Starting phenix.real_space_refine on Fri Jul 3 18:52:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7svw_25455/07_2026/7svw_25455.cif Found real_map, /net/cci-nas-00/data/ceres_data/7svw_25455/07_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_25455/07_2026/7svw_25455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7svw_25455/07_2026/7svw_25455.map" model { file = "/net/cci-nas-00/data/ceres_data/7svw_25455/07_2026/7svw_25455.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7svw_25455/07_2026/7svw_25455.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7svw_25455/07_2026/7svw_25455.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7svw_25455/07_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-dev-6108/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: 2.81, per 1000 atoms: 0.18 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: 1.10 Conformation dependent library (CDL) restraints added in 539.7 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: 1.56 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: 2.74 Time building geometry restraints manager: 1.56 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: 21922 2.91 - 5.82: 969 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: 1.740 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.440 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.550 ------------------------------------------------------------------------------- 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= 0.848 Angle : 1.497 14.555 23172 Z= 1.103 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 1.49666 / 1.10 (23172) hydrogen bonds : bond 0.18197 / 19.60 ( 698) hydrogen bonds : angle 6.92160 / 8.92 ( 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 : 0.494 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: 0.8431 (mmm) REVERT: B 137 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7705 (mtt90) REVERT: B 179 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.6943 (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: 0.7829 (mp) REVERT: D 77 ARG cc_start: 0.6841 (OUTLIER) cc_final: 0.6281 (tpt-90) REVERT: D 129 MET cc_start: 0.8612 (tpp) cc_final: 0.7642 (tpt) REVERT: D 132 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7383 (tmtp) REVERT: D 179 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7195 (mmm160) REVERT: D 405 ASP cc_start: 0.6642 (m-30) cc_final: 0.6396 (t0) outliers start: 36 outliers final: 10 residues processed: 244 average time/residue: 0.1608 time to fit residues: 53.0471 Evaluate side-chains 113 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 97 time to evaluate : 0.517 ------------------------------------------------------------------------------- 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 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 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: 8.9990 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: 0.6980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.5040 ------------------------------------------------------------------------------- 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 = 0.3929 r_free = 0.3929 target = 0.117116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.092449 restraints weight = 41922.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.093153 restraints weight = 28394.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.093698 restraints weight = 21622.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.093895 restraints weight = 18001.956| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.094166 restraints weight = 16601.374| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 16528 Z= 0.166 Angle : 0.688 7.875 23172 Z= 0.393 Chirality : 0.042 0.212 2564 Planarity : 0.006 0.148 2342 Dihedral : 24.029 155.356 3783 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.24 % Allowed : 6.65 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.21), residues: 1464 helix: 1.29 (0.23), residues: 498 sheet: -0.36 (0.31), residues: 220 loop : 0.18 (0.22), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG C 513 TYR 0.012 0.001 TYR D 459 PHE 0.022 0.002 PHE D 426 TRP 0.021 0.002 TRP C 275 HIS 0.009 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.17 (16528) covalent geometry : angle 0.68781 / 0.39 (23172) hydrogen bonds : bond 0.05509 / 6.07 ( 698) hydrogen bonds : angle 5.01419 / 6.67 ( 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 143 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 114 time to evaluate : 0.527 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 