Starting phenix.real_space_refine on Sat May 2 21:11:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ite_60859/05_2026/9ite_60859_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ite_60859/05_2026/9ite_60859.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ite_60859/05_2026/9ite_60859.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ite_60859/05_2026/9ite_60859.map" model { file = "/net/cci-nas-00/data/ceres_data/9ite_60859/05_2026/9ite_60859_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ite_60859/05_2026/9ite_60859_neut.cif" } resolution = 3.06 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= 0.041 sd= 0.148 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 1 5.49 5 S 63 5.16 5 C 5649 2.51 5 N 1458 2.21 5 O 1627 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8798 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1676 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 3, 'TRANS': 210} Chain breaks: 1 Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 5, 'GLN:plan1': 3, 'GLU:plan': 2, 'HIS:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 65 Chain: "B" Number of atoms: 2540 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2540 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2, 'GLN:plan1': 4, 'ARG:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 48 Chain: "E" Number of atoms: 1759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1759 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 4} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 413 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 20 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "R" Number of atoms: 2279 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2279 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 10, 'TRANS': 278} Chain breaks: 1 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 2, 'PHE:plan': 1, 'ARG:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 32 Chain: "R" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 131 Unusual residues: {'CLR': 3, 'NKP': 1, 'PLM': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 2.20, per 1000 atoms: 0.25 Number of scatterers: 8798 At special positions: 0 Unit cell: (93.5, 118.8, 138.6, 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 63 16.00 P 1 15.00 O 1627 8.00 N 1458 7.00 C 5649 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 9 " - pdb=" SG CYS R 263 " distance=2.03 Simple disulfide: pdb=" SG CYS R 89 " - pdb=" SG CYS R 168 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.80 Conformation dependent library (CDL) restraints added in 312.5 milliseconds 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2130 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 36.5% alpha, 23.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 6 through 31 removed outlier: 4.125A pdb=" N THR A 28 " --> pdb=" O SER A 24 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TYR A 29 " --> pdb=" O ARG A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 52 Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 117 through 129 removed outlier: 3.620A pdb=" N ILE A 128 " --> pdb=" O ASP A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 135 Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.721A pdb=" N GLN A 154 " --> pdb=" O GLU A 150 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N ILE A 155 " --> pdb=" O GLU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 161 removed outlier: 3.803A pdb=" N ASP A 160 " --> pdb=" O SER A 157 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N TYR A 161 " --> pdb=" O ILE A 158 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 157 through 161' Processing helix chain 'A' and resid 171 through 185 removed outlier: 3.554A pdb=" N VAL A 175 " --> pdb=" O CYS A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 227 removed outlier: 3.577A pdb=" N LYS A 225 " --> pdb=" O HIS A 221 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 removed outlier: 3.571A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.799A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.710A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.107A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 23 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.598A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 48 removed outlier: 