Starting phenix.real_space_refine on Tue Dec 31 12:26:49 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7svw_25455/12_2024/7svw_25455.cif Found real_map, /net/cci-nas-00/data/ceres_data/7svw_25455/12_2024/7svw_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_25455/12_2024/7svw_25455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7svw_25455/12_2024/7svw_25455.map" model { file = "/net/cci-nas-00/data/ceres_data/7svw_25455/12_2024/7svw_25455.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7svw_25455/12_2024/7svw_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-5532/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: 9.64, per 1000 atoms: 0.61 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: 4.23 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: 6.30 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: 6.26 Time building geometry restraints manager: 4.79 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: 1.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.550 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 41.150 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.790 ------------------------------------------------------------------------------- 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= 0.762 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 *********************** 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 : 1.553 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: 0.4033 time to fit residues: 132.2491 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 : 1.560 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7187 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= 0.206 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 *********************** 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 : 1.530 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 77 ARG cc_start: 0.7048 (OUTLIER) cc_final: 0.6669 (tpt170) REVERT: B 405 ASP cc_start: 0.6768 (m-30) cc_final: 0.6428 (t70) REVERT: B 453 ILE cc_start: 0.7620 (OUTLIER) cc_final: 0.7342 (pp) REVERT: C 516 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7756 (mp) REVERT: D 223 ARG cc_start: 0.8948 (OUTLIER) cc_final: 0.8572 (ptm160) REVERT: D 469 LEU cc_start: 0.7098 (tp) cc_final: 0.6883 (tt) outliers start: 32 outliers final: 18 residues processed: 138 average time/residue: 0.3398 time to fit residues: 66.6520 Evaluate side-chains 99 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 77 time to evaluate : 1.506 ------------------------------------------------------------------------------- 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 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 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 82 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 149 optimal weight: 1.9990 chunk 161 optimal weight: 8.9990 chunk 132 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 50 optimal weight: 6.9990 chunk 119 optimal weight: 0.5980 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 16528 Z= 0.286 Angle : 0.650 10.229 23172 Z= 0.360 Chirality : 0.041 0.147 2564 Planarity : 0.005 0.051 2342 Dihedral : 24.625 150.170 3756 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 3.48 % Allowed : 8.58 % Favored : 87.94 % 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: 0.86 (0.22), residues: 1464 helix: 1.67 (0.22), residues: 498 sheet: -0.09 (0.33), residues: 206 loop : 0.11 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 275 HIS 0.006 0.001 HIS B 105 PHE 0.020 0.002 PHE D 110 TYR 0.012 0.001 TYR D 285 ARG 0.009 0.001 ARG B 415 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 90 time to evaluate : 1.464 Fit side-chains REVERT: A 463 ASN cc_start: 0.7891 (t0) cc_final: 0.7338 (p0) REVERT: B 77 ARG cc_start: 0.7024 (OUTLIER) cc_final: 0.6671 (tpt-90) REVERT: B 129 MET cc_start: 0.8962 (ttm) cc_final: 0.8637 (ttt) REVERT: B 381 MET cc_start: 0.7655 (pmm) cc_final: 0.7415 (pmm) REVERT: C 516 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7951 (mp) REVERT: D 129 MET cc_start: 0.8915 (ttm) cc_final: 0.8566 (ttt) REVERT: D 223 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8808 (ptm160) outliers start: 45 outliers final: 25 residues processed: 123 average time/residue: 0.3057 time to fit residues: 55.4205 Evaluate side-chains 99 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 71 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 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 453 ILE Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 46 LEU Chi-restraints excluded: chain B residue 77 ARG Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 381 MET Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 429 LEU Chi-restraints excluded: chain C residue 453 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 76 LEU Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 446 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 147 optimal weight: 0.2980 chunk 112 optimal weight: 2.9990 chunk 77 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 100 optimal weight: 5.9990 chunk 149 optimal weight: 0.6980 chunk 158 optimal weight: 4.9990 chunk 78 optimal weight: 0.9990 chunk 141 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 503 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7307 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16528 Z= 0.176 Angle : 0.557 10.324 23172 Z= 0.310 Chirality : 0.037 0.149 2564 Planarity : 0.004 0.038 2342 Dihedral : 24.424 150.102 3750 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 2.24 % Allowed : 11.44 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.16 (0.22), residues: 1464 helix: 2.21 (0.23), residues: 500 sheet: 0.05 (0.34), residues: 196 loop : 0.07 (0.23), residues: 768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 225 HIS 0.004 0.001 HIS D 473 PHE 0.030 0.001 PHE C 306 TYR 0.018 0.001 TYR D 431 ARG 0.004 0.000 ARG B 415 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2928 Ramachandran restraints generated. 