Starting phenix.real_space_refine on Sat Sep 12 06:09:25 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7cal_30334/09_2026/7cal_30334.cif Found real_map, /net/cci-nas-00/data/ceres_data/7cal_30334/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7cal_30334/09_2026/7cal_30334.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7cal_30334/09_2026/7cal_30334.cif" model { file = "/net/cci-nas-00/data/ceres_data/7cal_30334/09_2026/7cal_30334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7cal_30334/09_2026/7cal_30334.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7cal_30334/09_2026/7cal_30334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7cal_30334/09_2026/7cal_30334.map" } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/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: 3.18, per 1000 atoms: 0.23 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: 1.22 Conformation dependent library (CDL) restraints added in 688.1 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: 2.00 Time building geometry restraints manager: 1.59 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 - 15.26: 7203 15.26 - 30.52: 888 30.52 - 45.78: 203 45.78 - 61.04: 42 61.04 - 76.30: 8 Dihedral angle restraints: 8344 sinusoidal: 3088 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 8341 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: 0.05 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: 1.430 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: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.970 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 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 : 14.516 76.300 4936 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/Z covalent geometry : bond 0.00747 / 0.33 (14472) covalent geometry : angle 1.09208 / 0.60 (19724) hydrogen bonds : bond 0.34895 / 22.26 ( 488) hydrogen bonds : angle 10.42048 / 7.23 ( 1404) Misc. bond : bond 0.00248 / 0.11 ( 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 : 0.566 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: 0.1277 time to fit residues: 57.2867 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 : 0.521 ------------------------------------------------------------------------------- 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... A 294 ASN A 301 HIS A 348 GLN A 365 ASN A 491 ASN B 294 ASN B 301 HIS 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: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.147819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.121378 restraints weight = 17748.133| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 2.11 r_work: 0.3228 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14480 Z= 0.141 Angle : 0.666 5.965 19724 Z= 0.359 Chirality : 0.046 0.177 2224 Planarity : 0.006 0.050 2452 Dihedral : 8.628 59.679 2076 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.60 % Favored : 88.18 % 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: -4.42 (0.17), residues: 1768 helix: -2.90 (0.13), residues: 964 sheet: None (None), residues: 0 loop : -2.89 (0.21), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 305 TYR 0.026 0.002 TYR C 114 PHE 0.022 0.002 PHE B 238 TRP 0.017 0.002 TRP D 62 HIS 0.003 0.001 HIS A 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (14472) covalent geometry : angle 0.66574 / 0.36 (19724) hydrogen bonds : bond 0.05494 / 3.51 ( 488) hydrogen bonds : angle 4.80217 / 3.28 ( 1404) Misc. bond : bond 0.00089 / 0.04 ( 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 325 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 300 time to evaluate : 0.430 Fit side-chains revert: symmetry clash REVERT: A 133 TYR cc_start: 0.8414 (t80) cc_final: 0.8024 (t80) REVERT: A 297 ASN cc_start: 0.8756 (t0) cc_final: 0.8499 (t0) REVERT: A 442 GLU cc_start: 0.7117 (pm20) cc_final: 0.6439 (pm20) REVERT: B 60 ARG cc_start: 0.7832 (mtp180) cc_final: 0.7036 (mtm-85) REVERT: B 297 ASN cc_start: 0.8766 (t0) cc_final: 0.8497 (t0) REVERT: B 442 GLU cc_start: 0.7138 (pm20) cc_final: 0.6467 (pm20) REVERT: B 464 LEU cc_start: 0.8517 (mp) cc_final: 0.8281 (mt) REVERT: C 60 ARG cc_start: 0.7823 (mtp180) cc_final: 0.7021 (mtm-85) REVERT: C 76 ILE cc_start: 0.8561 (pt) cc_final: 0.8119 (mt) REVERT: C 297 ASN cc_start: 0.8724 (t0) cc_final: 0.8480 (t0) REVERT: C 442 GLU cc_start: 0.7061 (pm20) cc_final: 0.6345 (pm20) REVERT: C 464 LEU cc_start: 0.8550 (mp) cc_final: 0.7797 (mp) REVERT: D 60 ARG cc_start: 0.7822 (mtp180) cc_final: 0.7024 (mtm-85) REVERT: D 297 ASN cc_start: 0.8717 (t0) cc_final: 0.8479 (t0) REVERT: D 442 GLU cc_start: 0.7034 (pm20) cc_final: 0.6329 (pm20) REVERT: D 464 LEU cc_start: 0.8546 (mp) cc_final: 0.8294 (mt) outliers start: 25 outliers final: 21 residues processed: 317 average time/residue: 0.1055 time to fit residues: 50.1392 Evaluate side-chains 303 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 282 time to evaluate : 0.322 ------------------------------------------------------------------------------- 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: 9.9990 chunk 16 optimal weight: 2.9990 chunk 146 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 137 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 118 optimal weight: 0.4980 chunk 110 optimal weight: 0.7980 chunk 83 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 284 ASN A 374 ASN A 407 GLN A 482 HIS B 284 ASN B 324 GLN B 374 ASN B 407 GLN C 407 GLN C 482 HIS D 407 GLN D 482 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.148976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.123410 restraints weight = 17869.210| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.86 r_work: 0.3230 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.2285 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= 0.136 Angle : 0.625 6.469 19724 Z= 0.329 Chirality : 0.045 0.177 2224 Planarity : 0.005 0.047 2452 Dihedral : 7.926 55.052 2076 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.43 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.65 % Favored : 88.12 % Rotamer: Outliers : 2.58 % Allowed : 15.83 % Favored : 81.59 % 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: -3.40 (0.19), residues: 1768 helix: -1.85 (0.16), residues: 996 sheet: None (None), residues: 0 loop : -2.75 (0.22), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 305 TYR 0.023 0.002 TYR C 114 PHE 0.021 0.001 PHE B 238 TRP 0.015 0.001 TRP B 302 HIS 0.008 0.001 HIS D 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 (14472) covalent geometry : angle 0.62519 / 0.33 (19724) hydrogen bonds : bond 0.04579 / 2.94 ( 488) hydrogen bonds : angle 4.25266 / 2.90 ( 1404) Misc. bond : bond 0.00112 / 0.06 ( 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 327 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 291 time to evaluate : 0.554 Fit side-chains revert: symmetry clash REVERT: A 133 TYR cc_start: 0.8481 (t80) cc_final: 0.8186 (t80) REVERT: A 297 ASN cc_start: 0.8748 (t0) cc_final: 0.8489 (t0) REVERT: A 442 GLU cc_start: 0.7186 (pm20) cc_final: 0.6549 (pm20) REVERT: B 60 ARG cc_start: 0.7844 (mtp180) cc_final: 0.7077 (mtm-85) REVERT: B 297 ASN cc_start: 0.8761 (t0) cc_final: 0.8509 (t0) REVERT: B 442 GLU cc_start: 0.7142 (pm20) cc_final: 0.6502 (pm20) REVERT: C 60 ARG cc_start: 0.7843 (mtp180) cc_final: 0.7087 (mtm-85) REVERT: C 297 ASN cc_start: 0.8724 (t0) cc_final: 0.8494 (t0) REVERT: C 442 GLU cc_start: 0.7124 (pm20) cc_final: 0.6436 (pm20) REVERT: D 60 ARG cc_start: 0.7877 (mtp180) cc_final: 0.7143 (mtm-85) REVERT: D 297 ASN cc_start: 0.8729 (t0) cc_final: 0.8488 (t0) REVERT: D 442 GLU cc_start: 0.7071 (pm20) cc_final: 0.6395 (pm20) outliers start: 36 outliers final: 30 residues processed: 314 average time/residue: 0.1161 time to fit residues: 54.4786 Evaluate side-chains 310 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 280 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 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 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 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 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 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 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 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: 9.9990 chunk 17 optimal weight: 3.9990 chunk 132 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 129 optimal weight: 1.9990 chunk 127 optimal weight: 0.0070 chunk 9 optimal weight: 0.0000 chunk 88 optimal weight: 6.