4.204A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'G' and resid 55 through 59 removed outlier: 3.790A pdb=" N ASN G 59 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 15 through 45 removed outlier: 3.575A pdb=" N GLY R 21 " --> pdb=" O TYR R 17 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N CYS R 22 " --> pdb=" O THR R 18 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET R 23 " --> pdb=" O LEU R 19 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N SER R 25 " --> pdb=" O GLY R 21 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU R 32 " --> pdb=" O PHE R 28 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N ILE R 33 " --> pdb=" O VAL R 29 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASN R 35 " --> pdb=" O GLY R 31 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N CYS R 36 " --> pdb=" O LEU R 32 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL R 45 " --> pdb=" O ILE R 41 " (cutoff:3.500A) Processing helix chain 'R' and resid 50 through 68 Processing helix chain 'R' and resid 69 through 80 removed outlier: 4.041A pdb=" N ARG R 73 " --> pdb=" O THR R 69 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 120 removed outlier: 3.862A pdb=" N CYS R 89 " --> pdb=" O GLY R 85 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER R 103 " --> pdb=" O ASN R 99 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE R 104 " --> pdb=" O MET R 100 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU R 105 " --> pdb=" O TYR R 101 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE R 110 " --> pdb=" O PHE R 106 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N TYR R 120 " --> pdb=" O LEU R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 129 through 146 Processing helix chain 'R' and resid 149 through 153 removed outlier: 3.899A pdb=" N VAL R 152 " --> pdb=" O ALA R 149 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE R 153 " --> pdb=" O PRO R 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 149 through 153' Processing helix chain 'R' and resid 173 through 178 removed outlier: 3.683A pdb=" N TRP R 177 " --> pdb=" O PRO R 173 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS R 178 " --> pdb=" O GLU R 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 173 through 178' Processing helix chain 'R' and resid 180 through 192 removed outlier: 3.803A pdb=" N ILE R 184 " --> pdb=" O TYR R 180 " (cutoff:3.500A) Processing helix chain 'R' and resid 193 through 212 Processing helix chain 'R' and resid 223 through 242 removed outlier: 4.043A pdb=" N VAL R 227 " --> pdb=" O ASN R 223 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU R 235 " --> pdb=" O ILE R 231 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N PHE R 238 " --> pdb=" O HIS R 234 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N PHE R 242 " --> pdb=" O PHE R 238 " (cutoff:3.500A) Processing helix chain 'R' and resid 242 through 256 removed outlier: 3.514A pdb=" N ASN R 246 " --> pdb=" O PHE R 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 273 Processing helix chain 'R' and resid 280 through 285 Processing helix chain 'R' and resid 286 through 291 Processing helix chain 'R' and resid 295 through 299 Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 75 removed outlier: 7.280A pdb=" N LYS A 35 " --> pdb=" O SER A 105 " (cutoff:3.500A) removed outlier: 8.269A pdb=" N LEU A 107 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LEU A 37 " --> pdb=" O LEU A 107 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LEU A 109 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LEU A 39 " --> pdb=" O LEU A 109 " (cutoff:3.500A) removed outlier: 8.943A pdb=" N ASP A 111 " --> pdb=" O LEU A 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.980A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.883A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.045A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.054A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.569A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.998A 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: 6.892A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.251A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.436A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.806A pdb=" N GLY B 244 " --> pdb=" O ASN B 230 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE B 232 