Starting phenix.real_space_refine on Sat Jun 14 02:15:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7svw_25455/06_2025/7svw_25455.cif Found real_map, /net/cci-nas-00/data/ceres_data/7svw_25455/06_2025/7svw_25455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7svw_25455/06_2025/7svw_25455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7svw_25455/06_2025/7svw_25455.map" model { file = "/net/cci-nas-00/data/ceres_data/7svw_25455/06_2025/7svw_25455.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7svw_25455/06_2025/7svw_25455.cif" } resolution = 3.69 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.27, per 1000 atoms: 0.59 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: 3.63 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 6.10 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: 6.24 Time building geometry restraints manager: 4.34 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: 1.710 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: 0.020 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 40.690 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.600 ------------------------------------------------------------------------------- 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 : 14.70 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP D 202 HIS 0.011 0.001 HIS D 105 PHE 0.025 0.001 PHE C 448 TYR 0.014 0.001 TYR D 278 ARG 0.002 0.000 ARG B 77 Details of bonding type rmsd hydrogen bonds : bond 0.18197 ( 698) hydrogen bonds : angle 6.92160 ( 1784) covalent geometry : bond 0.01161 (16528) covalent geometry : angle 1.46054 (23172) *********************** 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 : 1.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 MET cc_start: 0.8635 (tpp) cc_final: 0.8429 (mmm) REVERT: B 137 ARG cc_start: 0.8474 (OUTLIER) cc_final: 0.7704 (mtt90) REVERT: B 179 ARG cc_start: 0.7496 (OUTLIER) cc_final: 0.6942 (mmm160) REVERT: B 381 MET cc_start: 0.7348 (pmm) cc_final: 0.7055 (pmm) REVERT: B 405 ASP cc_start: 0.6571 (m-30) cc_final: 0.6303 (t0) REVERT: C 516 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7827 (mp) REVERT: D 77 ARG cc_start: 0.6841 (OUTLIER) cc_final: 0.6281 (tpt-90) REVERT: D 129 MET cc_start: 0.8612 (tpp) cc_final: 0.7639 (tpt) REVERT: D 132 LYS cc_start: 0.7888 (OUTLIER) cc_final: 0.7381 (tmtp) REVERT: D 179 ARG cc_start: 0.7736 (OUTLIER) cc_final: 0.7194 (mmm160) outliers start: 36 outliers final: 10 residues processed: 244 average time/residue: 0.4138 time to fit residues: 134.7998 Evaluate side-chains 111 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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 138 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 66 optimal weight: 0.9990 chunk 128 optimal weight: 0.3980 chunk 49 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 95 optimal weight: 4.9990 chunk 148 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 299 GLN D 43 GLN D 342 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.115106 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.090212 restraints weight = 42321.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.090928 restraints weight = 28307.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.091456 restraints weight = 21465.448| |-----------------------------------------------------------------------------| r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.2615 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= 0.160 Angle : 0.626 8.080 23172 Z= 0.349 Chirality : 0.039 0.140 2564 Planarity : 0.005 0.060 2342 Dihedral : 23.865 152.603 3783 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.47 % Allowed : 7.11 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.22), residues: 1464 helix: 1.75 (0.23), residues: 500 sheet: -0.07 (0.33), residues: 208 loop : 0.37 (0.23), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 275 HIS 0.007 0.001 HIS A 296 PHE 0.020 0.002 PHE D 426 TYR 0.012 0.001 TYR D 459 ARG 0.008 0.001 ARG C 513 Details of bonding type rmsd hydrogen bonds : bond 0.04416 ( 698) hydrogen bonds : angle 4.56044 ( 1784) covalent geometry : bond 0.00345 (16528) covalent geometry : angle 0.62586 (23172) *********************** 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 145 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 113 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 LYS cc_start: 0.7366 (ptpt) cc_final: 0.6829 (ptpp) REVERT: A 407 ASP cc_start: 0.5604 (m-30) cc_final: 0.5374 (m-30) REVERT: A 514 ASP cc_start: 0.6845 (OUTLIER) cc_final: 0.6594 (t0) REVERT: B 77 ARG cc_start: 0.6982 (OUTLIER) cc_final: 0.6477 (tpt170) REVERT: B 405 ASP cc_start: 0.7568 (m-30) cc_final: 0.6967 (t70) REVERT: B 431 TYR cc_start: 0.7245 (m-80) cc_final: 0.6824 (m-80) REVERT: B 453 ILE cc_start: 0.8028 (OUTLIER) cc_final: 0.7703 (pp) REVERT: C 270 LYS cc_start: 0.7374 (ptpt) cc_final: 0.6825 (ptpp) REVERT: D 223 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8824 (ptm160) REVERT: D 469 LEU cc_start: 0.7342 (tp) cc_final: 0.7024 (tt) outliers start: 32 outliers final: 18 residues processed: 138 average time/residue: 0.4466 time to fit residues: 88.8381 Evaluate side-chains 102 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 2.