LEU cc_start: 0.6652 (tp) cc_final: 0.6443 (tp) REVERT: B 405 ASP cc_start: 0.7752 (m-30) cc_final: 0.7102 (t70) REVERT: B 431 TYR cc_start: 0.7450 (m-80) cc_final: 0.6867 (m-80) REVERT: B 453 ILE cc_start: 0.7712 (OUTLIER) cc_final: 0.7348 (pp) REVERT: C 513 ARG cc_start: 0.6985 (tmt170) cc_final: 0.6748 (tmt170) REVERT: D 223 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8886 (ptm160) REVERT: D 405 ASP cc_start: 0.7759 (m-30) cc_final: 0.7083 (t70) outliers start: 29 outliers final: 15 residues processed: 137 average time/residue: 0.1561 time to fit residues: 29.9509 Evaluate side-chains 100 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 223 ARG 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: 2.9990 chunk 87 optimal weight: 5.9990 chunk 120 optimal weight: 0.5980 chunk 74 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 4 optimal weight: 20.0000 chunk 106 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.111096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.086257 restraints weight = 42677.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.086220 restraints weight = 32358.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.087198 restraints weight = 26204.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.087307 restraints weight = 19733.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.087485 restraints weight = 18926.702| |-----------------------------------------------------------------------------| r_work (final): 0.3392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 16528 Z= 0.225 Angle : 0.708 8.634 23172 Z= 0.393 Chirality : 0.043 0.224 2564 Planarity : 0.005 0.053 2342 Dihedral : 24.652 148.917 3754 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.55 % Allowed : 8.58 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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 (0.21), residues: 1464 helix: 1.23 (0.23), residues: 500 sheet: -0.27 (0.32), residues: 202 loop : -0.10 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 380 TYR 0.038 0.002 TYR D 435 PHE 0.030 0.003 PHE D 468 TRP 0.010 0.002 TRP C 390 HIS 0.008 0.002 HIS D 206 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.23 (16528) covalent geometry : angle 0.70786 / 0.39 (23172) hydrogen bonds : bond 0.05740 / 6.42 ( 698) hydrogen bonds : angle 4.76375 / 6.38 ( 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 127 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 94 time to evaluate : 0.553 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 ASP cc_start: 0.5811 (m-30) cc_final: 0.5474 (m-30) REVERT: B 129 MET cc_start: 0.8857 (ttm) cc_final: 0.8501 (ttt) REVERT: B 272 HIS cc_start: 0.7626 (OUTLIER) cc_final: 0.6625 (m-70) REVERT: B 381 MET cc_start: 0.7744 (pmm) cc_final: 0.7198 (pmm) REVERT: B 405 ASP cc_start: 0.7678 (m-30) cc_final: 0.7036 (t70) REVERT: B 415 ARG cc_start: 0.7408 (mpt90) cc_final: 0.7110 (mpt180) REVERT: B 431 TYR cc_start: 0.7340 (m-80) cc_final: 0.7032 (m-80) REVERT: B 453 ILE cc_start: 0.8115 (pt) cc_final: 0.7704 (pp) REVERT: B 465 GLN cc_start: 0.6128 (mm-40) cc_final: 0.5925 (mm-40) REVERT: C 304 LEU cc_start: 0.8596 (mt) cc_final: 0.8336 (mp) REVERT: C 407 ASP cc_start: 0.5989 (m-30) cc_final: 0.5594 (m-30) REVERT: D 129 MET cc_start: 0.8789 (ttm) cc_final: 0.8448 (ttt) REVERT: D 405 ASP cc_start: 0.7745 (m-30) cc_final: 0.7070 (t70) REVERT: D 415 ARG cc_start: 0.7414 (mpt90) cc_final: 0.7028 (mpt180) REVERT: D 465 GLN cc_start: 0.6180 (mm-40) cc_final: 0.5970 (mm-40) outliers start: 33 outliers final: 15 residues processed: 121 average time/residue: 0.1336 time to fit residues: 24.0920 Evaluate side-chains 91 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 75 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 377 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: 1.9990 chunk 130 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 83 optimal weight: 0.7980 chunk 156 optimal weight: 0.5980 chunk 76 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 134 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3855 r_free = 0.3855 target = 0.112499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.087750 restraints weight = 41911.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.088365 restraints weight = 26802.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.088926 restraints weight = 21276.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.089097 restraints weight = 16616.