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA B 242 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N PHE B 234 " --> pdb=" O ALA B 240 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ALA B 240 " --> pdb=" O PHE B 234 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.822A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.945A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 3.693A pdb=" N ARG E 98 " --> pdb=" O PHE E 110 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 147 through 149 removed outlier: 4.089A pdb=" N GLU E 247 " --> pdb=" O VAL E 148 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU E 175 " --> pdb=" O TYR E 191 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N TYR E 191 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N TRP E 177 " --> pdb=" O LEU E 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 156 through 161 Processing sheet with id=AB5, first strand: chain 'R' and resid 157 through 158 removed outlier: 4.154A pdb=" N ALA R 167 " --> pdb=" O HIS R 158 " (cutoff:3.500A) 408 hydrogen bonds defined for protein. 1137 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: 1.27 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2785 1.34 - 1.46: 2147 1.46 - 1.58: 3964 1.58 - 1.70: 0 1.70 - 1.82: 89 Bond restraints: 8985 Sorted by residual: bond pdb=" OAF NKP R 401 " pdb=" PAC NKP R 401 " ideal model delta sigma weight residual 1.638 1.819 -0.181 2.00e-02 2.50e+03 8.21e+01 bond pdb=" OAD NKP R 401 " pdb=" PAC NKP R 401 " ideal model delta sigma weight residual 1.696 1.521 0.175 2.00e-02 2.50e+03 7.65e+01 bond pdb=" OAB NKP R 401 " pdb=" PAC NKP R 401 " ideal model delta sigma weight residual 1.683 1.510 0.173 2.00e-02 2.50e+03 7.45e+01 bond pdb=" CAG NKP R 401 " pdb=" OAF NKP R 401 " ideal model delta sigma weight residual 1.450 1.342 0.108 2.00e-02 2.50e+03 2.92e+01 bond pdb=" CA GLN E 143 " pdb=" C GLN E 143 " ideal model delta sigma weight residual 1.531 1.576 -0.045 1.08e-02 8.57e+03 1.71e+01 ... (remaining 8980 not shown) Histogram of bond angle deviations from ideal: 0.00 - 12.40: 12205 12.40 - 24.79: 2 24.79 - 37.19: 0 37.19 - 49.58: 0 49.58 - 61.98: 1 Bond angle restraints: 12208 Sorted by residual: angle pdb=" OAB NKP R 401 " pdb=" PAC NKP R 401 " pdb=" OAD NKP R 401 " ideal model delta sigma weight residual 53.21 115.19 -61.98 3.00e+00 1.11e-01 4.27e+02 angle pdb=" OAB NKP R 401 " pdb=" PAC NKP R 401 " pdb=" OAF NKP R 401 " ideal model delta sigma weight residual 115.22 101.05 14.17 3.00e+00 1.11e-01 2.23e+01 angle pdb=" C LYS A 94 " pdb=" CA LYS A 94 " pdb=" CB LYS A 94 " ideal model delta sigma weight residual 110.37 103.32 7.05 1.54e+00 4.22e-01 2.10e+01 angle pdb=" C ILE A 76 " pdb=" CA ILE A 76 " pdb=" CB ILE A 76 " ideal model delta sigma weight residual 111.29 118.49 -7.20 1.64e+00 3.72e-01 1.93e+01 angle pdb=" C VAL E 225 " pdb=" CA VAL E 225 " pdb=" CB VAL E 225 " ideal model delta sigma weight residual 110.83 104.39 6.44 1.49e+00 4.50e-01 1.87e+01 ... (remaining 12203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 4957 17.62 - 35.24: 404 35.24 - 52.86: 83 52.86 - 70.48: 18 70.48 - 88.10: 2 Dihedral angle restraints: 5464 sinusoidal: 2171 harmonic: 3293 Sorted by residual: dihedral pdb=" CA ILE R 275 " pdb=" C ILE R 275 " pdb=" N THR R 276 " pdb=" CA THR R 276 " ideal model delta harmonic sigma weight residual 180.00 160.04 19.96 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA TRP B 82 " pdb=" C TRP B 82 " pdb=" N ASP B 83 " pdb=" CA ASP B 83 " ideal model delta harmonic sigma weight residual 180.00 160.24 19.76 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA TYR R 292 " pdb=" C TYR R 292 " pdb=" N PHE R 293 " pdb=" CA PHE R 293 " ideal model delta harmonic sigma weight residual 180.00 -160.39 -19.61 0 5.00e+00 4.00e-02 1.54e+01 ... (remaining 5461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 1243 0.070 - 0.141: 160 0.141 - 0.211: 14 0.211 - 0.281: 3 0.281 - 0.351: 3 Chirality restraints: 1423 Sorted by residual: chirality pdb=" CAH NKP R 401 " pdb=" CAG NKP R 401 " pdb=" CAI NKP R 401 " pdb=" OBC NKP R 401 " both_signs ideal model delta sigma weight residual False -2.84 -2.49 -0.35 2.00e-01 2.50e+01 3.09e+00 chirality pdb=" C14 CLR R 601 " pdb=" C13 CLR R 601 " pdb=" C15 CLR R 601 " pdb=" C8 CLR R 601 " both_signs ideal model delta sigma weight residual False -2.32 -2.65 