Starting phenix.real_space_refine on Sat Sep 12 11:50:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7svw_25455/09_2026/7svw_25455.cif Found real_map, /net/cci-nas-00/data/ceres_data/7svw_25455/09_2026/7svw_25455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7svw_25455/09_2026/7svw_25455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7svw_25455/09_2026/7svw_25455.map" model { file = "/net/cci-nas-00/data/ceres_data/7svw_25455/09_2026/7svw_25455.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7svw_25455/09_2026/7svw_25455.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7svw_25455/09_2026/7svw_25455.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7svw_25455/09_2026/7svw_25455.cif" } resolution = 3.69 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= 0.002 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: 6 Type Number sf(0) Gaussians P 184 5.49 5 Mg 2 5.21 5 S 44 5.16 5 C 9350 2.51 5 N 2892 2.21 5 O 3358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.01s 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: 15830 Number of models: 1 Model: "" Number of chains: 12 Chain: "1" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1021 Classifications: {'DNA': 50} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 49} Chain: "2" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 615 Classifications: {'DNA': 30} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 29} Chain: "3" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 301 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "4" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1021 Classifications: {'DNA': 50} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 49} Chain: "5" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 615 Classifications: {'DNA': 30} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 29} Chain: "6" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 301 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2382 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 11, 'TRANS': 284} Chain breaks: 3 Chain: "B" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3595 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 19, 'TRANS': 426} Chain: "C" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2382 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 11, 'TRANS': 284} Chain breaks: 3 Chain: "D" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3595 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 19, 'TRANS': 426} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.52, per 1000 atoms: 0.22 Number of scatterers: 15830 At special positions: 0 Unit cell: (107.73, 126.35, 155.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 44 16.00 P 184 15.00 Mg 2 11.99 O 3358 8.00 N 2892 7.00 C 9350 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.61 Conformation dependent library (CDL) restraints added in 642.2 milliseconds 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2756 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 16 sheets defined 41.4% alpha, 22.1% beta 79 base pairs and 146 stacking pairs defined. Time for finding SS restraints: 1.91 Creating SS restraints... Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 323 through 331 Processing helix chain 'A' and resid 332 through 335 Processing helix chain 'A' and resid 357 through 372 Processing helix chain 'A' and resid 373 through 376 Processing helix chain 'A' and resid 385 through 393 Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 436 through 440 Processing helix chain 'A' and resid 483 through 502 removed outlier: 3.937A pdb=" N THR A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 497 " --> pdb=" O ARG A 493 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 519 Processing helix chain 'B' and resid 39 through 54 removed outlier: 4.378A pdb=" N GLU B 54 " --> pdb=" O GLN B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 73 Processing helix chain 'B' and resid 78 through 90 Processing helix chain 'B' and resid 91 through 95 Processing helix chain 'B' and resid 108 through 123 Processing helix chain 'B' and resid 130 through 145 Processing helix chain 'B' and resid 152 through 160 Processing helix chain 'B' and resid 160 through 171 removed outlier: 4.072A pdb=" N GLN B 167 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 266 through 270 Processing helix chain 'B' and resid 289 through 293 Processing helix chain 'B' and resid 294 through 305 Processing helix chain 'B' and resid 322 through 331 removed outlier: 3.952A pdb=" N THR B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 335 Processing helix chain 'B' and resid 357 through 372 Processing helix chain 'B' and resid 385 through 393 Processing helix chain 'B' and resid 402 through 410 removed outlier: 3.888A pdb=" N ASP B 407 " --> pdb=" O ARG B 404 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'C' and resid 251 through 261 Processing helix chain 'C' and resid 266 through 270 Processing helix chain 'C' and resid 296 through 305 Processing helix chain 'C' and resid 323 through 331 Processing helix chain 'C' and resid 332 through 335 Processing helix chain 'C' and resid 357 through 372 Processing helix chain 'C' and resid 373 through 376 Processing helix chain 'C' and resid 385 through 393 Processing helix chain 'C' and resid 402 through 407 Processing helix chain 'C' and resid 436 through 440 Processing helix chain 'C' and resid 483 through 499 Processing helix chain 'C' and resid 505 through 519 removed outlier: 3.714A pdb=" N VAL C 510 " --> pdb=" O LEU C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 54 removed outlier: 4.378A pdb=" N GLU D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 73 Processing helix chain 'D' and resid 77 through 90 removed outlier: 4.166A pdb=" N ARG D 81 " --> pdb=" O ARG D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 95 Processing helix chain 'D' and resid 108 through 123 Processing helix chain 'D' and resid 130 through 145 Processing helix chain 'D' and resid 152 through 160 Processing helix chain 'D' and resid 160 through 171 removed outlier: 4.072A pdb=" N GLN D 167 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN D 168 " --> pdb=" O LEU D 164 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 261 Processing helix chain 'D' and resid 266 through 270 Processing helix chain 'D' and resid 289 through 293 Processing helix chain 'D' and resid 294 through 305 Processing helix chain 'D' and resid 322 through 331 removed outlier: 3.982A pdb=" N THR