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.089306 restraints weight = 16011.876| |-----------------------------------------------------------------------------| r_work (final): 0.3423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16528 Z= 0.137 Angle : 0.585 6.533 23172 Z= 0.333 Chirality : 0.039 0.175 2564 Planarity : 0.004 0.039 2342 Dihedral : 24.683 151.727 3752 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.16 % Allowed : 9.43 % Favored : 88.41 % 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: 0.70 (0.22), residues: 1464 helix: 1.67 (0.23), residues: 500 sheet: -0.34 (0.32), residues: 202 loop : -0.04 (0.23), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 513 TYR 0.017 0.001 TYR D 197 PHE 0.017 0.002 PHE C 468 TRP 0.011 0.001 TRP A 225 HIS 0.003 0.001 HIS A 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.14 (16528) covalent geometry : angle 0.58472 / 0.33 (23172) hydrogen bonds : bond 0.04398 / 4.89 ( 698) hydrogen bonds : angle 4.34703 / 5.81 ( 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 110 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: B 77 ARG cc_start: 0.6882 (OUTLIER) cc_final: 0.6552 (tpt170) REVERT: B 272 HIS cc_start: 0.7627 (OUTLIER) cc_final: 0.6646 (m-70) REVERT: B 405 ASP cc_start: 0.7767 (m-30) cc_final: 0.7114 (t70) REVERT: B 415 ARG cc_start: 0.7546 (mpt90) cc_final: 0.7219 (mpt90) REVERT: B 431 TYR cc_start: 0.7384 (m-80) cc_final: 0.6914 (m-80) REVERT: B 446 LEU cc_start: 0.8442 (mp) cc_final: 0.7643 (mm) REVERT: B 453 ILE cc_start: 0.8139 (OUTLIER) cc_final: 0.7820 (pt) REVERT: C 407 ASP cc_start: 0.5590 (m-30) cc_final: 0.5250 (m-30) REVERT: D 129 MET cc_start: 0.8781 (ttm) cc_final: 0.8367 (ttt) REVERT: D 405 ASP cc_start: 0.7834 (m-30) cc_final: 0.7178 (t70) REVERT: D 446 LEU cc_start: 0.8350 (mp) cc_final: 0.7577 (mm) REVERT: D 453 ILE cc_start: 0.8222 (OUTLIER) cc_final: 0.7964 (pp) outliers start: 28 outliers final: 18 residues processed: 105 average time/residue: 0.1269 time to fit residues: 20.2446 Evaluate side-chains 90 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 68 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 365 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 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 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 377 ILE Chi-restraints excluded: chain D residue 453 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 91 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 11 optimal weight: 7.9990 chunk 89 optimal weight: 6.9990 chunk 28 optimal weight: 6.9990 chunk 113 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 108 optimal weight: 0.0870 overall best weight: 1.1362 ------------------------------------------------------------------------------- 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 = 0.3828 r_free = 0.3828 target = 0.110882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.086266 restraints weight = 42102.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.086293 restraints weight = 28867.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.087074 restraints weight = 22982.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.087256 restraints weight = 17456.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.087468 restraints weight = 16454.749| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.3528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16528 Z= 0.163 Angle : 0.604 13.852 23172 Z= 0.338 Chirality : 0.040 0.168 2564 Planarity : 0.004 0.043 2342 Dihedral : 24.841 150.336 3752 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.70 % Allowed : 10.97 % Favored : 86.32 % 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: 0.72 (0.22), residues: 1464 helix: 1.80 (0.23), residues: 500 sheet: -0.21 (0.34), residues: 184 loop : -0.16 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 447 TYR 0.012 0.001 TYR D 459 PHE 0.028 0.002 PHE B 468 TRP 0.009 0.001 TRP A 225 HIS 0.004 0.001 HIS B 309 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.16 (16528) covalent geometry : angle 0.60445 / 0.34 (23172) hydrogen bonds : bond 0.04612 / 5.15 ( 698) hydrogen bonds : angle 4.25430 / 5.64 ( 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 107 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 72 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 77 ARG cc_start: 0.6772 (OUTLIER) cc_final: 0.6516 (tpt-90) REVERT: B 272 HIS cc_start: 0.7696 (OUTLIER) cc_final: 0.6887 (m-70) REVERT: B 405 ASP cc_start: 0.7893 (m-30) cc_final: 0.7351 (t70) REVERT: B 415 ARG cc_start: 0.7480 (mpt90) cc_final: 0.7206 (mpt90) REVERT: B 431 TYR cc_start: 0.7395 (m-80) cc_final: 0.6958 (m-80) REVERT: B 446 LEU cc_start: 0.8587 (mp) cc_final: 0.8031 (mm) REVERT: D 129 