Starting phenix.real_space_refine on Sat Jun 7 21:35:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hf7_34715/06_2025/8hf7_34715.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hf7_34715/06_2025/8hf7_34715.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hf7_34715/06_2025/8hf7_34715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hf7_34715/06_2025/8hf7_34715.map" model { file = "/net/cci-nas-00/data/ceres_data/8hf7_34715/06_2025/8hf7_34715.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hf7_34715/06_2025/8hf7_34715.cif" } resolution = 3.8 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= 0.003 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: 4 Type Number sf(0) Gaussians S 28 5.16 5 C 5784 2.51 5 N 1478 2.21 5 O 1688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8978 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4424 Classifications: {'peptide': 563} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 550} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 4424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4424 Classifications: {'peptide': 563} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 550} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 65 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'UNK:plan-1': 13} Unresolved non-hydrogen planarities: 13 Chain: "C" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 65 Classifications: {'peptide': 13} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'TRANS': 12} Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'UNK:plan-1': 13} Unresolved non-hydrogen planarities: 13 Time building chain proxies: 9.26, per 1000 atoms: 1.03 Number of scatterers: 8978 At special positions: 0 Unit cell: (80.652, 81.51, 140.712, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 28 16.00 O 1688 8.00 N 1478 7.00 C 5784 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: 3.96 Conformation dependent library (CDL) restraints added in 1.8 seconds 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2176 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 7 sheets defined 63.6% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 158 through 163 removed outlier: 4.082A pdb=" N VAL A 162 " --> pdb=" O ILE A 158 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS A 163 " --> pdb=" O PRO A 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 158 through 163' Processing helix chain 'A' and resid 167 through 188 removed outlier: 3.749A pdb=" N VAL A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR A 179 " --> pdb=" O THR A 175 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 182 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 183 " --> pdb=" O THR A 179 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLY A 185 " --> pdb=" O ILE A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 250 removed outlier: 4.358A pdb=" N ILE A 239 " --> pdb=" O GLN A 235 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASP A 240 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N VAL A 241 " --> pdb=" O LEU A 237 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N HIS A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE A 250 " --> pdb=" O ILE A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 260 removed outlier: 3.902A pdb=" N PHE A 257 " --> pdb=" O PRO A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 272 Processing helix chain 'A' and resid 275 through 277 No H-bonds generated for 'chain 'A' and resid 275 through 277' Processing helix chain 'A' and resid 278 through 304 removed outlier: 3.836A pdb=" N THR A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N VAL A 290 " --> pdb=" O ILE A 286 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N SER A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU A 298 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N VAL A 299 " --> pdb=" O ILE A 295 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ASN A 304 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 312 Processing helix chain 'A' and resid 313 through 325 removed outlier: 4.013A pdb=" N ILE A 317 " --> pdb=" O LEU A 313 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N TYR A 318 " --> pdb=" O ALA A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 326 through 353 removed outlier: 4.426A pdb=" N GLU A 330 " --> pdb=" O MET A 326 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N ARG A 334 " --> pdb=" O GLU A 330 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ASP A 335 " --> pdb=" O LYS A 331 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N ASN A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 removed outlier: 3.769A pdb=" N ILE A 357 " --> pdb=" O GLY A 353 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER A 359 " --> pdb=" O GLU A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 363 through 416 removed outlier: 4.446A pdb=" N LYS A 369 " --> pdb=" O GLN A 365 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ASP A 416 " --> pdb=" O VAL A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 444 removed outlier: 4.376A pdb=" N VAL A 432 " --> pdb=" O ASN A 428 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N TYR A 433 " --> pdb=" O THR A 429 " (cutoff:3.500A) Proline residue: A 437 - end of helix Processing helix chain 'A' and resid 444 through 459 Processing helix chain 'A' and resid 522 through 527 Processing helix chain 'A' and resid 528 through 532 removed outlier: 3.622A pdb=" N VAL A 531 " --> pdb=" O LYS A 528 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ASN A 532 " --> pdb=" O MET A 529 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 528 through 532' Processing helix chain 'A' and resid 553 through 558 removed outlier: 4.235A pdb=" N GLN A 558 " --> pdb=" O LYS A 554 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 579 removed outlier: 3.728A pdb=" N ASN A 577 " --> pdb=" O THR A 573 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 578 " --> pdb=" O ILE A 574 