Starting phenix.real_space_refine on Wed Mar 4 14:11:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7cal_30334/03_2026/7cal_30334.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cal_30334/03_2026/7cal_30334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7cal_30334/03_2026/7cal_30334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cal_30334/03_2026/7cal_30334.map" model { file = "/net/cci-nas-00/data/ceres_data/7cal_30334/03_2026/7cal_30334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cal_30334/03_2026/7cal_30334.cif" } resolution = 3.2 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 64 5.16 5 C 9292 2.51 5 N 2288 2.21 5 O 2416 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 56 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14064 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3465 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 425} Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 7, 'TYR:plan': 3, 'ASP:plan': 5, 'GLN:plan1': 5, 'ASN:plan1': 3, 'GLU:plan': 7, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 139 Chain: "B" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3465 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 425} Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 7, 'TYR:plan': 3, 'ASP:plan': 5, 'GLN:plan1': 5, 'ASN:plan1': 3, 'GLU:plan': 7, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 139 Chain: "C" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3465 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 425} Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 7, 'TYR:plan': 3, 'ASP:plan': 5, 'GLN:plan1': 5, 'ASN:plan1': 3, 'GLU:plan': 7, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 139 Chain: "D" Number of atoms: 3465 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3465 Classifications: {'peptide': 444} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 425} Unresolved non-hydrogen bonds: 199 Unresolved non-hydrogen angles: 246 Unresolved non-hydrogen dihedrals: 165 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 7, 'TYR:plan': 3, 'ASP:plan': 5, 'GLN:plan1': 5, 'ASN:plan1': 3, 'GLU:plan': 7, 'PHE:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 139 Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.77, per 1000 atoms: 0.20 Number of scatterers: 14064 At special positions: 0 Unit cell: (112.554, 112.554, 115.596, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 64 16.00 P 4 15.00 O 2416 8.00 N 2288 7.00 C 9292 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.33 Conformation dependent library (CDL) restraints added in 546.1 milliseconds 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3408 Finding SS restraints... Secondary structure from input PDB file: 76 helices and 4 sheets defined 51.1% alpha, 1.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 61 through 72 removed outlier: 3.502A pdb=" N VAL A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU A 68 " --> pdb=" O MET A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 83 removed outlier: 3.663A pdb=" N PHE A 79 " --> pdb=" O TRP A 75 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N PHE A 81 " --> pdb=" O CYS A 77 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA A 82 " --> pdb=" O PRO A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 109 removed outlier: 3.798A pdb=" N ASN A 99 " --> pdb=" O ASP A 95 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP A 105 " --> pdb=" O PHE A 101 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE A 106 " --> pdb=" O PHE A 102 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ILE A 107 " --> pdb=" O ALA A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 137 removed outlier: 3.584A pdb=" N ALA A 130 " --> pdb=" O PRO A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 154 removed outlier: 3.762A pdb=" N LEU A 154 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 161 through 166 Processing helix chain 'A' and resid 167 through 174 removed outlier: 3.636A pdb=" N LEU A 170 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG A 171 " --> pdb=" O SER A 168 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG A 174 " --> pdb=" O ARG A 171 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 186 removed outlier: 3.654A pdb=" N LEU A 181 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA A 183 " --> pdb=" O SER A 179 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG A 184 " --> pdb=" O SER A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 214 removed outlier: 3.722A pdb=" N CYS A 198 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR A 199 " --> pdb=" O TRP A 195 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR A 205 " --> pdb=" O LEU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 222 Processing helix chain 'A' and resid 247 through 259 Processing helix chain 'A' and resid 270 through 282 removed outlier: 3.691A pdb=" N LEU A 275 " --> pdb=" O PRO A 271 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 303 removed outlier: 3.594A pdb=" N GLY A 286 " --> pdb=" O MET A 282 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR A 290 " --> pdb=" O GLY A 286 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 323 removed outlier: 3.652A pdb=" N ALA A 320 " --> pdb=" O ALA A 316 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN A 323 " --> pdb=" O PHE A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 344 removed outlier: 4.479A pdb=" N GLN A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS A 336 " --> pdb=" O GLN A 332 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE A 337 " --> pdb=" O MET A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 367 removed outlier: 3.817A pdb=" N ASN A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 373 removed outlier: 3.644A pdb=" N VAL A 372 " --> pdb=" O PHE A 368 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 379 removed outlier: 3.512A pdb=" N PHE A 378 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN A 379 " --> pdb=" O TYR A 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 375 through 379' Processing helix chain 'A' and resid 482 through 491 removed outlier: 4.203A pdb=" N VAL A 488 " --> pdb=" O ASP A 484 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE A 489 " --> pdb=" O ASP A 485 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET A 490 " --> pdb=" O GLY A 486 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 72 removed outlier: 3.501A pdb=" N VAL B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU B 68 " --> pdb=" O MET B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 83 removed outlier: 3.664A pdb=" N PHE B 79 " --> pdb=" O TRP B 75 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE B 81 " --> pdb=" O CYS B 77 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA B 82 " --> pdb=" O PRO B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 109 removed outlier: 3.797A pdb=" N ASN B 99 " --> pdb=" O ASP B 95 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B 103 " --> pdb=" O ASN B 99 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP B 105 " --> pdb=" O PHE B 101 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE B 106 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE B 107 " --> pdb=" O ALA B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 137 removed outlier: 3.583A pdb=" N ALA B 130 " --> pdb=" O PRO B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 154 removed outlier: 3.762A pdb=" N LEU B 154 " --> pdb=" O LEU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 161 through 166 Processing helix chain 'B' and resid 167 through 174 removed outlier: 3.636A pdb=" N LEU B 170 " --> pdb=" O LEU B 167 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG B 171 " --> pdb=" O SER B 168 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG B 174 " --> pdb=" O ARG B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 186 removed outlier: 3.654A pdb=" N LEU B 181 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 183 " --> pdb=" O SER B 179 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG B 184 " --> pdb=" O SER B 180 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 214 removed outlier: 3.723A pdb=" N CYS B 198 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR B 199 " --> pdb=" O TRP B 195 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR B 205 " --> pdb=" O LEU B 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 247 through 259 Processing helix chain 'B' and resid 270 through 282 removed outlier: 3.692A pdb=" N LEU B 275 " --> pdb=" O PRO B 271 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 303 removed outlier: 3.593A pdb=" N GLY B 286 " --> pdb=" O MET B 282 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR B 290 " --> pdb=" O GLY B 286 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY B 293 " --> pdb=" O ALA B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 323 removed outlier: 3.652A pdb=" N ALA B 320 " --> pdb=" O ALA B 316 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N ASN B 323 " --> pdb=" O PHE B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 344 removed outlier: 4.478A pdb=" N GLN B 332 " --> pdb=" O ASP B 328 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS B 336 " --> pdb=" O GLN B 332 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ILE B 337 " --> pdb=" O MET B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 367 removed outlier: 3.816A pdb=" N ASN B 365 " --> pdb=" O SER B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 373 removed outlier: 3.643A pdb=" N VAL B 372 " --> pdb=" O PHE B 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 379 removed outlier: 3.512A pdb=" N PHE B 378 " --> pdb=" O ILE B 375 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN B 379 " --> pdb=" O TYR B 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 375 through 379' Processing helix chain 'B' and resid 482 through 491 removed outlier: 4.202A pdb=" N VAL B 488 " --> pdb=" O ASP B 484 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE B 489 " --> pdb=" O ASP B 485 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET B 490 " --> pdb=" O GLY B 486 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 72 removed outlier: 3.501A pdb=" N VAL C 67 " --> pdb=" O GLU C 63 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU C 68 " --> pdb=" O MET C 64 " (cutoff:3.500A) Processing helix chain 'C' and resid 75 through 83 removed outlier: 3.663A pdb=" N PHE C 79 " --> pdb=" O TRP C 75 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE C 81 " --> pdb=" O CYS C 77 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA C 82 " --> pdb=" O PRO C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 109 removed outlier: 3.797A pdb=" N ASN C 99 " --> pdb=" O ASP C 95 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ALA C 103 " --> pdb=" O ASN C 99 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP C 105 " --> pdb=" O PHE C 101 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE C 106 " --> pdb=" O PHE C 102 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE C 107 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 137 removed outlier: 3.583A pdb=" N ALA C 130 " --> pdb=" O PRO C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 154 removed outlier: 3.762A pdb=" N LEU C 154 " --> pdb=" O LEU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 161 through 166 Processing helix chain 'C' and resid 167 through 174 removed outlier: 3.636A pdb=" N LEU C 170 " --> pdb=" O LEU C 167 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG C 171 " --> pdb=" O SER C 168 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG C 174 " --> pdb=" O ARG C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 186 removed outlier: 3.653A pdb=" N LEU C 181 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ALA C 183 " --> pdb=" O SER C 179 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG C 184 " --> pdb=" O SER C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 214 removed outlier: 3.722A pdb=" N CYS C 198 " --> pdb=" O PHE C 194 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR C 199 " --> pdb=" O TRP C 195 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR C 205 " --> pdb=" O LEU C 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 222 Processing helix chain 'C' and resid 247 through 259 Processing helix chain 'C' and resid 270 through 282 removed outlier: 3.692A pdb=" N LEU C 275 " --> pdb=" O PRO C 271 " (cutoff:3.500A) Processing helix chain 'C' and resid 282 through 303 removed outlier: 3.593A pdb=" N GLY C 286 " --> pdb=" O MET C 282 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N TYR C 290 " --> pdb=" O GLY C 286 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N GLY C 293 " --> pdb=" O ALA C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 304 through 323 removed outlier: 3.652A pdb=" N ALA C 320 " --> pdb=" O ALA C 316 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASN C 323 " --> pdb=" O PHE C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 344 removed outlier: 4.478A pdb=" N GLN C 332 " --> pdb=" O ASP C 328 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS C 336 " --> pdb=" O GLN C 332 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE C 337 " --> pdb=" O MET C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 367 removed outlier: 3.816A pdb=" N ASN C 365 " --> pdb=" O SER C 361 " (cutoff:3.500A) Processing helix chain 'C' and resid 368 through 373 removed outlier: 3.644A pdb=" N VAL C 372 " --> pdb=" O PHE C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 379 removed outlier: 3.512A pdb=" N PHE C 378 " --> pdb=" O ILE C 375 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLN C 379 " --> pdb=" O TYR C 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 375 through 379' Processing helix chain 'C' and resid 482 through 491 removed outlier: 4.202A pdb=" N VAL C 488 " --> pdb=" O ASP C 484 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE C 489 " --> pdb=" O ASP C 485 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N MET C 490 " --> pdb=" O GLY C 486 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.502A