D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 335 Processing helix chain 'D' and resid 357 through 372 Processing helix chain 'D' and resid 385 through 393 Processing helix chain 'D' and resid 402 through 410 removed outlier: 3.888A pdb=" N ASP D 407 " --> pdb=" O ARG D 404 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 440 Processing sheet with id=AA1, first strand: chain 'A' and resid 236 through 243 removed outlier: 6.815A pdb=" N VAL A 229 " --> pdb=" O MET A 238 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE A 240 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR A 227 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU A 242 " --> pdb=" O TRP A 225 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N TRP A 225 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASP A 287 " --> pdb=" O CYS A 204 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N HIS A 206 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N PHE A 284 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ARG A 311 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR A 286 " --> pdb=" O ARG A 311 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 411 through 417 removed outlier: 5.793A pdb=" N LYS A 412 " --> pdb=" O PHE A 448 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N PHE A 448 " --> pdb=" O LYS A 412 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N SER A 414 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU A 446 " --> pdb=" O SER A 414 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR A 443 " --> pdb=" O GLN A 461 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLN A 461 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ASP A 449 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N THR A 455 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 15.480A pdb=" N ASP A 452 " --> pdb=" O GLN A 475 " (cutoff:3.500A) removed outlier: 11.849A pdb=" N GLN A 475 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N THR A 454 " --> pdb=" O HIS A 473 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N HIS A 473 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE A 456 " --> pdb=" O ARG A 471 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ARG A 471 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL A 458 " --> pdb=" O LEU A 469 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N MET A 430 " --> pdb=" O GLN A 475 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 411 through 417 removed outlier: 5.793A pdb=" N LYS A 412 " --> pdb=" O PHE A 448 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N PHE A 448 " --> pdb=" O LYS A 412 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N SER A 414 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU A 446 " --> pdb=" O SER A 414 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR A 443 " --> pdb=" O GLN A 461 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLN A 461 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ASP A 449 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N THR A 455 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 15.480A pdb=" N ASP A 452 " --> pdb=" O GLN A 475 " (cutoff:3.500A) removed outlier: 11.849A pdb=" N GLN A 475 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N THR A 454 " --> pdb=" O HIS A 473 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N HIS A 473 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE A 456 " --> pdb=" O ARG A 471 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ARG A 471 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL A 458 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 184 through 186 Processing sheet with id=AA5, first strand: chain 'B' and resid 237 through 243 removed outlier: 6.335A pdb=" N ILE B 237 " --> pdb=" O ASP B 231 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ASP B 231 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TRP B 202 " --> pdb=" O TYR B 285 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 213 through 214 Processing sheet with id=AA7, first strand: chain 'B' and resid 411 through 417 removed outlier: 5.586A pdb=" N LYS B 412 " --> pdb=" O PHE B 448 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N PHE B 448 " --> pdb=" O LYS B 412 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N SER B 414 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LEU B 446 " --> pdb=" O SER B 414 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N THR B 443 " --> pdb=" O GLN B 461 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLN B 461 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ASP B 449 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N THR B 455 " --> pdb=" O ASP B 449 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ARG B 460 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N PHE B 468 " --> pdb=" O ARG B 460 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU B 462 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLU B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 424 through 425 Processing sheet with id=AA9, first strand: chain 'C' and resid 236 through 243 removed outlier: 6.816A pdb=" N VAL C 229 " --> pdb=" O MET C 238 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE C 240 " --> pdb=" O THR C 227 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR C 227 " --> pdb=" O ILE C 240 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU C 242 " --> pdb=" O TRP C 225 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TRP C 225 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASP C 287 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N HIS C 206 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N PHE C 284 " --> pdb=" O HIS C 309 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ARG C 311 " --> pdb=" O PHE C 284 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N THR C 286 " --> pdb=" O ARG C 311 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 411 through 417 removed outlier: 5.793A pdb=" N LYS C 412 " --> pdb=" O PHE C 448 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N PHE C 448 " --> pdb=" O LYS C 412 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N SER C 414 " --> pdb=" O LEU C 446 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU C 446 " --> pdb=" O SER C 414 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR C 443 " --> pdb=" O GLN C 461 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLN C 461 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ASP C 449 