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.7004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 ASN B 374 ASN C 284 ASN C 374 ASN D 284 ASN D 374 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.152506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.127244 restraints weight = 17733.541| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 1.84 r_work: 0.3267 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3139 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3139 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2594 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= 0.112 Angle : 0.576 5.869 19724 Z= 0.303 Chirality : 0.044 0.166 2224 Planarity : 0.004 0.045 2452 Dihedral : 7.436 53.458 2076 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.37 % Favored : 88.40 % Rotamer: Outliers : 3.01 % Allowed : 17.12 % Favored : 79.87 % 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: -2.85 (0.20), residues: 1768 helix: -1.35 (0.16), residues: 996 sheet: None (None), residues: 0 loop : -2.58 (0.23), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 305 TYR 0.020 0.001 TYR A 114 PHE 0.025 0.001 PHE C 140 TRP 0.013 0.001 TRP B 302 HIS 0.002 0.001 HIS C 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 (14472) covalent geometry : angle 0.57619 / 0.30 (19724) hydrogen bonds : bond 0.03773 / 2.42 ( 488) hydrogen bonds : angle 4.00133 / 2.75 ( 1404) Misc. bond : bond 0.00118 / 0.06 ( 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 334 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 292 time to evaluate : 0.548 Fit side-chains REVERT: A 133 TYR cc_start: 0.8428 (t80) cc_final: 0.8137 (t80) REVERT: A 297 ASN cc_start: 0.8697 (t0) cc_final: 0.8472 (t0) REVERT: A 425 THR cc_start: 0.9098 (OUTLIER) cc_final: 0.8880 (t) REVERT: A 442 GLU cc_start: 0.7084 (pm20) cc_final: 0.6415 (pm20) REVERT: B 297 ASN cc_start: 0.8696 (t0) cc_final: 0.8454 (t0) REVERT: B 425 THR cc_start: 0.9105 (OUTLIER) cc_final: 0.8891 (t) REVERT: B 442 GLU cc_start: 0.7005 (pm20) cc_final: 0.6343 (pm20) REVERT: C 425 THR cc_start: 0.9098 (OUTLIER) cc_final: 0.8881 (t) REVERT: C 442 GLU cc_start: 0.7001 (pm20) cc_final: 0.6335 (pm20) REVERT: D 425 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8878 (t) REVERT: D 442 GLU cc_start: 0.6985 (pm20) cc_final: 0.6332 (pm20) REVERT: D 464 LEU cc_start: 0.8263 (mp) cc_final: 0.7447 (mp) outliers start: 42 outliers final: 29 residues processed: 321 average time/residue: 0.1078 time to fit residues: 52.4667 Evaluate side-chains 304 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 271 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 D residue 52 ILE 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 59 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 129 optimal weight: 1.9990 chunk 175 optimal weight: 0.8980 chunk 124 optimal weight: 0.7980 chunk 87 optimal weight: 9.9990 chunk 52 optimal weight: 1.9990 chunk 118 optimal weight: 3.9990 chunk 111 optimal weight: 0.0570 chunk 142 optimal weight: 6.9990 chunk 127 optimal weight: 0.9990 overall best weight: 0.7300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 354 ASN A 374 ASN B 354 ASN B 374 ASN C 297 ASN C 374 ASN D 297 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 = 0.3731 r_free = 0.3731 target = 0.151776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.126217 restraints weight = 17704.759| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 1.86 r_work: 0.3266 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2807 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= 0.113 Angle : 0.592 8.370 19724 Z= 0.307 Chirality : 0.044 0.164 2224 