pdb=" N VAL D 67 " --> pdb=" O GLU D 63 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU D 68 " --> pdb=" O MET D 64 " (cutoff:3.500A) Processing helix chain 'D' and resid 75 through 83 removed outlier: 3.664A pdb=" N PHE D 79 " --> pdb=" O TRP D 75 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N PHE D 81 " --> pdb=" O CYS D 77 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA D 82 " --> pdb=" O PRO D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 93 through 109 removed outlier: 3.797A pdb=" N ASN D 99 " --> pdb=" O ASP D 95 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA D 103 " --> pdb=" O ASN D 99 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ASP D 105 " --> pdb=" O PHE D 101 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE D 106 " --> pdb=" O PHE D 102 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE D 107 " --> pdb=" O ALA D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 137 removed outlier: 3.585A pdb=" N ALA D 130 " --> pdb=" O PRO D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 154 removed outlier: 3.761A pdb=" N LEU D 154 " --> pdb=" O LEU D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 161 through 166 Processing helix chain 'D' and resid 167 through 174 removed outlier: 3.636A pdb=" N LEU D 170 " --> pdb=" O LEU D 167 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG D 171 " --> pdb=" O SER D 168 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG D 174 " --> pdb=" O ARG D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 186 removed outlier: 3.654A pdb=" N LEU D 181 " --> pdb=" O ARG D 177 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ARG D 184 " --> pdb=" O SER D 180 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 214 removed outlier: 3.722A pdb=" N CYS D 198 " --> pdb=" O PHE D 194 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR D 199 " --> pdb=" O TRP D 195 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N THR D 205 " --> pdb=" O LEU D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 217 through 222 Processing helix chain 'D' and resid 247 through 259 Processing helix chain 'D' and resid 270 through 282 removed outlier: 3.691A pdb=" N LEU D 275 " --> pdb=" O PRO D 271 " (cutoff:3.500A) Processing helix chain 'D' and resid 282 through 303 removed outlier: 3.593A pdb=" N GLY D 286 " --> pdb=" O MET D 282 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR D 290 " --> pdb=" O GLY D 286 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLY D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 304 through 323 removed outlier: 3.652A pdb=" N ALA D 320 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN D 323 " --> pdb=" O PHE D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 344 removed outlier: 4.478A pdb=" N GLN D 332 " --> pdb=" O ASP D 328 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS D 336 " --> pdb=" O GLN D 332 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE D 337 " --> pdb=" O MET D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 367 removed outlier: 3.817A pdb=" N ASN D 365 " --> pdb=" O SER D 361 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 373 removed outlier: 3.644A pdb=" N VAL D 372 " --> pdb=" O PHE D 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 375 through 379 removed outlier: 3.512A pdb=" N PHE D 378 " --> pdb=" O ILE D 375 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN D 379 " --> pdb=" O TYR D 376 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 375 through 379' Processing helix chain 'D' and resid 482 through 491 removed outlier: 4.202A pdb=" N VAL D 488 " --> pdb=" O ASP D 484 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE D 489 " --> pdb=" O ASP D 485 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N MET D 490 " --> pdb=" O GLY D 486 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 432 through 434 removed outlier: 3.992A pdb=" N VAL A 422 " --> pdb=" O PHE A 434 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 432 through 434 removed outlier: 3.993A pdb=" N VAL B 422 " --> pdb=" O PHE B 434 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 432 through 434 removed outlier: 3.993A pdb=" N VAL C 422 " --> pdb=" O PHE C 434 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 432 through 434 removed outlier: 3.993A pdb=" N VAL D 422 " --> pdb=" O PHE D 434 " (cutoff:3.500A) 488 hydrogen bonds defined for protein. 1404 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 1.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2413 1.32 - 1.44: 4093 1.44 - 1.56: 7854 1.56 - 1.68: 0 1.68 - 1.80: 112 Bond restraints: 14472 Sorted by residual: bond pdb=" O13 3PE A 701 " pdb=" P 3PE A 701 " ideal model delta sigma weight residual 1.654 1.751 -0.097 2.00e-02 2.50e+03 2.35e+01 bond pdb=" O13 3PE D 701 " pdb=" P 3PE D 701 " ideal model delta sigma weight residual 1.654 1.750 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" O13 3PE C 701 " pdb=" P 3PE C 701 " ideal model delta sigma weight residual 1.654 1.750 -0.096 2.00e-02 2.50e+03 2.32e+01 bond pdb=" O13 3PE B 701 " pdb=" P 3PE B 701 " ideal model delta sigma weight residual 1.654 1.750 -0.096 2.00e-02 2.50e+03 2.31e+01 bond pdb=" O11 3PE A 701 " pdb=" P 3PE A 701 " ideal model delta sigma weight residual 1.644 1.696 -0.052 2.00e-02 2.50e+03 6.78e+00 ... (remaining 14467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.41: 18908 2.41 - 4.83: 643 4.83 - 7.24: 125 7.24 - 9.65: 40 9.65 - 12.07: 8 Bond angle restraints: 19724 Sorted by residual: angle pdb=" N VAL B 142 " pdb=" CA VAL B 142 " pdb=" C VAL B 142 " ideal model delta sigma weight residual 113.22 107.25 5.97 1.23e+00 6.61e-01 2.36e+01 angle pdb=" N VAL D 142 " pdb=" CA VAL D 142 " pdb=" C VAL D 142 " ideal model delta sigma weight residual 113.22 107.30 5.92 1.23e+00 6.61e-01 2.32e+01 angle pdb=" N VAL C 142 " pdb=" CA VAL C 142 " pdb=" C VAL C 142 " ideal model delta sigma weight residual 113.22 107.30 5.92 1.23e+00 6.61e-01 2.31e+01 angle pdb=" N VAL A 142 " pdb=" CA VAL A 142 " pdb=" C VAL A 142 " ideal model delta sigma weight residual 113.22 107.31 5.91 1.23e+00 6.61e-01 2.31e+01 angle pdb=" C VAL C 426 " pdb=" N TYR C 427 " pdb=" CA TYR C 427 " ideal model delta sigma weight residual 120.38 126.93 -6.55 1.46e+00 4.69e-01 2.01e+01 ... (remaining 19719 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 7474 17.93 - 35.86: 752 35.86 - 53.79: 143 53.79 - 71.72: 11 71.72 - 89.64: 12 Dihedral angle restraints: 8392 sinusoidal: 3136 harmonic: 5256 Sorted by residual: dihedral pdb=" CA MET C 476 " pdb=" C MET C 476 " pdb=" N SER C 477 " pdb=" CA SER C 477 " ideal model delta harmonic sigma weight residual -180.00 -157.39 -22.61 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA MET D 476 " pdb=" C MET D 476 " pdb=" N SER D 477 " pdb=" CA SER D 477 " ideal model delta harmonic sigma weight residual 180.00 -157.41 -22.59 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA MET A 476 " pdb=" C MET A 476 " pdb=" N SER A 477 " pdb=" CA SER A 477 " ideal model delta harmonic sigma