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N THR C 455 " --> pdb=" O ASP C 449 " (cutoff:3.500A) removed outlier: 15.480A pdb=" N ASP C 452 " --> pdb=" O GLN C 475 " (cutoff:3.500A) removed outlier: 11.849A pdb=" N GLN C 475 " --> pdb=" O ASP C 452 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N THR C 454 " --> pdb=" O HIS C 473 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N HIS C 473 " --> pdb=" O THR C 454 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE C 456 " --> pdb=" O ARG C 471 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ARG C 471 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL C 458 " --> pdb=" O LEU C 469 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N MET C 430 " --> pdb=" O GLN C 475 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 411 through 417 removed outlier: 5.793A pdb=" N LYS C 412 " --> pdb=" O PHE C 448 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N PHE C 448 " --> pdb=" O LYS C 412 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N SER C 414 " --> pdb=" O LEU C 446 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU C 446 " --> pdb=" O SER C 414 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR C 443 " --> pdb=" O GLN C 461 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLN C 461 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ASP C 449 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N THR C 455 " --> pdb=" O ASP C 449 " (cutoff:3.500A) removed outlier: 15.480A pdb=" N ASP C 452 " --> pdb=" O GLN C 475 " (cutoff:3.500A) removed outlier: 11.849A pdb=" N GLN C 475 " --> pdb=" O ASP C 452 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N THR C 454 " --> pdb=" O HIS C 473 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N HIS C 473 " --> pdb=" O THR C 454 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE C 456 " --> pdb=" O ARG C 471 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ARG C 471 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL C 458 " --> pdb=" O LEU C 469 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 184 through 186 Processing sheet with id=AB4, first strand: chain 'D' and resid 237 through 243 removed outlier: 6.336A pdb=" N ILE D 237 " --> pdb=" O ASP D 231 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASP D 231 " --> pdb=" O ILE D 237 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TRP D 202 " --> pdb=" O TYR D 285 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 213 through 214 Processing sheet with id=AB6, first strand: chain 'D' and resid 411 through 417 removed outlier: 5.586A pdb=" N LYS D 412 " --> pdb=" O PHE D 448 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N PHE D 448 " --> pdb=" O LYS D 412 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N SER D 414 " --> pdb=" O LEU D 446 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LEU D 446 " --> pdb=" O SER D 414 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N THR D 443 " --> pdb=" O GLN D 461 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLN D 461 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ASP D 449 " --> pdb=" O THR D 455 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N THR D 455 " --> pdb=" O ASP D 449 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG D 460 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N PHE D 468 " --> pdb=" O ARG D 460 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU D 462 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLU D 466 " --> pdb=" O GLU D 462 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 424 through 425 524 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 196 hydrogen bonds 392 hydrogen bond angles 0 basepair planarities 79 basepair parallelities 146 stacking parallelities Total time for adding SS restraints: 3.18 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 2202 1.29 - 1.42: 5060 1.42 - 1.55: 8830 1.55 - 1.68: 374 1.68 - 1.81: 62 Bond restraints: 16528 Sorted by residual: bond pdb=" C ARG B 81 " pdb=" O ARG B 81 " ideal model delta sigma weight residual 1.236 1.162 0.074 1.22e-02 6.72e+03 3.66e+01 bond pdb=" C ARG D 81 " pdb=" O ARG D 81 " ideal model delta sigma weight residual 1.236 1.162 0.074 1.22e-02 6.72e+03 3.66e+01 bond pdb=" CA ARG B 81 " pdb=" C ARG B 81 " ideal model delta sigma weight residual 1.524 1.447 0.076 1.32e-02 5.74e+03 3.35e+01 bond pdb=" CA ARG D 81 " pdb=" C ARG D 81 " ideal model delta sigma weight residual 1.524 1.448 0.076 1.32e-02 5.74e+03 3.28e+01 bond pdb=" C1' DT 2 1 " pdb=" N1 DT 2 1 " ideal model delta sigma weight residual 1.468 1.548 -0.080 1.40e-02 5.10e+03 3.27e+01 ... (remaining 16523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 21921 2.91 - 5.82: 970 5.82 - 8.73: 217 8.73 - 11.64: 54 11.64 - 14.56: 10 Bond angle restraints: 23172 Sorted by residual: angle pdb=" C ARG B 223 " pdb=" N PRO B 224 " pdb=" CA PRO B 224 " ideal model delta sigma weight residual 120.31 131.63 -11.32 9.80e-01 1.04e+00 1.33e+02 angle pdb=" C ARG D 223 " pdb=" N PRO D 224 " pdb=" CA PRO D 224 " ideal model delta sigma weight residual 120.03 130.21 -10.18 9.90e-01 1.02e+00 1.06e+02 angle pdb=" C ARG A 223 " pdb=" N PRO A 224 " pdb=" CA PRO A 224 " ideal model delta sigma weight residual 120.31 130.15 -9.84 9.80e-01 1.04e+00 1.01e+02 angle pdb=" C ARG C 223 " pdb=" N PRO C 224 " pdb=" CA PRO C 224 " ideal model delta sigma weight residual 120.31 130.11 -9.80 9.80e-01 1.04e+00 9.99e+01 angle pdb=" N GLY C 279 " pdb=" CA GLY C 279 " pdb=" C GLY C 279 " ideal model delta sigma weight residual 112.18 124.80 -12.62 1.34e+00 5.57e-01 8.87e+01 ... (remaining 23167 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.95: 8251 26.95 - 53.89: 1056 53.89 - 80.84: 135 80.84 - 107.79: 5 107.79 - 134.74: 1 Dihedral angle restraints: 9448 sinusoidal: 5160 harmonic: 4288 Sorted by residual: dihedral pdb=" CD ARG B 380 " pdb=" NE ARG B 380 " pdb=" CZ ARG B 380 " pdb=" NH1 ARG B 380 " ideal model delta sinusoidal sigma weight residual 0.00 80.95 -80.95 1 1.00e+01 1.00e-02 8.09e+01 dihedral pdb=" CD ARG D 99 " pdb=" NE ARG D 99 " pdb=" CZ ARG D 99 " pdb=" NH1 ARG D 99 " ideal model delta sinusoidal sigma weight residual 0.00 -77.04 77.04 1 1.00e+01 1.00e-02 7.45e+01 dihedral pdb=" CA TYR D 435 " pdb=" C TYR D 435 " pdb=" N LEU D 436 " pdb=" CA LEU D 436 " ideal model delta harmonic sigma weight residual -180.00 -154.76 -25.24 0 5.00e+00 4.00e-02 2.55e+01 ... (remaining 9445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 2272 0.108 - 0.217: 254 0.217 - 0.325: 