Starting phenix.real_space_refine on Tue Mar 3 19:23:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/21du_67602/03_2026/21du_67602_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/21du_67602/03_2026/21du_67602.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/21du_67602/03_2026/21du_67602_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/21du_67602/03_2026/21du_67602_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/21du_67602/03_2026/21du_67602.map" default_real_map = "/net/cci-nas-00/data/ceres_data/21du_67602/03_2026/21du_67602.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.058 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: 4 Type Number sf(0) Gaussians S 55 5.16 5 C 5121 2.51 5 N 1399 2.21 5 O 1483 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8058 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1943 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 234} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "B" Number of atoms: 2570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2570 Classifications: {'peptide': 339} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 1, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 29 Chain: "C" Number of atoms: 403 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 403 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "N" Number of atoms: 933 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 933 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 120} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 2189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2189 Classifications: {'peptide': 278} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 6, 'TRANS': 271} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 49 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 1, 'ASN:plan1': 2, 'GLU:plan': 3, 'ARG:plan': 1, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 45 Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'OR9': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.72, per 1000 atoms: 0.21 Number of scatterers: 8058 At special positions: 0 Unit cell: (78.183, 100.674, 123.165, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 55 16.00 O 1483 8.00 N 1399 7.00 C 5121 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 930 " - pdb=" SG CYS R1013 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 272.8 milliseconds 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1932 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 40.7% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.687A pdb=" N MET A 18 " --> pdb=" O GLU A 14 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 53 Processing helix chain 'A' and resid 54 through 56 No H-bonds generated for 'chain 'A' and resid 54 through 56' Processing helix chain 'A' and resid 95 through 101 removed outlier: 3.560A pdb=" N ASN A 101 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 130 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.334A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 removed outlier: 4.199A pdb=" N ARG A 169 " --> pdb=" O PRO A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 204 removed outlier: 3.712A pdb=" N ILE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 removed outlier: 3.506A pdb=" N TYR A 243 " --> pdb=" O HIS A 239 " (cutoff:3.500A) Processing helix chain 'B' and resid 3 through 26 Processing helix chain 'C' and resid 9 through 25 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.621A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 844 through 848 removed outlier: 3.762A pdb=" N ASP R 848 " --> pdb=" O VAL R 845 " (cutoff:3.500A) Processing helix chain 'R' and resid 858 through 889 removed outlier: 4.057A pdb=" N PHE R 889 " --> pdb=" O THR R 885 " (cutoff:3.500A) Processing helix chain 'R' and resid 895 through 923 removed outlier: 3.944A pdb=" N GLY R 919 " --> pdb=" O PHE R 915 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N TRP R 920 " --> pdb=" O LEU R 916 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N SER R 923 " --> pdb=" O GLY R 919 " (cutoff:3.500A) Processing helix chain 'R' and resid 926 through 959 removed outlier: 3.849A pdb=" N CYS R 930 " --> pdb=" O VAL R 926 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL R 933 " --> pdb=" O LEU R 929 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA R 952 " --> pdb=" O MET R 948 " (cutoff:3.500A) Processing helix chain 'R' and resid 969 through 993 Proline residue: R 982 - end of helix Processing