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 579 " --> pdb=" O LEU A 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 573 through 579' Processing helix chain 'A' and resid 587 through 596 removed outlier: 3.655A pdb=" N ILE A 591 " --> pdb=" O THR A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 634 removed outlier: 3.707A pdb=" N ILE A 630 " --> pdb=" O GLN A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 653 through 665 removed outlier: 3.631A pdb=" N ILE A 665 " --> pdb=" O VAL A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 678 through 682 removed outlier: 3.865A pdb=" N GLU A 682 " --> pdb=" O THR A 679 " (cutoff:3.500A) Processing helix chain 'A' and resid 704 through 708 removed outlier: 3.939A pdb=" N GLN A 707 " --> pdb=" O LEU A 704 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLY A 708 " --> pdb=" O LEU A 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 704 through 708' Processing helix chain 'A' and resid 710 through 717 removed outlier: 3.529A pdb=" N LEU A 714 " --> pdb=" O PHE A 710 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 163 removed outlier: 4.042A pdb=" N VAL B 162 " --> pdb=" O ILE B 158 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS B 163 " --> pdb=" O PRO B 159 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 158 through 163' Processing helix chain 'B' and resid 167 through 183 removed outlier: 3.560A pdb=" N LEU B 173 " --> pdb=" O ALA B 169 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA B 174 " --> pdb=" O ASN B 170 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N LEU B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N VAL B 178 " --> pdb=" O ALA B 174 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N THR B 179 " --> pdb=" O THR B 175 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 188 Processing helix chain 'B' and resid 202 through 250 removed outlier: 4.478A pdb=" N ILE B 239 " --> pdb=" O GLN B 235 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ASP B 240 " --> pdb=" O ARG B 236 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N VAL B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N HIS B 248 " --> pdb=" O SER B 244 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N PHE B 250 " --> pdb=" O ILE B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 260 removed outlier: 3.829A pdb=" N PHE B 257 " --> pdb=" O PRO B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 272 Processing helix chain 'B' and resid 275 through 277 No H-bonds generated for 'chain 'B' and resid 275 through 277' Processing helix chain 'B' and resid 278 through 304 removed outlier: 3.820A pdb=" N THR B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL B 290 " --> pdb=" O ILE B 286 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N SER B 291 " --> pdb=" O PHE B 287 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N LEU B 298 " --> pdb=" O VAL B 294 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL B 299 " --> pdb=" O ILE B 295 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ASN B 304 " --> pdb=" O LEU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 305 through 312 Processing helix chain 'B' and resid 313 through 325 removed outlier: 4.036A pdb=" N ILE B 317 " --> pdb=" O LEU B 313 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N TYR B 318 " --> pdb=" O ALA B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 353 removed outlier: 4.131A pdb=" N GLU B 330 " --> pdb=" O MET B 326 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N ARG B 334 " --> pdb=" O GLU B 330 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ASP B 335 " --> pdb=" O LYS B 331 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ASN B 340 " --> pdb=" O THR B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 361 removed outlier: 3.721A pdb=" N ILE B 357 " --> pdb=" O GLY B 353 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER B 359 " --> pdb=" O GLU B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 363 through 416 removed outlier: 4.469A pdb=" N LYS B 369 " --> pdb=" O GLN B 365 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N ASP B 416 " --> pdb=" O VAL B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 444 removed outlier: 4.391A pdb=" N VAL B 432 " --> pdb=" O ASN B 428 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N TYR B 433 " --> pdb=" O THR B 429 " (cutoff:3.500A) Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 444 through 459 Processing helix chain 'B' and resid 459 through 464 removed outlier: 3.874A pdb=" N VAL B 464 " --> pdb=" O GLU B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 527 Processing helix chain 'B' and resid 528 through 532 removed outlier: 3.889A pdb=" N VAL B 531 " --> pdb=" O LYS B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 553 through 558 removed outlier: 4.228A pdb=" N GLN B 558 " --> pdb=" O LYS B 554 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 579 removed outlier: 3.514A pdb=" N LEU B 578 " --> pdb=" O ILE B 574 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LEU B 579 " --> pdb=" O LEU B 575 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 574 through 579' Processing helix chain 'B' and resid 587 through 596 removed outlier: 3.741A pdb=" N ILE B 591 " --> pdb=" O THR B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 634 removed outlier: 3.602A pdb=" N ILE B 630 " --> pdb=" O GLN B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 653 through 665 removed outlier: 3.586A pdb=" N ARG B 659 " --> pdb=" O LEU B 655 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ILE B 665 " --> pdb=" O VAL B 661 " (cutoff:3.500A) Processing helix chain 'B' and resid 678 through 682 removed outlier: 3.857A pdb=" N GLU B 682 " --> pdb=" O THR B 679 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 708 removed outlier: 3.927A pdb=" N GLN B 707 " --> pdb=" O LEU B 704 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY B 708 " --> pdb=" O LEU B 705 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 704 through 