weight residual -180.00 -157.41 -22.59 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 8389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1424 0.053 - 0.106: 640 0.106 - 0.159: 122 0.159 - 0.213: 30 0.213 - 0.266: 8 Chirality restraints: 2224 Sorted by residual: chirality pdb=" CA TYR A 114 " pdb=" N TYR A 114 " pdb=" C TYR A 114 " pdb=" CB TYR A 114 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CA TYR C 114 " pdb=" N TYR C 114 " pdb=" C TYR C 114 " pdb=" CB TYR C 114 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.73e+00 chirality pdb=" CA TYR B 114 " pdb=" N TYR B 114 " pdb=" C TYR B 114 " pdb=" CB TYR B 114 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.68e+00 ... (remaining 2221 not shown) Planarity restraints: 2452 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 77 " -0.038 5.00e-02 4.00e+02 5.73e-02 5.26e+00 pdb=" N PRO A 78 " 0.099 5.00e-02 4.00e+02 pdb=" CA PRO A 78 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 78 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS D 77 " 0.038 5.00e-02 4.00e+02 5.72e-02 5.23e+00 pdb=" N PRO D 78 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO D 78 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 78 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS C 77 " 0.038 5.00e-02 4.00e+02 5.71e-02 5.22e+00 pdb=" N PRO C 78 " -0.099 5.00e-02 4.00e+02 pdb=" CA PRO C 78 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 78 " 0.033 5.00e-02 4.00e+02 ... (remaining 2449 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3961 2.79 - 3.32: 11786 3.32 - 3.85: 21570 3.85 - 4.37: 25689 4.37 - 4.90: 44276 Nonbonded interactions: 107282 Sorted by model distance: nonbonded pdb=" O TYR C 252 " pdb=" OG1 THR C 256 " model vdw 2.265 3.040 nonbonded pdb=" O TYR A 252 " pdb=" OG1 THR A 256 " model vdw 2.265 3.040 nonbonded pdb=" O TYR B 252 " pdb=" OG1 THR B 256 " model vdw 2.265 3.040 nonbonded pdb=" O TYR D 252 " pdb=" OG1 THR D 256 " model vdw 2.266 3.040 nonbonded pdb=" O SER A 152 " pdb=" OG SER A 152 " model vdw 2.348 3.040 ... (remaining 107277 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.290 Find NCS groups from input model: 0.100 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 : 0.007 0.097 14480 Z= 0.333 Angle : 1.092 12.067 19724 Z= 0.604 Chirality : 0.060 0.266 2224 Planarity : 0.007 0.057 2452 Dihedral : 14.988 89.644 4984 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.23 % Allowed : 14.03 % Favored : 85.75 % Rotamer: Outliers : 0.00 % Allowed : 12.61 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -6.34 (0.13), residues: 1768 helix: -4.72 (0.06), residues: 928 sheet: None (None), residues: 0 loop : -3.52 (0.18), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 246 TYR 0.037 0.003 TYR A 114 PHE 0.036 0.002 PHE C 238 TRP 0.016 0.002 TRP C 302 HIS 0.005 0.002 HIS B 301 Details of bonding type rmsd covalent geometry : bond 0.00747 (14472) covalent geometry : angle 1.09208 (19724) hydrogen bonds : bond 0.34895 ( 488) hydrogen bonds : angle 10.42048 ( 1404) Misc. bond : bond 0.00248 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: A 186 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7595 (mt-10) REVERT: A 442 GLU cc_start: 0.6713 (pm20) cc_final: 0.5937 (pm20) REVERT: B 60 ARG cc_start: 0.7672 (mtp-110) cc_final: 0.7246 (mtm-85) REVERT: B 442 GLU cc_start: 0.6639 (pm20) cc_final: 0.5939 (pm20) REVERT: C 60 ARG cc_start: 0.7658 (mtp-110) cc_final: 0.7275 (mtm-85) REVERT: C 442 GLU cc_start: 0.6647 (pm20) cc_final: 0.5901 (pm20) REVERT: D 60 ARG cc_start: 0.7662 (mtp-110) cc_final: 0.7283 (mtm-85) REVERT: D 442 GLU cc_start: 0.6654 (pm20) cc_final: 0.5903 (pm20) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.1226 time to fit residues: 54.4881 Evaluate side-chains 254 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 ASN A 301 HIS A 348 GLN A 365 ASN A 491 ASN B 294 ASN B 301 HIS B 348 GLN B 365 ASN B 491 ASN C 294 ASN C 301 HIS C 365 ASN C 491 ASN D 294 ASN D 301 HIS D 365 ASN D 491 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.147907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.121447 restraints weight = 17752.103| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.11 r_work: 0.3231 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14480 Z= 0.139 Angle : 0.664 5.903 19724 Z= 0.358 Chirality : 0.046 0.178 2224 Planarity : 0.006 0.050 2452 Dihedral : 9.742 61.989 2124 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.65 % Favored : 88.12 % Rotamer: Outliers : 1.79 % Allowed : 15.62 % Favored : 82.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -4.41 (0.17), residues: 1768 helix: -2.88 (0.13), residues: 968 sheet: None (None), residues: 0 loop : -2.91 (0.21), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 305 TYR 0.025 0.002 TYR C 114 PHE 0.022 0.002 PHE D 111 TRP 0.017 0.002 TRP B 62 HIS 0.002 0.001 HIS B 431 Details of bonding type rmsd covalent geometry : bond 0.00307 (14472) covalent geometry : angle 0.66442 (19724) hydrogen bonds : bond 0.05357 ( 488) hydrogen bonds : angle 4.77567 ( 1404) Misc. bond : bond 0.00101 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 293 time to evaluate : 0.502 Fit side-chains revert: symmetry clash REVERT: A 133 TYR cc_start: 0.8399 (t80) cc_final: 0.8013 (t80) REVERT: A 297 ASN cc_start: 0.8754 (t0) cc_final: 0.8488 (t0) REVERT: A 442 GLU cc_start: 0.7132 (pm20) cc_final: 0.6454 (pm20) REVERT: A 485 ASP cc_start: 0.8511 (t0) cc_final: 0.8302 (t0) REVERT: B 60 ARG cc_start: 0.7833 (mtp180) cc_final: 0.7032 (mtm-85) REVERT: B 297 ASN cc_start: 0.8762 (t0) cc_final: 0.8485 (t0) REVERT: B 442 GLU cc_start: 0.7136 (pm20) cc_final: 0.6464 (pm20) REVERT: B 446 GLU cc_start: 0.5778 (tt0) cc_final: 0.5512 (mt-10) REVERT: B 464 LEU cc_start: 0.8508 (mp) cc_final: 0.8273 (mt) REVERT: C 60 ARG cc_start: 0.7820 (mtp180) cc_final: 0.7018 (mtm-85) REVERT: C 297 ASN cc_start: 0.8724 (t0) cc_final: 0.8469 (t0) REVERT: C 442 GLU cc_start: 0.7060 (pm20) cc_final: 0.6335 (pm20) REVERT: D 60 ARG cc_start: 0.7827 (mtp180) cc_final: 0.7033 (mtm-85) REVERT: D 297 ASN cc_start: 0.8716 (t0) cc_final: 0.8457 (t0) REVERT: D 442 GLU cc_start: 0.7036 (pm20) cc_final: 0.6327 (pm20) REVERT: D 446 GLU cc_start: 0.6005 (tt0) cc_final: 0.5719 (mt-10) REVERT: D 464 LEU cc_start: 0.8535 (mp) cc_final: 0.8285 (mt) outliers start: 25 outliers final: 21 residues processed: 310 average time/residue: 0.1167 time to fit residues: 53.4938 Evaluate side-chains 298 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 277 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 244 TRP Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 244 TRP Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 244 TRP Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 462 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 54 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 146 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 137 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 110 optimal weight: 0.3980 chunk 83 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN B 284 