Starting phenix.real_space_refine on Wed Mar 4 18:52:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7svw_25455/03_2026/7svw_25455.cif Found real_map, /net/cci-nas-00/data/ceres_data/7svw_25455/03_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 { model { file = "/net/cci-nas-00/data/ceres_data/7svw_25455/03_2026/7svw_25455.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7svw_25455/03_2026/7svw_25455.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7svw_25455/03_2026/7svw_25455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7svw_25455/03_2026/7svw_25455.map" } 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-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15830 Number of models: 1 Model: "" Number of chains: 12 Chain: "1" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1021 Classifications: {'DNA': 50} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 49} Chain: "2" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 615 Classifications: {'DNA': 30} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 29} Chain: "3" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 301 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "4" Number of atoms: 1021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1021 Classifications: {'DNA': 50} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 49} Chain: "5" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 615 Classifications: {'DNA': 30} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 29} Chain: "6" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 301 Classifications: {'DNA': 15} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 14} Chain: "A" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2382 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 11, 'TRANS': 284} Chain breaks: 3 Chain: "B" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3595 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 19, 'TRANS': 426} Chain: "C" Number of atoms: 2382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 2382 Classifications: {'peptide': 296} Link IDs: {'PTRANS': 11, 'TRANS': 284} Chain breaks: 3 Chain: "D" Number of atoms: 3595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3595 Classifications: {'peptide': 446} Link IDs: {'PTRANS': 19, 'TRANS': 426} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.82, per 1000 atoms: 0.24 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: 1.53 Conformation dependent library (CDL) restraints added in 724.9 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: 2.51 Creating SS restraints... Processing helix chain 'A' and resid 251 through 261 Processing helix chain 'A' and resid 266 through 270 Processing helix chain 'A' and resid 296 through 305 Processing helix chain 'A' and resid 323 through 331 Processing helix chain 'A' and resid 332 through 335 Processing helix chain 'A' and resid 357 through 372 Processing helix chain 'A' and resid 373 through 376 Processing helix chain 'A' and resid 385 through 393 Processing helix chain 'A' and resid 402 through 407 Processing helix chain 'A' and resid 436 through 440 Processing helix chain 'A' and resid 483 through 502 removed outlier: 3.937A pdb=" N THR A 496 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA A 497 " --> pdb=" O ARG A 493 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ILE A 501 " --> pdb=" O ALA A 497 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER A 502 " --> pdb=" O GLY A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 505 through 519 Processing helix chain 'B' and resid 39 through 54 removed outlier: 4.378A pdb=" N GLU B 54 " --> pdb=" O GLN B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 73 Processing helix chain 'B' and resid 78 through 90 Processing helix chain 'B' and resid 91 through 95 Processing helix chain 'B' and resid 108 through 123 Processing helix chain 'B' and resid 130 through 145 Processing helix chain 'B' and resid 152 through 160 Processing helix chain 'B' and resid 160 through 171 removed outlier: 4.072A pdb=" N GLN B 167 " --> pdb=" O ILE B 163 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N GLN B 168 " --> pdb=" O LEU B 164 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS B 169 " --> pdb=" O GLU B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 261 Processing helix chain 'B' and resid 266 through 270 Processing helix chain 'B' and resid 289 through 293 Processing helix chain 'B' and resid 294 through 305 Processing helix chain 'B' and resid 322 through 331 removed outlier: 3.952A pdb=" N THR B 326 " --> pdb=" O ARG B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 335 Processing helix chain 'B' and resid 357 through 372 Processing helix chain 'B' and resid 385 through 393 Processing helix chain 'B' and resid 402 through 410 removed outlier: 3.888A pdb=" N ASP B 407 " --> pdb=" O ARG B 404 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 440 Processing helix chain 'C' and resid 251 through 261 Processing helix chain 'C' and resid 266 through 270 Processing helix chain 'C' and resid 296 through 305 Processing helix chain 'C' and resid 323 through 331 Processing helix chain 'C' and resid 332 through 335 Processing helix chain 'C' and resid 357 through 372 Processing helix chain 'C' and resid 373 through 376 Processing helix chain 'C' and resid 385 through 393 Processing helix chain 'C' and resid 402 through 407 Processing helix chain 'C' and resid 436 through 440 Processing helix chain 'C' and resid 483 through 499 Processing helix chain 'C' and resid 505 through 519 removed outlier: 