24 0.325 - 0.433: 11 0.433 - 0.541: 3 Chirality restraints: 2564 Sorted by residual: chirality pdb=" C3' DT 5 1 " pdb=" C4' DT 5 1 " pdb=" O3' DT 5 1 " pdb=" C2' DT 5 1 " both_signs ideal model delta sigma weight residual False -2.73 -2.19 -0.54 2.00e-01 2.50e+01 7.32e+00 chirality pdb=" CA ASN D 32 " pdb=" N ASN D 32 " pdb=" C ASN D 32 " pdb=" CB ASN D 32 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.70e+00 chirality pdb=" CA ASN B 32 " pdb=" N ASN B 32 " pdb=" C ASN B 32 " pdb=" CB ASN B 32 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.69e+00 ... (remaining 2561 not shown) Planarity restraints: 2342 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 380 " 1.091 9.50e-02 1.11e+02 4.89e-01 1.44e+02 pdb=" NE ARG B 380 " -0.066 2.00e-02 2.50e+03 pdb=" CZ ARG B 380 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG B 380 " 0.010 2.00e-02 2.50e+03 pdb=" NH2 ARG B 380 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 99 " -1.078 9.50e-02 1.11e+02 4.83e-01 1.41e+02 pdb=" NE ARG D 99 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG D 99 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG D 99 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG D 99 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 389 " 0.051 2.00e-02 2.50e+03 1.04e-01 1.08e+02 pdb=" C ARG B 389 " -0.179 2.00e-02 2.50e+03 pdb=" O ARG B 389 " 0.070 2.00e-02 2.50e+03 pdb=" N TRP B 390 " 0.058 2.00e-02 2.50e+03 ... (remaining 2339 not shown) Histogram of nonbonded interaction distances: 0.95 - 1.74: 12 1.74 - 2.53: 107 2.53 - 3.32: 17805 3.32 - 4.11: 41929 4.11 - 4.90: 68322 Warning: very small nonbonded interaction distances. Nonbonded interactions: 128175 Sorted by model distance: nonbonded pdb=" OP2 DG 6 12 " pdb=" NH1 ARG B 416 " model vdw 0.955 3.120 nonbonded pdb=" OP2 DG 3 12 " pdb=" NH1 ARG D 416 " model vdw 1.224 3.120 nonbonded pdb=" C7 DT 2 1 " pdb=" N ARG B 179 " model vdw 1.460 3.540 nonbonded pdb=" OP2 DG 6 12 " pdb=" CZ ARG B 416 " model vdw 1.486 3.270 nonbonded pdb=" O2 DT 5 16 " pdb=" NH2 ARG B 99 " model vdw 1.558 3.120 ... (remaining 128170 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain '1' selection = chain '4' } ncs_group { reference = chain '2' selection = chain '5' } ncs_group { reference = chain '3' selection = chain '6' } ncs_group { reference = chain 'A' selection = chain 'C' } ncs_group { reference = chain 'B' 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.700 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 17.060 Find NCS groups from input model: 0.190 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:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 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 : 0.012 0.080 16528 Z= 0.849 Angle : 1.498 14.555 23172 Z= 1.104 Chirality : 0.078 0.541 2564 Planarity : 0.018 0.489 2342 Dihedral : 20.294 134.736 6692 Min Nonbonded Distance : 0.955 Molprobity Statistics. All-atom Clashscore : 14.67 Ramachandran Plot: Outliers : 0.27 % Allowed : 3.96 % Favored : 95.77 % Rotamer: Outliers : 2.78 % Allowed : 2.40 % Favored : 94.82 % Cbeta Deviations : 0.65 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.20), residues: 1464 helix: 0.31 (0.21), residues: 494 sheet: 0.05 (0.34), residues: 178 loop : 0.07 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 77 TYR 0.014 0.001 TYR D 278 PHE 0.025 0.001 PHE C 448 TRP 0.007 0.001 TRP D 202 HIS 0.011 0.001 HIS D 105 Details of bonding type rmsd/Z covalent geometry : bond 0.01204 / 0.85 (16528) covalent geometry : angle 1.49784 / 1.10 (23172) hydrogen bonds : bond 0.18197 / 19.66 ( 698) hydrogen bonds : angle 6.92160 / 8.93 ( 1784) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 214 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 MET cc_start: 0.8635 (tpp) cc_final: 0.8429 (mmm) REVERT: B 137 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7711 (mtt90) REVERT: B 179 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.6942 (mmm160) REVERT: B 381 MET cc_start: 0.7348 (pmm) cc_final: 0.7054 (pmm) REVERT: B 405 ASP cc_start: 0.6571 (m-30) cc_final: 0.6245 (t0) REVERT: C 516 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7827 (mp) REVERT: D 77 ARG cc_start: 0.6841 (OUTLIER) cc_final: 0.6288 (tpt-90) REVERT: D 99 ARG cc_start: 0.6691 (OUTLIER) cc_final: 0.6371 (ttt-90) REVERT: D 129 MET cc_start: 0.8612 (tpp) cc_final: 0.7643 (tpt) REVERT: D 132 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7381 (tmtp) REVERT: D 179 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7198 (mmm160) REVERT: D 405 ASP cc_start: 0.6642 (m-30) cc_final: 0.6397 (t0) outliers start: 36 outliers final: 12 residues processed: 244 average time/residue: 0.1854 time to fit residues: 61.4879 Evaluate side-chains 116 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 501 ILE Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 512 ASP Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 99 ARG Chi-restraints excluded: chain B residue 106 ARG Chi-restraints excluded: chain B residue 137 ARG Chi-restraints excluded: chain B residue 179 ARG Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 77 ARG Chi-restraints excluded: chain D residue 99 ARG Chi-restraints excluded: chain D residue 132 LYS Chi-restraints excluded: chain D residue 179 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0270 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.5240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 GLN C 299 GLN D 342 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.116984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.092197 restraints weight = 41852.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.092763 restraints weight = 28238.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.093393 restraints weight = 21221.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.093544 restraints weight = 17984.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.093868 restraints weight = 16492.437| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16528 Z= 0.170 Angle : 0.689 7.556 23172 Z= 0.395 Chirality : 0.042 0.217 2564 Planarity : 0.006 0.155 2342 Dihedral : 24.019 154.169 3795 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.55 % Allowed : 6.88 % Favored : 90.