Starting phenix.real_space_refine on Tue Feb 3 22:55:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ncq_49266/02_2026/9ncq_49266.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ncq_49266/02_2026/9ncq_49266.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.51 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ncq_49266/02_2026/9ncq_49266.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ncq_49266/02_2026/9ncq_49266.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ncq_49266/02_2026/9ncq_49266.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ncq_49266/02_2026/9ncq_49266.map" } resolution = 3.51 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= 0.027 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 29 5.16 5 C 4679 2.51 5 N 1377 2.21 5 O 1465 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7550 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 670 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'TRANS': 90} Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "B" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 655 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 85} Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 648 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 86} Unresolved non-hydrogen bonds: 45 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 14 Chain: "G" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 355 Classifications: {'peptide': 71} Incomplete info: {'truncation_to_alanine': 62} Link IDs: {'TRANS': 70} Chain breaks: 1 Unresolved non-hydrogen bonds: 223 Unresolved non-hydrogen angles: 283 Unresolved non-hydrogen dihedrals: 180 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'TYR:plan': 2, 'ASN:plan1': 5, 'GLU:plan': 5, 'ASP:plan': 5, 'GLN:plan1': 5, 'ARG:plan': 1, 'TRP:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 108 Chain: "C" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 706 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'TRANS': 93} Unresolved non-hydrogen bonds: 41 Unresolved non-hydrogen angles: 51 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 22 Chain: "F" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 425 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'TRANS': 83} Unresolved non-hydrogen bonds: 252 Unresolved non-hydrogen angles: 320 Unresolved non-hydrogen dihedrals: 203 Unresolved non-hydrogen chiralities: 28 Planarities with less than four sites: {'TYR:plan': 2, 'GLN:plan1': 6, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 5, 'GLU:plan': 5, 'ASP:plan': 5, 'TRP:plan': 1, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 123 Chain: "D" Number of atoms: 605 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 605 Classifications: {'peptide': 86} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'TRANS': 85} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 95 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3, 'GLN:plan1': 1, 'ASN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "H" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 691 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 1, 'TRANS': 88} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 3, 'GLU:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 32 Chain: "I" Number of atoms: 695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 695 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 1, 'TRANS': 92} Unresolved non-hydrogen bonds: 67 Unresolved non-hydrogen angles: 80 Unresolved non-hydrogen dihedrals: 54 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ASP:plan': 2, 'ARG:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 46 Chain: "L" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 723 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 1, 'TRANS': 93} Unresolved non-hydrogen bonds: 48 Unresolved non-hydrogen angles: 59 Unresolved non-hydrogen dihedrals: 39 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'PHE:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 40 Chain: "K" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 693 Classifications: {'peptide': 90} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 1, 'TRANS': 88} Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'PHE:plan': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 25 Chain: "J" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 684 Classifications: {'peptide': 91} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 1, 'TRANS': 89} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 62 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1, 'ARG:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 35 Time building chain proxies: 2.10, per 1000 atoms: 0.28 Number of scatterers: 7550 At special positions: 0 Unit cell: (100.28, 91.56, 107.91, 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 29 16.00 O 1465 8.00 N 1377 7.00 C 4679 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.66 Conformation dependent library (CDL) restraints added in 272.1 milliseconds 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2046 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 0 sheets defined 84.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 232 through 240 removed outlier: 3.611A pdb=" N ILE A 236 " --> pdb=" O TYR A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 250 removed outlier: 3.922A pdb=" N GLY A 247 " --> pdb=" O SER A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 255 through 265 removed outlier: 3.571A pdb=" N ASP A 260 " --> pdb=" O GLU A 256 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLU A 261 " --> pdb=" O ALA A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 285 Processing helix chain 'A' and resid 290 through 300 Processing helix chain 'A' and resid 303 through 318 Processing helix chain 'B' and resid 232 through 237 removed outlier: 3.501A pdb=" N ALA B 237 " --> pdb=" O ILE B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 240 No H-bonds generated for 'chain 'B' and resid 238 through 240' Processing helix chain 'B' and resid 242 through 252 Processing helix chain 'B' and resid 255 through 266 removed outlier: 3.564A pdb=" N ASN B 266 " --> pdb=" O ILE B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 286 removed outlier: 3.508A pdb=" N GLN B 273 " --> pdb=" O ASP B 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 301 Processing helix chain 'B' and resid 303 through 313 removed outlier: 3.640A pdb=" N ILE B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N GLN B 311 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N THR B 312 " --> pdb=" O GLU B 308 " (cutoff:3.500A) Processing helix chain 'E' and resid 232 through 238 Processing helix chain 'E' and resid 241 through 253 Processing helix chain 'E' and resid 255 through 266 removed outlier: 3.618A pdb=" N ILE E 259 " --> pdb=" O ASN E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 285 Processing helix chain 'E' and resid 290 through 301 removed outlier: 3.571A pdb=" N ALA E 301 " --> pdb=" O ASP E 297 " (cutoff:3.500A) Processing helix chain 'E' and resid 303 through 314 removed outlier: 3.619A pdb=" N LYS E 309 " --> pdb=" O THR E 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 237 Processing helix chain 'G' and resid 256 through 266 Processing helix chain 'G' and resid 269 through 286 Processing helix chain 'G' and resid 289 through 301 Processing helix chain 'G' and resid 303 through 315 Processing helix chain 