3.714A pdb=" N VAL C 510 " --> pdb=" O LEU C 506 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 54 removed outlier: 4.378A pdb=" N GLU D 54 " --> pdb=" O GLN D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 73 Processing helix chain 'D' and resid 77 through 90 removed outlier: 4.166A pdb=" N ARG D 81 " --> pdb=" O ARG D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 95 Processing helix chain 'D' and resid 108 through 123 Processing helix chain 'D' and resid 130 through 145 Processing helix chain 'D' and resid 152 through 160 Processing helix chain 'D' and resid 160 through 171 removed outlier: 4.072A pdb=" N GLN D 167 " --> pdb=" O ILE D 163 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN D 168 " --> pdb=" O LEU D 164 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LYS D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 261 Processing helix chain 'D' and resid 266 through 270 Processing helix chain 'D' and resid 289 through 293 Processing helix chain 'D' and resid 294 through 305 Processing helix chain 'D' and resid 322 through 331 removed outlier: 3.982A pdb=" N THR D 326 " --> pdb=" O ARG D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 332 through 335 Processing helix chain 'D' and resid 357 through 372 Processing helix chain 'D' and resid 385 through 393 Processing helix chain 'D' and resid 402 through 410 removed outlier: 3.888A pdb=" N ASP D 407 " --> pdb=" O ARG D 404 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ILE D 408 " --> pdb=" O ASP D 405 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 440 Processing sheet with id=AA1, first strand: chain 'A' and resid 236 through 243 removed outlier: 6.815A pdb=" N VAL A 229 " --> pdb=" O MET A 238 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE A 240 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR A 227 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU A 242 " --> pdb=" O TRP A 225 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N TRP A 225 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASP A 287 " --> pdb=" O CYS A 204 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N HIS A 206 " --> pdb=" O ASP A 287 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N PHE A 284 " --> pdb=" O HIS A 309 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ARG A 311 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N THR A 286 " --> pdb=" O ARG A 311 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 411 through 417 removed outlier: 5.793A pdb=" N LYS A 412 " --> pdb=" O PHE A 448 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N PHE A 448 " --> pdb=" O LYS A 412 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N SER A 414 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU A 446 " --> pdb=" O SER A 414 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR A 443 " --> pdb=" O GLN A 461 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLN A 461 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ASP A 449 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N THR A 455 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 15.480A pdb=" N ASP A 452 " --> pdb=" O GLN A 475 " (cutoff:3.500A) removed outlier: 11.849A pdb=" N GLN A 475 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N THR A 454 " --> pdb=" O HIS A 473 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N HIS A 473 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE A 456 " --> pdb=" O ARG A 471 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ARG A 471 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL A 458 " --> pdb=" O LEU A 469 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N MET A 430 " --> pdb=" O GLN A 475 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 411 through 417 removed outlier: 5.793A pdb=" N LYS A 412 " --> pdb=" O PHE A 448 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N PHE A 448 " --> pdb=" O LYS A 412 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N SER A 414 " --> pdb=" O LEU A 446 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU A 446 " --> pdb=" O SER A 414 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR A 443 " --> pdb=" O GLN A 461 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N GLN A 461 " --> pdb=" O THR A 443 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ASP A 449 " --> pdb=" O THR A 455 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N THR A 455 " --> pdb=" O ASP A 449 " (cutoff:3.500A) removed outlier: 15.480A pdb=" N ASP A 452 " --> pdb=" O GLN A 475 " (cutoff:3.500A) removed outlier: 11.849A pdb=" N GLN A 475 " --> pdb=" O ASP A 452 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N THR A 454 " --> pdb=" O HIS A 473 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N HIS A 473 " --> pdb=" O THR A 454 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE A 456 " --> pdb=" O ARG A 471 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ARG A 471 " --> pdb=" O ILE A 456 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL A 458 " --> pdb=" O LEU A 469 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 184 through 186 Processing sheet with id=AA5, first strand: chain 'B' and resid 237 through 243 removed outlier: 6.335A pdb=" N ILE B 237 " --> pdb=" O ASP B 231 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N ASP B 231 " --> pdb=" O ILE B 237 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TRP B 202 " --> pdb=" O TYR B 285 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 213 through 214 Processing sheet with id=AA7, first strand: chain 'B' and