Planarity : 0.004 0.045 2452 Dihedral : 7.165 55.827 2076 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 3.99 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.75 % Favored : 89.03 % Rotamer: Outliers : 4.51 % Allowed : 16.69 % Favored : 78.80 % 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: -2.65 (0.20), residues: 1768 helix: -1.12 (0.16), residues: 1032 sheet: None (None), residues: 0 loop : -2.64 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 60 TYR 0.021 0.001 TYR B 114 PHE 0.024 0.001 PHE A 140 TRP 0.011 0.001 TRP A 302 HIS 0.002 0.001 HIS A 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.11 (14472) covalent geometry : angle 0.59151 / 0.31 (19724) hydrogen bonds : bond 0.03727 / 2.40 ( 488) hydrogen bonds : angle 3.85022 / 2.64 ( 1404) Misc. bond : bond 0.00085 / 0.04 ( 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 353 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 290 time to evaluate : 0.442 Fit side-chains REVERT: A 99 ASN cc_start: 0.8620 (t0) cc_final: 0.8413 (t0) REVERT: A 297 ASN cc_start: 0.8703 (t0) cc_final: 0.8465 (t0) REVERT: A 425 THR cc_start: 0.9103 (OUTLIER) cc_final: 0.8873 (t) REVERT: A 442 GLU cc_start: 0.6993 (pm20) cc_final: 0.6258 (pm20) REVERT: B 60 ARG cc_start: 0.7898 (ttp-110) cc_final: 0.7118 (mtm-85) REVERT: B 99 ASN cc_start: 0.8590 (t0) cc_final: 0.8379 (t0) REVERT: B 297 ASN cc_start: 0.8704 (t0) cc_final: 0.8454 (t0) REVERT: B 425 THR cc_start: 0.9090 (OUTLIER) cc_final: 0.8865 (t) REVERT: B 442 GLU cc_start: 0.6948 (pm20) cc_final: 0.6197 (pm20) REVERT: C 60 ARG cc_start: 0.7948 (ttp-110) cc_final: 0.7709 (ttp-110) REVERT: C 425 THR cc_start: 0.9101 (OUTLIER) cc_final: 0.8866 (t) REVERT: C 442 GLU cc_start: 0.6914 (pm20) cc_final: 0.6178 (pm20) REVERT: D 60 ARG cc_start: 0.7991 (ttp-110) cc_final: 0.7753 (ttp-110) REVERT: D 425 THR cc_start: 0.9083 (OUTLIER) cc_final: 0.8878 (t) REVERT: D 442 GLU cc_start: 0.6925 (pm20) cc_final: 0.6126 (pm20) outliers start: 63 outliers final: 37 residues processed: 324 average time/residue: 0.1093 time to fit residues: 52.9103 Evaluate side-chains 316 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 275 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 247 TYR 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 247 TYR 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 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 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 176 random chunks: chunk 156 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 74 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 104 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 ASN B 374 ASN C 297 ASN C 374 ASN D 297 ASN D 374 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.145892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.120124 restraints weight = 17878.914| |-----------------------------------------------------------------------------| r_work (start): 0.3322 rms_B_bonded: 1.88 r_work: 0.3212 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3079 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14480 Z= 0.165 Angle : 0.646 8.293 19724 Z= 0.335 Chirality : 0.046 0.170 2224 Planarity : 0.004 0.046 2452 Dihedral : 7.590 58.278 2076 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.65 % Favored : 88.12 % Rotamer: Outliers : 4.01 % Allowed : 17.69 % Favored : 78.30 % 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: -2.60 (0.20), residues: 1768 helix: -1.05 (0.16), residues: 1024 sheet: None (None), residues: 0 loop : -2.68 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 60 TYR 0.022 0.002 TYR B 114 PHE 0.025 0.002 PHE C 140 TRP 0.011 0.001 TRP D 62 HIS 0.003 0.001 HIS D 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.16 (14472) covalent geometry : angle 0.64570 / 0.33 (19724) hydrogen bonds : bond 0.04472 / 2.86 ( 488) hydrogen bonds : angle 4.00384 / 2.75 ( 1404) Misc. bond : bond 0.00083 / 0.04 ( 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 342 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 286 time