708' Processing helix chain 'B' and resid 710 through 717 removed outlier: 3.529A pdb=" N LEU B 714 " --> pdb=" O PHE B 710 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 500 through 503 removed outlier: 5.706A pdb=" N VAL A 489 " --> pdb=" O ASP A 502 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N PHE A 486 " --> pdb=" O SER A 542 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N SER A 542 " --> pdb=" O PHE A 486 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N GLN A 488 " --> pdb=" O GLU A 540 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N GLU A 540 " --> pdb=" O GLN A 488 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 671 through 674 removed outlier: 3.720A pdb=" N PHE A 673 " --> pdb=" O VAL A 513 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LYS A 512 " --> pdb=" O LYS A 686 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N VAL A 688 " --> pdb=" O LYS A 512 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA A 514 " --> pdb=" O VAL A 688 " (cutoff:3.500A) removed outlier: 8.152A pdb=" N LEU A 690 " --> pdb=" O ALA A 514 " (cutoff:3.500A) removed outlier: 7.636A pdb=" N VAL A 687 " --> pdb=" O GLU A 698 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N GLU A 698 " --> pdb=" O VAL A 687 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N VAL A 689 " --> pdb=" O VAL A 696 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N VAL A 696 " --> pdb=" O VAL A 689 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 560 through 562 Processing sheet with id=AA4, first strand: chain 'B' and resid 500 through 503 removed outlier: 5.705A pdb=" N VAL B 489 " --> pdb=" O ASP B 502 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N PHE B 486 " --> pdb=" O SER B 542 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N SER B 542 " --> pdb=" O PHE B 486 " (cutoff:3.500A) removed outlier: 5.312A pdb=" N GLN B 488 " --> pdb=" O GLU B 540 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N GLU B 540 " --> pdb=" O GLN B 488 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 671 through 674 removed outlier: 3.784A pdb=" N PHE B 673 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LYS B 512 " --> pdb=" O LYS B 686 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL B 688 " --> pdb=" O LYS B 512 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ALA B 514 " --> pdb=" O VAL B 688 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N LEU B 690 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N VAL B 687 " --> pdb=" O GLU B 698 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N GLU B 698 " --> pdb=" O VAL B 687 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL B 689 " --> pdb=" O VAL B 696 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL B 696 " --> pdb=" O VAL B 689 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 560 through 562 Processing sheet with id=AA7, first strand: chain 'B' and resid 572 through 573 removed outlier: 3.844A pdb=" N GLY B 572 " --> pdb=" O THR B 616 " (cutoff:3.500A) 457 hydrogen bonds defined for protein. 1338 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.93 Time building geometry restraints manager: 3.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1536 1.32 - 1.45: 2192 1.45 - 1.57: 5322 1.57 - 1.69: 0 1.69 - 1.82: 56 Bond restraints: 9106 Sorted by residual: bond pdb=" CA UNK D 4 " pdb=" C UNK D 4 " ideal model delta sigma weight residual 1.525 1.433 0.092 2.10e-02 2.27e+03 1.92e+01 bond pdb=" CA GLN B 612 " pdb=" C GLN B 612 " ideal model delta sigma weight residual 1.531 1.482 0.049 1.12e-02 7.97e+03 1.89e+01 bond pdb=" CA UNK D 10 " pdb=" C UNK D 10 " ideal model delta sigma weight residual 1.525 1.435 0.090 2.10e-02 2.27e+03 1.84e+01 bond pdb=" CA THR B 613 " pdb=" C THR B 613 " ideal model delta sigma weight residual 1.522 1.473 0.049 1.31e-02 5.83e+03 1.38e+01 bond pdb=" CA UNK C 10 " pdb=" C UNK C 10 " ideal model delta sigma weight residual 1.525 1.452 0.073 2.10e-02 2.27e+03 1.21e+01 ... (remaining 9101 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 11643 2.51 - 5.03: 520 5.03 - 7.54: 112 7.54 - 10.05: 52 10.05 - 12.57: 15 Bond angle restraints: 12342 Sorted by residual: angle pdb=" N ASN B 610 " pdb=" CA ASN B 610 " pdb=" C ASN B 610 " ideal model delta sigma weight residual 111.87 101.49 10.38 1.41e+00 5.03e-01 5.42e+01 angle pdb=" N MET A 607 " pdb=" CA MET A 607 " pdb=" C MET A 607 " ideal model delta sigma weight residual 109.24 99.38 9.86 1.39e+00 5.18e-01 5.03e+01 angle pdb=" C UNK D 12 " pdb=" CA UNK D 12 " pdb=" CB UNK D 12 " ideal model delta sigma weight residual 110.08 121.43 -11.35 1.90e+00 2.77e-01 3.57e+01 angle pdb=" C SER B 501 " pdb=" N ASP B 502 " pdb=" CA ASP B 502 " ideal model delta sigma weight residual 122.46 129.65 -7.19 1.41e+00 5.03e-01 2.60e+01 angle pdb=" C SER A 501 " pdb=" N ASP A 502 " pdb=" CA ASP A 502 " ideal model delta sigma weight residual 122.46 129.62 -7.16 1.41e+00 5.03e-01 2.58e+01 ... (remaining 12337 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.72: 4991 17.72 - 35.43: 436 35.43 - 53.15: 74 53.15 - 70.86: 15 70.86 - 88.58: 6 Dihedral angle restraints: 5522 sinusoidal: 2152 harmonic: 3370 Sorted by residual: dihedral pdb=" C UNK D 12 " pdb=" N UNK D 12 " pdb=" CA UNK D 12 " pdb=" CB UNK D 12 " ideal model delta harmonic sigma weight residual -122.60 -139.73 17.13 0 2.50e+00 1.60e-01 4.69e+01 dihedral pdb=" N UNK D 12 " pdb=" C UNK D 12 " pdb=" CA UNK D 12 " pdb=" CB UNK D 12 " ideal model delta harmonic sigma weight residual 122.80 137.07 -14.27 0 2.50e+00 1.60e-01 3.26e+01 dihedral pdb=" CA THR B 195 " pdb=" C THR B 195 " pdb=" N TYR B 196 " pdb=" CA TYR B 196 " ideal model delta harmonic sigma weight residual -180.00 -151.96 -28.04 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 5519 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1406 0.122 - 0.244: 94 0.244 - 0.366: 11 0.366 - 0.489: 2 0.489 - 0.611: 1 Chirality restraints: 1514 Sorted by residual: chirality pdb=" CA UNK D 12 " pdb=" N UNK D 12 " pdb=" C UNK D 12 " pdb=" CB UNK D 12 " both_signs ideal model delta sigma weight residual False 2.52 1.91 0.61 2.00e-01 2.50e+01 9.33e+00 chirality pdb=" CB VAL A 414 " pdb=" CA VAL A 414 " pdb=" CG1 VAL A 414 " pdb=" CG2 VAL A 414 " both_signs ideal model delta sigma weight residual False -2.63 -2.22 -0.40 2.00e-01 2.50e+01 4.09e+00 chirality pdb=" CB VAL B 414 " pdb=" CA VAL B 414 " pdb=" CG1 VAL B 414 " pdb=" CG2 VAL B 414 " both_signs ideal model delta sigma weight residual False -2.63 -2.24 -0.39 2.00e-01 2.50e+01 3.72e+00 ... (remaining 1511 not shown) Planarity restraints: 1544 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY A 166 " 0.019 2.00e-02 2.50e+03 3.62e-02 1.31e+01 pdb=" C GLY A 166 " -0.063 2.00e-02 2.50e+03 pdb=" O GLY A 166 " 0.023 2.00e-02 2.50e+03 pdb=" N LEU A 167 " 0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 197 " 0.056 5.00e-02 4.00e+02 8.66e-02 1.20e+01 pdb=" N PRO A 198 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 198 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 198 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA UNK D 5 " 0.015 2.00e-02 2.50e+03 3.20e-02 1.02e+01 pdb=" C UNK D 5 " -0.055 2.00e-02 2.50e+03 pdb=" O UNK D 5 " 0.021 2.00e-02 2.50e+03 pdb=" N UNK D 6 " 0.019 2.00e-02 2.50e+03 ... (remaining 1541 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 2573 2.82 - 3.34: 8523 3.34 - 3.86: 14897 3.86 - 4.38: 15743 4.38 - 4.90: 26484 Nonbonded interactions: 68220 Sorted by model distance: nonbonded pdb=" CB ASN B 561 " pdb=" CD2 LEU B 643 " model vdw 2.294 3.860 nonbonded pdb=" CB ASN A 561 " pdb=" CD2 LEU A 643 " model vdw 2.309 3.860 nonbonded pdb=" O LEU A 279 " pdb=" OG1 THR A 282 " model vdw 2.325 3.040 nonbonded pdb=" O LEU B 279 " pdb=" OG1 THR B 282 " model vdw 2.327 3.040 nonbonded pdb=" OG SER A 519 " pdb=" O SER B 651 " model vdw 2.331 3.040 ... (remaining 68215 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' 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: 28.890 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: 0.380 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 28.950 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 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 : 0.006 0.092 9106 Z= 0.340 Angle : 1.342 12.566 12342 Z= 0.674 Chirality : 0.069 0.611 1514 Planarity : 0.007 0.087 1544 Dihedral : 14.022 88.580 3346 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.62 % Allowed : 5.88 % Favored : 93.49 % Rotamer: Outliers : 0.61 % Allowed : 1.92 % Favored : 97.47 % Cbeta Deviations : 0.18 % 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: -3.03 (0.21), residues: 1122 helix: -1.77 (0.17), residues: 634 sheet: -1.21 (0.59), residues: 48 loop : -2.28 (0.25), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 408 HIS 0.002 0.001 HIS A 676 PHE 0.041 0.002 PHE A 257 TYR 0.023 0.002 TYR A 559 ARG 0.004 0.001 ARG A 629 Details of bonding type rmsd hydrogen bonds : bond 0.14547 ( 457) hydrogen bonds : angle 5.60355 ( 1338) covalent geometry : bond 0.00616 ( 9106) covalent geometry : angle 1.34201 (12342) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 172 time to evaluate : 1.029 Fit side-chains REVERT: A 192 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8347 (mp) REVERT: A 563 LEU cc_start: 0.8801 (tp) cc_final: 0.8442 (tt) REVERT: A 662 ASP cc_start: 0.9026 (m-30) cc_final: 0.8657 (m-30) REVERT: B 431 LEU cc_start: 0.8845 (tp) cc_final: 0.8636 (mt) REVERT: B 529 MET cc_start: 0.9375 (pmm) cc_final: 0.9061 (pmm) REVERT: B 563 LEU cc_start: 0.8368 (tt) cc_final: 0.8112 (tt) outliers start: 6 outliers final: 3 residues processed: 177 average time/residue: 0.1700 time to fit residues: 44.4693 Evaluate side-chains 126 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 122 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 613 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 96 optimal weight: 0.9980 chunk 86 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 34 optimal weight: 30.0000 chunk 54 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 273 ASN A 445 GLN B 273 ASN B 588 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.101667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.078708 restraints weight = 39083.174| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.080873 restraints weight = 22287.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.082275 restraints weight = 15203.627| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 9106 Z= 0.238 Angle : 0.824 10.373 12342 Z= 0.424 Chirality : 0.046 0.236 1514 Planarity : 0.005 0.033 1544 Dihedral : 6.199 51.753 1242 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.45 % Allowed : 5.17 % Favored : 94.39 % Rotamer: Outliers : 2.83 % Allowed : 12.35 % Favored : 84.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.95 (0.24), residues: 1122 helix: 0.18 (0.21), residues: 620 sheet: -1.11 (0.76), residues: 34 loop : -1.66 (0.26), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 408 HIS 0.004 0.001 HIS A 490 PHE 0.018 0.002 PHE A 257 TYR 0.028 0.002 TYR B 188 ARG 0.008 0.001 ARG B 593 Details of bonding type rmsd hydrogen bonds : bond 0.07522 ( 457) hydrogen bonds : angle 4.58477 ( 1338) covalent geometry : bond 0.00510 ( 9106) covalent geometry : angle 0.82354 (12342) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 129 time to evaluate : 1.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 300 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.9044 (mm) REVERT: A 529 MET cc_start: 0.9589 (pmm) cc_final: 0.9272 (pmm) REVERT: A 561 ASN cc_start: 0.8852 (t0) cc_final: 0.8237 (t0) REVERT: B 300 LEU cc_start: 0.9228 (mm) cc_final: 0.8981 (mm) REVERT: B 529 MET cc_start: 0.9501 (pmm) cc_final: 0.9142 (pmm) outliers start: 28 outliers final: 19 residues processed: 150 average time/residue: 0.1703 time to fit residues: 38.9018 Evaluate side-chains 130 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 110 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 613 THR Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 252 LEU Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 662 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 4 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 86 optimal weight: 0.7980 chunk 98 optimal weight: 0.2980 chunk 81 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 97 optimal weight: 20.0000 chunk 51 optimal weight: 0.5980 chunk 109 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 10 optimal weight: 7.