resid 411 through 417 removed outlier: 5.586A pdb=" N LYS B 412 " --> pdb=" O PHE B 448 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N PHE B 448 " --> pdb=" O LYS B 412 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N SER B 414 " --> pdb=" O LEU B 446 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LEU B 446 " --> pdb=" O SER B 414 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N THR B 443 " --> pdb=" O GLN B 461 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLN B 461 " --> pdb=" O THR B 443 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ASP B 449 " --> pdb=" O THR B 455 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N THR B 455 " --> pdb=" O ASP B 449 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N ARG B 460 " --> pdb=" O PHE B 468 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N PHE B 468 " --> pdb=" O ARG B 460 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU B 462 " --> pdb=" O GLU B 466 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N GLU B 466 " --> pdb=" O GLU B 462 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 424 through 425 Processing sheet with id=AA9, first strand: chain 'C' and resid 236 through 243 removed outlier: 6.816A pdb=" N VAL C 229 " --> pdb=" O MET C 238 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N ILE C 240 " --> pdb=" O THR C 227 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N THR C 227 " --> pdb=" O ILE C 240 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N LEU C 242 " --> pdb=" O TRP C 225 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N TRP C 225 " --> pdb=" O LEU C 242 " (cutoff:3.500A) removed outlier: 4.754A pdb=" N ASP C 287 " --> pdb=" O CYS C 204 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N HIS C 206 " --> pdb=" O ASP C 287 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N PHE C 284 " --> pdb=" O HIS C 309 " (cutoff:3.500A) removed outlier: 7.474A pdb=" N ARG C 311 " --> pdb=" O PHE C 284 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N THR C 286 " --> pdb=" O ARG C 311 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 411 through 417 removed outlier: 5.793A pdb=" N LYS C 412 " --> pdb=" O PHE C 448 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N PHE C 448 " --> pdb=" O LYS C 412 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N SER C 414 " --> pdb=" O LEU C 446 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU C 446 " --> pdb=" O SER C 414 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR C 443 " --> pdb=" O GLN C 461 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLN C 461 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ASP C 449 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N THR C 455 " --> pdb=" O ASP C 449 " (cutoff:3.500A) removed outlier: 15.480A pdb=" N ASP C 452 " --> pdb=" O GLN C 475 " (cutoff:3.500A) removed outlier: 11.849A pdb=" N GLN C 475 " --> pdb=" O ASP C 452 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N THR C 454 " --> pdb=" O HIS C 473 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N HIS C 473 " --> pdb=" O THR C 454 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE C 456 " --> pdb=" O ARG C 471 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ARG C 471 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL C 458 " --> pdb=" O LEU C 469 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N MET C 430 " --> pdb=" O GLN C 475 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 411 through 417 removed outlier: 5.793A pdb=" N LYS C 412 " --> pdb=" O PHE C 448 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N PHE C 448 " --> pdb=" O LYS C 412 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N SER C 414 " --> pdb=" O LEU C 446 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N LEU C 446 " --> pdb=" O SER C 414 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N THR C 443 " --> pdb=" O GLN C 461 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N GLN C 461 " --> pdb=" O THR C 443 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N ASP C 449 " --> pdb=" O THR C 455 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N THR C 455 " --> pdb=" O ASP C 449 " (cutoff:3.500A) removed outlier: 15.480A pdb=" N ASP C 452 " --> pdb=" O GLN C 475 " (cutoff:3.500A) removed outlier: 11.849A pdb=" N GLN C 475 " --> pdb=" O ASP C 452 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N THR C 454 " --> pdb=" O HIS C 473 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N HIS C 473 " --> pdb=" O THR C 454 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N ILE C 456 " --> pdb=" O ARG C 471 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N ARG C 471 " --> pdb=" O ILE C 456 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL C 458 " --> pdb=" O LEU C 469 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 184 through 186 Processing sheet with id=AB4, first strand: chain 'D' and resid 237 through 243 removed outlier: 6.336A pdb=" N ILE D 237 " --> pdb=" O ASP D 231 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ASP D 231 " --> pdb=" O ILE D 237 " (cutoff:3.500A) removed outlier: 5.974A pdb=" N TRP D 202 " --> pdb=" O TYR D 285 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 213 through 214 Processing sheet with id=AB6, first strand: chain 'D' and resid 411 through 417 removed outlier: 5.586A pdb=" N LYS D 412 " --> pdb=" O PHE D 448 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N PHE D 448 " --> pdb=" O LYS D 412 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N SER D 414 " --> pdb=" O LEU