to evaluate : 0.503 Fit side-chains revert: symmetry clash REVERT: A 76 ILE cc_start: 0.8677 (pt) cc_final: 0.8329 (mt) REVERT: A 99 ASN cc_start: 0.8608 (t0) cc_final: 0.8407 (t0) REVERT: A 297 ASN cc_start: 0.8806 (t0) cc_final: 0.8598 (t0) REVERT: A 302 TRP cc_start: 0.7007 (m100) cc_final: 0.6748 (m100) REVERT: A 425 THR cc_start: 0.9104 (OUTLIER) cc_final: 0.8887 (t) REVERT: B 60 ARG cc_start: 0.7934 (ttp-110) cc_final: 0.7634 (ttp-110) REVERT: B 76 ILE cc_start: 0.8688 (pt) cc_final: 0.8337 (mt) REVERT: B 302 TRP cc_start: 0.6991 (m100) cc_final: 0.6732 (m100) REVERT: B 425 THR cc_start: 0.9088 (OUTLIER) cc_final: 0.8870 (t) REVERT: C 60 ARG cc_start: 0.7917 (ttp-110) cc_final: 0.7613 (ttp-110) REVERT: C 76 ILE cc_start: 0.8675 (pt) cc_final: 0.8358 (mt) REVERT: C 324 GLN cc_start: 0.8754 (mt0) cc_final: 0.8536 (mp10) REVERT: C 425 THR cc_start: 0.9085 (OUTLIER) cc_final: 0.8867 (t) REVERT: D 60 ARG cc_start: 0.7933 (ttp-110) cc_final: 0.7624 (ttp-110) REVERT: D 76 ILE cc_start: 0.8694 (pt) cc_final: 0.8366 (mt) REVERT: D 324 GLN cc_start: 0.8751 (mt0) cc_final: 0.8532 (mp10) REVERT: D 425 THR cc_start: 0.9094 (OUTLIER) cc_final: 0.8881 (t) outliers start: 56 outliers final: 39 residues processed: 319 average time/residue: 0.1079 time to fit residues: 52.3422 Evaluate side-chains 328 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 285 time to evaluate : 0.525 ------------------------------------------------------------------------------- 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 254 SER 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 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 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 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 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 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: 1.9990 chunk 171 optimal weight: 2.9990 chunk 77 optimal weight: 0.1980 chunk 53 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 87 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 131 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 ASN B 99 ASN B 374 ASN C 99 ASN C 354 ASN C 374 ASN D 99 ASN D 354 ASN D 374 ASN D 482 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.147962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.121771 restraints weight = 17852.210| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.92 r_work: 0.3225 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2896 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= 0.127 Angle : 0.598 7.838 19724 Z= 0.310 Chirality : 0.045 0.167 2224 Planarity : 0.004 0.045 2452 Dihedral : 7.391 59.998 2076 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.14 % Favored : 88.63 % Rotamer: Outliers : 4.51 % Allowed : 17.55 % Favored : 77.94 % 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: -2.24 (0.20), residues: 1768 helix: -0.75 (0.17), residues: 1012 sheet: None (None), residues: 0 loop : -2.50 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 60 TYR 0.022 0.001 TYR C 114 PHE 0.026 0.001 PHE A 140 TRP 0.013 0.001 TRP A 302 HIS 0.015 0.001 HIS D 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (14472) covalent geometry : angle 0.59762 / 0.31 (19724) hydrogen bonds : bond 0.03907 / 2.51 ( 488) hydrogen bonds : angle 3.87521 / 2.66 ( 1404) Misc. bond : bond 0.00074 / 0.04 ( 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 343 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 280 time to evaluate : 0.556 Fit side-chains REVERT: A 60 ARG cc_start: 0.7732 (mtm-85) cc_final: 0.6950 (mtm-85) REVERT: A 99 ASN cc_start: 0.8540 (t0) cc_final: 0.8335 (t0) REVERT: A 297 ASN cc_start: 0.8760 (t0) cc_final: 0.8488 (t0) REVERT: A 425 THR cc_start: 0.9123 (OUTLIER) cc_final: 0.8900 (t) REVERT: B 60 ARG cc_start: 0.7925 (ttp-110) cc_final: 0.7626 (ttp-110) REVERT: B 425 THR cc_start: 0.9125 (OUTLIER) cc_final: 0.8904 (t) REVERT: C 60 ARG cc_start: 0.7941 (ttp-110) cc_final: 0.7619 (ttp-110) REVERT: C 425 THR cc_start: 0.9108 (OUTLIER) cc_final: 0.8882 (t) REVERT: D 