1464 Oldfield, 0 Emsley, 1464 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 91 time to evaluate : 1.601 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 463 ASN cc_start: 0.7792 (t0) cc_final: 0.7295 (p0) REVERT: B 59 THR cc_start: 0.6591 (m) cc_final: 0.6358 (m) REVERT: B 129 MET cc_start: 0.8919 (ttm) cc_final: 0.8509 (ttm) REVERT: C 463 ASN cc_start: 0.7892 (t0) cc_final: 0.7238 (p0) REVERT: D 59 THR cc_start: 0.6608 (m) cc_final: 0.6366 (m) REVERT: D 129 MET cc_start: 0.8845 (ttm) cc_final: 0.8437 (ttt) REVERT: D 223 ARG cc_start: 0.9031 (OUTLIER) cc_final: 0.8726 (ptm160) outliers start: 29 outliers final: 16 residues processed: 113 average time/residue: 0.2992 time to fit residues: 50.9101 Evaluate side-chains 93 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 76 time to evaluate : 1.651 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 228 THR Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 494 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 381 MET Chi-restraints excluded: chain C residue 406 LEU 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 223 ARG Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 446 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 132 optimal weight: 1.9990 chunk 89 optimal weight: 0.0070 chunk 2 optimal weight: 1.9990 chunk 118 optimal weight: 0.7980 chunk 65 optimal weight: 0.8980 chunk 135 optimal weight: 0.2980 chunk 109 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16528 Z= 0.156 Angle : 0.541 9.403 23172 Z= 0.299 Chirality : 0.036 0.148 2564 Planarity : 0.004 0.036 2342 Dihedral : 24.441 149.473 3744 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 2.16 % Allowed : 11.98 % Favored : 85.86 % 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: 1.27 (0.22), residues: 1464 helix: 2.33 (0.23), residues: 500 sheet: 0.11 (0.35), residues: 196 loop : 0.11 (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 B 296 PHE 0.027 0.001 PHE B 468 TYR 0.009 0.001 TYR D 431 ARG 0.005 0.000 ARG B 447 *********************** 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 110 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 82 time to evaluate : 1.581 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 463 ASN cc_start: 0.7418 (t0) cc_final: 0.7214 (p0) REVERT: B 129 MET cc_start: 0.8927 (ttm) cc_final: 0.8489 (ttt) REVERT: B 381 MET cc_start: 0.7150 (pmm) cc_final: 0.6924 (pmm) REVERT: C 463 ASN cc_start: 0.7435 (t0) cc_final: 0.7174 (p0) REVERT: D 223 ARG cc_start: 0.9009 (OUTLIER) cc_final: 0.8724 (ptm160) outliers start: 28 outliers final: 16 residues processed: 102 average time/residue: 0.3004 time to fit residues: 45.6137 Evaluate side-chains 91 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 1.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 365 LEU 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 72 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 399 VAL Chi-restraints excluded: chain D residue 446 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 53 optimal weight: 0.9990 chunk 142 optimal weight: 2.9990 chunk 31 optimal weight: 0.9990 chunk 93 optimal weight: 0.4980 chunk 39 optimal weight: 2.9990 chunk 158 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 73 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 52 optimal weight: 0.7980 chunk 83 optimal weight: 4.9990 overall best weight: 0.8586 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.4624 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= 0.193 Angle : 0.565 9.260 23172 Z= 0.311 Chirality : 0.037 0.142 2564 Planarity : 0.004 0.053 2342 Dihedral : 24.480 147.556 3744 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 2.24 % Allowed : 12.21 % 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: 1.18 (0.23), residues: 1464 helix: 2.27 (0.23), residues: 500 sheet: 0.05 (0.35), residues: 198 loop : 0.04 (0.24), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 225 HIS 0.003 0.001 HIS D 105 PHE 0.020 0.002 PHE C 306 TYR 0.008 0.001 TYR D 431 ARG 0.009 0.000 ARG B 404 *********************** 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 110 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 81 time to evaluate : 1.733 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 129 MET cc_start: 0.8967 (ttm) cc_final: 0.8540 (ttt) REVERT: C 463 ASN cc_start: 0.7429 (t0) cc_final: 0.7194 (p0) REVERT: D 223 ARG cc_start: 0.9003 (OUTLIER) cc_final: 0.8729 (ptm160) outliers start: 29 outliers final: 21 residues processed: 101 average time/residue: 0.3201 time to fit residues: 47.9109 Evaluate side-chains 93 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 1.