D 446 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N LEU D 446 " --> pdb=" O SER D 414 " (cutoff:3.500A) removed outlier: 8.593A pdb=" N THR D 443 " --> pdb=" O GLN D 461 " (cutoff:3.500A) removed outlier: 5.225A pdb=" N GLN D 461 " --> pdb=" O THR D 443 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ASP D 449 " --> pdb=" O THR D 455 " (cutoff:3.500A) removed outlier: 7.760A pdb=" N THR D 455 " --> pdb=" O ASP D 449 " (cutoff:3.500A) removed outlier: 5.909A pdb=" N ARG D 460 " --> pdb=" O PHE D 468 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N PHE D 468 " --> pdb=" O ARG D 460 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU D 462 " --> pdb=" O GLU D 466 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N GLU D 466 " --> pdb=" O GLU D 462 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 424 through 425 524 hydrogen bonds defined for protein. 1392 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 196 hydrogen bonds 392 hydrogen bond angles 0 basepair planarities 79 basepair parallelities 146 stacking parallelities Total time for adding SS restraints: 3.47 Time building geometry restraints manager: 2.00 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=" CA LEU B 94 " pdb=" C LEU B 94 " ideal model delta sigma weight residual 1.522 1.443 0.079 1.40e-02 5.10e+03 3.21e+01 ... (remaining 16523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.91: 21926 2.91 - 5.82: 965 5.82 - 8.73: 216 8.73 - 11.64: 56 11.64 - 14.56: 9 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 - 0.094: 2227 0.094 - 0.188: 269 0.188 - 0.282: 42 0.282 - 0.377: 17 0.377 - 0.471: 9 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 -2.66 -2.19 -0.47 2.00e-01 2.50e+01 5.54e+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: 2.470 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.890 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 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 0.079 16528 Z= 0.778 Angle : 1.461 14.555 23172 Z= 1.036 Chirality : 0.074 0.471 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 covalent geometry : bond 0.01161 (16528) covalent geometry : angle 1.46054 (23172) hydrogen bonds : bond 0.18197 ( 698) hydrogen bonds : angle 6.92160 ( 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 : 0.419 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: 0.1860 time to fit residues: 60.8215 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 : 0.536 ------------------------------------------------------------------------------- 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: 2.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0980 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0270 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 overall best weight: 0.5240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN A 503 ASN A 508 GLN C 299 GLN D 43 GLN D 342 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.116442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.091684 restraints weight = 42125.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.092425 restraints weight = 27885.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.092994 restraints weight = 21378.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.093180 restraints weight = 18285.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.093435 restraints weight = 17022.960| |-----------------------------------------------------------------------------| r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7689 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16528 Z= 0.149 Angle : 0.619 8.581 23172 Z= 0.344 Chirality : 0.038 0.152 2564 Planarity : 0.005 0.050 2342 Dihedral : 23.830 153.434 3783 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.32 % Allowed : 6.72 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.22), residues: 1464 helix: 1.64 (0.23), residues: 510 sheet: -0.16 (0.31), residues: 220 loop : 0.30 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 513 TYR 0.012 0.001 TYR D 459 PHE 0.021 0.002 PHE D 426 TRP 0.009 0.002 TRP C 275 HIS 0.007 0.001 HIS A 296 Details of bonding type rmsd covalent geometry : bond 0.00318 (16528) covalent geometry : angle 0.61929 (23172) hydrogen bonds : bond 0.04180 ( 698) hydrogen bonds : angle 4.50181 ( 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 152 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 122 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 407 ASP cc_start: 0.5539 (m-30) cc_final: 0.5294 (m-30) REVERT: A 514 ASP cc_start: 0.6831 (OUTLIER) cc_final: 0.6613 (t0) REVERT: B 77 ARG cc_start: 0.7074 (OUTLIER) cc_final: 0.6770 (tpt170) REVERT: B 405 ASP cc_start: 0.7706 (m-30) cc_final: 0.7165 (t0) REVERT: B 431 TYR cc_start: 0.7190 (m-80) cc_final: 0.6793 (m-80) REVERT: B 453 ILE cc_start: 0.7898 (OUTLIER) cc_final: 0.7644 (pp) REVERT: B 469 LEU cc_start: 0.7077 (tp) cc_final: 0.6857 (tp) REVERT: D 223 ARG cc_start: 0.9072 (OUTLIER) cc_final: 0.8749 (ptm160) REVERT: D 405 ASP cc_start: 0.7812 (m-30) cc_final: 0.7138 (t0) REVERT: D 469 LEU cc_start: 0.7305 (tp) cc_final: 0.7007 (tt) outliers start: 30 outliers final: 17 residues processed: 149 average time/residue: 0.1553 time to fit residues: 32.7547 Evaluate side-chains 100 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 79 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 452 ASP Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 500 THR 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 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 77 ARG 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 C residue 429 LEU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 46 LEU Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 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: 7.9990 chunk 120 optimal weight: 0.0050 chunk 74 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 83 optimal weight: 0.4980 chunk 4 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 101 optimal weight: 0.0670 chunk 12 optimal weight: 2.9990 overall best weight: 1.