helix chain 'R' and resid 994 through 999 removed outlier: 3.562A pdb=" N VAL R 998 " --> pdb=" O ASN R 994 " (cutoff:3.500A) Processing helix chain 'R' and resid 1017 through 1024 Processing helix chain 'R' and resid 1025 through 1053 removed outlier: 3.566A pdb=" N PHE R1029 " --> pdb=" O CYS R1025 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL R1042 " --> pdb=" O ALA R1038 " (cutoff:3.500A) Processing helix chain 'R' and resid 1059 through 1077 removed outlier: 3.765A pdb=" N PHE R1075 " --> pdb=" O VAL R1071 " (cutoff:3.500A) Processing helix chain 'R' and resid 1079 through 1081 No H-bonds generated for 'chain 'R' and resid 1079 through 1081' Processing helix chain 'R' and resid 1082 through 1087 removed outlier: 3.819A pdb=" N PHE R1086 " --> pdb=" O GLY R1082 " (cutoff:3.500A) Processing helix chain 'R' and resid 1091 through 1105 removed outlier: 3.584A pdb=" N PHE R1095 " --> pdb=" O LEU R1091 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N TYR R1097 " --> pdb=" O ILE R1093 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LEU R1098 " --> pdb=" O PRO R1094 " (cutoff:3.500A) Processing helix chain 'R' and resid 1105 through 1115 Processing helix chain 'R' and resid 1120 through 1125 Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 76 removed outlier: 3.607A pdb=" N HIS A 34 " --> pdb=" O ASN A 80 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N VAL A 86 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA A 105 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.648A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.729A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 6.313A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 148 through 151 removed outlier: 6.729A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.027A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ASP B 212 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N MET B 217 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.580A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASP B 254 " --> pdb=" O GLN B 259 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.547A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 8 removed outlier: 3.629A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 58 through 60 removed outlier: 5.340A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1164 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.25 Time building geometry restraints manager: 0.95 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2644 1.34 - 1.46: 1982 1.46 - 1.58: 3520 1.58 - 1.70: 2 1.70 - 1.81: 80 Bond restraints: 8228 Sorted by residual: bond pdb=" C10 OR9 R1201 " pdb=" N01 OR9 R1201 " ideal model delta sigma weight residual 1.450 1.256 0.194 2.00e-02 2.50e+03 9.45e+01 bond pdb=" C03 OR9 R1201 " pdb=" C08 OR9 R1201 " ideal model delta sigma weight residual 1.500 1.577 -0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C05 OR9 R1201 " pdb=" C06 OR9 R1201 " ideal model delta sigma weight residual 1.513 1.590 -0.077 2.00e-02 2.50e+03 1.47e+01 bond pdb=" C07 OR9 R1201 " pdb=" C12 OR9 R1201 " ideal model delta sigma weight residual 1.395 1.456 -0.061 2.00e-02 2.50e+03 9.34e+00 bond pdb=" C07 OR9 R1201 " pdb=" C09 OR9 R1201 " ideal model delta sigma weight residual 1.477 1.417 0.060 2.00e-02 2.50e+03 8.91e+00 ... (remaining 8223 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.01: 11121 3.01 - 6.02: 31 6.02 - 9.03: 1 9.03 - 12.05: 0 12.05 - 15.06: 1 Bond angle restraints: 11154 Sorted by residual: angle pdb=" C03 OR9 R1201 " pdb=" C01 OR9 R1201 " pdb=" N01 OR9 R1201 " ideal model delta sigma weight residual 112.42 97.36 15.06 3.00e+00 1.11e-01 2.52e+01 angle pdb=" CA PRO C 53 " pdb=" N PRO C 53 " pdb=" CD PRO C 53 " ideal model delta sigma weight residual 112.00 107.25 4.75 1.40e+00 5.10e-01 1.15e+01 angle pdb=" CB MET N 34 " pdb=" CG MET N 34 " pdb=" SD MET N 34 " ideal model delta sigma weight residual 112.70 121.14 -8.44 3.00e+00 1.11e-01 7.91e+00 angle pdb=" N VAL N 48 " pdb=" CA VAL N 48 " pdb=" C VAL N 48 " ideal model delta sigma weight residual 113.53 110.85 2.68 9.80e-01 1.04e+00 7.50e+00 angle pdb=" N GLN A 52 " pdb=" CA GLN A 52 " pdb=" C GLN A 52 " ideal model delta sigma weight residual 111.14 113.97 -2.83 1.08e+00 8.57e-01 6.86e+00 ... (remaining 11149 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 4142 17.98 - 35.96: 547 35.96 - 53.94: 136 53.94 - 71.92: 20 71.92 - 89.90: 8 Dihedral angle restraints: 4853 sinusoidal: 1855 harmonic: 2998 Sorted by residual: dihedral pdb=" CB CYS R 930 " pdb=" SG CYS R 930 " pdb=" SG CYS R1013 " pdb=" CB CYS R1013 " ideal model delta sinusoidal sigma weight residual 93.00 177.37 -84.37 1 1.00e+01 1.00e-02 8.66e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -5.51 -80.49 1 1.00e+01 1.00e-02 8.01e+01 dihedral pdb=" CA ASP N 50 " pdb=" CB ASP N 50 " pdb=" CG ASP N 50 " pdb=" OD1 ASP N 50 " ideal model delta sinusoidal sigma weight residual -30.00 -90.21 60.21 1 2.00e+01 2.50e-03 1.21e+01 ... (remaining 4850 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1085 0.057 - 0.113: 146 0.113 - 0.170: 19 0.170 - 0.227: 0 0.227 - 0.283: 1 Chirality restraints: 1251 Sorted by residual: chirality pdb=" C01 OR9 R1201 " pdb=" C02 OR9 R1201 " pdb=" C03 OR9 R1201 " pdb=" N01 OR9 R1201 " both_signs ideal model delta sigma weight residual False -2.48 -2.77 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CA GLU A 179 " pdb=" N GLU A 179 " pdb=" C GLU A 179 " pdb=" CB GLU A 179 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CB ILE B 43 " pdb=" CA ILE B 43 " pdb=" CG1 ILE B 43 " pdb=" CG2 ILE B 43 " both_signs ideal model delta sigma weight residual False 2.64 2.78 -0.14 2.00e-01 2.50e+01 4.86e-01 ... (remaining 1248 not shown) Planarity restraints: 1427 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR C 52 " 0.067 5.00e-02 4.00e+02 9.90e-02 1.57e+01 pdb=" N PRO C 53 " -0.171 5.00e-02 4.00e+02 pdb=" CA PRO C 53 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO C 53 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP N 90 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.10e+00 pdb=" CG ASP N 90 " -0.025 2.00e-02 2.50e+03 pdb=" OD1 ASP N 90 " 0.009 2.00e-02 2.50e+03 pdb=" OD2 ASP N 90 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS N 87 " 0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO N 88 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO N 88 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO N 88 " 0.020 5.00e-02 4.00e+02 ... (remaining 1424 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 914 2.75 - 3.29: 7569 3.29 - 3.83: 13859 3.83 - 4.36: 15903 4.36 - 4.90: 28292 Nonbonded interactions: 66537 Sorted by model distance: nonbonded pdb=" O SER A 204 " pdb=" OG SER A 204 " model vdw 2.214 3.040 nonbonded pdb=" NE2 HIS B 54 " pdb=" OG SER B 72 " model vdw 2.266 3.120 nonbonded pdb=" O GLY R1000 " pdb=" NE2 GLN R1016 " model vdw 2.283 3.120 nonbonded pdb=" OH TYR A 243 " pdb=" OE2 GLU R 951 " model vdw 2.302 3.040 nonbonded pdb=" OG SER R 868 " pdb=" OG SER R1100 " model vdw 2.306 3.040 ... (remaining 66532 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.980 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 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 : 0.004 0.194 8231 Z= 0.189 Angle : 0.501 15.058 11160 Z= 0.281 Chirality : 0.040 0.283 1251 Planarity : 0.004 0.099 1427 Dihedral : 17.046 89.897 2912 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.36 % Allowed : 28.50 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.27), residues: 1025 helix: 2.44 (0.27), residues: 377 sheet: 1.09 (0.33), residues: 231 loop : -0.77 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG R 968 TYR 0.007 0.001 TYR N 60 PHE 0.015 0.001 PHE R1075 TRP 0.013 0.001 TRP B 169 HIS 0.002 0.000 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 8228) covalent geometry : angle 0.50112 (11154) SS BOND : bond 0.00314 ( 3) SS BOND : angle 0.63424 ( 6) hydrogen bonds : bond 0.14958 ( 404) hydrogen bonds : angle 5.07473 ( 1164) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 109 time to evaluate : 0.216 Fit side-chains REVERT: R 886 TYR cc_start: 0.7862 (m-80) cc_final: 0.7624 (m-80) REVERT: R 1044 MET cc_start: 0.8145 (mmt) cc_final: 0.7660 (tpt) outliers start: 3 outliers final: 1 residues processed: 112 average time/residue: 0.5145 time to fit residues: 61.3387 Evaluate side-chains 105 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 996 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 30.0000 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 123 ASN N 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.184543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.122859 restraints weight = 8383.632| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 2.29 r_work: 0.3308 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.3146 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3146 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 8231 Z= 0.272 Angle : 0.640 9.052 11160 Z= 0.342 Chirality : 0.047 0.159 1251 Planarity : 0.005 0.063 1427 Dihedral : 4.337 25.191 1144 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 5.23 % Allowed : 25.53 % Favored : 69.