLU cc_start: 0.5296 (OUTLIER) cc_final: 0.4844 (tp30) REVERT: N 25 GLN cc_start: 0.7565 (mm-40) cc_final: 0.7305 (mt0) REVERT: N 65 GLN cc_start: 0.8292 (mt0) cc_final: 0.7987 (mp10) REVERT: N 95 ASP cc_start: 0.7621 (t70) cc_final: 0.7106 (t70) REVERT: N 103 MET cc_start: 0.7904 (OUTLIER) cc_final: 0.7594 (ttp) REVERT: N 108 LEU cc_start: 0.8062 (mp) cc_final: 0.7793 (mp) REVERT: N 168 SER cc_start: 0.8778 (OUTLIER) cc_final: 0.8530 (t) REVERT: N 261 LYS cc_start: 0.8250 (mtpm) cc_final: 0.7700 (ttpt) outliers start: 31 outliers final: 14 residues processed: 181 average time/residue: 1.6909 time to fit residues: 330.3201 Evaluate side-chains 179 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 156 time to evaluate : 1.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET 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 M residue 111 GLU Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain O residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 104 optimal weight: 0.0980 chunk 100 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 115 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 148 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- 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 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN M 27 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3978 r_free = 0.3978 target = 0.160139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.108212 restraints weight = 16666.368| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.60 r_work: 0.3155 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 17053 Z= 0.174 Angle : 0.601 10.004 24250 Z= 0.348 Chirality : 0.037 0.206 2721 Planarity : 0.004 0.043 2062 Dihedral : 28.780 167.491 4605 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.53 % Allowed : 26.08 % Favored : 71.39 % 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: 1.18 (0.24), residues: 1275 helix: 2.06 (0.22), residues: 575 sheet: 0.65 (0.37), residues: 196 loop : -0.66 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 193 HIS 0.004 0.001 HIS M 249 PHE 0.012 0.001 PHE O 254 TYR 0.018 0.002 TYR B 88 ARG 0.007 0.000 ARG H 96 Details of bonding type rmsd hydrogen bonds : bond 0.04131 ( 892) hydrogen bonds : angle 3.42712 ( 2271) SS BOND : bond 0.00250 ( 5) SS BOND : angle 1.01380 ( 10) covalent geometry : bond 0.00394 (17048) covalent geometry : angle 0.60098 (24240) ********************** 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 184 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 156 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.7648 (tp30) cc_final: 0.7402 (mm-30) REVERT: B 52 GLU cc_start: 0.6911 (mp0) cc_final: 0.6572 (mm-30) REVERT: B 74 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7537 (mt-10) REVERT: B 84 MET cc_start: 0.8256 (mmm) cc_final: 0.7990 (tpt) REVERT: C 36 LYS cc_start: 0.8571 (mmmm) cc_final: 0.8243 (mmmt) REVERT: C 42 ARG cc_start: 0.7415 (mtp85) cc_final: 0.6839 (mtp85) REVERT: D 60 ASN cc_start: 0.7681 (OUTLIER) cc_final: 0.7237 (m-40) REVERT: D 113 LYS cc_start: 0.7343 (ttmt) cc_final: 0.6872 (ttpt) REVERT: E 40 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.6715 (ttt-90) REVERT: E 90 MET cc_start: 0.7611 (OUTLIER) cc_final: 0.6630 (mtp) REVERT: F 35 ARG cc_start: 0.7928 (mtp-110) cc_final: 0.7610 (mtp85) REVERT: G 71 ARG cc_start: 0.7403 (ttm110) cc_final: 0.7153 (ttm170) REVERT: G 73 ASN cc_start: 0.7701 (t0) cc_final: 0.7092 (t0) REVERT: H 68 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6877 (mt-10) REVERT: H 82 LYS cc_start: 0.7605 (mtmm) cc_final: 0.7108 (mtmm) REVERT: M 38 THR cc_start: 0.7201 (p) cc_final: 0.6896 (t) REVERT: M 111 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7829 (pp20) REVERT: M 235 ASN cc_start: 0.7740 (OUTLIER) cc_final: 0.6873 (m110) REVERT: N 23 GLU cc_start: 0.5293 (OUTLIER) cc_final: 0.4842 (tp30) REVERT: N 25 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7332 (mt0) REVERT: N 65 GLN cc_start: 0.8283 (mt0) cc_final: 0.7980 (mp10) REVERT: N 95 ASP cc_start: 0.7599 (t70) cc_final: 0.7111 (t70) REVERT: N 103 MET cc_start: 0.7894 (OUTLIER) cc_final: 0.7568 (ttp) REVERT: N 108 LEU cc_start: 0.8057 (mp) cc_final: 0.7807 (mp) REVERT: N 162 MET cc_start: 0.8898 (mmt) cc_final: 0.8243 (mmm) REVERT: N 261 LYS cc_start: 0.8128 (mtpm) cc_final: 0.7747 (ttpt) outliers start: 28 outliers final: 15 residues processed: 174 average time/residue: 1.7197 time to fit residues: 322.5270 Evaluate side-chains 178 residues out of total 1111 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET 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 M residue 111 GLU Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain O residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 21 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 38 optimal weight: 0.5980 chunk 119 optimal weight: 6.9990 chunk 67 optimal weight: 0.0980 chunk 110 optimal weight: 5.9990 chunk 151 optimal weight: 10.0000 chunk 6 optimal weight: 4.9990 chunk 35 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 overall best weight: 1.5182 ------------------------------------------------------------------------------- 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 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN M 27 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 = 0.3979 r_free = 0.3979 target = 0.160220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.108271 restraints weight = 16642.314| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.59 r_work: 0.3157 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17053 Z= 0.185 Angle : 0.595 8.250 24250 Z= 0.345 Chirality : 0.037 0.207 2721 Planarity : 0.004 0.038 2062 Dihedral : 28.664 167.477 4605 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.71 % Allowed : 25.99 % Favored : 71.30 % 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: 1.20 (0.24), residues: 1275 helix: 2.09 (0.22), residues: 575 sheet: 0.62 (0.37), residues: 196 loop : -0.65 (0.28), residues: 504 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 0.012 0.001 PHE O 254 TYR 0.016 0.002 TYR D 37 ARG 0.009 0.000 ARG N 176 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 892) hydrogen bonds : angle 3.38852 ( 2271) SS BOND : bond 0.00258 ( 5) SS BOND : angle 1.03647 ( 10) covalent geometry : bond 0.00422 (17048) covalent geometry : angle 0.59443 (24240) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14104.63 seconds wall clock time: 239 minutes 43.40 seconds (14383.40 seconds total)