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" C14 CLR R 701 " pdb=" C13 CLR R 701 " pdb=" C15 CLR R 701 " pdb=" C8 CLR R 701 " both_signs ideal model delta sigma weight residual False -2.32 -2.61 0.30 2.00e-01 2.50e+01 2.20e+00 ... (remaining 1420 not shown) Planarity restraints: 1520 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP E 74 " 0.078 5.00e-02 4.00e+02 1.21e-01 2.33e+01 pdb=" N PRO E 75 " -0.209 5.00e-02 4.00e+02 pdb=" CA PRO E 75 " 0.064 5.00e-02 4.00e+02 pdb=" CD PRO E 75 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 96 " -0.035 2.00e-02 2.50e+03 2.90e-02 2.10e+01 pdb=" CG TRP A 96 " 0.078 2.00e-02 2.50e+03 pdb=" CD1 TRP A 96 " -0.032 2.00e-02 2.50e+03 pdb=" CD2 TRP A 96 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 96 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 96 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 96 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 96 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 96 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP A 96 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS R 213 " -0.048 5.00e-02 4.00e+02 7.45e-02 8.88e+00 pdb=" N PRO R 214 " 0.129 5.00e-02 4.00e+02 pdb=" CA PRO R 214 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO R 214 " -0.041 5.00e-02 4.00e+02 ... (remaining 1517 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 2922 2.84 - 3.36: 7306 3.36 - 3.87: 13029 3.87 - 4.39: 14807 4.39 - 4.90: 27482 Nonbonded interactions: 65546 Sorted by model distance: nonbonded pdb=" O ASP B 333 " pdb=" OG SER B 334 " model vdw 2.326 3.040 nonbonded pdb=" NE ARG B 22 " pdb=" OD2 ASP B 258 " model vdw 2.335 3.120 nonbonded pdb=" NH2 ARG E 203 " pdb=" OD2 ASP E 224 " model vdw 2.369 3.120 nonbonded pdb=" OD1 ASP A 73 " pdb=" NZ LYS A 82 " model vdw 2.369 3.120 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.377 3.040 ... (remaining 65541 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 1.080 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.950 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.181 8987 Z= 0.273 Angle : 0.968 61.981 12212 Z= 0.466 Chirality : 0.051 0.351 1423 Planarity : 0.006 0.121 1520 Dihedral : 13.542 88.100 3328 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.43 (0.25), residues: 1114 helix: 1.25 (0.29), residues: 360 sheet: 0.31 (0.30), residues: 259 loop : -1.85 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 184 TYR 0.010 0.002 TYR E 50 PHE 0.018 0.002 PHE B 292 TRP 0.078 0.003 TRP A 96 HIS 0.004 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00563 ( 8985) covalent geometry : angle 0.96796 (12208) SS BOND : bond 0.00061 ( 2) SS BOND : angle 0.74780 ( 4) hydrogen bonds : bond 0.14317 ( 401) hydrogen bonds : angle 5.80689 ( 1137) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.320 Fit side-chains REVERT: B 258 ASP cc_start: 0.7048 (t70) cc_final: 0.6798 (t0) REVERT: E 224 ASP cc_start: 0.8096 (m-30) cc_final: 0.7437 (m-30) REVERT: G 27 ARG cc_start: 0.7725 (mtt90) cc_final: 0.7492 (mtt90) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.1087 time to fit residues: 17.5931 Evaluate side-chains 103 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 103 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 ASN A 185 ASN A 198 HIS B 239 ASN E 113 GLN ** R 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 283 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.121769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.094068 restraints weight = 13698.977| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 2.09 r_work: 0.3016 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8987 Z= 0.223 Angle : 0.707 10.838 12212 Z= 0.370 Chirality : 0.047 0.231 1423 Planarity : 0.006 0.078 1520 Dihedral : 7.940 82.384 1455 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.40 % Allowed : 5.70 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: -0.23 (0.25), residues: 1114 helix: 1.44 (0.29), residues: 372 sheet: 0.34 (0.31), residues: 254 loop : -1.76 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 184 TYR 0.013 0.002 TYR E 103 PHE 0.021 0.002 PHE R 115 TRP 0.050 0.003 TRP A 96 HIS 0.006 0.002 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00545 ( 8985) covalent geometry : angle 0.70705 (12208) SS BOND : bond 0.00019 ( 2) SS BOND : angle 1.04556 ( 4) hydrogen bonds : bond 0.07020 ( 401) hydrogen