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.26), residues: 1025 helix: 2.27 (0.26), residues: 372 sheet: 0.64 (0.32), residues: 237 loop : -0.82 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 132 TYR 0.020 0.002 TYR A 191 PHE 0.027 0.003 PHE R1075 TRP 0.014 0.002 TRP R 947 HIS 0.005 0.002 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00646 ( 8228) covalent geometry : angle 0.63922 (11154) SS BOND : bond 0.00372 ( 3) SS BOND : angle 1.46482 ( 6) hydrogen bonds : bond 0.06054 ( 404) hydrogen bonds : angle 4.61532 ( 1164) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 115 time to evaluate : 0.258 Fit side-chains REVERT: B 294 CYS cc_start: 0.8044 (OUTLIER) cc_final: 0.7746 (m) REVERT: B 303 ASP cc_start: 0.7831 (p0) cc_final: 0.7622 (p0) REVERT: C 21 MET cc_start: 0.4737 (ttt) cc_final: 0.4169 (mpt) REVERT: N 35 ASN cc_start: 0.7988 (m-40) cc_final: 0.7782 (m110) REVERT: N 118 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.6886 (mtm180) REVERT: R 886 TYR cc_start: 0.7921 (m-80) cc_final: 0.7502 (m-80) REVERT: R 1044 MET cc_start: 0.8401 (mmt) cc_final: 0.8189 (tpt) outliers start: 44 outliers final: 23 residues processed: 144 average time/residue: 0.4734 time to fit residues: 72.7497 Evaluate side-chains 129 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 104 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 29 VAL Chi-restraints excluded: chain A residue 127 SER Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 996 ASN Chi-restraints excluded: chain R residue 1019 VAL Chi-restraints excluded: chain R residue 1024 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 56 optimal weight: 0.9980 chunk 82 optimal weight: 9.9990 chunk 89 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 52 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 69 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 12 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN B 340 ASN R 954 HIS ** R1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.189575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.142249 restraints weight = 8318.591| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.40 r_work: 0.3365 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3207 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8231 Z= 0.157 Angle : 0.524 8.006 11160 Z= 0.280 Chirality : 0.043 0.150 1251 Planarity : 0.004 0.054 1427 Dihedral : 4.056 25.358 1144 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 4.99 % Allowed : 26.84 % Favored : 68.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.27), residues: 1025 helix: 2.36 (0.27), residues: 371 sheet: 0.61 (0.33), residues: 230 loop : -0.92 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 208 TYR 0.014 0.001 TYR A 191 PHE 0.016 0.001 PHE A 74 TRP 0.014 0.002 TRP A 96 HIS 0.004 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 8228) covalent geometry : angle 0.52294 (11154) SS BOND : bond 0.00571 ( 3) SS BOND : angle 1.27807 ( 6) hydrogen bonds : bond 0.04692 ( 404) hydrogen bonds : angle 4.34157 ( 1164) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 106 time to evaluate : 0.287 Fit side-chains revert: symmetry clash REVERT: B 136 SER cc_start: 0.8220 (OUTLIER) cc_final: 0.7956 (p) REVERT: B 259 GLN cc_start: 0.8092 (pt0) cc_final: 0.7854 (pt0) REVERT: B 303 ASP cc_start: 0.7824 (p0) cc_final: 0.7610 (p0) REVERT: N 38 ARG cc_start: 0.7848 (OUTLIER) cc_final: 0.7610 (ptm-80) REVERT: R 886 TYR cc_start: 0.8046 (m-80) cc_final: 0.7585 (m-80) REVERT: R 1044 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8173 (tpt) outliers start: 42 outliers final: 18 residues processed: 134 average time/residue: 0.4923 time to fit residues: 70.2035 Evaluate side-chains 121 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 100 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 909 LEU Chi-restraints excluded: chain R residue 976 ILE Chi-restraints excluded: chain R residue 1019 VAL Chi-restraints excluded: chain R residue 1044 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 91 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 50 optimal weight: 0.9990 chunk 81 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 51 optimal weight: 0.3980 chunk 37 optimal weight: 0.6980 chunk 73 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN ** R1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.192129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.131813 restraints weight = 8432.934| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.28 r_work: 0.3405 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work: 0.3242 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8231 Z= 0.129 Angle : 0.489 7.511 11160 Z= 0.263 Chirality : 0.042 0.150 1251 Planarity : 0.003 0.049 1427 Dihedral : 3.797 23.531 1142 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 5.46 % Allowed : 25.89 % Favored : 68.