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 THR 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 32 optimal weight: 0.7980 chunk 60 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 163 optimal weight: 0.2980 chunk 154 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 27 optimal weight: 7.9990 chunk 125 optimal weight: 0.9990 chunk 138 optimal weight: 0.8980 chunk 118 optimal weight: 0.9990 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 299 GLN B 413 GLN C 299 GLN C 503 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.112635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.088335 restraints weight = 43932.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.089022 restraints weight = 27948.904| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.089559 restraints weight = 20357.525| |-----------------------------------------------------------------------------| r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7822 moved from start: 0.3452 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 16528 Z= 0.149 Angle : 0.573 9.071 23172 Z= 0.319 Chirality : 0.038 0.136 2564 Planarity : 0.004 0.044 2342 Dihedral : 24.263 150.164 3756 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.55 % Allowed : 8.58 % Favored : 88.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.22), residues: 1464 helix: 2.00 (0.23), residues: 500 sheet: -0.20 (0.32), residues: 216 loop : 0.37 (0.24), residues: 748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 225 HIS 0.003 0.001 HIS C 296 PHE 0.024 0.002 PHE D 468 TYR 0.012 0.001 TYR B 435 ARG 0.009 0.001 ARG B 415 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 698) hydrogen bonds : angle 4.00438 ( 1784) covalent geometry : bond 0.00327 (16528) covalent geometry : angle 0.57270 (23172) *********************** 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: 33 poor density : 97 time to evaluate : 1.599 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 270 LYS cc_start: 0.7200 (ptpt) cc_final: 0.6583 (ptpp) REVERT: A 407 ASP cc_start: 0.5712 (m-30) cc_final: 0.5394 (m-30) REVERT: A 463 ASN cc_start: 0.8426 (t0) cc_final: 0.7526 (p0) REVERT: B 129 MET cc_start: 0.8887 (ttm) cc_final: 0.8537 (ttt) REVERT: B 381 MET cc_start: 0.7540 (pmm) cc_final: 0.7324 (pmm) REVERT: B 405 ASP cc_start: 0.7834 (m-30) cc_final: 0.7332 (t0) REVERT: B 413 GLN cc_start: 0.7283 (OUTLIER) cc_final: 0.6661 (tm-30) REVERT: B 446 LEU cc_start: 0.7780 (mp) cc_final: 0.7291 (mt) REVERT: C 270 LYS cc_start: 0.7284 (ptpt) cc_final: 0.6666 (ptpp) REVERT: C 407 ASP cc_start: 0.5558 (m-30) cc_final: 0.5286 (m-30) REVERT: C 463 ASN cc_start: 0.8295 (t0) cc_final: 0.7412 (p0) REVERT: D 129 MET cc_start: 0.8812 (ttm) cc_final: 0.8397 (ttt) REVERT: D 223 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.8795 (ptm160) outliers start: 33 outliers final: 15 residues processed: 126 average time/residue: 0.3103 time to fit residues: 57.5138 Evaluate side-chains 95 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 78 time to evaluate : 1.693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 494 LEU 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 181 THR Chi-restraints excluded: chain B residue 413 GLN 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 516 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 18 optimal weight: 3.9990 chunk 159 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 147 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 123 optimal weight: 2.9990 chunk 149 optimal weight: 0.4980 chunk 58 optimal weight: 2.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 ASN D 413 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.110011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.085733 restraints weight = 44129.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.086575 restraints weight = 29257.