'C' and resid 232 through 240 Processing helix chain 'C' and resid 241 through 251 Processing helix chain 'C' and resid 255 through 266 removed outlier: 3.986A pdb=" N ILE C 259 " --> pdb=" O ASN C 255 " (cutoff:3.500A) Processing helix chain 'C' and resid 269 through 285 removed outlier: 3.979A pdb=" N VAL C 275 " --> pdb=" O ALA C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 301 Processing helix chain 'C' and resid 303 through 318 removed outlier: 3.800A pdb=" N ALA C 307 " --> pdb=" O LEU C 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 240 Processing helix chain 'F' and resid 241 through 251 Processing helix chain 'F' and resid 255 through 266 Processing helix chain 'F' and resid 269 through 286 Processing helix chain 'F' and resid 290 through 301 Processing helix chain 'F' and resid 303 through 315 removed outlier: 3.685A pdb=" N LYS F 309 " --> pdb=" O THR F 305 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE F 310 " --> pdb=" O LEU F 306 " (cutoff:3.500A) Processing helix chain 'D' and resid 232 through 238 removed outlier: 3.550A pdb=" N GLY D 238 " --> pdb=" O THR D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 253 removed outlier: 3.691A pdb=" N LYS D 251 " --> pdb=" O GLY D 247 " (cutoff:3.500A) Processing helix chain 'D' and resid 255 through 266 Processing helix chain 'D' and resid 269 through 286 removed outlier: 3.516A pdb=" N GLN D 273 " --> pdb=" O ASP D 269 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL D 275 " --> pdb=" O ALA D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 301 removed outlier: 4.196A pdb=" N LEU D 294 " --> pdb=" O ALA D 290 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE D 295 " --> pdb=" O TYR D 291 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LYS D 296 " --> pdb=" O ASP D 292 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ALA D 301 " --> pdb=" O ASP D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 314 removed outlier: 4.043A pdb=" N ILE D 310 " --> pdb=" O LEU D 306 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N GLN D 311 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N THR D 312 " --> pdb=" O GLU D 308 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ILE D 313 " --> pdb=" O LYS D 309 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ILE D 314 " --> pdb=" O ILE D 310 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 306 through 314' Processing helix chain 'H' and resid 96 through 106 removed outlier: 3.630A pdb=" N ASN H 102 " --> pdb=" O CYS H 98 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASP H 106 " --> pdb=" O ASN H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 119 removed outlier: 4.518A pdb=" N LEU H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 133 Processing helix chain 'H' and resid 136 through 153 Processing helix chain 'H' and resid 154 through 156 No H-bonds generated for 'chain 'H' and resid 154 through 156' Processing helix chain 'H' and resid 157 through 168 Processing helix chain 'H' and resid 171 through 184 Processing helix chain 'I' and resid 95 through 105 removed outlier: 3.911A pdb=" N ALA I 100 " --> pdb=" O ASP I 96 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N VAL I 103 " --> pdb=" O ALA I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 119 removed outlier: 4.197A pdb=" N LEU I 115 " --> pdb=" O ASP I 111 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA I 116 " --> pdb=" O TRP I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 131 Processing helix chain 'I' and resid 136 through 152 removed outlier: 3.826A pdb=" N TRP I 148 " --> pdb=" O SER I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 153 through 156 Processing helix chain 'I' and resid 157 through 168 Processing helix chain 'I' and resid 170 through 187 removed outlier: 3.514A pdb=" N VAL I 180 " --> pdb=" O LEU I 176 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU I 186 " --> pdb=" O GLN I 182 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N GLN I 187 " --> pdb=" O ALA I 183 " (cutoff:3.500A) Processing helix chain 'L' and resid 95 through 106 removed outlier: 3.589A pdb=" N ALA L 99 " --> pdb=" O GLU L 95 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ALA L 100 " --> pdb=" O ASP L 96 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE L 101 " --> pdb=" O LEU L 97 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ASN L 102 " --> pdb=" O CYS L 98 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N VAL L 103 " --> pdb=" O ALA L 99 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ILE L 104 " --> pdb=" O ALA L 100 " (cutoff:3.500A) Processing helix chain 'L' and resid 111 through 119 removed outlier: 4.041A pdb=" N LEU L 115 " --> pdb=" O ASP L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 133 Processing helix chain 'L' and resid 136 through 153 Processing helix chain 'L' and resid 154 through 156 No H-bonds generated for 'chain 'L' and resid 154 through 156' Processing helix chain 'L' and resid 157 through 168 Processing helix chain 'L' and resid 171 through 188 removed outlier: 3.533A pdb=" N ALA L 183 " --> pdb=" O GLU L 179 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 106 removed outlier: 3.565A pdb=" N ALA K 100 " --> pdb=" O ASP K 96 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL K 103 " --> pdb=" O ALA K 99 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ILE K 104 " --> pdb=" O ALA K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 118 removed outlier: 4.293A pdb=" N LEU K 115 " --> pdb=" O ASP K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 133 removed outlier: 3.534A pdb=" N ILE K 126 " --> pdb=" O SER K 122 " (cutoff:3.500A) Processing helix chain 'K' and resid 137 through 153 Processing helix chain 'K' and resid 157 through 168 Processing helix chain 'K' and resid 171 through 184 Processing helix chain 'J' and resid 95 through 106 removed outlier: 3.565A pdb=" N ALA J 99 " --> pdb=" O GLU J 95 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL J 103 " --> pdb=" O ALA J 99 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP J 106 " --> pdb=" O ASN J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 119 removed outlier: 4.214A pdb=" N LEU J 115 " --> pdb=" O ASP J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 133 Processing helix chain 'J' and resid 137 through 153 removed outlier: 3.565A pdb=" N LEU J 145 " --> pdb=" O VAL J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 163 Processing helix chain 'J' and resid 163 through 168 removed outlier: 3.781A pdb=" N SER J 167 " --> pdb=" O GLY J 163 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N CYS J 168 " --> pdb=" O ALA J 164 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 163 through 168' Processing helix chain 'J' and resid 170 through 184 533 hydrogen bonds defined for protein. 