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.27), residues: 1025 helix: 2.45 (0.27), residues: 371 sheet: 0.50 (0.32), residues: 235 loop : -0.92 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 208 TYR 0.014 0.001 TYR A 191 PHE 0.016 0.001 PHE R1075 TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8228) covalent geometry : angle 0.48906 (11154) SS BOND : bond 0.00433 ( 3) SS BOND : angle 0.88801 ( 6) hydrogen bonds : bond 0.04245 ( 404) hydrogen bonds : angle 4.17928 ( 1164) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 110 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 152 LYS cc_start: 0.6303 (tttt) cc_final: 0.5984 (ttmt) REVERT: B 136 SER cc_start: 0.8190 (OUTLIER) cc_final: 0.7929 (p) REVERT: B 303 ASP cc_start: 0.7804 (p0) cc_final: 0.7593 (p0) REVERT: N 38 ARG cc_start: 0.7843 (OUTLIER) cc_final: 0.7626 (ptm-80) REVERT: R 886 TYR cc_start: 0.8081 (m-80) cc_final: 0.7567 (m-80) outliers start: 46 outliers final: 27 residues processed: 138 average time/residue: 0.4657 time to fit residues: 68.7016 Evaluate side-chains 132 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 103 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 976 ILE Chi-restraints excluded: chain R residue 1019 VAL Chi-restraints excluded: chain R residue 1024 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 53 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 75 optimal weight: 20.0000 chunk 21 optimal weight: 0.0270 chunk 96 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 37 optimal weight: 0.0970 overall best weight: 0.9038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN R1036 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.193846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.149587 restraints weight = 8379.404| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 2.34 r_work: 0.3319 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.3165 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7738 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8231 Z= 0.151 Angle : 0.515 7.866 11160 Z= 0.275 Chirality : 0.042 0.153 1251 Planarity : 0.004 0.047 1427 Dihedral : 3.905 22.425 1142 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 5.46 % Allowed : 26.01 % Favored : 68.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.27), residues: 1025 helix: 2.49 (0.27), residues: 368 sheet: 0.43 (0.32), residues: 235 loop : -0.95 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 208 TYR 0.016 0.001 TYR A 191 PHE 0.015 0.001 PHE A 74 TRP 0.012 0.001 TRP A 96 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8228) covalent geometry : angle 0.51405 (11154) SS BOND : bond 0.00660 ( 3) SS BOND : angle 1.60044 ( 6) hydrogen bonds : bond 0.04419 ( 404) hydrogen bonds : angle 4.20423 ( 1164) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 103 time to evaluate : 0.271 Fit side-chains revert: symmetry clash REVERT: B 136 SER cc_start: 0.8327 (OUTLIER) cc_final: 0.8063 (p) REVERT: B 303 ASP cc_start: 0.7746 (p0) cc_final: 0.7531 (p0) REVERT: N 38 ARG cc_start: 0.8008 (OUTLIER) cc_final: 0.7775 (ptm-80) REVERT: N 83 MET cc_start: 0.5895 (OUTLIER) cc_final: 0.5681 (mtp) REVERT: R 886 TYR cc_start: 0.8166 (m-80) cc_final: 0.7671 (m-80) outliers start: 46 outliers final: 26 residues processed: 133 average time/residue: 0.4503 time to fit residues: 64.2885 Evaluate side-chains 130 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain A residue 238 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 38 ARG Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 909 LEU Chi-restraints excluded: chain R residue 976 ILE Chi-restraints excluded: chain R residue 1019 VAL Chi-restraints excluded: chain R residue 1024 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 89 optimal weight: 0.0670 chunk 67 optimal weight: 0.0270 chunk 74 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 55 optimal weight: 0.7980 chunk 48 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.3776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 ASN A 89 GLN B 259 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.193539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.134189 restraints weight = 8321.394| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 2.25 r_work: 0.3425 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3262 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8231 Z= 0.106 Angle : 0.472 6.685 11160 Z= 0.253 Chirality : 0.041 0.150 1251 Planarity : 0.003 0.046 1427 Dihedral : 3.683 21.093 1142 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.63 % Allowed : 26.96 % Favored : 68.