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 299 GLN C 199 ASN C 299 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.110343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.085718 restraints weight = 44514.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.087444 restraints weight = 28635.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.087593 restraints weight = 22341.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.087715 restraints weight = 18000.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.087912 restraints weight = 16998.444| |-----------------------------------------------------------------------------| r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16528 Z= 0.198 Angle : 0.632 9.419 23172 Z= 0.350 Chirality : 0.040 0.142 2564 Planarity : 0.005 0.047 2342 Dihedral : 24.474 147.906 3756 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 3.01 % Allowed : 8.58 % 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: 0.95 (0.22), residues: 1464 helix: 1.76 (0.23), residues: 500 sheet: -0.24 (0.32), residues: 208 loop : 0.22 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 404 TYR 0.011 0.001 TYR D 435 PHE 0.021 0.002 PHE D 468 TRP 0.010 0.002 TRP D 275 HIS 0.005 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00445 (16528) covalent geometry : angle 0.63217 (23172) hydrogen bonds : bond 0.04533 ( 698) hydrogen bonds : angle 4.26857 ( 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 130 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 91 time to evaluate : 0.503 Fit side-chains REVERT: A 306 PHE cc_start: 0.7911 (p90) cc_final: 0.7624 (p90) REVERT: A 407 ASP cc_start: 0.5862 (m-30) cc_final: 0.5509 (m-30) REVERT: A 463 ASN cc_start: 0.8185 (t0) cc_final: 0.7551 (p0) REVERT: B 129 MET cc_start: 0.8918 (ttm) cc_final: 0.8570 (ttt) REVERT: B 405 ASP cc_start: 0.7767 (m-30) cc_final: 0.7211 (t70) REVERT: B 431 TYR cc_start: 0.7206 (m-80) cc_final: 0.6912 (m-80) REVERT: B 453 ILE cc_start: 0.8074 (pt) cc_final: 0.7795 (pt) REVERT: D 129 MET cc_start: 0.8875 (ttm) cc_final: 0.8500 (ttt) REVERT: D 223 ARG cc_start: 0.9100 (OUTLIER) cc_final: 0.8826 (ptm160) REVERT: D 405 ASP cc_start: 0.7853 (m-30) cc_final: 0.7321 (t70) outliers start: 39 outliers final: 23 residues processed: 124 average time/residue: 0.1308 time to fit residues: 23.9985 Evaluate side-chains 100 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 76 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 381 MET Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 465 GLN 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 Chi-restraints excluded: chain D residue 408 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 13 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 130 optimal weight: 5.9990 chunk 85 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 76 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 1 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 ASN B 413 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.111171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.087756 restraints weight = 44530.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.087774 restraints weight = 33264.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.089020 restraints weight = 27725.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.088967 restraints weight = 21908.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.089241 restraints weight = 19991.813| |-----------------------------------------------------------------------------| r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.3992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 16528 Z= 0.151 Angle : 0.565 10.740 23172 Z= 0.313 Chirality : 0.037 0.154 2564 Planarity : 0.004 0.038 2342 Dihedral : 24.380 149.245 3744 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.55 % Allowed : 10.82 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.22), residues: 1464 helix: 2.15 (0.23), residues: 500 sheet: -0.23 (0.33), residues: 210 loop : 0.13 (0.24), residues: 754 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 513 TYR 0.012 0.001 TYR D 431 PHE 0.024 0.001 PHE C 306 TRP 0.010 0.001 TRP C 225 HIS 0.003 0.001 HIS B 206 Details of bonding type rmsd covalent geometry : bond 0.00333 (16528) covalent geometry : angle 0.56544 (23172) hydrogen bonds : bond 0.03717 ( 698) hydrogen bonds : angle 3.96816 ( 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 120 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 87 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: A 463 ASN cc_start: 0.8117 (t0) cc_final: 0.7472 (p0) REVERT: B 381 MET cc_start: 0.7430 (pmm) cc_final: 0.7227 (pmm) REVERT: B 405 ASP cc_start: 0.7871 (m-30) cc_final: 0.7605 (t0) REVERT: B 431 TYR cc_start: 0.7117 (m-80) cc_final: 0.6893 (m-80) REVERT: C 463 ASN cc_start: 0.8098 (t0) cc_final: 0.7460 (p0) REVERT: D 129 MET cc_start: 0.8780 (ttm) cc_final: 0.8367 (ttt) REVERT: D 223 ARG cc_start: 0.9080 (OUTLIER) cc_final: 0.8850 (ptm160) REVERT: D 405 ASP cc_start: 0.7898 (m-30) cc_final: 0.7579 (t0) REVERT: D 465 GLN cc_start: 0.6378 (mm-40) cc_final: 0.6146 (mm-40) outliers start: 33 outliers final: 18 residues processed: 113 average time/residue: 0.1218 time to fit residues: 21.2474 Evaluate side-chains 96 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 446 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 91 optimal weight: 0.4980 chunk 36 optimal weight: 0.6980 chunk 84 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 28 optimal weight: 0.4980 chunk 113 optimal weight: 0.9980 chunk 149 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 108 optimal weight: 0.0030 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3865 r_free = 0.3865 target = 0.112059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.088614 restraints weight = 45127.