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 365 LEU 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 72 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 213 LEU Chi-restraints excluded: chain C residue 406 LEU Chi-restraints excluded: chain C residue 408 ILE Chi-restraints excluded: chain C residue 411 MET Chi-restraints excluded: chain C residue 453 ILE Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 72 LEU Chi-restraints excluded: chain D residue 76 LEU Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 399 VAL 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 152 optimal weight: 0.0060 chunk 17 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 chunk 89 optimal weight: 0.8980 chunk 133 optimal weight: 0.6980 chunk 88 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 96 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 overall best weight: 0.6596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 465 GLN D 465 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7305 moved from start: 0.4805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 16528 Z= 0.168 Angle : 0.545 8.136 23172 Z= 0.302 Chirality : 0.036 0.141 2564 Planarity : 0.004 0.047 2342 Dihedral : 24.430 148.196 3744 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 2.40 % Allowed : 11.98 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.26 (0.23), residues: 1464 helix: 2.37 (0.23), residues: 500 sheet: 0.22 (0.36), residues: 198 loop : 0.03 (0.24), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 225 HIS 0.003 0.001 HIS A 217 PHE 0.029 0.002 PHE B 468 TYR 0.007 0.001 TYR D 459 ARG 0.007 0.000 ARG B 404 *********************** 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 110 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 79 time to evaluate : 1.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 129 MET cc_start: 0.8970 (ttm) cc_final: 0.8534 (ttt) REVERT: D 223 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8695 (ptm160) outliers start: 31 outliers final: 22 residues processed: 100 average time/residue: 0.3181 time to fit residues: 46.8009 Evaluate side-chains 93 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 70 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 76 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 408 ILE Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain C residue 406 LEU 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 76 LEU Chi-restraints excluded: chain D residue 223 ARG Chi-restraints excluded: chain D residue 377 ILE Chi-restraints excluded: chain D residue 399 VAL 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 97 optimal weight: 0.7980 chunk 63 optimal weight: 2.9990 chunk 94 optimal weight: 6.9990 chunk 47 optimal weight: 0.0040 chunk 31 optimal weight: 0.9980 chunk 30 optimal weight: 0.0370 chunk 100 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 overall best weight: 0.4870 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 465 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7289 moved from start: 0.4942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16528 Z= 0.154 Angle : 0.544 8.014 23172 Z= 0.301 Chirality : 0.036 0.161 2564 Planarity : 0.004 0.058 2342 Dihedral : 24.412 147.760 3742 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.93 % Allowed : 12.75 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.17 (0.23), residues: 1464 helix: 2.24 (0.23), residues: 508 sheet: 0.29 (0.36), residues: 198 loop : -0.06 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 225 HIS 0.003 0.001 HIS B 296 PHE 0.019 0.001 PHE C 306 TYR 0.008 0.001 TYR D 459 ARG 0.012 0.000 ARG D 404 *********************** 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 105 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 80 time to evaluate : 1.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 129 MET cc_start: 0.8957 (ttm) cc_final: 0.8525 (ttt) REVERT: D 223 ARG cc_start: 0.8974 (OUTLIER) cc_final: 0.8707 (ptm160) outliers start: 25 outliers final: 19 residues processed: 99 average time/residue: 0.3440 time to fit residues: 48.8594 Evaluate side-chains 93 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 1.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain A residue 516 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain C residue 406 LEU 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 223 ARG 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 143 optimal weight: 0.8980 chunk 151 optimal weight: 1.9990 chunk 138 optimal weight: 0.5980 chunk 147 optimal weight: 0.0770 chunk 88 optimal weight: 6.9990 chunk 64 optimal weight: 0.7980 chunk 115 optimal weight: 5.9990 chunk 45 optimal weight: 3.9990 chunk 133 optimal weight: 0.0000 chunk 139 optimal weight: 0.9980 chunk 146 optimal weight: 0.1980 overall best weight: 0.