ASN B 374 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.149865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.124052 restraints weight = 17798.172| |-----------------------------------------------------------------------------| r_work (start): 0.3368 rms_B_bonded: 1.89 r_work: 0.3262 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3129 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14480 Z= 0.117 Angle : 0.600 6.897 19724 Z= 0.314 Chirality : 0.044 0.169 2224 Planarity : 0.004 0.046 2452 Dihedral : 8.899 58.874 2124 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.14 % Favored : 88.63 % Rotamer: Outliers : 2.08 % Allowed : 16.12 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -3.21 (0.19), residues: 1768 helix: -1.72 (0.16), residues: 968 sheet: None (None), residues: 0 loop : -2.61 (0.22), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 305 TYR 0.021 0.002 TYR C 114 PHE 0.020 0.001 PHE C 238 TRP 0.013 0.001 TRP B 302 HIS 0.002 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00259 (14472) covalent geometry : angle 0.59967 (19724) hydrogen bonds : bond 0.04250 ( 488) hydrogen bonds : angle 4.14161 ( 1404) Misc. bond : bond 0.00101 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 296 time to evaluate : 0.509 Fit side-chains revert: symmetry clash REVERT: A 297 ASN cc_start: 0.8714 (t0) cc_final: 0.8468 (t0) REVERT: A 425 THR cc_start: 0.9187 (p) cc_final: 0.8928 (t) REVERT: A 442 GLU cc_start: 0.7050 (pm20) cc_final: 0.6398 (pm20) REVERT: B 60 ARG cc_start: 0.7834 (mtp180) cc_final: 0.7054 (mtm-85) REVERT: B 297 ASN cc_start: 0.8696 (t0) cc_final: 0.8446 (t0) REVERT: B 425 THR cc_start: 0.9244 (p) cc_final: 0.8977 (t) REVERT: B 442 GLU cc_start: 0.6995 (pm20) cc_final: 0.6407 (pm20) REVERT: C 60 ARG cc_start: 0.7839 (mtp180) cc_final: 0.7060 (mtm-85) REVERT: C 148 PHE cc_start: 0.7964 (m-80) cc_final: 0.7763 (m-80) REVERT: C 297 ASN cc_start: 0.8673 (t0) cc_final: 0.8443 (t0) REVERT: C 442 GLU cc_start: 0.6967 (pm20) cc_final: 0.6321 (pm20) REVERT: D 60 ARG cc_start: 0.7836 (mtp180) cc_final: 0.7063 (mtm-85) REVERT: D 148 PHE cc_start: 0.7957 (m-80) cc_final: 0.7757 (m-80) REVERT: D 297 ASN cc_start: 0.8678 (t0) cc_final: 0.8437 (t0) REVERT: D 425 THR cc_start: 0.9246 (p) cc_final: 0.8968 (t) REVERT: D 442 GLU cc_start: 0.6967 (pm20) cc_final: 0.6313 (pm20) outliers start: 29 outliers final: 23 residues processed: 323 average time/residue: 0.1132 time to fit residues: 54.5094 Evaluate side-chains 303 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 280 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 244 TRP Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 244 TRP Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 244 TRP Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 462 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 174 optimal weight: 5.9990 chunk 17 optimal weight: 5.9990 chunk 132 optimal weight: 6.9990 chunk 103 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 129 optimal weight: 2.9990 chunk 127 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 ASN A 374 ASN A 407 GLN B 374 ASN B 407 GLN C 284 ASN C 374 ASN C 407 GLN D 284 ASN D 374 ASN D 407 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.143879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.117654 restraints weight = 18148.273| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 1.93 r_work: 0.3197 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8044 moved from start: 0.2392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14480 Z= 0.181 Angle : 0.655 6.149 19724 Z= 0.348 Chirality : 0.047 0.181 2224 Planarity : 0.004 0.047 2452 Dihedral : 9.118 57.531 2124 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.22 % Favored : 87.56 % Rotamer: Outliers : 3.80 % Allowed : 16.62 % Favored : 79.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -3.15 (0.19), residues: 1768 helix: -1.61 (0.16), residues: 1032 sheet: None (None), residues: 0 loop : -2.71 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 305 TYR 0.025 0.002 TYR D 114 PHE 0.023 0.002 PHE C 140 TRP 0.012 0.001 TRP B 302 HIS 0.004 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00430 (14472) covalent geometry : angle 0.65481 (19724) hydrogen bonds : bond 0.04700 ( 488) hydrogen bonds : angle 4.19795 ( 1404) Misc. bond : bond 0.00117 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 348 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 295 time to evaluate : 0.514 Fit side-chains REVERT: A 76 ILE cc_start: 0.8643 (pt) cc_final: 0.8233 (mt) REVERT: A 425 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8894 (t) REVERT: B 76 ILE cc_start: 0.8605 (pt) cc_final: 0.8233 (mt) REVERT: B 425 THR cc_start: 0.9116 (OUTLIER) cc_final: 0.8885 (t) REVERT: B 442 GLU cc_start: 0.7293 (pm20) cc_final: 0.6535 (pm20) REVERT: B 464 LEU cc_start: 0.8422 (mp) cc_final: 0.8204 (mt) REVERT: C 76 ILE cc_start: 0.8655 (pt) cc_final: 0.8265 (mt) REVERT: C 148 PHE cc_start: 0.8039 (m-80) cc_final: 0.7733 (m-80) REVERT: C 425 THR cc_start: 0.9117 (OUTLIER) cc_final: 0.8885 (t) REVERT: C 464 LEU cc_start: 0.8462 (mp) cc_final: 0.8229 (mt) REVERT: D 76 ILE cc_start: 0.8597 (pt) cc_final: 0.8237 (mt) REVERT: D 148 PHE cc_start: 0.8023 (m-80) cc_final: 0.7719 (m-80) REVERT: D 425 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8873 (t) REVERT: D 442 GLU cc_start: 0.7286 (pm20) cc_final: 0.6532 (pm20) REVERT: D 464 LEU cc_start: 0.8446 (mp) cc_final: 0.8183 (mt) outliers start: 53 outliers final: 37 residues processed: 323 average time/residue: 0.1132 time to fit residues: 54.4783 Evaluate side-chains 327 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 286 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 244 TRP Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 433 GLN Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 433 GLN Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 244 TRP Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 433 GLN Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 244 TRP Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 433 GLN Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 462 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 59 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 129 optimal weight: 0.7980 chunk 175 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 87 optimal weight: 10.0000 chunk 52 optimal weight: 3.9990 chunk 118 optimal weight: 0.1980 chunk 111 optimal weight: 1.9990 chunk 142 optimal weight: 0.4980 chunk 127 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN B 374 ASN C 374 ASN D 374 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.146669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.120133 restraints weight = 17971.190| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.95 r_work: 0.3214 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14480 Z= 0.134 Angle : 0.612 8.645 19724 Z= 0.320 Chirality : 0.045 0.175 2224 Planarity : 0.004 0.045 2452 Dihedral : 8.881 58.241 2124 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.97 % Favored : 88.80 % Rotamer: Outliers : 4.08 % Allowed : 16.98 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.70 (0.20), residues: 1768 helix: -1.20 (0.16), residues: 1000 sheet: None (None), residues: 0 loop : -2.56 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 60 TYR 0.022 0.001 TYR C 114 PHE 0.024 0.001 PHE A 140 TRP 0.015 0.001 TRP B 302 HIS 0.003 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00310 (14472) covalent geometry : angle 0.61200 (19724) hydrogen bonds : bond 0.04038 ( 488) hydrogen bonds : angle 4.00948 ( 1404) Misc. bond : bond 0.00089 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 303 time to evaluate : 0.377 Fit side-chains REVERT: A 425 THR cc_start: 0.9112 (OUTLIER) cc_final: 0.8879 (t) REVERT: B 425 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8869 (t) REVERT: B 442 GLU cc_start: 0.7133 (pm20) cc_final: 0.6333 (pm20) REVERT: C 76 ILE cc_start: 0.8600 (pt) cc_final: 0.8290 (mt) REVERT: C 99 ASN cc_start: 0.8656 (t0) cc_final: 0.8439 (t0) REVERT: C 148 PHE cc_start: 0.8003 (m-80) cc_final: 0.7654 (m-80) REVERT: C 425 THR cc_start: 0.9111 (OUTLIER) cc_final: 0.8881 (t) REVERT: C 442 GLU cc_start: 0.7126 (pm20) cc_final: 0.6317 (pm20) REVERT: D 148 PHE cc_start: 0.7991 (m-80) cc_final: 0.7651 (m-80) REVERT: D 425 THR cc_start: 0.9102 (p) cc_final: 0.8864 (t) REVERT: D 442 GLU cc_start: 0.7137 (pm20) cc_final: 0.6320 (pm20) outliers start: 57 outliers final: 39 residues processed: 335 average time/residue: 0.1036 time to fit residues: 52.4077 Evaluate side-chains 329 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 287 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 244 TRP Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 244 TRP Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 244 TRP Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 462 THR Chi-restraints excluded: chain D residue 488 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 156 optimal weight: 0.5980 chunk 61 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 83 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 74 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 76 optimal weight: 4.9990 chunk 62 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN B 374 ASN C 374 ASN D 374 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.144948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.118645 restraints weight = 17949.925| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 1.93 r_work: 0.3201 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14480 Z= 0.153 Angle : 0.637 8.002 19724 Z= 0.329 Chirality : 0.046 0.176 2224 Planarity : 0.004 0.045 2452 Dihedral : 8.921 59.632 2124 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.60 % Favored : 88.18 % Rotamer: Outliers : 4.44 % Allowed : 16.98 % Favored : 78.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.67 (0.20), residues: 1768 helix: -1.02 (0.17), residues: 1004 sheet: None (None), residues: 0 loop : -2.80 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 60 TYR 0.023 0.002 TYR B 114 PHE 0.025 0.002 PHE D 140 TRP 0.013 0.001 TRP B 302 HIS 0.003 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00363 (14472) covalent geometry : angle 0.63707 (19724) hydrogen bonds : bond 0.04282 ( 488) hydrogen bonds : angle 4.01660 ( 1404) Misc. bond : bond 0.00089 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 283 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 76 ILE cc_start: 0.8609 (pt) cc_final: 0.8307 (mt) REVERT: A 425 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8884 (t) REVERT: B 60 ARG cc_start: 0.7919 (ttp-110) cc_final: 0.7663 (ttp-110) REVERT: B 76 ILE cc_start: 0.8630 (pt) cc_final: 0.8312 (mt) REVERT: B 99 ASN cc_start: 0.8645 (t0) cc_final: 0.8426 (t0) REVERT: B 425 THR cc_start: 0.9084 (OUTLIER) cc_final: 0.8861 (t) REVERT: C 76 ILE cc_start: 0.8627 (pt) cc_final: 0.8337 (mt) REVERT: C 99 ASN cc_start: 0.8603 (t0) cc_final: 0.8396 (t0) REVERT: C 148 PHE cc_start: 0.7992 (m-80) cc_final: 0.7606 (m-80) REVERT: C 425 THR cc_start: 0.9093 (OUTLIER) cc_final: 0.8872 (t) REVERT: D 60 ARG cc_start: 0.7945 (ttp-110) cc_final: 0.7666 (ttp-110) REVERT: D 76 ILE cc_start: 0.8641 (pt) cc_final: 0.8324 (mt) REVERT: D 99 ASN cc_start: 0.8618 (t0) cc_final: 0.8412 (t0) REVERT: D 148 PHE cc_start: 0.8000 (m-80) cc_final: 0.7628 (m-80) REVERT: D 425 THR cc_start: 0.9087 (OUTLIER) cc_final: 0.8866 (t) REVERT: D 464 LEU cc_start: 0.8372 (mp) cc_final: 0.8138 (mt) outliers start: 62 outliers final: 45 residues processed: 323 average time/residue: 0.1071 time to fit residues: 52.2927 Evaluate side-chains 328 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 279 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 244 TRP Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 244 TRP Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 244 TRP Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 462 THR Chi-restraints excluded: chain D residue 488 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 172 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 53 optimal weight: 0.0980 chunk 38 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 105 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 131 optimal weight: 10.0000 chunk 52 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 354 ASN A 374 ASN B 354 ASN B 374 ASN C 354 ASN C 374 ASN D 354 ASN D 374 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.147410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.121168 restraints weight = 17880.944| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.93 r_work: 0.3226 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3090 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.2894 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14480 Z= 0.126 Angle : 0.614 8.467 19724 Z= 0.313 Chirality : 0.044 0.167 2224 Planarity : 0.004 0.045 2452 Dihedral : 8.712 59.115 2124 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.43 % Favored : 88.35 % Rotamer: Outliers : 3.87 % Allowed : 17.62 % Favored : 78.