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.089393 restraints weight = 31048.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.089757 restraints weight = 25158.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.090028 restraints weight = 21502.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.090199 restraints weight = 20507.106| |-----------------------------------------------------------------------------| r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 16528 Z= 0.125 Angle : 0.540 8.663 23172 Z= 0.298 Chirality : 0.036 0.153 2564 Planarity : 0.004 0.036 2342 Dihedral : 24.391 149.948 3744 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 2.32 % Allowed : 11.90 % 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: 1.32 (0.22), residues: 1464 helix: 2.30 (0.23), residues: 500 sheet: 0.22 (0.36), residues: 186 loop : 0.17 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 447 TYR 0.012 0.001 TYR D 459 PHE 0.027 0.001 PHE B 468 TRP 0.009 0.001 TRP C 225 HIS 0.003 0.001 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00268 (16528) covalent geometry : angle 0.53961 (23172) hydrogen bonds : bond 0.03375 ( 698) hydrogen bonds : angle 3.80590 ( 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 117 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 87 time to evaluate : 0.464 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 ASN cc_start: 0.7804 (t0) cc_final: 0.7459 (p0) REVERT: B 349 ASP cc_start: 0.8111 (m-30) cc_final: 0.7781 (t0) REVERT: B 431 TYR cc_start: 0.7004 (m-80) cc_final: 0.6730 (m-80) REVERT: B 465 GLN cc_start: 0.6365 (mm-40) cc_final: 0.6135 (mm-40) REVERT: C 463 ASN cc_start: 0.8020 (t0) cc_final: 0.7477 (p0) REVERT: C 513 ARG cc_start: 0.7353 (tmt170) cc_final: 0.6876 (tpt90) REVERT: D 405 ASP cc_start: 0.7945 (m-30) cc_final: 0.7706 (t0) outliers start: 30 outliers final: 19 residues processed: 106 average time/residue: 0.1389 time to fit residues: 21.4957 Evaluate side-chains 95 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 381 MET Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 446 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 58 optimal weight: 4.9990 chunk 8 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 101 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 375 GLN B 384 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.104350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.080058 restraints weight = 42380.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.080382 restraints weight = 26392.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.080870 restraints weight = 22479.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.081055 restraints weight = 18224.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.081176 restraints weight = 17196.498| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 16528 Z= 0.311 Angle : 0.715 8.603 23172 Z= 0.392 Chirality : 0.044 0.150 2564 Planarity : 0.006 0.076 2342 Dihedral : 24.867 145.566 3742 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 3.48 % Allowed : 11.13 % Favored : 85.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.22), residues: 1464 helix: 1.65 (0.23), residues: 494 sheet: -0.74 (0.32), residues: 232 loop : -0.34 (0.24), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 447 TYR 0.010 0.002 TYR C 278 PHE 0.025 0.003 PHE D 306 TRP 0.011 0.002 TRP D 178 HIS 0.007 0.001 HIS B 105 Details of bonding type rmsd covalent geometry : bond 0.00717 (16528) covalent geometry : angle 0.71462 (23172) hydrogen bonds : bond 0.05557 ( 698) hydrogen bonds : angle 4.59586 ( 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 129 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 84 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: A 463 ASN cc_start: 0.8222 (t0) cc_final: 0.7633 (p0) REVERT: B 431 TYR cc_start: 0.7309 (m-80) cc_final: 0.6697 (m-80) REVERT: C 463 ASN cc_start: 0.8178 (t0) cc_final: 0.7432 (p0) REVERT: D 405 ASP cc_start: 0.8008 (m-30) cc_final: 0.7602 (t70) outliers start: 45 outliers final: 28 residues processed: 118 average time/residue: 0.1195 time to fit residues: 21.3689 Evaluate side-chains 101 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 73 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 445 ASN Chi-restraints excluded: chain A residue 453 ILE Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 496 THR Chi-restraints excluded: chain A residue 500 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 446 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 19 optimal weight: 7.9990 chunk 45 optimal weight: 0.9990 chunk 50 optimal weight: 2.9990 chunk 131 optimal weight: 0.8980 chunk 132 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 81 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.104768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.078069 restraints weight = 43538.