1596 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: 0.79 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1815 1.33 - 1.45: 1295 1.45 - 1.57: 4459 1.57 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 7608 Sorted by residual: bond pdb=" CA ARG I 114 " pdb=" C ARG I 114 " ideal model delta sigma weight residual 1.524 1.406 0.118 1.26e-02 6.30e+03 8.71e+01 bond pdb=" C ARG I 114 " pdb=" N LEU I 115 " ideal model delta sigma weight residual 1.334 1.279 0.055 1.27e-02 6.20e+03 1.88e+01 bond pdb=" C ARG I 114 " pdb=" O ARG I 114 " ideal model delta sigma weight residual 1.237 1.213 0.023 1.16e-02 7.43e+03 4.09e+00 bond pdb=" CA ARG I 114 " pdb=" CB ARG I 114 " ideal model delta sigma weight residual 1.529 1.499 0.030 1.58e-02 4.01e+03 3.62e+00 bond pdb=" CB GLU C 256 " pdb=" CG GLU C 256 " ideal model delta sigma weight residual 1.520 1.566 -0.046 3.00e-02 1.11e+03 2.31e+00 ... (remaining 7603 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 10234 1.76 - 3.52: 96 3.52 - 5.28: 9 5.28 - 7.04: 7 7.04 - 8.80: 2 Bond angle restraints: 10348 Sorted by residual: angle pdb=" N ARG I 114 " pdb=" CA ARG I 114 " pdb=" C ARG I 114 " ideal model delta sigma weight residual 111.14 104.51 6.63 1.08e+00 8.57e-01 3.77e+01 angle pdb=" CA GLU C 256 " pdb=" CB GLU C 256 " pdb=" CG GLU C 256 " ideal model delta sigma weight residual 114.10 122.90 -8.80 2.00e+00 2.50e-01 1.94e+01 angle pdb=" C ARG I 114 " pdb=" CA ARG I 114 " pdb=" CB ARG I 114 " ideal model delta sigma weight residual 110.90 104.03 6.87 1.58e+00 4.01e-01 1.89e+01 angle pdb=" C GLN J 169 " pdb=" CA GLN J 169 " pdb=" CB GLN J 169 " ideal model delta sigma weight residual 117.23 111.72 5.51 1.36e+00 5.41e-01 1.64e+01 angle pdb=" CB GLU C 256 " pdb=" CG GLU C 256 " pdb=" CD GLU C 256 " ideal model delta sigma weight residual 112.60 118.21 -5.61 1.70e+00 3.46e-01 1.09e+01 ... (remaining 10343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 4074 18.00 - 36.00: 422 36.00 - 54.00: 107 54.00 - 72.00: 25 72.00 - 90.00: 12 Dihedral angle restraints: 4640 sinusoidal: 1534 harmonic: 3106 Sorted by residual: dihedral pdb=" C ARG I 114 " pdb=" N ARG I 114 " pdb=" CA ARG I 114 " pdb=" CB ARG I 114 " ideal model delta harmonic sigma weight residual -122.60 -112.49 -10.11 0 2.50e+00 1.60e-01 1.64e+01 dihedral pdb=" CA ASP K 131 " pdb=" CB ASP K 131 " pdb=" CG ASP K 131 " pdb=" OD1 ASP K 131 " ideal model delta sinusoidal sigma weight residual -30.00 -86.85 56.85 1 2.00e+01 2.50e-03 1.09e+01 dihedral pdb=" CB GLU L 130 " pdb=" CG GLU L 130 " pdb=" CD GLU L 130 " pdb=" OE1 GLU L 130 " ideal model delta sinusoidal sigma weight residual 0.00 90.00 -90.00 1 3.00e+01 1.11e-03 1.07e+01 ... (remaining 4637 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 752 0.027 - 0.053: 367 0.053 - 0.079: 137 0.079 - 0.106: 28 0.106 - 0.132: 6 Chirality restraints: 1290 Sorted by residual: chirality pdb=" CB THR J 157 " pdb=" CA THR J 157 " pdb=" OG1 THR J 157 " pdb=" CG2 THR J 157 " both_signs ideal model delta sigma weight residual False 2.55 2.42 0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CB VAL B 239 " pdb=" CA VAL B 239 " pdb=" CG1 VAL B 239 " pdb=" CG2 VAL B 239 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA THR J 157 " pdb=" N THR J 157 " pdb=" C THR J 157 " pdb=" CB THR J 157 " both_signs ideal model delta sigma weight residual False 2.53 2.41 0.12 2.00e-01 2.50e+01 3.66e-01 ... (remaining 1287 not shown) Planarity restraints: 1348 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG I 113 " 0.014 2.00e-02 2.50e+03 2.89e-02 8.34e+00 pdb=" C ARG I 113 " -0.050 2.00e-02 2.50e+03 pdb=" O ARG I 113 " 0.019 2.00e-02 2.50e+03 pdb=" N ARG I 114 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 281 " 0.016 2.00e-02 2.50e+03 1.30e-02 4.19e+00 pdb=" CG TRP C 281 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP C 281 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP C 281 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 281 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 281 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 281 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 281 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 281 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 281 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN L 118 " -0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" C GLN L 118 " 0.032 2.00e-02 2.50e+03 pdb=" O GLN L 118 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU L 119 " -0.011 2.00e-02 2.50e+03 ... (remaining 1345 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 47 2.63 - 3.20: 7024 3.20 - 3.77: 12036 3.77 - 4.33: 14959 4.33 - 4.90: 24481 Nonbonded interactions: 58547 Sorted by model distance: nonbonded pdb=" O GLN I 118 " pdb=" NE2 GLN I 118 " model vdw 2.067 3.120 nonbonded pdb=" NH1 ARG H 166 " pdb=" OD1 ASN H 171 " model vdw 2.268 3.120 nonbonded pdb=" O TYR I 133 " pdb=" NE ARG I 140 " model vdw 2.281 3.120 nonbonded pdb=" ND2 ASN A 252 " pdb=" OD2 ASP A 297 " model vdw 2.287 3.120 nonbonded pdb=" OH TYR B 232 " pdb=" O ILE B 313 " model vdw 2.292 3.040 ... (remaining 58542 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 232 through 237 and (name N or name CA or name C or name \ O or name CB )) or resid 238 or (resid 239 through 246 and (name N or name CA or \ name C or name O or name CB )) or resid 247 or (resid 248 through 252 and (name \ N or name CA or name C or name O or name CB )) or resid 253 or (resid 254 throu \ gh 263 and (name N or name CA or name C or name O or name CB )) or resid 264 or \ (resid 265 through 276 and (name N or name CA or name C or name O or name CB )) \ or resid 277 through 278 or (resid 279 through 285 and (name N or name CA or nam \ e C or name O or name CB )) or resid 286 or (resid 287 through 313 and (name N o \ r name CA or name C or name O or name CB )))) selection = (chain 'B' and ((resid 232 through 237 and (name N or name CA or name C or name \ O or name CB )) or resid 238 or (resid 239 through 246 and (name N or name CA or \ name C or name O or name CB )) or resid 247 or (resid 248 through 252 and (name \ N or name CA or name C or name O or name CB )) or resid 253 or (resid 254 throu \ gh 263 and (name N or name CA or name C or name O or name CB )) or resid 264 or \ (resid 265 through 276 and (name N or name CA or name C or name O or name CB )) \ or resid 277 through 278 or (resid 279 through 285 and (name N or name CA or nam \ e C or name O or name CB )) or resid 286 or (resid 287 through 313 and (name N o \ r name CA or name C or name O or name CB )))) selection = (chain 'C' and ((resid 232 through 237 and (name N or name CA or name C or name \ O or name CB )) or resid 238 or (resid 239 through 246 and (name N or name CA or \ name C or name O or name CB )) or resid 247 or (resid 248 through 252 and (name \ N or name CA or name C or name O or name CB )) or resid 253 or (resid 254 throu \ gh 263 and (name N or name CA or name C or name O or name CB )) or resid 264 or \ (resid 265 through 276 and (name N or name CA or name C or name O or name CB )) \ or resid 277 through 278 or (resid 279 through 285 and (name N or name CA or nam \ e C or name O or name CB )) or resid 286 or (resid 287 through 313 and (name N o \ r name CA or name C or name O or name CB )))) selection = (chain 'D' and ((resid 232 through 237 and (name N or name CA or name C or name \ O or name CB )) or (resid 238 through 246 and (name N or name CA or name C or na \ me O or name CB )) or resid 247 or (resid 248 through 252 and (name N or name CA \ or name C or name O or name CB )) or resid 253 or (resid 254 through 263 and (n \ ame N or name CA or name C or name O or name CB )) or resid 264 through 265 or ( \ resid 266 through 276 and (name N or name CA or name C or name O or name CB )) o \ r resid 277 through 278 or (resid 279 through 285 and (name N or name CA or name \ C or name O or name CB )) or resid 286 or (resid 287 through 313 and (name N or \ name CA or name C or name O or name CB )))) selection = (chain 'E' and ((resid 232 through 237 and (name N or name CA or name C or name \ O or name CB )) or resid 238 or (resid 239 through 246 and (name N or name CA or \ name C or name O or name CB )) or resid 247 or (resid 248 through 252 and (name \ N or name CA or name C or name O or name CB )) or resid 253 or (resid 254 throu \ gh 263 and (name N or name CA or name C or name O or name CB )) or resid 264 or \ (resid 265 through 276 and (name N or name CA or name C or name O or name CB )) \ or resid 277 through 278 or (resid 279 through 285 and (name N or name CA or nam \ e C or name O or name CB )) or resid 286 or (resid 287 through 313 and (name N o \ r name CA or name C or name O or name CB )))) selection = (chain 'F' and resid 232 through 313) } ncs_group { reference = (chain 'H' and ((resid 95 through 97 and (name N or name CA or name C or name O \ or name CB )) or resid 98 through 100 or (resid 101 and (name N or name CA or na \ me C or name O or name CB )) or resid 102 through 109 or (resid 110 through 111 \ and (name N or name CA or name C or name O or name CB )) or resid 112 or (resid \ 113 and (name N or name CA or name C or name O or name CB )) or resid 114 throug \ h 116 or (resid 117 and (name N or name CA or name C or name O or name CB )) or \ resid 118 through 119 or (resid 120 through 121 and (name N or name CA or name C \ or name O or name CB )) or resid 122 through 145 or (resid 146 and (name N or n \ ame CA or name C or name O or name CB )) or resid 147 through 148 or (resid 149 \ and (name N or name CA or name C or name O or name CB )) or resid 150 or (resid \ 151 and (name N or name CA or name C or name O or name CB )) or resid 152 or (re \ sid 153 through 157 and (name N or name CA or name C or name O or name CB )) or \ resid 158 through 159 or (resid 160 and (name N or name CA or name C or name O o \ r name CB )) or resid 161 through 180 or (resid 181 and (name N or name CA or na \ me C or name O or name CB )) or resid 182 through 183 or (resid 184 and (name N \ or name CA or name C or name O or name CB )))) selection = (chain 'I' and ((resid 95 through 97 and (name N or name CA or name C or name O \ or name CB )) or resid 98 through 100 or (resid 101 and (name N or name CA or na \ me C or name O or name CB )) or resid 102 through 105 or (resid 106 and (name N \ or name CA or name C or name O or name CB )) or resid 107 through 109 or (resid \ 110 through 111 and (name N or name CA or name C or name O or name CB )) or resi \ d 112 through 120 or (resid 121 and (name N or name CA or name C or name O or na \ me CB )) or resid 122 through 131 or (resid 132 and (name N or name CA or name C \ or name O or name CB )) or resid 133 through 145 or (resid 146 and (name N or n \ ame CA or name C or name O or name CB )) or resid 147 through 159 or (resid 160 \ and (name N or name CA or name C or name O or name CB )) or resid 161 through 16 \ 8 or (resid 169 and (name N or name CA or name C or name O or name CB )) or resi \ d 170 through 180 or (resid 181 and (name N or name CA or name C or name O or na \ me CB )) or resid 182 through 184)) selection = (chain 'J' and ((resid 95 through 97 and (name N or name CA or name C or name O \ or name CB )) or resid 98 through 100 or (resid 101 and (name N or name CA or na \ me C or name O or name CB )) or resid 102 through 105 or (resid 106 and (name N \ or name CA or name C or name O or name CB )) or resid 107 through 116 or (resid \ 117 and (name N or name CA or name C or name O or name CB )) or resid 118 throug \ h 131 or (resid 132 and (name N or name CA or name C or name O or name CB )) or \ resid 133 through 141 or (resid 142 and (name N or name CA or name C or name O o \ r name CB )) or resid 143 through 148 or (resid 149 and (name N or name CA or na \ me C or name O or name CB )) or resid 150 or (resid 151 and (name N or name CA o \ r name C or name O or name CB )) or resid 152 through 154 or (resid 155 through \ 157 and (name N or name CA or name C or name O or name CB )) or resid 158 throug \ h 159 or (resid 160 and (name N or name CA or name C or name O or name CB )) or \ resid 161 through 168 or (resid 169 and (name N or name CA or name C or name O o \ r name CB )) or resid 170 through 184)) selection = (chain 'K' and ((resid 95 through 97 and (name N or name CA or name C or name O \ or name CB )) or resid 98 through 105 or (resid 106 and (name N or name CA or na \ me C or name O or name CB )) or resid 107 through 109 or (resid 110 through 111 \ and (name N or name CA or name C or name O or name CB )) or resid 112 or (resid \ 113 and (name N or name CA or name C or name O or name CB )) or resid 114 throug \ h 116 or (resid 117 and (name N or name CA or name C or name O or name CB )) or \ resid 118 through 119 or (resid 120 through 121 and (name N or name CA or name C \ or name O or name CB )) or resid 122 through 131 or (resid 132 and (name N or n \ ame CA or name C or name O or name CB )) or resid 133 through 141 or (resid 142 \ and (name N or name CA or name C or name O or name CB )) or resid 143 through 14 \ 5 or (resid 146 and (name N or name CA or name C or name O or name CB )) or resi \ d 147 through 150 or (resid 151 and (name N or name CA or name C or name O or na \ me CB )) or resid 152 through 154 or (resid 155 through 157 and (name N or name \ CA or name C or name O or name CB )) or resid 158 through 168 or (resid 169 and \ (name N or name CA or name C or name O or name CB )) or resid 170 through 180 or \ (resid 181 and (name N or name CA or name C or name O or name CB )) or resid 18 \ 2 through 184)) selection = (chain 'L' and ((resid 95 through 97 and (name N or name CA or name C or name O \ or name CB )) or resid 98 through 105 or (resid 106 and (name N or name CA or na \ me C or name O or name CB )) or resid 107 through 109 or (resid 110 through 111 \ and (name N or name CA or name C or name O or name CB )) or resid 112 through 11 \ 6 or (resid 117 and (name N or name CA or name C or name O or name CB )) or resi \ d 118 through 119 or (resid 120 through 121 and (name N or name CA or name C or \ name O or name CB )) or resid 122 through 141 or (resid 142 and (name N or name \ CA or name C or name O or name CB )) or resid 143 through 145 or (resid 146 and \ (name N or name CA or name C or name O or name CB )) or resid 147 through 148 or \ (resid 149 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 0 or (resid 151 and (name N or name CA or name C or name O or name CB )) or resi \ d 152 or (resid 153 through 157 and (name N or name CA or name C or name O or na \ me CB )) or resid 158 through 159 or (resid 160 and (name N or name CA or name C \ or name O or name CB )) or resid 161 through 168 or (resid 169 and (name N or n \ ame CA or name C or name O or name CB )) or resid 170 through 180 or (resid 181 \ and (name N or name CA or name C or name O or name CB )) or resid 182 through 18 \ 4)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.470 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: 0.000 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.360 Find NCS groups from input model: 0.180 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 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 : 0.003 0.118 7608 Z= 0.167 Angle : 0.490 8.798 10348 Z= 0.295 Chirality : 0.035 0.132 1290 Planarity : 0.002 0.029 1348 Dihedral : 17.130 89.995 2594 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 27.19 % Favored : 72.