bonds : angle 4.86794 ( 1137) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.333 Fit side-chains REVERT: B 258 ASP cc_start: 0.7757 (t70) cc_final: 0.7527 (t0) REVERT: G 27 ARG cc_start: 0.7740 (mtt90) cc_final: 0.7455 (mtt90) REVERT: G 48 ASP cc_start: 0.7799 (t0) cc_final: 0.7567 (t0) REVERT: R 36 CYS cc_start: 0.7235 (p) cc_final: 0.6900 (m) REVERT: R 75 PHE cc_start: 0.8239 (t80) cc_final: 0.7965 (t80) outliers start: 13 outliers final: 9 residues processed: 121 average time/residue: 0.1103 time to fit residues: 18.0474 Evaluate side-chains 115 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 106 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain E residue 187 GLN Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 138 THR Chi-restraints excluded: chain R residue 188 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 64 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 72 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 106 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN E 113 GLN R 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.125385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.098358 restraints weight = 13667.142| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.97 r_work: 0.3102 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8987 Z= 0.107 Angle : 0.539 6.217 12212 Z= 0.290 Chirality : 0.042 0.158 1423 Planarity : 0.004 0.061 1520 Dihedral : 6.967 81.276 1455 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 0.86 % Allowed : 9.57 % Favored : 89.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.11 (0.26), residues: 1114 helix: 1.86 (0.29), residues: 371 sheet: 0.53 (0.30), residues: 275 loop : -1.77 (0.27), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 256 TYR 0.012 0.001 TYR R 97 PHE 0.014 0.001 PHE B 199 TRP 0.033 0.002 TRP A 96 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00225 ( 8985) covalent geometry : angle 0.53949 (12208) SS BOND : bond 0.00175 ( 2) SS BOND : angle 0.55175 ( 4) hydrogen bonds : bond 0.04604 ( 401) hydrogen bonds : angle 4.37884 ( 1137) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.341 Fit side-chains REVERT: B 201 SER cc_start: 0.8457 (t) cc_final: 0.8253 (p) REVERT: B 258 ASP cc_start: 0.7663 (t70) cc_final: 0.7429 (t0) REVERT: E 224 ASP cc_start: 0.8253 (m-30) cc_final: 0.7763 (m-30) REVERT: G 27 ARG cc_start: 0.7865 (mtt90) cc_final: 0.7583 (mtt90) outliers start: 8 outliers final: 5 residues processed: 120 average time/residue: 0.1160 time to fit residues: 18.6242 Evaluate side-chains 110 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 105 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 156 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 82 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 66 optimal weight: 0.0980 chunk 59 optimal weight: 2.9990 chunk 103 optimal weight: 0.0980 chunk 51 optimal weight: 3.9990 chunk 1 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN B 259 GLN E 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.125652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.098381 restraints weight = 13841.619| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 2.07 r_work: 0.3085 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.1248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8987 Z= 0.116 Angle : 0.540 6.193 12212 Z= 0.288 Chirality : 0.042 0.165 1423 Planarity : 0.004 0.052 1520 Dihedral : 6.840 83.437 1455 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.75 % Allowed : 11.18 % Favored : 88.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.26 (0.26), residues: 1114 helix: 2.00 (0.29), residues: 371 sheet: 0.54 (0.30), residues: 282 loop : -1.68 (0.28), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 184 TYR 0.012 0.001 TYR R 40 PHE 0.013 0.001 PHE B 199 TRP 0.026 0.002 TRP A 96 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8985) covalent geometry : angle 0.53957 (12208) SS BOND : bond 0.00141 ( 2) SS BOND : angle 0.54860 ( 4) hydrogen bonds : bond 0.04704 ( 401) hydrogen bonds : angle 4.28460 ( 1137) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 105 time to evaluate : 0.254 Fit side-chains REVERT: E 224 ASP cc_start: 0.8270 (m-30) cc_final: 0.7753 (m-30) REVERT: G 27 ARG cc_start: 0.7850 (mtt90) cc_final: 0.7536 (mtt90) outliers start: 7 outliers final: 5 residues processed: 107 