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.080071 restraints weight = 22741.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.081312 restraints weight = 15395.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.082080 restraints weight = 12240.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.082523 restraints weight = 10728.170| |-----------------------------------------------------------------------------| r_work (final): 0.3319 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 16528 Z= 0.170 Angle : 0.590 8.160 23172 Z= 0.327 Chirality : 0.038 0.152 2564 Planarity : 0.004 0.039 2342 Dihedral : 24.673 147.645 3742 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.85 % Allowed : 12.83 % Favored : 85.32 % 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: 1.97 (0.23), residues: 498 sheet: -0.23 (0.35), residues: 200 loop : -0.28 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 404 TYR 0.009 0.001 TYR D 459 PHE 0.017 0.002 PHE C 468 TRP 0.011 0.001 TRP C 225 HIS 0.003 0.001 HIS D 105 Details of bonding type rmsd covalent geometry : bond 0.00380 (16528) covalent geometry : angle 0.58951 (23172) hydrogen bonds : bond 0.04051 ( 698) hydrogen bonds : angle 4.14077 ( 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 101 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 77 time to evaluate : 0.641 Fit side-chains REVERT: A 463 ASN cc_start: 0.8236 (t0) cc_final: 0.7554 (p0) REVERT: B 431 TYR cc_start: 0.7169 (m-80) cc_final: 0.6549 (m-80) REVERT: C 355 ARG cc_start: 0.6771 (tmm160) cc_final: 0.6122 (ttp80) REVERT: C 463 ASN cc_start: 0.8049 (t0) cc_final: 0.7397 (p0) outliers start: 24 outliers final: 19 residues processed: 95 average time/residue: 0.1596 time to fit residues: 21.8285 Evaluate side-chains 87 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 68 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 446 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 99 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 139 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 93 optimal weight: 0.7980 chunk 60 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 90 optimal weight: 0.8980 chunk 137 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.105773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.079324 restraints weight = 43676.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.081370 restraints weight = 22444.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.082638 restraints weight = 15023.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.083405 restraints weight = 11894.922| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.083805 restraints weight = 10405.136| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16528 Z= 0.145 Angle : 0.564 7.816 23172 Z= 0.313 Chirality : 0.037 0.147 2564 Planarity : 0.004 0.068 2342 Dihedral : 24.607 147.535 3742 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.93 % Allowed : 13.29 % Favored : 84.78 % 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: 0.96 (0.23), residues: 1464 helix: 2.16 (0.23), residues: 498 sheet: 0.10 (0.36), residues: 186 loop : -0.20 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 404 TYR 0.009 0.001 TYR A 431 PHE 0.031 0.001 PHE B 468 TRP 0.010 0.001 TRP C 225 HIS 0.003 0.001 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00323 (16528) covalent geometry : angle 0.56449 (23172) hydrogen bonds : bond 0.03646 ( 698) hydrogen bonds : angle 3.96184 ( 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 97 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 72 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: A 463 ASN cc_start: 0.7874 (t0) cc_final: 0.7532 (p0) REVERT: B 431 TYR cc_start: 0.6994 (m-80) cc_final: 0.6446 (m-80) REVERT: C 355 ARG cc_start: 0.6785 (tmm160) cc_final: 0.6382 (ttp80) REVERT: C 463 ASN cc_start: 0.7713 (t0) cc_final: 0.7388 (p0) REVERT: C 516 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.8194 (mp) outliers start: 25 outliers final: 13 residues processed: 92 average time/residue: 0.1508 time to fit residues: 19.8900 Evaluate side-chains 82 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain C residue 516 LEU Chi-restraints excluded: chain D residue 72 LEU 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: 0.9990 chunk 91 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 145 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 119 optimal weight: 0.9980 chunk 113 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.105309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.081565 restraints weight = 43012.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.081650 restraints weight = 26889.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.082263 restraints weight = 22579.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.082486 restraints weight = 17276.