MET cc_start: 0.8820 (ttm) cc_final: 0.8401 (ttt) REVERT: D 405 ASP cc_start: 0.7878 (m-30) cc_final: 0.7294 (t70) REVERT: D 446 LEU cc_start: 0.8402 (mp) cc_final: 0.7551 (mm) REVERT: D 453 ILE cc_start: 0.8227 (OUTLIER) cc_final: 0.7953 (pp) outliers start: 35 outliers final: 18 residues processed: 102 average time/residue: 0.1194 time to fit residues: 19.1412 Evaluate side-chains 90 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 384 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 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 408 ILE Chi-restraints excluded: chain B residue 423 CYS 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 377 ILE Chi-restraints excluded: chain D residue 453 ILE 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: 1.9990 chunk 101 optimal weight: 0.0980 chunk 162 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 87 optimal weight: 2.9990 chunk 11 optimal weight: 7.9990 chunk 80 optimal weight: 0.9980 chunk 141 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 413 GLN B 465 GLN D 445 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.108854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.084815 restraints weight = 44138.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.085445 restraints weight = 31065.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.086101 restraints weight = 27597.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.086142 restraints weight = 20436.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.086347 restraints weight = 19509.013| |-----------------------------------------------------------------------------| r_work (final): 0.3401 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.3967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16528 Z= 0.198 Angle : 0.643 7.849 23172 Z= 0.357 Chirality : 0.042 0.169 2564 Planarity : 0.005 0.038 2342 Dihedral : 25.002 148.627 3749 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.09 % Allowed : 11.13 % Favored : 85.78 % 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: 0.37 (0.22), residues: 1464 helix: 1.72 (0.23), residues: 500 sheet: -0.85 (0.32), residues: 208 loop : -0.38 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 416 TYR 0.019 0.002 TYR D 435 PHE 0.019 0.002 PHE B 306 TRP 0.010 0.002 TRP A 225 HIS 0.006 0.001 HIS D 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.20 (16528) covalent geometry : angle 0.64316 / 0.36 (23172) hydrogen bonds : bond 0.04906 / 5.46 ( 698) hydrogen bonds : angle 4.33258 / 5.72 ( 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 116 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 76 time to evaluate : 0.549 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 411 MET cc_start: 0.7999 (mtp) cc_final: 0.7741 (mtp) REVERT: B 77 ARG cc_start: 0.6802 (OUTLIER) cc_final: 0.6413 (tpt-90) REVERT: B 381 MET cc_start: 0.7749 (pmm) cc_final: 0.7252 (pmm) REVERT: B 405 ASP cc_start: 0.7915 (m-30) cc_final: 0.7621 (t0) REVERT: B 413 GLN cc_start: 0.6917 (OUTLIER) cc_final: 0.6210 (tm-30) REVERT: B 431 TYR cc_start: 0.7304 (m-80) cc_final: 0.7040 (m-80) REVERT: B 446 LEU cc_start: 0.8681 (mp) cc_final: 0.8255 (mm) REVERT: B 453 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.8028 (pt) REVERT: D 223 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8743 (ptm160) REVERT: D 405 ASP cc_start: 0.7903 (m-30) cc_final: 0.7528 (t0) REVERT: D 446 LEU cc_start: 0.8466 (mp) cc_final: 0.7965 (mm) outliers start: 40 outliers final: 22 residues processed: 107 average time/residue: 0.1310 time to fit residues: 21.5962 Evaluate side-chains 93 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 67 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 384 GLN 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 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 413 GLN Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 453 ILE Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain C residue 245 ASP 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 D residue 34 ILE Chi-restraints excluded: chain D residue 72 LEU 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 399 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 19 optimal weight: 6.9990 chunk 45 optimal weight: 0.4980 chunk 50 optimal weight: 1.9990 chunk 131 optimal weight: 2.9990 chunk 132 optimal weight: 0.6980 chunk 130 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 20.0000 chunk 96 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 81 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.3830 r_free = 0.3830 target = 0.110132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.086360 restraints weight = 44149.