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.27), residues: 1033 helix: 1.13 (0.18), residues: 839 sheet: None (None), residues: 0 loop : -1.35 (0.46), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 146 TYR 0.005 0.001 TYR B 232 PHE 0.006 0.001 PHE E 248 TRP 0.034 0.002 TRP C 281 HIS 0.003 0.001 HIS L 160 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 7608) covalent geometry : angle 0.49011 (10348) hydrogen bonds : bond 0.16786 ( 533) hydrogen bonds : angle 5.14859 ( 1596) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 126 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 232 TYR cc_start: 0.6581 (m-10) cc_final: 0.6364 (m-10) REVERT: A 263 LYS cc_start: 0.7434 (ttpt) cc_final: 0.6990 (tptt) REVERT: C 251 LYS cc_start: 0.6934 (ttmt) cc_final: 0.6644 (mttp) REVERT: H 147 ILE cc_start: 0.6784 (mt) cc_final: 0.6501 (pt) REVERT: L 161 LEU cc_start: 0.8047 (tp) cc_final: 0.7749 (tp) REVERT: K 150 ASN cc_start: 0.7758 (t0) cc_final: 0.7521 (m110) REVERT: K 167 SER cc_start: 0.7320 (m) cc_final: 0.6892 (p) outliers start: 0 outliers final: 0 residues processed: 126 average time/residue: 0.0944 time to fit residues: 15.5673 Evaluate side-chains 97 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 0.0040 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.0770 chunk 100 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 overall best weight: 0.4950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 ASN ** B 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 ASN L 107 ASN K 107 ASN K 155 ASN K 182 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.209114 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.186696 restraints weight = 8974.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.190952 restraints weight = 5749.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.193826 restraints weight = 3703.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.193433 restraints weight = 2694.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.193622 restraints weight = 2266.830| |-----------------------------------------------------------------------------| r_work (final): 0.4431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6307 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7608 Z= 0.106 Angle : 0.449 6.653 10348 Z= 0.248 Chirality : 0.036 0.113 1290 Planarity : 0.002 0.018 1348 Dihedral : 3.417 20.058 1099 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 3.36 % Allowed : 25.15 % Favored : 71.49 % 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: 1.49 (0.27), residues: 1033 helix: 1.41 (0.18), residues: 862 sheet: None (None), residues: 0 loop : -1.00 (0.48), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 166 TYR 0.007 0.001 TYR I 133 PHE 0.004 0.001 PHE E 248 TRP 0.019 0.002 TRP C 281 HIS 0.003 0.001 HIS L 160 Details of bonding type rmsd covalent geometry : bond 0.00229 ( 7608) covalent geometry : angle 0.44919 (10348) hydrogen bonds : bond 0.03117 ( 533) hydrogen bonds : angle 3.48736 ( 1596) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.283 Fit side-chains REVERT: A 263 LYS cc_start: 0.7256 (ttpt) cc_final: 0.6858 (tptt) REVERT: B 313 ILE cc_start: 0.5096 (OUTLIER) cc_final: 0.4817 (mt) REVERT: E 264 ASN cc_start: 0.7434 (m-40) cc_final: 0.7189 (m110) REVERT: K 150 ASN cc_start: 0.7494 (t0) cc_final: 0.7194 (m110) REVERT: K 167 SER cc_start: 0.6968 (m) cc_final: 0.6605 (p) outliers start: 23 outliers final: 10 residues processed: 124 average time/residue: 0.0761 time to fit residues: 12.7152 Evaluate side-chains 105 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain K residue 165 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 52 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 75 optimal weight: 8.9990 chunk 70 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 31 optimal weight: 5.9990 chunk 13 optimal weight: 0.5980 chunk 10 optimal weight: 0.7980 chunk 43 optimal weight: 9.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 ASN B 283 GLN ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 266 ASN L 118 GLN K 107 ASN K 155 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.201227 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.180247 restraints weight = 9261.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.181259 restraints weight = 7108.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.182961 restraints weight = 5487.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4291 r_free = 0.4291 target = 0.183752 restraints weight = 4235.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.183837 restraints weight = 3855.137| |-----------------------------------------------------------------------------| r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6483 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 7608 Z= 0.131 Angle : 0.495 10.260 10348 Z= 0.264 Chirality : 0.037 0.125 1290 Planarity : 0.003 0.025 1348 Dihedral : 3.574 20.120 1099 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 5.12 % Allowed : 26.17 % Favored : 68.71 % 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: 1.30 (0.27), residues: 1033 helix: 1.30 (0.18), residues: 855 sheet: None (None), residues: 0 loop : -1.06 (0.47), residues: 178 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 146 TYR 0.008 0.001 TYR H 133 PHE 0.005 0.001 PHE H 101 TRP 0.022 0.002 TRP L 148 HIS 0.003 0.001 HIS C 285 Details of bonding type rmsd covalent geometry : bond 0.00306 ( 7608) covalent geometry : angle 0.49537 (10348) hydrogen bonds : bond 0.03328 ( 533) hydrogen bonds : angle 3.55354 ( 1596) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 113 time to evaluate : 0.338 Fit side-chains REVERT: A 263 LYS cc_start: 0.7444 (ttpt) cc_final: 0.7061 (tptt) REVERT: B 252 ASN cc_start: 0.7613 (OUTLIER) cc_final: 0.6973 (t0) REVERT: B 297 ASP cc_start: 0.6175 (m-30) cc_final: 0.5747 (m-30) REVERT: B 313 ILE cc_start: 0.5551 (OUTLIER) cc_final: 0.5174 (mt) REVERT: E 264 ASN cc_start: 0.7400 (m-40) cc_final: 0.6905 (m110) REVERT: C 233 ILE cc_start: 0.7089 (OUTLIER) cc_final: 0.6760 (pt) REVERT: H 118 GLN cc_start: 0.7776 (tm-30) cc_final: 0.7431 (tm-30) REVERT: K 167 SER cc_start: 0.7069 (m) cc_final: 0.6831 (p) REVERT: J 170 MET cc_start: 0.7385 (OUTLIER) cc_final: 0.6901 (mtm) outliers start: 35 outliers final: 16 residues processed: 139 average time/residue: 0.0722 time to fit residues: 13.6025 Evaluate side-chains 118 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 284 LEU Chi-restraints excluded: chain B residue 252 ASN Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain C residue 233 ILE Chi-restraints excluded: chain C residue 293 THR Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 165 LEU Chi-restraints excluded: chain K residue 176 LEU Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain J residue 170 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 71 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 52 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 8 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 17 optimal weight: 0.0670 chunk 0 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 118 GLN K 107 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.203861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.183539 restraints weight = 9229.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.184374 restraints weight = 7794.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.186513 restraints weight = 5544.