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.41 (0.20), residues: 1768 helix: -0.79 (0.17), residues: 1008 sheet: None (None), residues: 0 loop : -2.73 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 60 TYR 0.022 0.001 TYR A 114 PHE 0.025 0.001 PHE A 140 TRP 0.012 0.001 TRP D 302 HIS 0.002 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00291 (14472) covalent geometry : angle 0.61360 (19724) hydrogen bonds : bond 0.03836 ( 488) hydrogen bonds : angle 3.89144 ( 1404) Misc. bond : bond 0.00076 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 278 time to evaluate : 0.506 Fit side-chains REVERT: A 60 ARG cc_start: 0.7766 (mtm-85) cc_final: 0.6883 (mtm-85) REVERT: A 99 ASN cc_start: 0.8570 (t0) cc_final: 0.8369 (t0) REVERT: A 297 ASN cc_start: 0.8783 (t0) cc_final: 0.8476 (t0) REVERT: A 425 THR cc_start: 0.9082 (OUTLIER) cc_final: 0.8871 (t) REVERT: A 442 GLU cc_start: 0.7148 (pm20) cc_final: 0.6546 (pm20) REVERT: B 60 ARG cc_start: 0.7972 (ttp-110) cc_final: 0.7655 (ttp-110) REVERT: B 297 ASN cc_start: 0.8797 (t0) cc_final: 0.8493 (t0) REVERT: B 425 THR cc_start: 0.9066 (OUTLIER) cc_final: 0.8856 (t) REVERT: C 297 ASN cc_start: 0.8803 (t0) cc_final: 0.8483 (t0) REVERT: C 425 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8859 (t) REVERT: C 442 GLU cc_start: 0.7154 (pm20) cc_final: 0.6555 (pm20) REVERT: D 60 ARG cc_start: 0.7933 (ttp-110) cc_final: 0.7620 (ttp-110) REVERT: D 148 PHE cc_start: 0.7988 (m-80) cc_final: 0.7598 (m-80) REVERT: D 297 ASN cc_start: 0.8804 (t0) cc_final: 0.8470 (t0) REVERT: D 425 THR cc_start: 0.9075 (OUTLIER) cc_final: 0.8872 (t) outliers start: 54 outliers final: 45 residues processed: 313 average time/residue: 0.1102 time to fit residues: 51.9211 Evaluate side-chains 315 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 266 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 244 TRP Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 244 TRP Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 244 TRP Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 462 THR Chi-restraints excluded: chain D residue 488 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 109 optimal weight: 2.9990 chunk 131 optimal weight: 7.9990 chunk 39 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 48 optimal weight: 0.1980 chunk 112 optimal weight: 0.8980 chunk 149 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 163 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 374 ASN B 99 ASN B 374 ASN C 99 ASN C 374 ASN D 99 ASN D 374 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.147153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.120751 restraints weight = 17862.354| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.93 r_work: 0.3222 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14480 Z= 0.124 Angle : 0.608 8.050 19724 Z= 0.310 Chirality : 0.044 0.165 2224 Planarity : 0.004 0.044 2452 Dihedral : 8.638 59.039 2124 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.31 % Favored : 88.46 % Rotamer: Outliers : 4.15 % Allowed : 17.84 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.23 (0.20), residues: 1768 helix: -0.59 (0.17), residues: 1004 sheet: None (None), residues: 0 loop : -2.72 (0.23), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 60 TYR 0.021 0.001 TYR C 114 PHE 0.025 0.001 PHE D 140 TRP 0.011 0.001 TRP B 302 HIS 0.003 0.001 HIS A 431 Details of bonding type rmsd covalent geometry : bond 0.00287 (14472) covalent geometry : angle 0.60777 (19724) hydrogen bonds : bond 0.03831 ( 488) hydrogen bonds : angle 3.84426 ( 1404) Misc. bond : bond 0.00084 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 266 time to evaluate : 0.552 Fit side-chains revert: symmetry clash REVERT: A 60 ARG cc_start: 0.7760 (mtm-85) cc_final: 0.6942 (mtm-85) REVERT: A 297 ASN cc_start: 0.8790 (t0) cc_final: 0.8455 (t0) REVERT: A 425 THR cc_start: 0.9080 (OUTLIER) cc_final: 0.8862 (t) REVERT: A 442 GLU cc_start: 0.7128 (pm20) cc_final: 0.6539 (pm20) REVERT: B 60 ARG cc_start: 0.7991 (ttp-110) cc_final: 0.7687 (ttp-110) REVERT: B 297 ASN cc_start: 0.8793 (t0) cc_final: 0.8499 (t0) REVERT: B 425 THR cc_start: 0.9072 (OUTLIER) cc_final: 0.8857 (t) REVERT: B 442 GLU cc_start: 0.7076 (pm20) cc_final: 0.6517 (pm20) REVERT: C 297 ASN cc_start: 0.8811 (t0) cc_final: 0.8495 (t0) REVERT: C 425 THR cc_start: 0.9063 (OUTLIER) cc_final: 0.8856 (t) REVERT: C 442 GLU cc_start: 0.7053 (pm20) cc_final: 0.6465 (pm20) REVERT: D 60 ARG cc_start: 0.7955 (ttp-110) cc_final: 0.7638 (ttp-110) REVERT: D 297 ASN cc_start: 0.8803 (t0) cc_final: 0.8475 (t0) REVERT: D 425 THR cc_start: 0.9067 (OUTLIER) cc_final: 0.8860 (t) REVERT: D 442 GLU cc_start: 0.7147 (pm20) cc_final: 0.6519 (pm20) outliers start: 58 outliers final: 47 residues processed: 305 average time/residue: 0.1097 time to fit residues: 50.1762 Evaluate side-chains 313 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 262 time to evaluate : 0.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 244 TRP Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 167 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 244 TRP Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 244 TRP Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 462 THR Chi-restraints excluded: chain D residue 488 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 68 optimal weight: 1.9990 chunk 128 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 135 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 104 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 125 optimal weight: 1.9990 chunk 1 optimal weight: 0.5980 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 374 ASN B 99 ASN B 374 ASN C 99 ASN C 374 ASN D 99 ASN D 374 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.149063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.122711 restraints weight = 17838.812| |-----------------------------------------------------------------------------| r_work (start): 0.3351 rms_B_bonded: 1.94 r_work: 0.3242 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14480 Z= 0.114 Angle : 0.603 9.886 19724 Z= 0.303 Chirality : 0.044 0.162 2224 Planarity : 0.004 0.044 2452 Dihedral : 8.436 59.268 2124 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.52 % Favored : 89.25 % Rotamer: Outliers : 4.15 % Allowed : 18.48 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -2.00 (0.21), residues: 1768 helix: -0.39 (0.17), residues: 1008 sheet: None (None), residues: 0 loop : -2.67 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 60 TYR 0.020 0.001 TYR A 114 PHE 0.027 0.001 PHE A 140 TRP 0.011 0.001 TRP C 302 HIS 0.002 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00260 (14472) covalent geometry : angle 0.60316 (19724) hydrogen bonds : bond 0.03597 ( 488) hydrogen bonds : angle 3.76928 ( 1404) Misc. bond : bond 0.00084 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 272 time to evaluate : 0.501 Fit side-chains REVERT: A 60 ARG cc_start: 0.7771 (mtm-85) cc_final: 0.6938 (mtm-85) REVERT: A 297 ASN cc_start: 0.8753 (t0) cc_final: 0.8448 (t0) REVERT: A 425 THR cc_start: 0.9087 (OUTLIER) cc_final: 0.8885 (t) REVERT: A 442 GLU cc_start: 0.6963 (pm20) cc_final: 0.6339 (pm20) REVERT: B 60 ARG cc_start: 0.8018 (ttp-110) cc_final: 0.7706 (ttp-110) REVERT: B 297 ASN cc_start: 0.8769 (t0) cc_final: 0.8464 (t0) REVERT: B 425 THR cc_start: 0.9059 (OUTLIER) cc_final: 0.8850 (t) REVERT: B 442 GLU cc_start: 0.6963 (pm20) cc_final: 0.6337 (pm20) REVERT: C 297 ASN cc_start: 0.8767 (t0) cc_final: 0.8445 (t0) REVERT: C 425 THR cc_start: 0.9043 (OUTLIER) cc_final: 0.8836 (t) REVERT: C 442 GLU cc_start: 0.6950 (pm20) cc_final: 0.6333 (pm20) REVERT: D 60 ARG cc_start: 0.7939 (ttp-110) cc_final: 0.7624 (ttp-110) REVERT: D 297 ASN cc_start: 0.8772 (t0) cc_final: 0.8437 (t0) REVERT: D 425 THR cc_start: 0.9070 (OUTLIER) cc_final: 0.8865 (t) REVERT: D 442 GLU cc_start: 0.6872 (pm20) cc_final: 0.6184 (pm20) outliers start: 58 outliers final: 49 residues processed: 313 average time/residue: 0.1028 time to fit residues: 48.4129 Evaluate side-chains 317 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 