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.27), residues: 1025 helix: 2.62 (0.27), residues: 368 sheet: 0.47 (0.32), residues: 235 loop : -0.92 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 208 TYR 0.014 0.001 TYR A 191 PHE 0.015 0.001 PHE R1109 TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 8228) covalent geometry : angle 0.47176 (11154) SS BOND : bond 0.00444 ( 3) SS BOND : angle 1.07599 ( 6) hydrogen bonds : bond 0.03831 ( 404) hydrogen bonds : angle 4.08612 ( 1164) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 110 time to evaluate : 0.274 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8752 (OUTLIER) cc_final: 0.8529 (m-80) REVERT: B 118 ASP cc_start: 0.8685 (p0) cc_final: 0.8117 (p0) REVERT: B 254 ASP cc_start: 0.8076 (t0) cc_final: 0.7853 (t0) REVERT: R 886 TYR cc_start: 0.8113 (m-80) cc_final: 0.7666 (m-80) REVERT: R 918 ASP cc_start: 0.7338 (t70) cc_final: 0.7024 (t0) outliers start: 39 outliers final: 24 residues processed: 134 average time/residue: 0.5271 time to fit residues: 75.1497 Evaluate side-chains 126 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 101 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 902 MET Chi-restraints excluded: chain R residue 909 LEU Chi-restraints excluded: chain R residue 976 ILE Chi-restraints excluded: chain R residue 1019 VAL Chi-restraints excluded: chain R residue 1024 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 82 optimal weight: 0.1980 chunk 81 optimal weight: 0.7980 chunk 55 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 70 optimal weight: 0.8980 chunk 26 optimal weight: 9.9990 chunk 100 optimal weight: 0.3980 chunk 29 optimal weight: 0.5980 chunk 59 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN N 84 ASN R 954 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.198638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.154901 restraints weight = 8329.439| |-----------------------------------------------------------------------------| r_work (start): 0.3766 rms_B_bonded: 2.35 r_work: 0.3431 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8231 Z= 0.117 Angle : 0.495 7.172 11160 Z= 0.263 Chirality : 0.041 0.150 1251 Planarity : 0.004 0.048 1427 Dihedral : 3.692 22.167 1142 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.16 % Allowed : 28.27 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.27), residues: 1025 helix: 2.59 (0.27), residues: 368 sheet: 0.44 (0.33), residues: 235 loop : -0.93 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 199 TYR 0.015 0.001 TYR A 191 PHE 0.014 0.001 PHE A 74 TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8228) covalent geometry : angle 0.49471 (11154) SS BOND : bond 0.00424 ( 3) SS BOND : angle 0.86732 ( 6) hydrogen bonds : bond 0.03914 ( 404) hydrogen bonds : angle 4.06741 ( 1164) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 109 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: A 152 LYS cc_start: 0.6459 (tttt) cc_final: 0.6170 (ttmt) REVERT: A 208 ARG cc_start: 0.8167 (mtm110) cc_final: 0.7780 (mtm110) REVERT: B 59 TYR cc_start: 0.8710 (OUTLIER) cc_final: 0.8491 (m-80) REVERT: N 83 MET cc_start: 0.6534 (ptp) cc_final: 0.6254 (ptp) REVERT: R 886 TYR cc_start: 0.8176 (m-80) cc_final: 0.7796 (m-80) outliers start: 35 outliers final: 26 residues processed: 134 average time/residue: 0.5277 time to fit residues: 75.3141 Evaluate side-chains 136 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 109 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 909 LEU Chi-restraints excluded: chain R residue 976 ILE Chi-restraints excluded: chain R residue 1019 VAL Chi-restraints excluded: chain R residue 1024 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 88 optimal weight: 0.6980 chunk 84 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 chunk 63 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 