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.087118 restraints weight = 24930.031| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.4041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 16528 Z= 0.180 Angle : 0.597 9.797 23172 Z= 0.329 Chirality : 0.039 0.154 2564 Planarity : 0.004 0.043 2342 Dihedral : 24.409 148.213 3744 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.78 % Allowed : 10.66 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.22), residues: 1464 helix: 2.10 (0.23), residues: 500 sheet: -0.02 (0.32), residues: 218 loop : 0.17 (0.24), residues: 746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 225 HIS 0.005 0.001 HIS B 105 PHE 0.023 0.002 PHE C 306 TYR 0.016 0.001 TYR B 431 ARG 0.007 0.001 ARG B 416 Details of bonding type rmsd hydrogen bonds : bond 0.04086 ( 698) hydrogen bonds : angle 4.05740 ( 1784) covalent geometry : bond 0.00402 (16528) covalent geometry : angle 0.59677 (23172) *********************** 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 119 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 83 time to evaluate : 1.683 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 LYS cc_start: 0.7004 (ptpt) cc_final: 0.6402 (ptpp) REVERT: A 463 ASN cc_start: 0.8158 (t0) cc_final: 0.7592 (p0) REVERT: B 405 ASP cc_start: 0.7932 (m-30) cc_final: 0.7687 (t0) REVERT: C 270 LYS cc_start: 0.7074 (ptpt) cc_final: 0.6485 (ptpp) REVERT: C 463 ASN cc_start: 0.8104 (t0) cc_final: 0.7403 (p0) REVERT: D 129 MET cc_start: 0.8841 (ttm) cc_final: 0.8418 (ttt) REVERT: D 223 ARG cc_start: 0.9104 (OUTLIER) cc_final: 0.8825 (ptm160) REVERT: D 413 GLN cc_start: 0.7042 (OUTLIER) cc_final: 0.6822 (tm-30) outliers start: 36 outliers final: 18 residues processed: 109 average time/residue: 0.2966 time to fit residues: 48.1917 Evaluate side-chains 98 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 1.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 429 LEU Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 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 Chi-restraints excluded: chain D residue 413 GLN 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 114 optimal weight: 2.9990 chunk 158 optimal weight: 5.9990 chunk 103 optimal weight: 0.0070 chunk 153 optimal weight: 0.9980 chunk 29 optimal weight: 0.0270 chunk 119 optimal weight: 0.2980 chunk 53 optimal weight: 0.0970 chunk 154 optimal weight: 0.8980 chunk 128 optimal weight: 0.9980 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 overall best weight: 0.2654 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 445 ASN D 43 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.109376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.085090 restraints weight = 43906.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.085523 restraints weight = 27226.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.086145 restraints weight = 20723.668| |-----------------------------------------------------------------------------| r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16528 Z= 0.117 Angle : 0.532 8.200 23172 Z= 0.294 Chirality : 0.036 0.148 2564 Planarity : 0.004 0.035 2342 Dihedral : 24.315 150.860 3744 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 1.70 % Allowed : 12.60 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.30 (0.23), residues: 1464 helix: 2.19 (0.23), residues: 510 sheet: 0.15 (0.36), residues: 196 loop : 0.22 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 225 HIS 0.004 0.001 HIS D 296 PHE 0.017 0.001 PHE A 468 TYR 0.011 0.001 TYR D 197 ARG 0.003 0.000 ARG C 367 Details of bonding type rmsd hydrogen bonds : bond 0.03215 ( 698) hydrogen bonds : angle 3.72860 ( 1784) covalent geometry : bond 0.00246 (16528) covalent geometry : angle 0.53237 (23172) *********************** 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 118 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 LYS cc_start: 0.7164 (ptpt) cc_final: 0.6500 (ptpp) REVERT: A 463 ASN cc_start: 0.7988 (t0) cc_final: 0.7524 (p0) REVERT: B 381 MET cc_start: 0.7226 (pmm) cc_final: 0.6915 (pmm) REVERT: B 405 ASP cc_start: 0.7993 (m-30) cc_final: 0.7757 (t0) REVERT: B 411 MET cc_start: 0.8036 (mtt) cc_final: 0.7786 (mtp) REVERT: B 413 GLN cc_start: 0.6933 (tp-100) cc_final: 0.6476 (tm-30) REVERT: B 446 LEU cc_start: 0.7844 (mp) cc_final: 0.7363 (mt) REVERT: C 270 LYS cc_start: 0.7141 (ptpt) cc_final: 0.6491 (ptpp) REVERT: C 463 ASN cc_start: 0.7924 (t0) cc_final: 0.7428 (p0) REVERT: C 513 ARG cc_start: 0.7345 (tmt170) cc_final: 0.6948 (tpt90) REVERT: D 423 CYS cc_start: 0.6508 (m) cc_final: 0.6085 (p) REVERT: D 430 MET cc_start: 0.8029 (tpp) cc_final: 0.7742 (tpp) outliers start: 22 outliers final: 12 residues processed: 114 average time/residue: 0.3329 time to fit residues: 55.4948 Evaluate side-chains 90 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 78 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 420 ARG 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 C residue 245 ASP Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 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 25 optimal weight: 0.0870 chunk 120 optimal weight: 0.2980 chunk 140 optimal weight: 0.6980 chunk 4 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 130 optimal weight: 0.1980 chunk 5 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 132 optimal weight: 0.9980 overall best weight: 0.4558 ------------------------------------------------------------------------------- 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 = 0.3801 r_free = 0.3801 target = 0.108922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.083098 restraints weight = 43721.