60 ARG cc_start: 0.7966 (ttp-110) cc_final: 0.7637 (ttp-110) REVERT: D 324 GLN cc_start: 0.8700 (mt0) cc_final: 0.8483 (mp10) REVERT: D 425 THR cc_start: 0.9115 (OUTLIER) cc_final: 0.8893 (t) outliers start: 63 outliers final: 43 residues processed: 323 average time/residue: 0.1112 time to fit residues: 54.4506 Evaluate side-chains 319 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 272 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 69 LEU 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 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 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 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 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: 3.9990 chunk 131 optimal weight: 8.9990 chunk 39 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 112 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 38 optimal weight: 9.9990 chunk 163 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 374 ASN B 99 ASN B 297 ASN B 374 ASN C 99 ASN C 297 ASN C 324 GLN C 374 ASN D 99 ASN D 297 ASN D 324 GLN D 374 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.141484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.115232 restraints weight = 18092.891| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 1.93 r_work: 0.3150 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 14480 Z= 0.228 Angle : 0.710 11.519 19724 Z= 0.366 Chirality : 0.049 0.186 2224 Planarity : 0.005 0.048 2452 Dihedral : 8.016 59.899 2076 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.23 % Allowed : 12.73 % Favored : 87.05 % Rotamer: Outliers : 4.23 % Allowed : 18.27 % Favored : 77.51 % 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: -2.54 (0.20), residues: 1768 helix: -0.95 (0.16), residues: 1024 sheet: None (None), residues: 0 loop : -2.74 (0.23), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 60 TYR 0.025 0.002 TYR D 114 PHE 0.025 0.002 PHE C 140 TRP 0.009 0.002 TRP A 302 HIS 0.004 0.001 HIS B 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.23 (14472) covalent geometry : angle 0.71015 / 0.37 (19724) hydrogen bonds : bond 0.04963 / 3.18 ( 488) hydrogen bonds : angle 4.14585 / 2.86 ( 1404) Misc. bond : bond 0.00119 / 0.06 ( 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 343 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 284 time to evaluate : 0.527 Fit side-chains REVERT: A 60 ARG cc_start: 0.7828 (mtm-85) cc_final: 0.7046 (mtm-85) REVERT: A 76 ILE cc_start: 0.8670 (pt) cc_final: 0.8343 (mt) REVERT: A 302 TRP cc_start: 0.7107 (m100) cc_final: 0.6881 (m100) REVERT: A 425 THR cc_start: 0.9130 (OUTLIER) cc_final: 0.8903 (t) REVERT: A 464 LEU cc_start: 0.8537 (mp) cc_final: 0.8327 (mt) REVERT: B 60 ARG cc_start: 0.7956 (ttp-110) cc_final: 0.7648 (ttp-110) REVERT: B 76 ILE cc_start: 0.8646 (pt) cc_final: 0.8331 (mt) REVERT: B 302 TRP cc_start: 0.7094 (m100) cc_final: 0.6883 (m100) REVERT: B 425 THR cc_start: 0.9130 (OUTLIER) cc_final: 0.8904 (t) REVERT: C 60 ARG cc_start: 0.7922 (ttp-110) cc_final: 0.7599 (ttp-110) REVERT: C 76 ILE cc_start: 0.8661 (pt) cc_final: 0.8341 (mt) REVERT: C 425 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8893 (t) REVERT: D 60 ARG cc_start: 0.7932 (ttp-110) cc_final: 0.7618 (ttp-110) REVERT: D 76 ILE cc_start: 0.8654 (pt) cc_final: 0.8349 (mt) REVERT: D 425 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8885 (t) outliers start: 59 outliers final: 45 residues processed: 323 average time/residue: 0.1077 time to fit residues: 52.7834 Evaluate side-chains 327 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 278 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 104 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 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 452 TYR 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 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: 0.9990 chunk 128 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 135 optimal weight: 4.9990 chunk 4 optimal weight: 0.0670 chunk 56 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 