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.187716 restraints weight = 3975.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.188008 restraints weight = 3306.763| |-----------------------------------------------------------------------------| r_work (final): 0.4368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6448 moved from start: 0.3091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7608 Z= 0.108 Angle : 0.465 7.444 10348 Z= 0.248 Chirality : 0.036 0.126 1290 Planarity : 0.002 0.017 1348 Dihedral : 3.438 18.814 1099 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 5.26 % Allowed : 24.85 % Favored : 69.88 % 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: 1.51 (0.27), residues: 1033 helix: 1.44 (0.18), residues: 862 sheet: None (None), residues: 0 loop : -1.07 (0.47), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 146 TYR 0.015 0.001 TYR B 291 PHE 0.007 0.001 PHE B 248 TRP 0.022 0.002 TRP L 148 HIS 0.002 0.001 HIS C 282 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 7608) covalent geometry : angle 0.46463 (10348) hydrogen bonds : bond 0.02888 ( 533) hydrogen bonds : angle 3.41157 ( 1596) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 109 time to evaluate : 0.189 Fit side-chains REVERT: A 263 LYS cc_start: 0.7472 (ttpt) cc_final: 0.7031 (tptt) REVERT: B 313 ILE cc_start: 0.5363 (OUTLIER) cc_final: 0.5068 (mt) REVERT: E 264 ASN cc_start: 0.7412 (m-40) cc_final: 0.7012 (m110) REVERT: H 118 GLN cc_start: 0.7683 (tm-30) cc_final: 0.7259 (tm-30) REVERT: I 170 MET cc_start: 0.6927 (mtt) cc_final: 0.6555 (mtt) REVERT: L 130 GLU cc_start: 0.6599 (tm-30) cc_final: 0.6333 (tt0) REVERT: K 167 SER cc_start: 0.7077 (m) cc_final: 0.6864 (p) REVERT: J 170 MET cc_start: 0.7225 (OUTLIER) cc_final: 0.6834 (mtm) outliers start: 36 outliers final: 20 residues processed: 135 average time/residue: 0.0650 time to fit residues: 12.1431 Evaluate side-chains 118 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 180 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 23 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 22 optimal weight: 0.5980 chunk 21 optimal weight: 2.9990 chunk 73 optimal weight: 0.5980 chunk 31 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 19 optimal weight: 0.0570 chunk 55 optimal weight: 1.9990 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4509 r_free = 0.4509 target = 0.203068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.182386 restraints weight = 9258.108| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.183814 restraints weight = 8139.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.185661 restraints weight = 5554.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.186275 restraints weight = 3835.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4313 r_free = 0.4313 target = 0.186371 restraints weight = 3662.303| |-----------------------------------------------------------------------------| r_work (final): 0.4357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6465 moved from start: 0.3270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7608 Z= 0.110 Angle : 0.468 7.009 10348 Z= 0.248 Chirality : 0.036 0.134 1290 Planarity : 0.002 0.017 1348 Dihedral : 3.434 18.861 1099 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.97 % Allowed : 25.58 % Favored : 69.44 % 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: 1.52 (0.27), residues: 1033 helix: 1.44 (0.18), residues: 861 sheet: None (None), residues: 0 loop : -1.03 (0.46), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 146 TYR 0.005 0.001 TYR I 133 PHE 0.004 0.001 PHE E 248 TRP 0.024 0.002 TRP L 148 HIS 0.002 0.001 HIS C 282 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 7608) covalent geometry : angle 0.46839 (10348) hydrogen bonds : bond 0.02915 ( 533) hydrogen bonds : angle 3.41136 ( 1596) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 106 time to evaluate : 0.225 Fit side-chains revert: symmetry clash REVERT: A 263 LYS cc_start: 0.7573 (ttpt) cc_final: 0.7175 (tptt) REVERT: B 313 ILE cc_start: 0.5688 (OUTLIER) cc_final: 0.5382 (mt) REVERT: E 264 ASN cc_start: 0.7403 (m-40) cc_final: 0.7001 (m110) REVERT: H 118 GLN cc_start: 0.7821 (tm-30) cc_final: 0.7460 (tm-30) REVERT: I 170 MET cc_start: 0.7020 (mtt) cc_final: 0.6532 (mtt) REVERT: K 167 SER cc_start: 0.7041 (m) cc_final: 0.6824 (p) REVERT: J 170 MET cc_start: 0.7296 (OUTLIER) cc_final: 0.6866 (mtm) outliers start: 34 outliers final: 24 residues processed: 130 average time/residue: 0.0725 time to fit residues: 12.9620 Evaluate side-chains 126 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 100 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain C residue 234 THR Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain H residue 179 GLU Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 123 ASP Chi-restraints excluded: chain K residue 176 LEU Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 180 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 91 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 74 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 282 HIS ** A 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 252 ASN ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 118 GLN L 118 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.200474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4263 r_free = 0.4263 target = 0.179586 restraints weight = 9293.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.181724 restraints weight = 7432.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.183495 restraints weight = 5199.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4276 r_free = 0.4276 target = 0.183610 restraints weight = 3504.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.183777 restraints weight = 3350.687| |-----------------------------------------------------------------------------| r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6527 moved from start: 0.3531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7608 Z= 0.131 Angle : 0.504 6.408 10348 Z= 0.269 Chirality : 0.037 0.135 1290 Planarity : 0.002 0.019 1348 Dihedral : 3.602 20.489 1099 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 5.12 % Allowed : 25.73 % Favored : 69.15 % 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: 1.35 (0.27), residues: 1033 helix: 1.31 (0.18), residues: 863 sheet: None (None), residues: 0 loop : -1.05 (0.47), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 146 TYR 0.010 0.001 TYR I 133 PHE 0.004 0.001 PHE H 101 TRP 0.026 0.002 TRP L 148 HIS 0.010 0.001 HIS A 282 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 7608) covalent geometry : angle 0.50378 (10348) hydrogen bonds : bond 0.03146 ( 533) hydrogen bonds : angle 3.52449 ( 1596) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 105 time to evaluate : 0.275 Fit side-chains revert: symmetry clash REVERT: A 263 LYS cc_start: 0.7548 (ttpt) cc_final: 0.7105 (tptt) REVERT: H 118 GLN cc_start: 0.7866 (tm-30) cc_final: 0.7566 (tm-30) REVERT: I 170 MET cc_start: 0.7064 (mtt) cc_final: 0.6655 (mtt) REVERT: K 106 ASP cc_start: 0.8106 (p0) cc_final: 0.7828 (p0) REVERT: K 167 SER cc_start: 0.7069 (m) cc_final: 0.6823 (p) REVERT: J 170 MET cc_start: 0.7354 (OUTLIER) cc_final: 0.6867 (mtm) outliers start: 35 outliers final: 25 residues processed: 130 average time/residue: 0.0716 time to fit residues: 12.6604 Evaluate side-chains 124 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 98 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 123 ASP Chi-restraints excluded: chain K residue 176 LEU Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 180 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 53 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 92 optimal weight: 0.9980 chunk 86 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 91 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 7 optimal weight: 5.