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.087276 restraints weight = 29862.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.087710 restraints weight = 26053.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.087836 restraints weight = 19399.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.088021 restraints weight = 18490.766| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 16528 Z= 0.130 Angle : 0.584 8.578 23172 Z= 0.326 Chirality : 0.039 0.161 2564 Planarity : 0.004 0.034 2342 Dihedral : 24.968 151.229 3749 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.01 % Allowed : 12.75 % 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: 0.67 (0.22), residues: 1464 helix: 1.96 (0.23), residues: 500 sheet: -0.38 (0.35), residues: 184 loop : -0.31 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 415 TYR 0.017 0.001 TYR B 197 PHE 0.019 0.002 PHE B 468 TRP 0.012 0.001 TRP A 225 HIS 0.003 0.001 HIS D 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.13 (16528) covalent geometry : angle 0.58427 / 0.33 (23172) hydrogen bonds : bond 0.04243 / 4.72 ( 698) hydrogen bonds : angle 4.08658 / 5.37 ( 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: 26 poor density : 80 time to evaluate : 0.540 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 463 ASN cc_start: 0.8037 (t0) cc_final: 0.7216 (p0) REVERT: B 77 ARG cc_start: 0.6651 (OUTLIER) cc_final: 0.6432 (tpt-90) REVERT: B 381 MET cc_start: 0.7599 (pmm) cc_final: 0.7300 (pmm) REVERT: B 405 ASP cc_start: 0.7889 (m-30) cc_final: 0.7608 (t0) REVERT: B 413 GLN cc_start: 0.7042 (OUTLIER) cc_final: 0.6528 (tm-30) REVERT: B 423 CYS cc_start: 0.6053 (OUTLIER) cc_final: 0.4960 (m) REVERT: B 431 TYR cc_start: 0.7342 (m-80) cc_final: 0.7072 (m-80) REVERT: B 446 LEU cc_start: 0.8579 (mp) cc_final: 0.8040 (mm) REVERT: D 223 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8738 (ptm160) REVERT: D 405 ASP cc_start: 0.7800 (m-30) cc_final: 0.7414 (t0) REVERT: D 413 GLN cc_start: 0.6624 (OUTLIER) cc_final: 0.6271 (tm-30) REVERT: D 446 LEU cc_start: 0.8357 (mp) cc_final: 0.7924 (mm) outliers start: 26 outliers final: 17 residues processed: 100 average time/residue: 0.1347 time to fit residues: 20.4215 Evaluate side-chains 94 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 384 GLN Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 THR 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 77 ARG 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 B residue 423 CYS Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 408 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 223 ARG Chi-restraints excluded: chain D residue 377 ILE 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 optimal weight: 0.5980 chunk 8 optimal weight: 10.0000 chunk 139 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 93 optimal weight: 0.0270 chunk 60 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 63 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 90 optimal weight: 0.7980 chunk 137 optimal weight: 0.9980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 413 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.108781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.084452 restraints weight = 42291.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.084661 restraints weight = 26718.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.085188 restraints weight = 20717.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.085532 restraints weight = 17185.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.085659 restraints weight = 16096.697| |-----------------------------------------------------------------------------| r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16528 Z= 0.125 Angle : 0.575 8.989 23172 Z= 0.321 Chirality : 0.039 0.157 2564 Planarity : 0.004 0.033 2342 Dihedral : 24.961 151.710 3748 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.01 % Allowed : 13.14 % 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: 0.77 (0.22), residues: 1464 helix: 2.05 (0.23), residues: 500 sheet: -0.34 (0.35), residues: 184 loop : -0.25 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 367 TYR 0.015 0.001 TYR B 435 PHE 0.017 0.001 PHE A 468 TRP 0.011 0.001 TRP A 225 HIS 0.003 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.12 (16528) covalent geometry : angle 0.57524 / 0.32 (23172) hydrogen bonds : bond 0.04055 / 4.52 ( 698) hydrogen bonds : angle 3.98607 / 5.24 ( 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 102 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 