48 optimal weight: 0.1980 chunk 55 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 96 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 340 ASN ** R1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.199353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.154199 restraints weight = 8165.607| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.14 r_work: 0.3445 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7722 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8231 Z= 0.118 Angle : 0.497 7.283 11160 Z= 0.264 Chirality : 0.041 0.199 1251 Planarity : 0.004 0.048 1427 Dihedral : 3.694 22.143 1142 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.28 % Allowed : 27.91 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.27), residues: 1025 helix: 2.59 (0.27), residues: 369 sheet: 0.41 (0.32), residues: 238 loop : -0.91 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 199 TYR 0.015 0.001 TYR A 191 PHE 0.015 0.001 PHE A 74 TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 8228) covalent geometry : angle 0.49685 (11154) SS BOND : bond 0.00415 ( 3) SS BOND : angle 0.76108 ( 6) hydrogen bonds : bond 0.03891 ( 404) hydrogen bonds : angle 4.04807 ( 1164) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 111 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 152 LYS cc_start: 0.6506 (tttt) cc_final: 0.6204 (ttmt) REVERT: A 208 ARG cc_start: 0.8202 (mtm110) cc_final: 0.7813 (mtm110) REVERT: B 136 SER cc_start: 0.8347 (OUTLIER) cc_final: 0.8063 (p) REVERT: B 197 ARG cc_start: 0.7673 (mtp-110) cc_final: 0.7432 (mtp-110) REVERT: R 886 TYR cc_start: 0.8171 (m-80) cc_final: 0.7744 (m-80) outliers start: 36 outliers final: 29 residues processed: 137 average time/residue: 0.4687 time to fit residues: 68.9335 Evaluate side-chains 134 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 104 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 138 GLU Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 909 LEU Chi-restraints excluded: chain R residue 976 ILE Chi-restraints excluded: chain R residue 1019 VAL Chi-restraints excluded: chain R residue 1024 THR Chi-restraints excluded: chain R residue 1095 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 47 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 84 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 42 optimal weight: 0.0040 chunk 5 optimal weight: 20.0000 chunk 70 optimal weight: 3.9990 overall best weight: 0.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 259 GLN ** R1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.198564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.153581 restraints weight = 8227.626| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.20 r_work: 0.3376 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 moved from start: 0.2332 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8231 Z= 0.131 Angle : 0.524 8.027 11160 Z= 0.279 Chirality : 0.042 0.183 1251 Planarity : 0.004 0.053 1427 Dihedral : 3.774 22.565 1142 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 4.04 % Allowed : 28.62 % Favored : 67.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.27), residues: 1025 helix: 2.54 (0.27), residues: 369 sheet: 0.39 (0.32), residues: 238 loop : -0.93 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 199 TYR 0.015 0.001 TYR A 191 PHE 0.016 0.001 PHE A 74 TRP 0.011 0.001 TRP A 96 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00297 ( 8228) covalent geometry : angle 0.51981 (11154) SS BOND : bond 0.00966 ( 3) SS BOND : angle 2.89372 ( 6) hydrogen bonds : bond 0.04070 ( 404) hydrogen bonds : angle 4.07601 ( 1164) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 107 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 132 ARG cc_start: 0.7212 (tpt-90) cc_final: 0.7005 (tpt-90) REVERT: B 136 SER cc_start: 0.8327 (OUTLIER) cc_final: 0.8037 (p) REVERT: B 197 ARG cc_start: 0.7622 (mtp-110) cc_final: 0.7381 (mtp-110) REVERT: N 83 MET cc_start: 0.6455 (ptp) cc_final: 0.6178 (ptp) REVERT: R 886 TYR cc_start: 0.8153 (m-80) cc_final: 0.7718 (m-80) outliers start: 34 outliers final: 29 residues processed: 131 average time/residue: 0.5131 time to fit residues: 71.7394 Evaluate side-chains 133 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 103 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 909 LEU Chi-restraints excluded: chain R residue 976 ILE Chi-restraints excluded: chain R residue 1019 VAL Chi-restraints excluded: chain R residue 1024 THR Chi-restraints excluded: chain R residue 1095 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 3 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 72 optimal weight: 0.4980 chunk 86 optimal weight: 0.4980 chunk 6 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 98 optimal weight: 0.0030 overall best weight: 0.