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 283 GLN ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 ASN L 118 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.202043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.181571 restraints weight = 9336.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4267 r_free = 0.4267 target = 0.180962 restraints weight = 6528.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.183211 restraints weight = 5815.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.183498 restraints weight = 4230.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.183659 restraints weight = 3825.000| |-----------------------------------------------------------------------------| r_work (final): 0.4335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6536 moved from start: 0.3724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7608 Z= 0.127 Angle : 0.499 6.761 10348 Z= 0.266 Chirality : 0.038 0.315 1290 Planarity : 0.003 0.029 1348 Dihedral : 3.582 18.134 1099 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 5.56 % Allowed : 25.88 % Favored : 68.57 % 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: 1.36 (0.27), residues: 1033 helix: 1.31 (0.18), residues: 863 sheet: None (None), residues: 0 loop : -1.03 (0.47), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 146 TYR 0.019 0.001 TYR B 291 PHE 0.007 0.001 PHE C 248 TRP 0.028 0.002 TRP C 281 HIS 0.002 0.001 HIS L 160 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 7608) covalent geometry : angle 0.49896 (10348) hydrogen bonds : bond 0.03091 ( 533) hydrogen bonds : angle 3.49294 ( 1596) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 110 time to evaluate : 0.265 Fit side-chains REVERT: A 263 LYS cc_start: 0.7540 (ttpt) cc_final: 0.7058 (tptt) REVERT: D 244 GLN cc_start: 0.5515 (OUTLIER) cc_final: 0.5276 (mp10) REVERT: H 118 GLN cc_start: 0.7858 (tm-30) cc_final: 0.7556 (tm-30) REVERT: I 170 MET cc_start: 0.7109 (mtt) cc_final: 0.6745 (mtt) REVERT: K 167 SER cc_start: 0.7108 (m) cc_final: 0.6820 (p) REVERT: J 170 MET cc_start: 0.7361 (OUTLIER) cc_final: 0.6913 (mtm) outliers start: 38 outliers final: 33 residues processed: 136 average time/residue: 0.0640 time to fit residues: 12.2069 Evaluate side-chains 136 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 101 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 LEU Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain C residue 306 LEU Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain D residue 244 GLN Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain L residue 147 ILE Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 123 ASP Chi-restraints excluded: chain K residue 176 LEU Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 180 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 37 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 68 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 53 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 0.0170 chunk 14 optimal weight: 0.6980 chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.7422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.200571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.180146 restraints weight = 9402.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.181071 restraints weight = 7684.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.182929 restraints weight = 5559.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.184118 restraints weight = 4087.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.184283 restraints weight = 3526.413| |-----------------------------------------------------------------------------| r_work (final): 0.4330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.3882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7608 Z= 0.126 Angle : 0.523 10.442 10348 Z= 0.277 Chirality : 0.037 0.184 1290 Planarity : 0.002 0.022 1348 Dihedral : 3.643 26.319 1099 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 5.56 % Allowed : 26.61 % Favored : 67.84 % 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: 1.30 (0.27), residues: 1033 helix: 1.27 (0.18), residues: 868 sheet: None (None), residues: 0 loop : -1.09 (0.47), residues: 165 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 146 TYR 0.007 0.001 TYR I 133 PHE 0.006 0.001 PHE C 248 TRP 0.023 0.002 TRP H 148 HIS 0.003 0.001 HIS C 282 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7608) covalent geometry : angle 0.52309 (10348) hydrogen bonds : bond 0.03099 ( 533) hydrogen bonds : angle 3.52332 ( 1596) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 105 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: A 251 LYS cc_start: 0.7616 (mttp) cc_final: 0.7369 (mptt) REVERT: A 263 LYS cc_start: 0.7525 (ttpt) cc_final: 0.7057 (tptt) REVERT: H 118 GLN cc_start: 0.7825 (tm-30) cc_final: 0.7546 (tm-30) REVERT: I 170 MET cc_start: 0.7139 (mtt) cc_final: 0.6742 (mtt) REVERT: L 130 GLU cc_start: 0.6631 (tm-30) cc_final: 0.6307 (tt0) REVERT: K 106 ASP cc_start: 0.8126 (p0) cc_final: 0.7845 (p0) REVERT: K 167 SER cc_start: 0.7127 (m) cc_final: 0.6857 (p) REVERT: J 170 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.6897 (mtm) outliers start: 38 outliers final: 29 residues processed: 132 average time/residue: 0.0736 time to fit residues: 13.1047 Evaluate side-chains 130 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 100 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 123 ASP Chi-restraints excluded: chain K residue 176 LEU Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 180 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 78 optimal weight: 0.9990 chunk 55 optimal weight: 0.0470 chunk 48 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.7680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 ASN J 160 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.199036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.178831 restraints weight = 9323.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.179607 restraints weight = 8839.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.181445 restraints weight = 6000.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.182223 restraints weight = 4173.