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.082657 restraints weight = 16236.897| |-----------------------------------------------------------------------------| r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.5287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16528 Z= 0.153 Angle : 0.581 13.853 23172 Z= 0.319 Chirality : 0.037 0.147 2564 Planarity : 0.004 0.058 2342 Dihedral : 24.596 146.468 3742 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.70 % Allowed : 13.37 % Favored : 84.93 % 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: 0.97 (0.23), residues: 1464 helix: 2.21 (0.23), residues: 498 sheet: 0.20 (0.38), residues: 176 loop : -0.25 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 404 TYR 0.011 0.001 TYR C 431 PHE 0.019 0.001 PHE A 468 TRP 0.009 0.001 TRP C 225 HIS 0.003 0.001 HIS A 217 Details of bonding type rmsd covalent geometry : bond 0.00344 (16528) covalent geometry : angle 0.58128 (23172) hydrogen bonds : bond 0.03754 ( 698) hydrogen bonds : angle 3.99435 ( 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 94 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 72 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 463 ASN cc_start: 0.7770 (t0) cc_final: 0.7422 (p0) REVERT: B 423 CYS cc_start: 0.6141 (OUTLIER) cc_final: 0.5282 (m) REVERT: B 431 TYR cc_start: 0.7016 (m-80) cc_final: 0.6449 (m-80) REVERT: C 355 ARG cc_start: 0.6768 (tmm160) cc_final: 0.6131 (ttp80) outliers start: 22 outliers final: 16 residues processed: 89 average time/residue: 0.1584 time to fit residues: 19.9313 Evaluate side-chains 83 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 66 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain D residue 72 LEU 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: 5.9990 chunk 133 optimal weight: 0.7980 chunk 95 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 33 optimal weight: 0.0000 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 96 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.106104 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.082380 restraints weight = 43138.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.083166 restraints weight = 26315.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.083524 restraints weight = 22145.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.083737 restraints weight = 16333.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.084154 restraints weight = 15243.485| |-----------------------------------------------------------------------------| r_work (final): 0.3339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.5370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 16528 Z= 0.139 Angle : 0.570 9.045 23172 Z= 0.313 Chirality : 0.037 0.148 2564 Planarity : 0.004 0.061 2342 Dihedral : 24.519 147.203 3742 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 1.31 % Allowed : 13.99 % 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: 1.05 (0.23), residues: 1464 helix: 2.29 (0.23), residues: 498 sheet: 0.26 (0.38), residues: 176 loop : -0.21 (0.23), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 404 TYR 0.010 0.001 TYR A 431 PHE 0.021 0.001 PHE A 468 TRP 0.010 0.001 TRP C 225 HIS 0.003 0.001 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00310 (16528) covalent geometry : angle 0.57043 (23172) hydrogen bonds : bond 0.03497 ( 698) hydrogen bonds : angle 3.90283 ( 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 85 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 68 time to evaluate : 0.538 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 463 ASN cc_start: 0.7672 (t0) cc_final: 0.7428 (p0) REVERT: A 499 LYS cc_start: 0.7542 (mtmt) cc_final: 0.7293 (ttmt) REVERT: B 431 TYR cc_start: 0.6546 (m-80) cc_final: 0.6000 (m-80) REVERT: C 355 ARG cc_start: 0.6696 (tmm160) cc_final: 0.6148 (ttp80) outliers start: 17 outliers final: 16 residues processed: 82 average time/residue: 0.1652 time to fit residues: 19.2265 Evaluate side-chains 82 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 465 GLN Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 446 LEU Chi-restraints excluded: chain C residue 214 VAL Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 465 GLN Chi-restraints excluded: chain D residue 72 LEU 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 81 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 25 optimal weight: 0.3980 chunk 21 optimal weight: 6.9990 chunk 60 optimal weight: 0.0370 chunk 131 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 30 optimal weight: 6.9990 chunk 134 optimal weight: 3.9990 chunk 144 optimal weight: 0.0870 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.107078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.083585 restraints weight = 42910.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.083404 restraints weight = 28045.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.084147 restraints weight = 23323.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.084338 restraints weight = 18195.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.084515 restraints weight = 16910.957| |-----------------------------------------------------------------------------| r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7851 moved from start: 0.5463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16528 Z= 0.125 Angle : 0.548 9.001 23172 Z= 0.302 Chirality : 0.036 0.147 2564 Planarity : 0.004 0.054 2342 Dihedral : 24.415 147.400 3742 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.47 % Allowed : 13.91 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.23), residues: 1464 helix: 2.27 (0.23), residues: 506 sheet: 0.28 (0.38), residues: 176 loop : -0.19 (0.24), residues: 782 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 404 TYR 0.009 0.001 TYR D 459 PHE 0.020 0.001 PHE A 468 TRP 0.009 0.001 TRP C 225 HIS 0.004 0.001 HIS D 296 Details of bonding type rmsd covalent geometry : bond 0.00273 (16528) covalent geometry : angle 0.54848 (23172) hydrogen bonds : bond 0.03325 ( 698) hydrogen bonds : angle 3.80294 ( 1784) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2195.95 seconds wall clock time: 38 minutes 43.45 seconds (2323.45 seconds total)