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.21), residues: 1464 helix: 1.33 (0.23), residues: 498 sheet: -0.31 (0.31), residues: 218 loop : 0.15 (0.22), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 513 TYR 0.011 0.001 TYR D 459 PHE 0.020 0.002 PHE D 426 TRP 0.024 0.002 TRP C 275 HIS 0.009 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.17 (16528) covalent geometry : angle 0.68923 / 0.39 (23172) hydrogen bonds : bond 0.05789 / 6.37 ( 698) hydrogen bonds : angle 5.05039 / 6.71 ( 1784) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 113 time to evaluate : 0.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 LEU cc_start: 0.6643 (tp) cc_final: 0.6440 (tp) REVERT: B 106 ARG cc_start: 0.8459 (OUTLIER) cc_final: 0.8180 (mtt90) REVERT: B 380 ARG cc_start: 0.7714 (OUTLIER) cc_final: 0.7467 (ttm170) REVERT: B 405 ASP cc_start: 0.7745 (m-30) cc_final: 0.7103 (t70) REVERT: B 431 TYR cc_start: 0.7461 (m-80) cc_final: 0.6868 (m-80) REVERT: B 453 ILE cc_start: 0.7732 (OUTLIER) cc_final: 0.7376 (pp) REVERT: C 513 ARG cc_start: 0.7086 (tmt170) cc_final: 0.6841 (tmt170) REVERT: D 132 LYS cc_start: 0.7634 (OUTLIER) cc_final: 0.6991 (tmtp) REVERT: D 405 ASP cc_start: 0.7774 (m-30) cc_final: 0.7076 (t0) outliers start: 33 outliers final: 16 residues processed: 139 average time/residue: 0.1811 time to fit residues: 34.5038 Evaluate side-chains 105 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 514 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 106 ARG Chi-restraints excluded: chain B residue 380 ARG Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 132 LYS Chi-restraints excluded: chain D residue 377 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 134 optimal weight: 3.9990 chunk 87 optimal weight: 5.9990 chunk 120 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 113 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 chunk 4 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 chunk 101 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 503 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.110797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.085391 restraints weight = 42277.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.086994 restraints weight = 27170.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.087710 restraints weight = 18598.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.087708 restraints weight = 16912.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.087865 restraints weight = 16440.084| |-----------------------------------------------------------------------------| r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.3120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 16528 Z= 0.225 Angle : 0.737 9.869 23172 Z= 0.404 Chirality : 0.045 0.250 2564 Planarity : 0.006 0.046 2342 Dihedral : 24.757 147.491 3762 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.94 % Allowed : 8.11 % Favored : 88.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.21), residues: 1464 helix: 1.13 (0.22), residues: 500 sheet: -0.04 (0.34), residues: 190 loop : -0.15 (0.22), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG B 380 TYR 0.041 0.002 TYR D 435 PHE 0.028 0.003 PHE D 468 TRP 0.011 0.002 TRP B 178 HIS 0.008 0.002 HIS D 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00483 / 0.22 (16528) covalent geometry : angle 0.73686 / 0.40 (23172) hydrogen bonds : bond 0.05854 / 6.55 ( 698) hydrogen bonds : angle 4.77589 / 6.39 ( 1784) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 97 time to evaluate : 0.613 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 ASP cc_start: 0.6049 (m-30) cc_final: 0.5655 (m-30) REVERT: B 77 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6410 (tpt-90) REVERT: B 129 MET cc_start: 0.8929 (ttm) cc_final: 0.8617 (ttt) REVERT: B 272 HIS cc_start: 0.7684 (OUTLIER) cc_final: 0.6712 (m-70) REVERT: B 381 MET cc_start: 0.7690 (pmm) cc_final: 0.7166 (pmm) REVERT: B 405 ASP cc_start: 0.7626 (m-30) cc_final: 0.6983 (t70) REVERT: B 431 TYR cc_start: 0.7366 (m-80) cc_final: 0.7063 (m-80) REVERT: B 453 ILE cc_start: 0.8199 (pt) cc_final: 0.7779 (pp) REVERT: B 465 GLN cc_start: 0.6064 (mm-40) cc_final: 0.5825 (mm-40) REVERT: C 407 ASP cc_start: 0.5998 (m-30) cc_final: 0.5591 (m-30) REVERT: D 129 MET cc_start: 0.8836 (ttm) cc_final: 0.8507 (ttt) REVERT: D 223 ARG cc_start: 0.9123 (OUTLIER) cc_final: 0.8827 (ptm160) REVERT: D 405 ASP cc_start: 0.7742 (m-30) cc_final: 0.7084 (t70) REVERT: D 453 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8067 (pp) REVERT: D 465 GLN cc_start: 0.6097 (mm-40) cc_final: 0.5864 (mm-40) outliers start: 38 outliers final: 17 residues processed: 128 average time/residue: 0.1459 time to fit residues: 27.2934 Evaluate side-chains 94 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 73 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 132 LYS Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 453 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 13 optimal weight: 9.9990 chunk 155 optimal weight: 0.9980 chunk 130 optimal weight: 0.4980 chunk 85 optimal weight: 7.9990 chunk 83 optimal weight: 1.9990 chunk 156 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 1 optimal weight: 10.0000 chunk 134 optimal weight: 2.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 GLN C 299 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.111990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.086811 restraints weight = 42247.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.087840 restraints weight = 26184.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.088215 restraints weight = 21249.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.088346 restraints weight = 17549.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.088547 restraints weight = 16281.314| |-----------------------------------------------------------------------------| r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16528 Z= 0.137 Angle : 0.595 6.827 23172 Z= 0.337 Chirality : 0.040 0.185 2564 Planarity : 0.004 0.040 2342 Dihedral : 24.725 151.194 3756 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.63 % Allowed : 9.12 % Favored : 88.