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.084391 restraints weight = 24098.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.085009 restraints weight = 16654.005| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7849 moved from start: 0.4431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16528 Z= 0.124 Angle : 0.539 7.319 23172 Z= 0.297 Chirality : 0.036 0.148 2564 Planarity : 0.004 0.053 2342 Dihedral : 24.306 149.038 3744 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.78 % Allowed : 12.67 % Favored : 85.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.23), residues: 1464 helix: 2.15 (0.23), residues: 510 sheet: 0.17 (0.35), residues: 196 loop : 0.22 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 225 HIS 0.003 0.001 HIS B 296 PHE 0.030 0.001 PHE B 468 TYR 0.007 0.001 TYR B 459 ARG 0.010 0.000 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.03232 ( 698) hydrogen bonds : angle 3.72577 ( 1784) covalent geometry : bond 0.00269 (16528) covalent geometry : angle 0.53901 (23172) *********************** 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 108 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 85 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.6699 (p0) cc_final: 0.6436 (t0) REVERT: A 270 LYS cc_start: 0.7005 (ptpt) cc_final: 0.6287 (ptpp) REVERT: A 463 ASN cc_start: 0.7929 (t0) cc_final: 0.7549 (p0) REVERT: B 405 ASP cc_start: 0.8016 (m-30) cc_final: 0.7613 (t0) REVERT: B 411 MET cc_start: 0.8061 (mtt) cc_final: 0.7838 (mtp) REVERT: B 446 LEU cc_start: 0.7622 (mp) cc_final: 0.7092 (mt) REVERT: C 215 ASP cc_start: 0.6705 (p0) cc_final: 0.6370 (t0) REVERT: C 270 LYS cc_start: 0.7132 (ptpt) cc_final: 0.6459 (ptpp) REVERT: C 463 ASN cc_start: 0.7899 (t0) cc_final: 0.7486 (p0) REVERT: D 465 GLN cc_start: 0.6526 (mm-40) cc_final: 0.6280 (mm-40) outliers start: 23 outliers final: 13 residues processed: 102 average time/residue: 0.3495 time to fit residues: 51.4200 Evaluate side-chains 93 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 1.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 420 ARG 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 C residue 213 LEU Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 446 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 58 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 124 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 44 optimal weight: 4.9990 chunk 126 optimal weight: 0.1980 chunk 127 optimal weight: 0.0000 chunk 27 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 overall best weight: 0.7986 ------------------------------------------------------------------------------- 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 = 0.3777 r_free = 0.3777 target = 0.107359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.082829 restraints weight = 43846.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.083179 restraints weight = 26248.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.083419 restraints weight = 21635.869| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 16528 Z= 0.145 Angle : 0.560 10.565 23172 Z= 0.308 Chirality : 0.037 0.150 2564 Planarity : 0.004 0.056 2342 Dihedral : 24.386 147.286 3744 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.62 % Allowed : 12.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.23), residues: 1464 helix: 2.27 (0.23), residues: 500 sheet: 0.36 (0.36), residues: 188 loop : 0.19 (0.24), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 178 HIS 0.003 0.001 HIS B 105 PHE 0.017 0.001 PHE A 468 TYR 0.017 0.001 TYR D 435 ARG 0.010 0.000 ARG D 404 Details of bonding type rmsd hydrogen bonds : bond 0.03526 ( 698) hydrogen bonds : angle 3.81338 ( 1784) covalent geometry : bond 0.00322 (16528) covalent geometry : angle 0.56040 (23172) *********************** 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 99 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 78 time to evaluate : 1.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.6539 (p0) cc_final: 0.6193 (t0) REVERT: A 270 LYS cc_start: 0.6881 (ptpt) cc_final: 0.6140 (ptpp) REVERT: A 463 ASN cc_start: 0.7942 (t0) cc_final: 0.7593 (p0) REVERT: B 405 ASP cc_start: 0.7997 (m-30) cc_final: 0.7775 (t70) REVERT: C 270 LYS cc_start: 0.6930 (ptpt) cc_final: 0.6212 (ptpp) REVERT: C 463 ASN cc_start: 0.7761 (t0) cc_final: 0.7354 (p0) outliers start: 21 outliers final: 13 residues processed: 96 average time/residue: 0.3159 time to fit residues: 44.3790 Evaluate side-chains 90 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 1.