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 HIS B 490 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.103483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.080658 restraints weight = 39772.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.082933 restraints weight = 22358.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.084393 restraints weight = 15047.442| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9106 Z= 0.143 Angle : 0.691 11.761 12342 Z= 0.342 Chirality : 0.042 0.221 1514 Planarity : 0.003 0.029 1544 Dihedral : 5.522 59.679 1239 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.36 % Allowed : 5.35 % Favored : 94.30 % Rotamer: Outliers : 3.44 % Allowed : 16.40 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.50 (0.25), residues: 1122 helix: 0.65 (0.21), residues: 640 sheet: -1.28 (0.77), residues: 34 loop : -1.71 (0.26), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP B 408 HIS 0.002 0.001 HIS A 676 PHE 0.013 0.001 PHE A 257 TYR 0.032 0.002 TYR B 559 ARG 0.003 0.000 ARG B 593 Details of bonding type rmsd hydrogen bonds : bond 0.06575 ( 457) hydrogen bonds : angle 4.30256 ( 1338) covalent geometry : bond 0.00301 ( 9106) covalent geometry : angle 0.69122 (12342) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 1.032 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 300 LEU cc_start: 0.9323 (OUTLIER) cc_final: 0.9017 (mm) REVERT: A 561 ASN cc_start: 0.8875 (t0) cc_final: 0.8287 (t0) REVERT: B 300 LEU cc_start: 0.9252 (mm) cc_final: 0.9023 (mm) REVERT: B 490 HIS cc_start: 0.9073 (OUTLIER) cc_final: 0.8870 (m-70) REVERT: B 529 MET cc_start: 0.9446 (pmm) cc_final: 0.9100 (pmm) outliers start: 34 outliers final: 22 residues processed: 151 average time/residue: 0.1629 time to fit residues: 38.7414 Evaluate side-chains 134 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 110 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 560 ILE Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 490 HIS Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 662 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 70 optimal weight: 0.9980 chunk 75 optimal weight: 9.9990 chunk 16 optimal weight: 5.9990 chunk 92 optimal weight: 30.0000 chunk 48 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 69 optimal weight: 5.9990 chunk 32 optimal weight: 0.0770 chunk 11 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 overall best weight: 1.3940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 ASN B 588 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.104534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.081859 restraints weight = 39307.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.084163 restraints weight = 22233.245| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.085593 restraints weight = 14946.559| |-----------------------------------------------------------------------------| r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9106 Z= 0.126 Angle : 0.674 12.526 12342 Z= 0.326 Chirality : 0.042 0.232 1514 Planarity : 0.003 0.031 1544 Dihedral : 4.979 40.847 1238 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.53 % Favored : 94.21 % Rotamer: Outliers : 3.44 % Allowed : 19.53 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.23 (0.25), residues: 1122 helix: 0.91 (0.21), residues: 644 sheet: -1.28 (0.77), residues: 34 loop : -1.66 (0.26), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 408 HIS 0.017 0.001 HIS B 490 PHE 0.011 0.001 PHE B 257 TYR 0.028 0.001 TYR B 559 ARG 0.003 0.000 ARG B 593 Details of bonding type rmsd hydrogen bonds : bond 0.05981 ( 457) hydrogen bonds : angle 4.11782 ( 1338) covalent geometry : bond 0.00254 ( 9106) covalent geometry : angle 0.67360 (12342) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 120 time to evaluate : 1.137 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 TYR cc_start: 0.4550 (t80) cc_final: 0.3810 (m-80) REVERT: A 300 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9020 (mm) REVERT: A 561 ASN cc_start: 0.8874 (t0) cc_final: 0.8289 (t0) REVERT: A 662 ASP cc_start: 0.9160 (m-30) cc_final: 0.8770 (p0) REVERT: B 490 HIS cc_start: 0.9037 (t-90) cc_final: 0.8685 (m-70) REVERT: B 529 MET cc_start: 0.9426 (pmm) cc_final: 0.9156 (pmm) outliers start: 34 outliers final: 24 residues processed: 146 average time/residue: 0.1827 time to fit residues: 41.1293 Evaluate side-chains 135 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 110 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 171 ILE Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 490 HIS Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 644 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 60 optimal weight: 6.9990 chunk 2 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 33 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 36 optimal weight: 0.3980 chunk 44 optimal weight: 20.0000 chunk 99 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 62 optimal weight: 0.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 490 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.104334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.081474 restraints weight = 39000.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.083784 restraints weight = 22215.