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN B 259 GLN ** R1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.200085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.154729 restraints weight = 8213.946| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.15 r_work: 0.3449 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8231 Z= 0.113 Angle : 0.505 7.820 11160 Z= 0.269 Chirality : 0.041 0.176 1251 Planarity : 0.004 0.057 1427 Dihedral : 3.700 21.675 1142 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.68 % Allowed : 29.22 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.27), residues: 1025 helix: 2.55 (0.27), residues: 369 sheet: 0.40 (0.32), residues: 238 loop : -0.91 (0.31), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG A 199 TYR 0.015 0.001 TYR A 191 PHE 0.015 0.001 PHE A 74 TRP 0.012 0.001 TRP B 169 HIS 0.002 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 8228) covalent geometry : angle 0.50139 (11154) SS BOND : bond 0.00657 ( 3) SS BOND : angle 2.54721 ( 6) hydrogen bonds : bond 0.03819 ( 404) hydrogen bonds : angle 4.03145 ( 1164) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 107 time to evaluate : 0.352 Fit side-chains revert: symmetry clash REVERT: A 152 LYS cc_start: 0.6477 (tttt) cc_final: 0.6187 (ttmt) REVERT: A 208 ARG cc_start: 0.8237 (mtm110) cc_final: 0.7847 (mtm110) REVERT: B 118 ASP cc_start: 0.8738 (p0) cc_final: 0.8138 (p0) REVERT: B 136 SER cc_start: 0.8317 (OUTLIER) cc_final: 0.8059 (p) REVERT: B 197 ARG cc_start: 0.7708 (mtp-110) cc_final: 0.7475 (mtp-110) REVERT: R 886 TYR cc_start: 0.8169 (m-80) cc_final: 0.7766 (m-80) REVERT: R 918 ASP cc_start: 0.7687 (t0) cc_final: 0.7379 (t0) REVERT: R 924 PHE cc_start: 0.7083 (m-80) cc_final: 0.6486 (m-10) outliers start: 31 outliers final: 24 residues processed: 130 average time/residue: 0.4975 time to fit residues: 69.1012 Evaluate side-chains 130 residues out of total 883 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 158 SER Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain A residue 236 GLN Chi-restraints excluded: chain B residue 81 ILE Chi-restraints excluded: chain B residue 88 ASN Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 136 SER Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 156 GLN Chi-restraints excluded: chain B residue 213 VAL Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 269 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain N residue 1 GLN Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain N residue 78 THR Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 909 LEU Chi-restraints excluded: chain R residue 976 ILE Chi-restraints excluded: chain R residue 1019 VAL Chi-restraints excluded: chain R residue 1095 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 78 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 25 optimal weight: 9.9990 chunk 9 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 43 optimal weight: 4.9990 chunk 54 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 259 GLN ** R1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.191603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.131445 restraints weight = 8276.587| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.24 r_work: 0.3290 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8231 Z= 0.160 Angle : 0.552 8.880 11160 Z= 0.293 Chirality : 0.043 0.178 1251 Planarity : 0.004 0.058 1427 Dihedral : 3.919 23.157 1142 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.80 % Allowed : 29.45 % Favored : 66.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.27), residues: 1025 helix: 2.46 (0.27), residues: 368 sheet: 0.34 (0.32), residues: 238 loop : -0.95 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 199 TYR 0.017 0.001 TYR A 191 PHE 0.016 0.001 PHE A 74 TRP 0.011 0.001 TRP A 96 HIS 0.003 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 8228) covalent geometry : angle 0.54959 (11154) SS BOND : bond 0.00696 ( 3) SS BOND : angle 2.36120 ( 6) hydrogen bonds : bond 0.04345 ( 404) hydrogen bonds : angle 4.16578 ( 1164) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3114.94 seconds wall clock time: 53 minutes 41.12 seconds (3221.12 seconds total)