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.182349 restraints weight = 3812.442| |-----------------------------------------------------------------------------| r_work (final): 0.4321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.4038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7608 Z= 0.126 Angle : 0.526 9.906 10348 Z= 0.280 Chirality : 0.038 0.276 1290 Planarity : 0.003 0.024 1348 Dihedral : 3.675 24.672 1099 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 5.41 % Allowed : 26.46 % Favored : 68.13 % 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: 1.24 (0.27), residues: 1033 helix: 1.23 (0.18), residues: 869 sheet: None (None), residues: 0 loop : -1.12 (0.46), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 146 TYR 0.021 0.001 TYR B 291 PHE 0.006 0.001 PHE C 248 TRP 0.022 0.002 TRP C 281 HIS 0.003 0.001 HIS C 282 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 7608) covalent geometry : angle 0.52608 (10348) hydrogen bonds : bond 0.03123 ( 533) hydrogen bonds : angle 3.51734 ( 1596) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 101 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 263 LYS cc_start: 0.7544 (ttpt) cc_final: 0.7077 (tptt) REVERT: E 313 ILE cc_start: 0.7516 (OUTLIER) cc_final: 0.6578 (tp) REVERT: H 118 GLN cc_start: 0.7876 (tm-30) cc_final: 0.7574 (tm-30) REVERT: I 170 MET cc_start: 0.7199 (mtt) cc_final: 0.6789 (mtt) REVERT: L 130 GLU cc_start: 0.6894 (tm-30) cc_final: 0.6286 (tt0) REVERT: K 106 ASP cc_start: 0.8123 (p0) cc_final: 0.7829 (p0) REVERT: K 167 SER cc_start: 0.7151 (m) cc_final: 0.6884 (p) REVERT: J 170 MET cc_start: 0.7285 (OUTLIER) cc_final: 0.6809 (mtm) outliers start: 37 outliers final: 33 residues processed: 123 average time/residue: 0.0644 time to fit residues: 11.1847 Evaluate side-chains 132 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 97 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 233 ILE Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 267 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 284 LEU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain D residue 235 THR Chi-restraints excluded: chain H residue 98 CYS Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain H residue 161 LEU Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 123 ASP Chi-restraints excluded: chain K residue 176 LEU Chi-restraints excluded: chain J residue 151 THR Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 170 MET Chi-restraints excluded: chain J residue 180 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 91 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 74 optimal weight: 0.0770 chunk 17 optimal weight: 0.0670 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.204249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.183688 restraints weight = 9344.917| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.185613 restraints weight = 8279.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.187434 restraints weight = 5607.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.188021 restraints weight = 3738.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.188069 restraints weight = 3419.145| |-----------------------------------------------------------------------------| r_work (final): 0.4364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6454 moved from start: 0.4126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 7608 Z= 0.106 Angle : 0.516 12.232 10348 Z= 0.273 Chirality : 0.037 0.284 1290 Planarity : 0.002 0.027 1348 Dihedral : 3.545 24.398 1099 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.53 % Allowed : 27.34 % Favored : 68.13 % 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: 1.52 (0.27), residues: 1033 helix: 1.42 (0.18), residues: 870 sheet: None (None), residues: 0 loop : -1.06 (0.47), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG L 146 TYR 0.006 0.001 TYR I 133 PHE 0.005 0.001 PHE B 248 TRP 0.025 0.002 TRP L 148 HIS 0.003 0.001 HIS J 160 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 7608) covalent geometry : angle 0.51594 (10348) hydrogen bonds : bond 0.02854 ( 533) hydrogen bonds : angle 3.34904 ( 1596) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2066 Ramachandran restraints generated. 1033 Oldfield, 0 Emsley, 1033 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 110 time to evaluate : 0.261 Fit side-chains revert: symmetry clash REVERT: A 263 LYS cc_start: 0.7449 (ttpt) cc_final: 0.6987 (tptt) REVERT: C 277 LEU cc_start: 0.7082 (OUTLIER) cc_final: 0.6748 (mp) REVERT: H 118 GLN cc_start: 0.7775 (tm-30) cc_final: 0.7475 (tm-30) REVERT: I 170 MET cc_start: 0.7104 (mtt) cc_final: 0.6731 (mtt) REVERT: L 130 GLU cc_start: 0.6815 (tm-30) cc_final: 0.6251 (tt0) REVERT: K 106 ASP cc_start: 0.8060 (p0) cc_final: 0.7723 (p0) REVERT: K 167 SER cc_start: 0.7095 (m) cc_final: 0.6814 (p) outliers start: 31 outliers final: 24 residues processed: 130 average time/residue: 0.0715 time to fit residues: 12.9952 Evaluate side-chains 125 residues out of total 941 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 100 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 ILE Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 280 ASN Chi-restraints excluded: chain A residue 305 THR Chi-restraints excluded: chain B residue 229 LEU Chi-restraints excluded: chain B residue 254 VAL Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain E residue 229 LEU Chi-restraints excluded: chain E residue 313 ILE Chi-restraints excluded: chain C residue 229 LEU Chi-restraints excluded: chain C residue 252 ASN Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 305 THR Chi-restraints excluded: chain H residue 120 LYS Chi-restraints excluded: chain H residue 121 VAL Chi-restraints excluded: chain H residue 147 ILE Chi-restraints excluded: chain H residue 151 THR Chi-restraints excluded: chain I residue 107 ASN Chi-restraints excluded: chain I residue 145 LEU Chi-restraints excluded: chain L residue 103 VAL Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain K residue 123 ASP Chi-restraints excluded: chain K residue 176 LEU Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 180 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.6980 chunk 9 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 51 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 44 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 73 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 252 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 252 ASN L 118 GLN J 160 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.200031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.179666 restraints weight = 9361.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.180416 restraints weight = 8370.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.182407 restraints weight = 5868.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.183874 restraints weight = 4182.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.183948 restraints weight = 3664.550| |-----------------------------------------------------------------------------| r_work (final): 0.4327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6522 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7608 Z= 0.133 Angle : 0.553 13.772 10348 Z= 0.291 Chirality : 0.039 0.271 1290 Planarity : 0.003 0.022 1348 Dihedral : 3.717 24.566 1099 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 4.39 % Allowed : 28.51 % Favored : 67.11 % 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: 1.27 (0.27), residues: 1033 helix: 1.22 (0.18), residues: 875 sheet: None (None), residues: 0 loop : -1.03 (0.47), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG I 146 TYR 0.022 0.001 TYR B 291 PHE 0.006 0.001 PHE C 248 TRP 0.027 0.003 TRP B 281 HIS 0.002 0.001 HIS C 282 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 7608) covalent geometry : angle 0.55348 (10348) hydrogen bonds : bond 0.03169 ( 533) hydrogen bonds : angle 3.54648 ( 1596) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1001.06 seconds wall clock time: 17 minutes 58.50 seconds (1078.50 seconds total)