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.085274 restraints weight = 14925.216| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.3164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9106 Z= 0.124 Angle : 0.679 12.304 12342 Z= 0.324 Chirality : 0.042 0.194 1514 Planarity : 0.003 0.031 1544 Dihedral : 4.843 39.174 1238 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.70 % Favored : 94.03 % Rotamer: Outliers : 3.64 % Allowed : 21.96 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.06 (0.25), residues: 1122 helix: 1.04 (0.21), residues: 642 sheet: -1.23 (0.79), residues: 34 loop : -1.57 (0.26), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 408 HIS 0.002 0.000 HIS A 676 PHE 0.010 0.001 PHE B 257 TYR 0.027 0.001 TYR B 559 ARG 0.002 0.000 ARG B 593 Details of bonding type rmsd hydrogen bonds : bond 0.05772 ( 457) hydrogen bonds : angle 4.11637 ( 1338) covalent geometry : bond 0.00255 ( 9106) covalent geometry : angle 0.67866 (12342) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 118 time to evaluate : 0.973 Fit side-chains REVERT: A 187 TYR cc_start: 0.4506 (t80) cc_final: 0.3736 (m-80) REVERT: A 300 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.9037 (mm) REVERT: A 561 ASN cc_start: 0.8861 (t0) cc_final: 0.8270 (t0) REVERT: A 662 ASP cc_start: 0.9149 (m-30) cc_final: 0.8762 (p0) REVERT: A 679 THR cc_start: 0.6427 (OUTLIER) cc_final: 0.6099 (t) REVERT: B 490 HIS cc_start: 0.8957 (OUTLIER) cc_final: 0.8674 (m-70) outliers start: 36 outliers final: 27 residues processed: 146 average time/residue: 0.1680 time to fit residues: 37.3304 Evaluate side-chains 138 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 108 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 644 ILE Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 490 HIS Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 573 THR Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 644 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 7 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 42 optimal weight: 10.0000 chunk 85 optimal weight: 0.8980 chunk 36 optimal weight: 30.0000 chunk 55 optimal weight: 20.0000 chunk 77 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 13 optimal weight: 0.2980 chunk 83 optimal weight: 0.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 490 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.103660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.080122 restraints weight = 38527.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.082449 restraints weight = 22155.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.083969 restraints weight = 14999.014| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.3363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9106 Z= 0.132 Angle : 0.707 12.731 12342 Z= 0.337 Chirality : 0.043 0.205 1514 Planarity : 0.003 0.033 1544 Dihedral : 4.825 36.934 1238 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.70 % Favored : 94.03 % Rotamer: Outliers : 4.05 % Allowed : 22.17 % Favored : 73.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.09 (0.25), residues: 1122 helix: 1.13 (0.22), residues: 632 sheet: -1.28 (0.80), residues: 34 loop : -1.37 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 408 HIS 0.004 0.001 HIS B 490 PHE 0.009 0.001 PHE A 256 TYR 0.040 0.001 TYR B 188 ARG 0.002 0.000 ARG B 593 Details of bonding type rmsd hydrogen bonds : bond 0.05837 ( 457) hydrogen bonds : angle 4.18032 ( 1338) covalent geometry : bond 0.00279 ( 9106) covalent geometry : angle 0.70709 (12342) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 109 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 187 TYR cc_start: 0.4534 (t80) cc_final: 0.3776 (m-80) REVERT: A 300 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9114 (mm) REVERT: A 561 ASN cc_start: 0.8897 (t0) cc_final: 0.8320 (t0) REVERT: A 607 MET cc_start: 0.8606 (ppp) cc_final: 0.8330 (pmm) REVERT: A 662 ASP cc_start: 0.9170 (m-30) cc_final: 0.8793 (p0) REVERT: A 679 THR cc_start: 0.6428 (OUTLIER) cc_final: 0.6092 (t) REVERT: B 559 TYR cc_start: 0.8463 (p90) cc_final: 0.7775 (p90) REVERT: B 679 THR cc_start: 0.6407 (OUTLIER) cc_final: 0.6080 (t) outliers start: 40 outliers final: 28 residues processed: 140 average time/residue: 0.1474 time to fit residues: 31.9036 Evaluate side-chains 135 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 104 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 271 ASP Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 679 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 36 optimal weight: 30.0000 chunk 57 optimal weight: 0.9980 chunk 86 optimal weight: 0.0670 chunk 29 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 28 optimal weight: 3.9990 chunk 110 optimal weight: 30.0000 chunk 83 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 62 optimal weight: 0.9990 overall best weight: 0.7118 ------------------------------------------------------------------------------- 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 = 0.4057 r_free = 0.4057 target = 0.105719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.082603 restraints weight = 39292.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.084980 restraints weight = 22524.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.086504 restraints weight = 15185.563| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.3434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9106 Z= 0.120 Angle : 0.700 13.664 12342 Z= 0.327 Chirality : 0.042 0.204 1514 Planarity : 0.003 0.032 1544 Dihedral : 4.615 35.236 1238 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.27 % Allowed : 5.97 % Favored : 93.76 % Rotamer: Outliers : 2.63 % Allowed : 24.29 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.19 (0.25), residues: 1122 helix: 1.25 (0.22), residues: 646 sheet: -1.15 (0.68), residues: 48 loop : -1.48 (0.27), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 408 HIS 0.002 0.000 HIS A 490 PHE 0.013 0.001 PHE A 256 TYR 0.029 0.001 TYR B 188 ARG 0.002 0.000 ARG B 627 Details of bonding type rmsd hydrogen bonds : bond 0.05188 ( 457) hydrogen bonds : angle 4.04470 ( 1338) covalent geometry : bond 0.00237 ( 9106) covalent geometry : angle 0.69967 (12342) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 