average time/residue: 0.1204 time to fit residues: 16.9817 Evaluate side-chains 112 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 107 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 156 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 54 optimal weight: 3.9990 chunk 88 optimal weight: 0.0170 chunk 74 optimal weight: 9.9990 chunk 64 optimal weight: 2.9990 chunk 98 optimal weight: 0.0270 chunk 106 optimal weight: 0.1980 chunk 105 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 239 ASN E 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.126026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.098563 restraints weight = 13750.524| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.02 r_work: 0.3107 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2960 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8987 Z= 0.107 Angle : 0.521 5.940 12212 Z= 0.279 Chirality : 0.041 0.157 1423 Planarity : 0.004 0.048 1520 Dihedral : 6.582 84.806 1455 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.18 % Allowed : 11.83 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.43 (0.26), residues: 1114 helix: 2.22 (0.29), residues: 365 sheet: 0.61 (0.30), residues: 284 loop : -1.59 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 256 TYR 0.010 0.001 TYR R 97 PHE 0.012 0.001 PHE B 199 TRP 0.024 0.002 TRP A 96 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00233 ( 8985) covalent geometry : angle 0.52101 (12208) SS BOND : bond 0.00166 ( 2) SS BOND : angle 0.47471 ( 4) hydrogen bonds : bond 0.04375 ( 401) hydrogen bonds : angle 4.14986 ( 1137) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.470 Fit side-chains REVERT: E 224 ASP cc_start: 0.8265 (m-30) cc_final: 0.7726 (m-30) REVERT: G 27 ARG cc_start: 0.7615 (mtt90) cc_final: 0.7393 (mtt90) outliers start: 11 outliers final: 8 residues processed: 115 average time/residue: 0.1126 time to fit residues: 17.5208 Evaluate side-chains 109 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain R residue 136 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 72 optimal weight: 0.6980 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 66 optimal weight: 0.0370 chunk 58 optimal weight: 0.8980 chunk 75 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 48 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 4.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.125464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.098138 restraints weight = 13700.163| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 1.99 r_work: 0.3079 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2931 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8987 Z= 0.123 Angle : 0.539 6.568 12212 Z= 0.287 Chirality : 0.042 0.173 1423 Planarity : 0.004 0.052 1520 Dihedral : 6.551 85.870 1455 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.29 % Allowed : 12.80 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.48 (0.26), residues: 1114 helix: 2.25 (0.29), residues: 365 sheet: 0.56 (0.29), residues: 292 loop : -1.53 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 256 TYR 0.013 0.001 TYR R 40 PHE 0.017 0.001 PHE B 241 TRP 0.022 0.002 TRP A 96 HIS 0.005 0.001 HIS A 198 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8985) covalent geometry : angle 0.53943 (12208) SS BOND : bond 0.00122 ( 2) SS BOND : angle 0.50005 ( 4) hydrogen bonds : bond 0.04697 ( 401) hydrogen bonds : angle 4.18281 ( 1137) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 106 time to evaluate : 0.351 Fit side-chains REVERT: E 224 ASP cc_start: 0.8318 (m-30) cc_final: 0.7802 (m-30) REVERT: R 292 TYR cc_start: 0.7693 (OUTLIER) cc_final: 0.6963 (p90) outliers start: 12 outliers final: 10 residues processed: 109 average time/residue: 0.1177 time to fit residues: 17.0851 Evaluate side-chains 116 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 188 ILE Chi-restraints excluded: chain R residue 292 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 31 optimal weight: 0.6980 chunk 69 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 93 optimal weight: 0.0870 chunk 90 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.126307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.099356 restraints weight = 13811.562| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 2.01 r_work: 0.3107 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2962 