ASN cc_start: 0.8149 (t0) cc_final: 0.7373 (p0) REVERT: B 381 MET cc_start: 0.7630 (pmm) cc_final: 0.7364 (pmm) REVERT: B 405 ASP cc_start: 0.8044 (m-30) cc_final: 0.7695 (t0) REVERT: B 423 CYS cc_start: 0.6660 (p) cc_final: 0.6394 (p) REVERT: B 431 TYR cc_start: 0.7399 (m-80) cc_final: 0.6959 (m-80) REVERT: B 446 LEU cc_start: 0.8509 (mp) cc_final: 0.8047 (mm) REVERT: C 463 ASN cc_start: 0.8201 (t0) cc_final: 0.7410 (p0) REVERT: D 223 ARG cc_start: 0.9086 (OUTLIER) cc_final: 0.8844 (ptm160) REVERT: D 405 ASP cc_start: 0.7997 (m-30) cc_final: 0.7593 (t0) REVERT: D 446 LEU cc_start: 0.8506 (mp) cc_final: 0.7958 (mm) outliers start: 26 outliers final: 22 residues processed: 96 average time/residue: 0.1259 time to fit residues: 18.7224 Evaluate side-chains 96 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 73 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 355 ARG Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 384 GLN Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 THR 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 307 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 408 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 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: 0.0170 chunk 91 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 145 optimal weight: 0.7980 chunk 89 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 113 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 413 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.107163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.082413 restraints weight = 43116.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.082861 restraints weight = 25922.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.083108 restraints weight = 20214.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.083540 restraints weight = 17367.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.083648 restraints weight = 16084.349| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 16528 Z= 0.124 Angle : 0.572 9.631 23172 Z= 0.318 Chirality : 0.039 0.157 2564 Planarity : 0.004 0.033 2342 Dihedral : 24.965 151.719 3744 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.85 % Allowed : 13.14 % Favored : 85.01 % 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: 0.81 (0.22), residues: 1464 helix: 2.09 (0.23), residues: 500 sheet: -0.30 (0.35), residues: 184 loop : -0.24 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 372 TYR 0.014 0.001 TYR B 435 PHE 0.033 0.002 PHE B 468 TRP 0.010 0.001 TRP A 225 HIS 0.003 0.001 HIS B 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00236 / 0.12 (16528) covalent geometry : angle 0.57242 / 0.32 (23172) hydrogen bonds : bond 0.03971 / 4.43 ( 698) hydrogen bonds : angle 3.93053 / 5.15 ( 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 104 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 80 time to evaluate : 0.547 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 ASN cc_start: 0.8374 (t0) cc_final: 0.7491 (p0) REVERT: B 381 MET cc_start: 0.7709 (pmm) cc_final: 0.7385 (pmm) REVERT: B 405 ASP cc_start: 0.8074 (m-30) cc_final: 0.7742 (t0) REVERT: B 431 TYR cc_start: 0.7281 (m-80) cc_final: 0.6898 (m-80) REVERT: B 446 LEU cc_start: 0.8557 (mp) cc_final: 0.8064 (mm) REVERT: C 463 ASN cc_start: 0.8357 (t0) cc_final: 0.7548 (p0) REVERT: D 223 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8795 (ptm160) REVERT: D 405 ASP cc_start: 0.8063 (m-30) cc_final: 0.7656 (t0) REVERT: D 446 LEU cc_start: 0.8594 (mp) cc_final: 0.8001 (mm) outliers start: 24 outliers final: 21 residues processed: 97 average time/residue: 0.1207 time to fit residues: 18.3421 Evaluate side-chains 98 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 384 GLN Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 496 THR 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 307 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 413 GLN Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 355 ARG Chi-restraints excluded: chain C residue 408 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 76 LEU 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: 9.9990 chunk 133 optimal weight: 0.0020 chunk 95 optimal weight: 10.0000 chunk 112 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 32 optimal weight: 2.9990 chunk 1 optimal weight: 9.9990 chunk 96 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 overall best weight: 1.6794 ------------------------------------------------------------------------------- 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 = 0.3732 r_free = 0.3732 target = 0.105215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.080413 restraints weight = 43312.