121 time to evaluate : 1.022 Fit side-chains revert: symmetry clash REVERT: A 187 TYR cc_start: 0.4411 (t80) cc_final: 0.3740 (m-80) REVERT: A 188 TYR cc_start: 0.7493 (OUTLIER) cc_final: 0.7086 (m-80) REVERT: A 300 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9067 (mm) REVERT: A 561 ASN cc_start: 0.8825 (t0) cc_final: 0.8301 (t0) REVERT: A 662 ASP cc_start: 0.9149 (m-30) cc_final: 0.8760 (p0) REVERT: A 679 THR cc_start: 0.6389 (OUTLIER) cc_final: 0.6087 (t) REVERT: B 561 ASN cc_start: 0.8968 (t0) cc_final: 0.8293 (t0) REVERT: B 679 THR cc_start: 0.6397 (OUTLIER) cc_final: 0.6081 (t) outliers start: 26 outliers final: 20 residues processed: 143 average time/residue: 0.1570 time to fit residues: 34.3292 Evaluate side-chains 132 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 108 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 188 TYR Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 282 THR Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 679 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 13 optimal weight: 6.9990 chunk 83 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 106 optimal weight: 10.0000 chunk 15 optimal weight: 7.9990 chunk 77 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 90 optimal weight: 6.9990 chunk 48 optimal weight: 9.9990 chunk 44 optimal weight: 20.0000 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 GLN A 588 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.099521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.076275 restraints weight = 40714.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.078465 restraints weight = 23478.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.079875 restraints weight = 16025.194| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9106 Z= 0.221 Angle : 0.803 14.064 12342 Z= 0.398 Chirality : 0.045 0.228 1514 Planarity : 0.003 0.034 1544 Dihedral : 5.151 39.664 1238 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.24 % Favored : 93.58 % Rotamer: Outliers : 4.35 % Allowed : 24.49 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -0.14 (0.25), residues: 1122 helix: 0.88 (0.21), residues: 636 sheet: -1.91 (0.78), residues: 36 loop : -1.33 (0.28), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.003 TRP A 408 HIS 0.004 0.001 HIS A 490 PHE 0.012 0.002 PHE B 486 TYR 0.030 0.002 TYR B 559 ARG 0.005 0.001 ARG A 627 Details of bonding type rmsd hydrogen bonds : bond 0.07151 ( 457) hydrogen bonds : angle 4.58646 ( 1338) covalent geometry : bond 0.00479 ( 9106) covalent geometry : angle 0.80265 (12342) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 104 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 TYR cc_start: 0.4782 (t80) cc_final: 0.4155 (m-80) REVERT: A 300 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.9152 (mm) REVERT: A 561 ASN cc_start: 0.9063 (t0) cc_final: 0.8455 (t0) REVERT: A 662 ASP cc_start: 0.9209 (m-30) cc_final: 0.8804 (p0) REVERT: A 679 THR cc_start: 0.6476 (OUTLIER) cc_final: 0.6133 (t) REVERT: B 561 ASN cc_start: 0.9155 (t0) cc_final: 0.8732 (t0) REVERT: B 662 ASP cc_start: 0.9496 (m-30) cc_final: 0.8975 (p0) REVERT: B 679 THR cc_start: 0.6436 (OUTLIER) cc_final: 0.6106 (t) outliers start: 43 outliers final: 29 residues processed: 140 average time/residue: 0.1576 time to fit residues: 34.4421 Evaluate side-chains 135 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 103 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 179 THR Chi-restraints excluded: chain A residue 232 VAL Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 290 VAL Chi-restraints excluded: chain A residue 300 LEU Chi-restraints excluded: chain A residue 344 SER Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 238 SER Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 344 SER Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 404 VAL Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 679 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 103 optimal weight: 5.9990 chunk 108 optimal weight: 0.3980 chunk 72 optimal weight: 1.9990 chunk 93 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 96 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 overall best weight: 2.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 490 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.101519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.078277 restraints weight = 39287.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.080487 restraints weight = 22734.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.081897 restraints weight = 15556.757| |-----------------------------------------------------------------------------| r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.4033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9106 Z= 0.150 Angle : 0.762 13.526 12342 Z= 0.360 Chirality : 0.044 0.217 1514 Planarity : 0.003 0.032 1544 Dihedral : 4.963 38.732 1238 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 14.01 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.42 % Favored : 93.49 % Rotamer: Outliers : 2.63 % Allowed : 25.71 % Favored : 71.