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8987 Z= 0.105 Angle : 0.514 5.804 12212 Z= 0.274 Chirality : 0.041 0.157 1423 Planarity : 0.004 0.045 1520 Dihedral : 6.375 86.205 1455 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.08 % Allowed : 13.44 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.57 (0.26), residues: 1114 helix: 2.35 (0.29), residues: 365 sheet: 0.58 (0.29), residues: 296 loop : -1.50 (0.28), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 27 TYR 0.010 0.001 TYR R 97 PHE 0.012 0.001 PHE R 96 TRP 0.022 0.002 TRP A 96 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 8985) covalent geometry : angle 0.51378 (12208) SS BOND : bond 0.00152 ( 2) SS BOND : angle 0.42073 ( 4) hydrogen bonds : bond 0.04266 ( 401) hydrogen bonds : angle 4.10072 ( 1137) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.224 Fit side-chains REVERT: E 224 ASP cc_start: 0.8294 (m-30) cc_final: 0.7742 (m-30) REVERT: R 292 TYR cc_start: 0.7717 (OUTLIER) cc_final: 0.6785 (p90) outliers start: 10 outliers final: 7 residues processed: 111 average time/residue: 0.1079 time to fit residues: 16.1158 Evaluate side-chains 109 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 101 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 292 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 44 optimal weight: 0.6980 chunk 88 optimal weight: 0.9990 chunk 58 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 63 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.127092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.099746 restraints weight = 13790.383| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.14 r_work: 0.3090 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8987 Z= 0.118 Angle : 0.535 6.376 12212 Z= 0.284 Chirality : 0.042 0.170 1423 Planarity : 0.004 0.050 1520 Dihedral : 6.397 87.138 1455 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 1.29 % Allowed : 13.66 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.61 (0.26), residues: 1114 helix: 2.39 (0.28), residues: 365 sheet: 0.64 (0.29), residues: 292 loop : -1.49 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 27 TYR 0.015 0.001 TYR R 40 PHE 0.012 0.001 PHE R 96 TRP 0.021 0.002 TRP A 96 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00268 ( 8985) covalent geometry : angle 0.53454 (12208) SS BOND : bond 0.00127 ( 2) SS BOND : angle 0.44612 ( 4) hydrogen bonds : bond 0.04572 ( 401) hydrogen bonds : angle 4.11897 ( 1137) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 104 time to evaluate : 0.335 Fit side-chains REVERT: B 239 ASN cc_start: 0.8909 (OUTLIER) cc_final: 0.8566 (t0) REVERT: E 224 ASP cc_start: 0.8292 (m-30) cc_final: 0.7696 (m-30) REVERT: R 292 TYR cc_start: 0.7720 (OUTLIER) cc_final: 0.6805 (p90) outliers start: 12 outliers final: 9 residues processed: 110 average time/residue: 0.1202 time to fit residues: 17.6549 Evaluate side-chains 112 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 156 VAL Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 292 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 59 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 75 optimal weight: 0.1980 chunk 104 optimal weight: 0.7980 chunk 48 optimal weight: 0.9990 chunk 63 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 109 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.125600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.098099 restraints weight = 13676.103| |-----------------------------------------------------------------------------| r_work (start): 0.3303 rms_B_bonded: 2.11 r_work: 0.3090 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8987 Z= 0.114 Angle : 0.527 5.917 12212 Z= 0.282 Chirality : 0.042 0.164 1423 Planarity : 0.004 0.047 1520 Dihedral : 6.349 87.379 1455 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.18 % Allowed : 13.98 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.64 (0.26), residues: 1114 helix: 2.41 (0.28), residues: 365 sheet: 0.63 (0.29), residues: 294 loop : -1.45 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 27 TYR 0.009 0.001 TYR R 97 PHE 0.013 0.001 PHE R 96 TRP 0.023 0.002 TRP A 96 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00256 ( 8985) covalent geometry : angle 0.52712 (12208) SS BOND : bond 0.00125 ( 2) SS BOND : angle 0.40191 ( 4) hydrogen bonds : bond 0.04461 ( 401) hydrogen bonds : angle 