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.22), residues: 1464 helix: 1.64 (0.23), residues: 500 sheet: -0.37 (0.32), residues: 202 loop : -0.10 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 404 TYR 0.015 0.001 TYR B 197 PHE 0.020 0.002 PHE A 324 TRP 0.012 0.001 TRP C 225 HIS 0.003 0.001 HIS D 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.14 (16528) covalent geometry : angle 0.59483 / 0.34 (23172) hydrogen bonds : bond 0.04456 / 4.96 ( 698) hydrogen bonds : angle 4.34692 / 5.79 ( 1784) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 73 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 ASP cc_start: 0.5626 (m-30) cc_final: 0.5297 (m-30) REVERT: B 77 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6678 (tpt-90) REVERT: B 129 MET cc_start: 0.8921 (ttm) cc_final: 0.8553 (ttt) REVERT: B 272 HIS cc_start: 0.7650 (OUTLIER) cc_final: 0.6721 (m-70) REVERT: B 405 ASP cc_start: 0.7748 (m-30) cc_final: 0.7093 (t70) REVERT: B 431 TYR cc_start: 0.7379 (m-80) cc_final: 0.6972 (m-80) REVERT: B 446 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.7405 (mt) REVERT: B 453 ILE cc_start: 0.8253 (OUTLIER) cc_final: 0.7837 (pp) REVERT: C 407 ASP cc_start: 0.5586 (m-30) cc_final: 0.5251 (m-30) REVERT: D 129 MET cc_start: 0.8799 (ttm) cc_final: 0.8390 (ttt) REVERT: D 223 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8727 (ptm160) REVERT: D 405 ASP cc_start: 0.7916 (m-30) cc_final: 0.7245 (t70) REVERT: D 446 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.7469 (mm) outliers start: 34 outliers final: 19 residues processed: 102 average time/residue: 0.1360 time to fit residues: 20.9097 Evaluate side-chains 94 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 132 LYS Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 446 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 91 optimal weight: 5.9990 chunk 36 optimal weight: 0.6980 chunk 84 optimal weight: 6.9990 chunk 70 optimal weight: 0.5980 chunk 11 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 13 optimal weight: 20.0000 chunk 108 optimal weight: 0.0060 overall best weight: 0.8198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 445 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.111530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.086312 restraints weight = 42701.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.088306 restraints weight = 26532.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.088223 restraints weight = 20353.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.088360 restraints weight = 16856.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.088496 restraints weight = 15463.742| |-----------------------------------------------------------------------------| r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16528 Z= 0.138 Angle : 0.587 11.153 23172 Z= 0.328 Chirality : 0.039 0.175 2564 Planarity : 0.004 0.042 2342 Dihedral : 24.802 150.997 3756 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.78 % Allowed : 10.43 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.22), residues: 1464 helix: 1.85 (0.23), residues: 500 sheet: -0.19 (0.34), residues: 184 loop : -0.13 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 460 TYR 0.017 0.001 TYR D 439 PHE 0.033 0.002 PHE D 468 TRP 0.009 0.001 TRP A 225 HIS 0.003 0.001 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (16528) covalent geometry : angle 0.58747 / 0.33 (23172) hydrogen bonds : bond 0.04302 / 4.83 ( 698) hydrogen bonds : angle 4.16779 / 5.52 ( 1784) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 79 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 406 LEU cc_start: 0.8614 (mm) cc_final: 0.8414 (mm) REVERT: B 77 ARG cc_start: 0.6696 (OUTLIER) cc_final: 0.6431 (tpt170) REVERT: B 129 MET cc_start: 0.8950 (ttm) cc_final: 0.8561 (ttm) REVERT: B 272 HIS cc_start: 0.7652 (OUTLIER) cc_final: 0.6845 (m-70) REVERT: B 381 MET cc_start: 0.7542 (pmm) cc_final: 0.7319 (pmm) REVERT: B 405 ASP cc_start: 0.7800 (m-30) cc_final: 0.7185 (t70) REVERT: B 446 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.7447 (mt) REVERT: C 406 LEU cc_start: 0.8572 (mm) cc_final: 0.8295 (mm) REVERT: D 129 MET cc_start: 0.8818 (ttm) cc_final: 0.8386 (ttt) REVERT: D 223 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8722 (ptm160) REVERT: D 405 ASP cc_start: 0.7964 (m-30) cc_final: 0.7295 (t70) REVERT: D 446 LEU cc_start: 0.8396 (OUTLIER) cc_final: 0.7785 (mm) outliers start: 36 outliers final: 21 residues processed: 108 average time/residue: 0.1359 time to fit residues: 22.1733 Evaluate side-chains 100 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 272 HIS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 132 LYS Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 446 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 58 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 1 optimal weight: 9.9990 chunk 32 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 162 optimal weight: 5.9990 chunk 104 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 11 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.105857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.081560 restraints weight = 44299.144| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.081778 restraints weight = 33607.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.082202 restraints weight = 32148.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.082440 restraints weight = 22755.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.082795 restraints weight = 20880.903| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.075 16528 Z= 0.379 Angle : 0.855 11.774 23172 Z= 0.457 Chirality : 0.051 0.231 2564 Planarity : 0.007 0.061 2342 Dihedral : 25.281 144.521 3756 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.64 % Favored : 95.22 % Rotamer: Outliers : 3.25 % Allowed : 11.51 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.21), residues: 1464 helix: 0.92 (0.22), residues: 496 sheet: -1.03 (0.31), residues: 220 loop : -0.71 (0.23), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.001 ARG D 447 TYR 0.023 0.003 TYR D 285 PHE 0.035 0.004 PHE D 306 TRP 0.018 0.003 TRP D 178 HIS 0.009 0.002 HIS D 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00834 / 0.38 (16528) covalent geometry : angle 0.85471 / 0.46 (23172) hydrogen bonds : bond 0.07042 / 7.83 ( 698) hydrogen bonds : angle 4.96957 / 6.51 ( 1784) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 72 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 129 MET cc_start: 0.9026 (ttm) cc_final: 0.8630 (ttt) REVERT: B 405 ASP cc_start: 0.7912 (m-30) cc_final: 0.7564 (t0) REVERT: B 431 TYR cc_start: 0.7436 (m-80) cc_final: 0.6934 (m-80) REVERT: B 446 LEU cc_start: 0.8975 (mp) cc_final: 0.8256 (mt) REVERT: C 516 LEU cc_start: 0.8437 (OUTLIER) cc_final: 0.8210 (mp) REVERT: D 405 ASP cc_start: 0.7948 (m-30) cc_final: 0.7593 (t0) REVERT: D 446 LEU cc_start: 0.8831 (mp) cc_final: 0.8330 (mm) outliers start: 42 outliers final: 27 residues processed: 107 average time/residue: 0.1305 time to fit residues: 21.3941 Evaluate side-chains 95 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 67 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 508 GLN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 377 ILE Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 132 LYS Chi-restraints excluded: chain D residue 307 VAL Chi-restraints excluded: chain D residue 377 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 19 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 130 optimal weight: 0.4980 chunk 59 optimal weight: 0.7980 chunk 9 optimal weight: 20.0000 chunk 96 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 81 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 413 GLN D 413 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.108953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.085078 restraints weight = 44053.