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.080981 restraints weight = 27025.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.081174 restraints weight = 20926.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.081534 restraints weight = 17480.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.081673 restraints weight = 16027.015| |-----------------------------------------------------------------------------| r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16528 Z= 0.202 Angle : 0.637 10.392 23172 Z= 0.351 Chirality : 0.041 0.168 2564 Planarity : 0.004 0.036 2342 Dihedral : 25.056 149.195 3744 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.70 % Allowed : 13.60 % 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: 0.57 (0.22), residues: 1464 helix: 1.96 (0.23), residues: 498 sheet: -0.44 (0.35), residues: 198 loop : -0.44 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 415 TYR 0.014 0.001 TYR B 435 PHE 0.019 0.002 PHE D 306 TRP 0.007 0.001 TRP A 225 HIS 0.005 0.001 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.20 (16528) covalent geometry : angle 0.63728 / 0.35 (23172) hydrogen bonds : bond 0.04710 / 5.23 ( 698) hydrogen bonds : angle 4.12827 / 5.38 ( 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 98 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 ASN cc_start: 0.8396 (t0) cc_final: 0.7509 (p0) REVERT: B 405 ASP cc_start: 0.8058 (m-30) cc_final: 0.7779 (t0) REVERT: B 431 TYR cc_start: 0.7284 (m-80) cc_final: 0.6871 (m-80) REVERT: B 446 LEU cc_start: 0.8703 (mp) cc_final: 0.8205 (mm) REVERT: C 463 ASN cc_start: 0.8363 (t0) cc_final: 0.7551 (p0) REVERT: D 223 ARG cc_start: 0.9132 (OUTLIER) cc_final: 0.8814 (ptm160) REVERT: D 405 ASP cc_start: 0.8134 (m-30) cc_final: 0.7807 (t0) REVERT: D 413 GLN cc_start: 0.6947 (OUTLIER) cc_final: 0.6237 (tm-30) REVERT: D 446 LEU cc_start: 0.8575 (mp) cc_final: 0.8165 (mm) outliers start: 22 outliers final: 15 residues processed: 96 average time/residue: 0.1318 time to fit residues: 19.3447 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 : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 384 GLN Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 496 THR 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 307 VAL Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain C residue 408 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 223 ARG 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 81 optimal weight: 0.0270 chunk 7 optimal weight: 9.9990 chunk 25 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 60 optimal weight: 0.9990 chunk 131 optimal weight: 2.9990 chunk 84 optimal weight: 0.0030 chunk 123 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 134 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.4850 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 413 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.105311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.080854 restraints weight = 42794.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.081819 restraints weight = 26393.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.082027 restraints weight = 22346.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.082208 restraints weight = 16954.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.082368 restraints weight = 15809.563| |-----------------------------------------------------------------------------| r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 moved from start: 0.4351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.199 16528 Z= 0.240 Angle : 0.832 59.200 23172 Z= 0.480 Chirality : 0.042 0.666 2564 Planarity : 0.004 0.049 2342 Dihedral : 25.059 149.230 3744 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.55 % Allowed : 13.76 % Favored : 84.70 % Cbeta Deviations : 0.07 % 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: 0.56 (0.22), residues: 1464 helix: 1.97 (0.23), residues: 498 sheet: -0.45 (0.35), residues: 198 loop : -0.45 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 389 TYR 0.105 0.002 TYR A 233 PHE 0.018 0.002 PHE D 306 TRP 0.008 0.001 TRP A 225 HIS 0.005 0.001 HIS B 105 Details of bonding type rmsd/Z covalent geometry : bond 0.00484 / 0.24 (16528) covalent geometry : angle 0.83207 / 0.48 (23172) hydrogen bonds : bond 0.04641 / 5.15 ( 698) hydrogen bonds : angle 4.12257 / 5.37 ( 1784) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2232.91 seconds wall clock time: 39 minutes 36.89 seconds (2376.89 seconds total)