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 420 ARG 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 C residue 408 ILE Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 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 25 optimal weight: 0.4980 chunk 90 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 154 optimal weight: 0.1980 chunk 38 optimal weight: 0.0980 chunk 134 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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 = 0.3793 r_free = 0.3793 target = 0.108582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.084794 restraints weight = 42839.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.084614 restraints weight = 27734.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.085426 restraints weight = 23036.979| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16528 Z= 0.122 Angle : 0.532 7.752 23172 Z= 0.295 Chirality : 0.036 0.147 2564 Planarity : 0.004 0.054 2342 Dihedral : 24.312 148.659 3744 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.62 % Allowed : 12.60 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.23), residues: 1464 helix: 2.24 (0.23), residues: 508 sheet: 0.52 (0.37), residues: 188 loop : 0.19 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 225 HIS 0.003 0.001 HIS D 296 PHE 0.029 0.001 PHE B 468 TYR 0.018 0.001 TYR D 435 ARG 0.009 0.000 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.03173 ( 698) hydrogen bonds : angle 3.74340 ( 1784) covalent geometry : bond 0.00264 (16528) covalent geometry : angle 0.53239 (23172) *********************** 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 107 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 86 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 LYS cc_start: 0.6888 (ptpt) cc_final: 0.6123 (ptpp) REVERT: A 463 ASN cc_start: 0.7692 (t0) cc_final: 0.7424 (p0) REVERT: B 431 TYR cc_start: 0.6293 (m-80) cc_final: 0.5716 (m-80) REVERT: C 270 LYS cc_start: 0.6872 (ptpt) cc_final: 0.6142 (ptpp) REVERT: C 463 ASN cc_start: 0.7707 (t0) cc_final: 0.7389 (p0) outliers start: 21 outliers final: 15 residues processed: 103 average time/residue: 0.3677 time to fit residues: 54.5036 Evaluate side-chains 92 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 1.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 420 ARG 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 C residue 245 ASP Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 446 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 129 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 141 optimal weight: 0.0970 chunk 86 optimal weight: 0.3980 chunk 31 optimal weight: 0.9980 chunk 150 optimal weight: 5.9990 chunk 153 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 121 optimal weight: 3.9990 chunk 108 optimal weight: 0.0980 overall best weight: 0.4778 ------------------------------------------------------------------------------- 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 = 0.3794 r_free = 0.3794 target = 0.108614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.084848 restraints weight = 43286.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.084752 restraints weight = 27410.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.085520 restraints weight = 23063.677| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.4929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16528 Z= 0.123 Angle : 0.535 8.025 23172 Z= 0.295 Chirality : 0.036 0.147 2564 Planarity : 0.004 0.056 2342 Dihedral : 24.310 147.176 3742 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.24 % Allowed : 12.98 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.23), residues: 1464 helix: 2.29 (0.23), residues: 508 sheet: 0.53 (0.37), residues: 188 loop : 0.20 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 225 HIS 0.006 0.001 HIS A 296 PHE 0.020 0.001 PHE A 468 TYR 0.021 0.001 TYR D 435 ARG 0.011 0.000 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.03164 ( 698) hydrogen bonds : angle 3.70054 ( 1784) covalent geometry : bond 0.00270 (16528) covalent geometry : angle 0.53510 (23172) *********************** 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 101 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 215 ASP cc_start: 0.6417 (p0) cc_final: 0.6094 (t0) REVERT: A 270 LYS cc_start: 0.6906 (ptpt) cc_final: 0.6166 (ptpp) REVERT: A 463 ASN cc_start: 0.7668 (t0) cc_final: 0.7447 (p0) REVERT: B 129 MET cc_start: 0.9016 (ttm) cc_final: 0.8557 (ttt) REVERT: B 425 GLN cc_start: 0.7508 (mm110) cc_final: 0.7047 (pm20) REVERT: B 431 TYR cc_start: 0.6418 (m-80) cc_final: 0.5839 (m-80) REVERT: C 215 ASP cc_start: 0.6382 (p0) cc_final: 0.6081 (t0) REVERT: C 270 LYS cc_start: 0.6865 (ptpt) cc_final: 0.6131 (ptpp) REVERT: C 463 ASN cc_start: 0.7657 (t0) cc_final: 0.7408 (p0) outliers start: 16 outliers final: 14 residues processed: 98 average time/residue: 0.3415 time to fit residues: 49.3131 Evaluate side-chains 94 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 1.550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 420 ARG 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 C residue 245 ASP Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 446 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 78 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 117 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 94 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 chunk 48 optimal weight: 0.0870 chunk 2 optimal weight: 1.9990 chunk 142 optimal weight: 1.9990 chunk 119 optimal weight: 0.7980 chunk 129 optimal weight: 0.8980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 413 GLN D 272 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.107229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.083407 restraints weight = 43329.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.083217 restraints weight = 27516.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.083998 restraints weight = 23297.280| |-----------------------------------------------------------------------------| r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.5093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16528 Z= 0.140 Angle : 0.549 8.464 23172 Z= 0.303 Chirality : 0.036 0.146 2564 Planarity : 0.004 0.065 2342 Dihedral : 24.377 146.436 3742 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.31 % Allowed : 12.98 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.23), residues: 1464 helix: 2.23 (0.23), residues: 508 sheet: 0.48 (0.36), residues: 188 loop : 0.15 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 225 HIS 0.007 0.001 HIS C 296 PHE 0.030 0.001 PHE B 468 TYR 0.021 0.001 TYR D 435 ARG 0.008 0.000 ARG B 404 Details of bonding type rmsd hydrogen bonds : bond 0.03435 ( 698) hydrogen bonds : angle 3.76649 ( 1784) covalent geometry : bond 0.00313 (16528) covalent geometry : angle 0.54950 (23172) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 1.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 270 LYS cc_start: 0.6869 (ptpt) cc_final: 0.6134 (ptpp) REVERT: A 463 ASN cc_start: 0.7677 (t0) cc_final: 0.7435 (p0) REVERT: B 129 MET cc_start: 0.9044 (ttm) cc_final: 0.8592 (ttt) REVERT: B 425 GLN cc_start: 0.7506 (mm110) cc_final: 0.7183 (pm20) REVERT: B 431 TYR cc_start: 0.6402 (m-80) cc_final: 0.5986 (m-80) REVERT: C 270 LYS cc_start: 0.6846 (ptpt) cc_final: 0.6135 (ptpp) REVERT: C 463 ASN cc_start: 0.7581 (t0) cc_final: 0.7292 (p0) outliers start: 17 outliers final: 15 residues processed: 94 average time/residue: 0.3467 time to fit residues: 48.8310 Evaluate side-chains 91 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 76 time to evaluate : 1.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 C residue 245 ASP Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 408 ILE Chi-restraints excluded: chain D residue 446 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 139 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 104 optimal weight: 0.9980 chunk 103 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 chunk 53 optimal weight: 0.0020 chunk 37 optimal weight: 0.5980 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 465 GLN C 463 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.107258 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.083437 restraints weight = 43251.937| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.083353 restraints weight = 26572.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.084116 restraints weight = 22203.615| |-----------------------------------------------------------------------------| r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.5201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16528 Z= 0.138 Angle : 0.547 8.813 23172 Z= 0.302 Chirality : 0.036 0.146 2564 Planarity : 0.004 0.053 2342 Dihedral : 24.346 147.190 3742 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.39 % Allowed : 13.45 % Favored : 85.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.23), residues: 1464 helix: 2.24 (0.23), residues: 508 sheet: 0.39 (0.36), residues: 188 loop : 0.12 (0.24), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 225 HIS 0.006 0.001 HIS C 296 PHE 0.020 0.001 PHE A 468 TYR 0.022 0.001 TYR D 435 ARG 0.017 0.000 ARG D 404 Details of bonding type rmsd hydrogen bonds : bond 0.03369 ( 698) hydrogen bonds : angle 3.71879 ( 1784) covalent geometry : bond 0.00308 (16528) covalent geometry : angle 0.54670 (23172) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4537.67 seconds wall clock time: 83 minutes 7.63 seconds (4987.63 seconds total)