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.085908 restraints weight = 30854.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.086171 restraints weight = 29322.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.086338 restraints weight = 20736.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.086515 restraints weight = 19235.793| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.4198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16528 Z= 0.139 Angle : 0.615 8.613 23172 Z= 0.343 Chirality : 0.041 0.175 2564 Planarity : 0.004 0.034 2342 Dihedral : 25.080 150.137 3756 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.85 % Allowed : 13.29 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.22), residues: 1464 helix: 1.70 (0.23), residues: 498 sheet: -0.72 (0.35), residues: 186 loop : -0.55 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 447 TYR 0.020 0.001 TYR D 435 PHE 0.020 0.002 PHE D 468 TRP 0.016 0.001 TRP A 225 HIS 0.004 0.001 HIS D 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.14 (16528) covalent geometry : angle 0.61459 / 0.34 (23172) hydrogen bonds : bond 0.04551 / 5.04 ( 698) hydrogen bonds : angle 4.28125 / 5.65 ( 1784) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 82 time to evaluate : 0.529 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 LEU cc_start: 0.8645 (mm) cc_final: 0.8436 (mm) REVERT: B 381 MET cc_start: 0.7864 (pmm) cc_final: 0.7594 (pmm) REVERT: B 405 ASP cc_start: 0.7805 (m-30) cc_final: 0.7455 (t0) REVERT: B 413 GLN cc_start: 0.7001 (OUTLIER) cc_final: 0.6424 (tm-30) REVERT: B 423 CYS cc_start: 0.6164 (p) cc_final: 0.5045 (m) REVERT: B 431 TYR cc_start: 0.7392 (m-80) cc_final: 0.7044 (m-80) REVERT: B 446 LEU cc_start: 0.8827 (mp) cc_final: 0.8146 (mm) REVERT: B 465 GLN cc_start: 0.6260 (mm-40) cc_final: 0.6052 (mm-40) REVERT: D 405 ASP cc_start: 0.7877 (m-30) cc_final: 0.7541 (t0) REVERT: D 413 GLN cc_start: 0.6936 (OUTLIER) cc_final: 0.6350 (tm-30) REVERT: D 446 LEU cc_start: 0.8663 (mp) cc_final: 0.7979 (mm) outliers start: 24 outliers final: 18 residues processed: 105 average time/residue: 0.1373 time to fit residues: 21.7330 Evaluate side-chains 99 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 79 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 132 LYS Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 413 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 99 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 56.6624 > 50:) chunk 8 optimal weight: 20.0000 chunk 139 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 137 optimal weight: 0.6980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.102599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.077849 restraints weight = 44207.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.078160 restraints weight = 28261.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.078573 restraints weight = 21799.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.078916 restraints weight = 17912.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.078999 restraints weight = 16972.438| |-----------------------------------------------------------------------------| r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 16528 Z= 0.305 Angle : 0.757 9.184 23172 Z= 0.409 Chirality : 0.046 0.235 2564 Planarity : 0.006 0.049 2342 Dihedral : 25.270 146.544 3749 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.63 % Allowed : 12.67 % Favored : 84.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.15 (0.22), residues: 1464 helix: 1.34 (0.23), residues: 496 sheet: -0.97 (0.33), residues: 212 loop : -0.79 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 513 TYR 0.019 0.002 TYR D 435 PHE 0.028 0.003 PHE D 306 TRP 0.011 0.002 TRP B 178 HIS 0.006 0.001 HIS D 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00676 / 0.30 (16528) covalent geometry : angle 0.75722 / 0.41 (23172) hydrogen bonds : bond 0.05953 / 6.63 ( 698) hydrogen bonds : angle 4.62874 / 6.07 ( 1784) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 79 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 405 ASP cc_start: 0.8142 (m-30) cc_final: 0.7743 (t0) REVERT: B 431 TYR cc_start: 0.7521 (m-80) cc_final: 0.6949 (m-80) REVERT: B 446 LEU cc_start: 0.9185 (mp) cc_final: 0.8961 (mp) REVERT: C 411 MET cc_start: 0.8568 (mtp) cc_final: 0.8121 (mtp) REVERT: D 223 ARG cc_start: 0.9155 (OUTLIER) cc_final: 0.8836 (ptm160) REVERT: D 405 ASP cc_start: 0.8033 (m-30) cc_final: 0.7694 (t0) REVERT: D 446 LEU cc_start: 0.9035 (mp) cc_final: 0.8498 (mm) REVERT: D 465 GLN cc_start: 0.6636 (mm-40) cc_final: 0.6367 (mm-40) outliers start: 34 outliers final: 27 residues processed: 105 average time/residue: 0.1353 time to fit residues: 21.6473 Evaluate side-chains 102 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 74 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 445 ASN Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 132 LYS Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 399 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 61 optimal weight: 0.6980 chunk 91 optimal weight: 2.9990 chunk 35 optimal weight: 9.9990 chunk 145 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 119 optimal weight: 0.6980 chunk 113 optimal weight: 0.0010 chunk 38 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 425 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.105551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.080921 restraints weight = 43420.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.081436 restraints weight = 25759.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.081817 restraints weight = 20336.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.082141 restraints weight = 17201.