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.03 (0.25), residues: 1122 helix: 1.03 (0.21), residues: 642 sheet: -1.98 (0.77), residues: 36 loop : -1.40 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 408 HIS 0.002 0.001 HIS B 490 PHE 0.012 0.001 PHE A 256 TYR 0.029 0.001 TYR B 559 ARG 0.003 0.000 ARG A 627 Details of bonding type rmsd hydrogen bonds : bond 0.06517 ( 457) hydrogen bonds : angle 4.34257 ( 1338) covalent geometry : bond 0.00323 ( 9106) covalent geometry : angle 0.76241 (12342) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 103 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 TYR cc_start: 0.4680 (t80) cc_final: 0.4073 (m-80) REVERT: A 561 ASN cc_start: 0.9024 (t0) cc_final: 0.8418 (t0) REVERT: A 662 ASP cc_start: 0.9207 (m-30) cc_final: 0.8823 (p0) REVERT: A 679 THR cc_start: 0.6430 (OUTLIER) cc_final: 0.6073 (t) REVERT: B 490 HIS cc_start: 0.8875 (OUTLIER) cc_final: 0.8671 (m-70) REVERT: B 561 ASN cc_start: 0.9083 (t0) cc_final: 0.8430 (t0) REVERT: B 679 THR cc_start: 0.6411 (OUTLIER) cc_final: 0.6071 (t) outliers start: 26 outliers final: 20 residues processed: 126 average time/residue: 0.1580 time to fit residues: 30.7153 Evaluate side-chains 126 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 103 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 375 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 429 THR Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 490 HIS Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 679 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 77 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 12 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 101 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 46 optimal weight: 9.9990 chunk 56 optimal weight: 20.0000 chunk 55 optimal weight: 7.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 490 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.101189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.077892 restraints weight = 39735.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.080088 restraints weight = 22993.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.081500 restraints weight = 15763.704| |-----------------------------------------------------------------------------| r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.4142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9106 Z= 0.155 Angle : 0.774 13.670 12342 Z= 0.367 Chirality : 0.044 0.237 1514 Planarity : 0.003 0.035 1544 Dihedral : 4.990 39.244 1238 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.51 % Favored : 93.40 % Rotamer: Outliers : 2.63 % Allowed : 25.30 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.05 (0.25), residues: 1122 helix: 1.04 (0.21), residues: 632 sheet: -2.02 (0.76), residues: 36 loop : -1.23 (0.28), residues: 454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP A 408 HIS 0.004 0.001 HIS B 490 PHE 0.012 0.001 PHE A 256 TYR 0.029 0.002 TYR B 559 ARG 0.003 0.000 ARG B 627 Details of bonding type rmsd hydrogen bonds : bond 0.06525 ( 457) hydrogen bonds : angle 4.35373 ( 1338) covalent geometry : bond 0.00335 ( 9106) covalent geometry : angle 0.77406 (12342) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2244 Ramachandran restraints generated. 1122 Oldfield, 0 Emsley, 1122 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 105 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 187 TYR cc_start: 0.4696 (t80) cc_final: 0.4128 (m-80) REVERT: A 561 ASN cc_start: 0.9040 (t0) cc_final: 0.8422 (t0) REVERT: A 662 ASP cc_start: 0.9208 (m-30) cc_final: 0.8839 (p0) REVERT: A 679 THR cc_start: 0.6407 (OUTLIER) cc_final: 0.6048 (t) REVERT: B 561 ASN cc_start: 0.9098 (t0) cc_final: 0.8655 (t0) REVERT: B 679 THR cc_start: 0.6378 (OUTLIER) cc_final: 0.6035 (t) outliers start: 26 outliers final: 22 residues processed: 127 average time/residue: 0.1631 time to fit residues: 31.9195 Evaluate side-chains 127 residues out of total 990 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 103 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 170 ASN Chi-restraints excluded: chain A residue 173 LEU Chi-restraints excluded: chain A residue 238 SER Chi-restraints excluded: chain A residue 289 ASP Chi-restraints excluded: chain A residue 351 ILE Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 414 VAL Chi-restraints excluded: chain A residue 525 THR Chi-restraints excluded: chain A residue 569 VAL Chi-restraints excluded: chain A residue 609 LEU Chi-restraints excluded: chain A residue 679 THR Chi-restraints excluded: chain B residue 192 ILE Chi-restraints excluded: chain B residue 290 VAL Chi-restraints excluded: chain B residue 351 ILE Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 414 VAL Chi-restraints excluded: chain B residue 429 THR Chi-restraints excluded: chain B residue 525 THR Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 609 LEU Chi-restraints excluded: chain B residue 644 ILE Chi-restraints excluded: chain B residue 679 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 114 random chunks: chunk 77 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 45 optimal weight: 8.9990 chunk 1 optimal weight: 0.0980 chunk 79 optimal weight: 0.8980 chunk 98 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 67 optimal weight: 0.0370 chunk 11 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 588 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4050 r_free = 0.4050 target = 0.105232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.082846 restraints weight = 39626.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.085239 restraints weight = 22230.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.086724 restraints weight = 14808.595| |-----------------------------------------------------------------------------| r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 moved from start: 0.4000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9106 Z= 0.129 Angle : 0.762 13.712 12342 Z= 0.349 Chirality : 0.044 0.213 1514 Planarity : 0.003 0.032 1544 Dihedral : 4.646 36.461 1238 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 11.48 Ramachandran Plot: Outliers : 0.18 % Allowed : 6.24 % Favored : 93.58 % Rotamer: Outliers : 2.02 % Allowed : 26.11 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.14 (0.25), residues: 1122 helix: 1.16 (0.21), residues: 656 sheet: -1.57 (0.79), residues: 34 loop : -1.44 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 408 HIS 0.003 0.001 HIS B 490 PHE 0.012 0.001 PHE A 256 TYR 0.028 0.001 TYR B 559 ARG 0.004 0.000 ARG B 627 Details of bonding type rmsd hydrogen bonds : bond 0.05466 ( 457) hydrogen bonds : angle 4.07432 ( 1338) covalent geometry : bond 0.00257 ( 9106) covalent geometry : angle 0.76191 (12342) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3198.91 seconds wall clock time: 57 minutes 45.77 seconds (3465.77 seconds total)