4.10364 ( 1137) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 104 time to evaluate : 0.310 Fit side-chains REVERT: B 239 ASN cc_start: 0.8917 (OUTLIER) cc_final: 0.8679 (t0) REVERT: E 224 ASP cc_start: 0.8307 (m-30) cc_final: 0.7781 (m-30) REVERT: R 126 THR cc_start: 0.7108 (p) cc_final: 0.6903 (p) REVERT: R 292 TYR cc_start: 0.7869 (OUTLIER) cc_final: 0.6827 (p90) outliers start: 11 outliers final: 7 residues processed: 110 average time/residue: 0.1102 time to fit residues: 16.2218 Evaluate side-chains 111 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 102 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 239 ASN Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 292 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 83 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 15 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 47 optimal weight: 0.0370 chunk 91 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.7860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.125719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.098426 restraints weight = 13650.737| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.05 r_work: 0.3097 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.49 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8987 Z= 0.117 Angle : 0.539 6.498 12212 Z= 0.289 Chirality : 0.042 0.167 1423 Planarity : 0.004 0.048 1520 Dihedral : 6.349 87.770 1455 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 1.08 % Allowed : 14.09 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.65 (0.26), residues: 1114 helix: 2.41 (0.28), residues: 365 sheet: 0.67 (0.29), residues: 292 loop : -1.46 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 27 TYR 0.017 0.001 TYR R 40 PHE 0.012 0.001 PHE R 96 TRP 0.022 0.002 TRP A 96 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8985) covalent geometry : angle 0.53910 (12208) SS BOND : bond 0.00121 ( 2) SS BOND : angle 0.41006 ( 4) hydrogen bonds : bond 0.04525 ( 401) hydrogen bonds : angle 4.15238 ( 1137) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2228 Ramachandran restraints generated. 1114 Oldfield, 0 Emsley, 1114 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.291 Fit side-chains REVERT: E 224 ASP cc_start: 0.8305 (m-30) cc_final: 0.7763 (m-30) REVERT: R 126 THR cc_start: 0.7137 (p) cc_final: 0.6919 (p) REVERT: R 292 TYR cc_start: 0.7882 (OUTLIER) cc_final: 0.6869 (p90) outliers start: 10 outliers final: 8 residues processed: 110 average time/residue: 0.1186 time to fit residues: 17.4239 Evaluate side-chains 114 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain B residue 308 LEU Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain R residue 129 THR Chi-restraints excluded: chain R residue 136 VAL Chi-restraints excluded: chain R residue 292 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 46 optimal weight: 3.9990 chunk 1 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 48 optimal weight: 0.8980 chunk 93 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.126967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.099801 restraints weight = 13645.581| |-----------------------------------------------------------------------------| r_work (start): 0.3300 rms_B_bonded: 2.09 r_work: 0.3088 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2942 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8987 Z= 0.121 Angle : 0.540 6.525 12212 Z= 0.289 Chirality : 0.042 0.169 1423 Planarity : 0.004 0.051 1520 Dihedral : 6.359 88.425 1455 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.85 % Favored : 95.15 % Rotamer: Outliers : 1.18 % Allowed : 14.30 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.12 % 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: 0.62 (0.26), residues: 1114 helix: 2.28 (0.28), residues: 371 sheet: 0.66 (0.29), residues: 292 loop : -1.42 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 27 TYR 0.009 0.001 TYR R 97 PHE 0.012 0.001 PHE R 96 TRP 0.024 0.002 TRP A 96 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00274 ( 8985) covalent geometry : angle 0.53962 (12208) SS BOND : bond 0.00116 ( 2) SS BOND : angle 0.41602 ( 4) hydrogen bonds : bond 0.04650 ( 401) hydrogen bonds : angle 4.15334 ( 1137) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2770.31 seconds wall clock time: 47 minutes 59.20 seconds (2879.20 seconds total)