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.082240 restraints weight = 16238.472| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 16528 Z= 0.128 Angle : 0.607 10.005 23172 Z= 0.338 Chirality : 0.040 0.172 2564 Planarity : 0.004 0.033 2342 Dihedral : 25.078 150.642 3749 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.62 % Allowed : 13.52 % Favored : 84.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.22), residues: 1464 helix: 1.92 (0.23), residues: 498 sheet: -0.21 (0.37), residues: 166 loop : -0.65 (0.23), residues: 800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 367 TYR 0.021 0.001 TYR D 435 PHE 0.037 0.002 PHE D 468 TRP 0.017 0.001 TRP A 225 HIS 0.004 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.13 (16528) covalent geometry : angle 0.60715 / 0.34 (23172) hydrogen bonds : bond 0.04265 / 4.72 ( 698) hydrogen bonds : angle 4.09198 / 5.40 ( 1784) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 87 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 406 LEU cc_start: 0.8676 (mm) cc_final: 0.8451 (mm) REVERT: B 381 MET cc_start: 0.7667 (pmm) cc_final: 0.7358 (pmm) REVERT: B 405 ASP cc_start: 0.7913 (m-30) cc_final: 0.7651 (t70) REVERT: B 431 TYR cc_start: 0.7293 (m-80) cc_final: 0.6891 (m-80) REVERT: B 446 LEU cc_start: 0.9012 (mp) cc_final: 0.8424 (mm) REVERT: D 223 ARG cc_start: 0.9081 (OUTLIER) cc_final: 0.8716 (ptm160) REVERT: D 405 ASP cc_start: 0.7925 (m-30) cc_final: 0.7645 (t70) REVERT: D 446 LEU cc_start: 0.8973 (mp) cc_final: 0.8363 (mm) outliers start: 21 outliers final: 16 residues processed: 106 average time/residue: 0.1362 time to fit residues: 21.9442 Evaluate side-chains 92 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 75 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 445 ASN Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 132 LYS Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 399 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 17 optimal weight: 20.0000 chunk 133 optimal weight: 0.9990 chunk 95 optimal weight: 10.0000 chunk 112 optimal weight: 0.5980 chunk 58 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 1 optimal weight: 9.9990 chunk 96 optimal weight: 0.9980 chunk 89 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 465 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.105273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.080848 restraints weight = 43080.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.080953 restraints weight = 27161.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.081255 restraints weight = 22218.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.081704 restraints weight = 18596.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.081845 restraints weight = 17283.731| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.4549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16528 Z= 0.141 Angle : 0.609 10.620 23172 Z= 0.335 Chirality : 0.040 0.172 2564 Planarity : 0.004 0.037 2342 Dihedral : 25.075 149.680 3746 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 1.39 % Allowed : 14.14 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.22), residues: 1464 helix: 1.97 (0.23), residues: 498 sheet: -0.31 (0.36), residues: 180 loop : -0.57 (0.23), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 416 TYR 0.018 0.001 TYR D 435 PHE 0.026 0.002 PHE B 468 TRP 0.011 0.001 TRP A 225 HIS 0.006 0.001 HIS A 217 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.14 (16528) covalent geometry : angle 0.60931 / 0.34 (23172) hydrogen bonds : bond 0.04338 / 4.83 ( 698) hydrogen bonds : angle 4.06003 / 5.34 ( 1784) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.548 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 463 ASN cc_start: 0.8269 (t0) cc_final: 0.7393 (p0) REVERT: B 381 MET cc_start: 0.7636 (pmm) cc_final: 0.7322 (pmm) REVERT: B 405 ASP cc_start: 0.8013 (m-30) cc_final: 0.7768 (t70) REVERT: B 431 TYR cc_start: 0.7189 (m-80) cc_final: 0.6879 (m-80) REVERT: B 446 LEU cc_start: 0.9049 (mp) cc_final: 0.8453 (mm) REVERT: D 223 ARG cc_start: 0.9110 (OUTLIER) cc_final: 0.8746 (ptm160) REVERT: D 405 ASP cc_start: 0.8051 (m-30) cc_final: 0.7657 (t70) REVERT: D 446 LEU cc_start: 0.9032 (mp) cc_final: 0.8422 (mm) outliers start: 18 outliers final: 14 residues processed: 93 average time/residue: 0.1463 time to fit residues: 20.2024 Evaluate side-chains 91 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 470 THR Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 132 LYS Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 465 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 81 optimal weight: 0.5980 chunk 7 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 21 optimal weight: 7.9990 chunk 60 optimal weight: 0.0980 chunk 131 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 123 optimal weight: 3.9990 chunk 30 optimal weight: 0.3980 chunk 134 optimal weight: 0.0970 chunk 144 optimal weight: 0.0970 overall best weight: 0.2576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 375 GLN D 413 GLN D 465 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.106713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.082496 restraints weight = 42779.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.082659 restraints weight = 26367.649| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.083249 restraints weight = 21753.250| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.083392 restraints weight = 18018.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.083557 restraints weight = 16656.317| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.4593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 16528 Z= 0.118 Angle : 0.591 10.215 23172 Z= 0.329 Chirality : 0.039 0.167 2564 Planarity : 0.004 0.034 2342 Dihedral : 25.002 150.760 3744 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.16 % Allowed : 14.45 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.22), residues: 1464 helix: 1.95 (0.23), residues: 508 sheet: -0.48 (0.36), residues: 188 loop : -0.52 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 416 TYR 0.020 0.001 TYR B 435 PHE 0.029 0.001 PHE D 468 TRP 0.014 0.001 TRP A 225 HIS 0.005 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.12 (16528) covalent geometry : angle 0.59126 / 0.33 (23172) hydrogen bonds : bond 0.03919 / 4.35 ( 698) hydrogen bonds : angle 3.91313 / 5.14 ( 1784) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2262.49 seconds wall clock time: 40 minutes 2.89 seconds (2402.89 seconds total)