264 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 244 TRP Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 425 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 99 ASN Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 244 TRP Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 425 THR Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 99 ASN Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 244 TRP Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 462 THR Chi-restraints excluded: chain D residue 488 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 12 optimal weight: 0.4980 chunk 88 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 132 optimal weight: 6.9990 chunk 140 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 135 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 284 ASN A 374 ASN B 99 ASN B 374 ASN C 99 ASN C 374 ASN D 99 ASN D 374 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.149153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.122762 restraints weight = 17879.418| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.94 r_work: 0.3244 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14480 Z= 0.114 Angle : 0.602 9.821 19724 Z= 0.302 Chirality : 0.043 0.161 2224 Planarity : 0.004 0.044 2452 Dihedral : 8.397 59.552 2124 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.71 % Favored : 88.07 % Rotamer: Outliers : 4.01 % Allowed : 18.34 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.87 (0.21), residues: 1768 helix: -0.30 (0.17), residues: 1012 sheet: None (None), residues: 0 loop : -2.60 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 60 TYR 0.020 0.001 TYR B 114 PHE 0.026 0.001 PHE C 140 TRP 0.010 0.001 TRP D 302 HIS 0.002 0.001 HIS D 301 Details of bonding type rmsd covalent geometry : bond 0.00259 (14472) covalent geometry : angle 0.60207 (19724) hydrogen bonds : bond 0.03586 ( 488) hydrogen bonds : angle 3.74708 ( 1404) Misc. bond : bond 0.00080 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3536 Ramachandran restraints generated. 1768 Oldfield, 0 Emsley, 1768 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 258 time to evaluate : 0.446 Fit side-chains REVERT: A 60 ARG cc_start: 0.7714 (mtm-85) cc_final: 0.6878 (mtm-85) REVERT: A 297 ASN cc_start: 0.8759 (t0) cc_final: 0.8466 (t0) REVERT: A 425 THR cc_start: 0.9095 (OUTLIER) cc_final: 0.8890 (t) REVERT: A 442 GLU cc_start: 0.6979 (pm20) cc_final: 0.6367 (pm20) REVERT: B 60 ARG cc_start: 0.8022 (ttp-110) cc_final: 0.7712 (ttp-110) REVERT: B 297 ASN cc_start: 0.8769 (t0) cc_final: 0.8471 (t0) REVERT: B 425 THR cc_start: 0.9067 (p) cc_final: 0.8856 (t) REVERT: B 442 GLU cc_start: 0.6994 (pm20) cc_final: 0.6380 (pm20) REVERT: C 297 ASN cc_start: 0.8767 (t0) cc_final: 0.8446 (t0) REVERT: C 425 THR cc_start: 0.9047 (p) cc_final: 0.8837 (t) REVERT: C 442 GLU cc_start: 0.6973 (pm20) cc_final: 0.6366 (pm20) REVERT: D 60 ARG cc_start: 0.8012 (ttp-110) cc_final: 0.7685 (ttp-110) REVERT: D 297 ASN cc_start: 0.8769 (t0) cc_final: 0.8443 (t0) REVERT: D 425 THR cc_start: 0.9057 (OUTLIER) cc_final: 0.8857 (t) REVERT: D 442 GLU cc_start: 0.6885 (pm20) cc_final: 0.6251 (pm20) outliers start: 56 outliers final: 47 residues processed: 299 average time/residue: 0.1087 time to fit residues: 48.4858 Evaluate side-chains 306 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 257 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 69 LEU Chi-restraints excluded: chain A residue 99 ASN Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 234 VAL Chi-restraints excluded: chain A residue 244 TRP Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 351 THR Chi-restraints excluded: chain A residue 425 THR Chi-restraints excluded: chain A residue 426 VAL Chi-restraints excluded: chain A residue 459 VAL Chi-restraints excluded: chain A residue 462 THR Chi-restraints excluded: chain A residue 488 VAL Chi-restraints excluded: chain B residue 52 ILE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 167 LEU Chi-restraints excluded: chain B residue 234 VAL Chi-restraints excluded: chain B residue 244 TRP Chi-restraints excluded: chain B residue 254 SER Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 426 VAL Chi-restraints excluded: chain B residue 459 VAL Chi-restraints excluded: chain B residue 462 THR Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain C residue 52 ILE Chi-restraints excluded: chain C residue 69 LEU Chi-restraints excluded: chain C residue 234 VAL Chi-restraints excluded: chain C residue 244 TRP Chi-restraints excluded: chain C residue 254 SER Chi-restraints excluded: chain C residue 351 THR Chi-restraints excluded: chain C residue 426 VAL Chi-restraints excluded: chain C residue 459 VAL Chi-restraints excluded: chain C residue 462 THR Chi-restraints excluded: chain C residue 488 VAL Chi-restraints excluded: chain D residue 52 ILE Chi-restraints excluded: chain D residue 69 LEU Chi-restraints excluded: chain D residue 234 VAL Chi-restraints excluded: chain D residue 244 TRP Chi-restraints excluded: chain D residue 254 SER Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 425 THR Chi-restraints excluded: chain D residue 426 VAL Chi-restraints excluded: chain D residue 459 VAL Chi-restraints excluded: chain D residue 462 THR Chi-restraints excluded: chain D residue 488 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 155 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 150 optimal weight: 0.2980 chunk 154 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 167 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 160 optimal weight: 0.8980 chunk 157 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN A 374 ASN B 99 ASN B 374 ASN C 99 ASN C 374 ASN D 99 ASN D 374 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.149907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.123911 restraints weight = 17749.961| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 1.90 r_work: 0.3253 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3120 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.3202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14480 Z= 0.112 Angle : 0.598 9.749 19724 Z= 0.300 Chirality : 0.043 0.159 2224 Planarity : 0.004 0.044 2452 Dihedral : 8.343 58.642 2124 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.09 % Favored : 88.69 % Rotamer: Outliers : 3.87 % Allowed : 18.70 % Favored : 77.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.79 (0.21), residues: 1768 helix: -0.18 (0.17), residues: 988 sheet: None (None), residues: 0 loop : -2.58 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 60 TYR 0.020 0.001 TYR C 114 PHE 0.025 0.001 PHE A 140 TRP 0.010 0.001 TRP D 302 HIS 0.002 0.001 HIS C 301 Details of bonding type rmsd covalent geometry : bond 0.00254 (14472) covalent geometry : angle 0.59840 (19724) hydrogen bonds : bond 0.03546 ( 488) hydrogen bonds : angle 3.72103 ( 1404) Misc. bond : bond 0.00083 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3436.07 seconds wall clock time: 59 minutes 22.79 seconds (3562.79 seconds total)