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 465 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7261 moved from start: 0.5037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16528 Z= 0.145 Angle : 0.543 8.962 23172 Z= 0.299 Chirality : 0.036 0.159 2564 Planarity : 0.004 0.051 2342 Dihedral : 24.363 147.872 3742 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 1.78 % Allowed : 12.98 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.24 (0.23), residues: 1464 helix: 2.30 (0.23), residues: 508 sheet: 0.29 (0.36), residues: 198 loop : -0.00 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 225 HIS 0.006 0.001 HIS A 296 PHE 0.033 0.001 PHE B 468 TYR 0.008 0.001 TYR D 459 ARG 0.012 0.000 ARG B 404 *********************** 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 106 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 83 time to evaluate : 1.423 Fit side-chains revert: symmetry clash REVERT: B 129 MET cc_start: 0.8961 (ttm) cc_final: 0.8525 (ttt) outliers start: 23 outliers final: 19 residues processed: 97 average time/residue: 0.3497 time to fit residues: 48.7235 Evaluate side-chains 92 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 73 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 406 LEU 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 72 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 245 ASP Chi-restraints excluded: chain C residue 406 LEU 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 446 LEU Chi-restraints excluded: chain D residue 465 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 96 optimal weight: 2.9990 chunk 155 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 chunk 108 optimal weight: 0.0470 chunk 163 optimal weight: 0.0970 chunk 150 optimal weight: 4.9990 chunk 130 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 79 optimal weight: 0.4980 overall best weight: 0.7078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 465 GLN D 464 ASN D 465 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.5124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16528 Z= 0.180 Angle : 0.570 12.564 23172 Z= 0.311 Chirality : 0.036 0.141 2564 Planarity : 0.004 0.061 2342 Dihedral : 24.396 146.908 3742 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 2.01 % Allowed : 12.91 % Favored : 85.09 % 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: 1.20 (0.23), residues: 1464 helix: 2.30 (0.23), residues: 508 sheet: 0.28 (0.35), residues: 198 loop : -0.05 (0.24), residues: 758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 225 HIS 0.006 0.001 HIS C 296 PHE 0.020 0.001 PHE A 468 TYR 0.014 0.001 TYR B 431 ARG 0.013 0.000 ARG B 404 ********************** 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: 26 poor density : 72 time to evaluate : 1.424 Fit side-chains revert: symmetry clash REVERT: B 129 MET cc_start: 0.8992 (ttm) cc_final: 0.8559 (ttt) REVERT: B 465 GLN cc_start: 0.6472 (OUTLIER) cc_final: 0.5482 (mm110) REVERT: D 423 CYS cc_start: 0.4041 (m) cc_final: 0.3619 (m) REVERT: D 465 GLN cc_start: 0.5792 (OUTLIER) cc_final: 0.5176 (mm110) outliers start: 26 outliers final: 18 residues processed: 90 average time/residue: 0.3311 time to fit residues: 43.4242 Evaluate side-chains 92 residues out of total 1294 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 72 time to evaluate : 1.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 245 ASP Chi-restraints excluded: chain A residue 406 LEU Chi-restraints excluded: chain A residue 411 MET Chi-restraints excluded: chain A residue 420 ARG Chi-restraints excluded: chain B residue 43 GLN Chi-restraints excluded: chain B residue 72 LEU Chi-restraints excluded: chain B residue 181 THR Chi-restraints excluded: chain B residue 399 VAL Chi-restraints excluded: chain B residue 423 CYS Chi-restraints excluded: chain B residue 465 GLN Chi-restraints excluded: chain C residue 245 ASP Chi-restraints excluded: chain C residue 406 LEU 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 Chi-restraints excluded: chain D residue 465 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 164 random chunks: chunk 103 optimal weight: 4.9990 chunk 138 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 119 optimal weight: 0.0060 chunk 19 optimal weight: 7.9990 chunk 36 optimal weight: 0.0470 chunk 130 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.4494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 465 GLN D 465 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.108226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.084481 restraints weight = 43148.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.084453 restraints weight = 27531.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.085246 restraints weight = 22979.109| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16528 Z= 0.156 Angle : 0.552 8.990 23172 Z= 0.302 Chirality : 0.036 0.148 2564 Planarity : 0.004 0.054 2342 Dihedral : 24.370 147.182 3740 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.78 % Allowed : 13.29 % Favored : 84.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.25 (0.23), residues: 1464 helix: 2.32 (0.23), residues: 508 sheet: 0.30 (0.36), residues: 198 loop : -0.00 (0.24), residues: 758 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 0.034 0.001 PHE B 468 TYR 0.013 0.001 TYR B 431 ARG 0.012 0.000 ARG B 404 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2514.55 seconds wall clock time: 47 minutes 41.76 seconds (2861.76 seconds total)