104 optimal weight: 0.8980 chunk 6 optimal weight: 0.9980 chunk 125 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 374 ASN A 482 HIS B 99 ASN B 374 ASN B 482 HIS C 99 ASN C 324 GLN C 374 ASN C 482 HIS D 99 ASN D 324 GLN D 374 ASN D 482 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.148541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.122186 restraints weight = 17891.780| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 1.95 r_work: 0.3238 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3103 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.3034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14480 Z= 0.116 Angle : 0.605 9.288 19724 Z= 0.310 Chirality : 0.044 0.165 2224 Planarity : 0.004 0.043 2452 Dihedral : 7.347 59.140 2076 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.92 % Favored : 88.86 % Rotamer: Outliers : 3.80 % Allowed : 18.48 % Favored : 77.72 % 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: -1.96 (0.21), residues: 1768 helix: -0.42 (0.17), residues: 996 sheet: None (None), residues: 0 loop : -2.51 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 60 TYR 0.022 0.001 TYR C 114 PHE 0.023 0.001 PHE A 140 TRP 0.016 0.001 TRP A 302 HIS 0.013 0.001 HIS A 482 Details of bonding type rmsd/Z covalent geometry : bond 0.00263 / 0.12 (14472) covalent geometry : angle 0.60520 / 0.31 (19724) hydrogen bonds : bond 0.03671 / 2.37 ( 488) hydrogen bonds : angle 3.88118 / 2.68 ( 1404) Misc. bond : bond 0.00059 / 0.03 ( 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 322 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 269 time to evaluate : 0.553 Fit side-chains REVERT: A 60 ARG cc_start: 0.7734 (mtm-85) cc_final: 0.6904 (mtm-85) REVERT: A 425 THR cc_start: 0.9103 (OUTLIER) cc_final: 0.8873 (t) REVERT: B 60 ARG cc_start: 0.7925 (ttp-110) cc_final: 0.7601 (ttp-110) REVERT: B 425 THR cc_start: 0.9109 (OUTLIER) cc_final: 0.8873 (t) REVERT: C 60 ARG cc_start: 0.7890 (ttp-110) cc_final: 0.7556 (ttp-110) REVERT: C 425 THR cc_start: 0.9095 (OUTLIER) cc_final: 0.8867 (t) REVERT: D 425 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8882 (t) outliers start: 53 outliers final: 41 residues processed: 308 average time/residue: 0.1051 time to fit residues: 48.5057 Evaluate side-chains 304 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 259 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL 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 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 B residue 69 LEU Chi-restraints excluded: chain B residue 99 ASN Chi-restraints excluded: chain B residue 104 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 247 TYR Chi-restraints excluded: chain B residue 254 SER 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 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 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 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 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: 1.9990 chunk 88 optimal weight: 6.9990 chunk 70 optimal weight: 1.9990 chunk 105 optimal weight: 0.0770 chunk 3 optimal weight: 0.6980 chunk 132 optimal weight: 6.9990 chunk 140 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 135 optimal weight: 0.5980 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 99 ASN A 374 ASN B 99 ASN B 373 HIS B 374 ASN C 99 ASN C 297 ASN C 374 ASN D 99 ASN D 297 ASN D 374 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.148171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.122172 restraints weight = 17992.331| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 1.92 r_work: 0.3233 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3100 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14480 Z= 0.124 Angle : 0.621 10.193 19724 Z= 0.316 Chirality : 0.045 0.166 2224 Planarity : 0.005 0.057 2452 Dihedral : 7.313 58.190 2076 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 4.79 Ramachandran Plot: Outliers : 0.23 % Allowed : 11.14 % Favored : 88.63 % Rotamer: Outliers : 3.72 % Allowed : 18.41 % Favored : 77.87 % 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: -1.97 (0.21), residues: 1768 helix: -0.31 (0.17), residues: 1000 sheet: None (None), residues: 0 loop : -2.71 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 60 TYR 0.022 0.001 TYR B 114 PHE 0.026 0.001 PHE C 140 TRP 0.011 0.001 TRP A 302 HIS 0.002 0.001 HIS A 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.12 (14472) covalent geometry : angle 0.62082 / 0.32 (19724) hydrogen bonds : bond 0.03801 / 2.43 ( 488) hydrogen bonds : angle 3.86742 / 2.67 ( 1404) Misc. bond : bond 0.00084 / 0.04 ( 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 316 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 264 time to evaluate : 0.432 Fit side-chains REVERT: A 60 ARG cc_start: 0.7759 (mtm-85) cc_final: 0.6946 (mtm-85) REVERT: A 425 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8880 (t) REVERT: A 442 GLU cc_start: 0.7117 (pm20) cc_final: 0.6493 (pm20) REVERT: B 60 ARG cc_start: 0.7973 (ttp-110) cc_final: 0.7649 (ttp-110) REVERT: B 425 THR cc_start: 0.9113 (OUTLIER) cc_final: 0.8876 (t) REVERT: B 442 GLU cc_start: 0.6965 (pm20) cc_final: 0.6324 (pm20) REVERT: C 60 ARG cc_start: 0.7974 (ttp-110) cc_final: 0.7588 (ttp-110) REVERT: C 425 THR cc_start: 0.9090 (OUTLIER) cc_final: 0.8854 (t) REVERT: C 442 GLU cc_start: 0.7004 (pm20) cc_final: 0.6342 (pm20) REVERT: D 60 ARG cc_start: 0.7954 (ttp-110) cc_final: 0.7587 (ttp-110) REVERT: D 425 THR cc_start: 0.9081 (OUTLIER) cc_final: 0.8855 (t) REVERT: D 442 GLU cc_start: 0.7057 (pm20) cc_final: 0.6423 (pm20) outliers start: 52 outliers final: 41 residues processed: 300 average time/residue: 0.1048 time to fit residues: 47.3419 Evaluate side-chains 301 residues out of total 1584 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 256 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 98 VAL Chi-restraints excluded: chain A residue 99 ASN 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 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 B residue 69 LEU Chi-restraints excluded: chain B residue 98 VAL Chi-restraints excluded: chain B residue 104 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 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 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 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 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 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: 0.7980 chunk 150 optimal weight: 0.0370 chunk 154 optimal weight: 0.9980 chunk 55 optimal weight: 8.9990 chunk 167 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 160 optimal weight: 0.2980 chunk 157 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3732 r_free = 0.3732 target = 0.151820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.126644 restraints weight = 17688.794| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.85 r_work: 0.3266 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3134 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.3209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14480 Z= 0.111 Angle : 0.602 9.874 19724 Z= 0.306 Chirality : 0.044 0.159 2224 Planarity : 0.005 0.060 2452 Dihedral : 7.072 57.092 2076 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.23 % Allowed : 10.69 % Favored : 89.08 % Rotamer: Outliers : 3.72 % Allowed : 18.41 % Favored : 77.87 % 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: -1.72 (0.21), residues: 1768 helix: -0.14 (0.17), residues: 1008 sheet: None (None), residues: 0 loop : -2.57 (0.23), residues: 760 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 0.024 0.001 PHE A 140 TRP 0.013 0.001 TRP A 302 HIS 0.002 0.001 HIS B 301 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (14472) covalent geometry : angle 0.60239 / 0.31 (19724) hydrogen bonds : bond 0.03554 / 2.28 ( 488) hydrogen bonds : angle 3.77955 / 2.61 ( 1404) Misc. bond : bond 0.00082 / 0.04 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3515.49 seconds wall clock time: 60 minutes 48.31 seconds (3648.31 seconds total)