Starting phenix.real_space_refine on Wed Sep 17 22:51:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rfh_19121/09_2025/8rfh_19121.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rfh_19121/09_2025/8rfh_19121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rfh_19121/09_2025/8rfh_19121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rfh_19121/09_2025/8rfh_19121.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rfh_19121/09_2025/8rfh_19121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rfh_19121/09_2025/8rfh_19121.map" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 54 atoms to isotropic. 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 58 5.16 5 C 7550 2.51 5 N 2032 2.21 5 O 2158 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11802 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5874 Classifications: {'peptide': 730} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 696} Chain breaks: 1 Chain: "B" Number of atoms: 5874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 730, 5874 Classifications: {'peptide': 730} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 696} Chain breaks: 1 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.34, per 1000 atoms: 0.28 Number of scatterers: 11802 At special positions: 0 Unit cell: (141.588, 78.66, 91.908, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 58 16.00 P 4 15.00 O 2158 8.00 N 2032 7.00 C 7550 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: 0.98 Conformation dependent library (CDL) restraints added in 562.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2752 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 12 sheets defined 43.6% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.45 Creating SS restraints... Processing helix chain 'A' and resid 157 through 170 Processing helix chain 'A' and resid 187 through 198 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 218 through 229 removed outlier: 3.575A pdb=" N LYS A 229 " --> pdb=" O ASN A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.662A pdb=" N HIS A 238 " --> pdb=" O LYS A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 256 removed outlier: 3.559A pdb=" N GLY A 256 " --> pdb=" O PHE A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 268 through 277 removed outlier: 3.520A pdb=" N TRP A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE A 277 " --> pdb=" O GLU A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 294 through 301 removed outlier: 4.287A pdb=" N ALA A 298 " --> pdb=" O ASP A 294 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N CYS A 301 " --> pdb=" O VAL A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 328 removed outlier: 3.550A pdb=" N ILE A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 348 removed outlier: 4.111A pdb=" N LEU A 339 " --> pdb=" O PRO A 335 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N SER A 340 " --> pdb=" O GLU A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 366 Processing helix chain 'A' and resid 368 through 382 Processing helix chain 'A' and resid 389 through 401 removed outlier: 3.763A pdb=" N ASN A 393 " --> pdb=" O PRO A 389 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LYS A 394 " --> pdb=" O GLU A 390 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 395 " --> pdb=" O ASN A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 415 removed outlier: 3.688A pdb=" N GLY A 415 " --> pdb=" O PHE A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 435 Processing helix chain 'A' and resid 445 through 460 Processing helix chain 'A' and resid 480 through 494 Processing helix chain 'A' and resid 511 through 516 Processing helix chain 'A' and resid 526 through 534 removed outlier: 3.534A pdb=" N LYS A 534 " --> pdb=" O PHE A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 565 Processing helix chain 'A' and resid 583 through 588 Processing helix chain 'A' and resid 605 through 611 Processing helix chain 'A' and resid 674 through 678 Processing helix chain 'A' and resid 679 through 685 Processing helix chain 'A' and resid 697 through 702 removed outlier: 3.862A pdb=" N LEU A 701 " --> pdb=" O LYS A 697 " (cutoff:3.500A) Processing helix chain 'A' and resid 708 through 715 removed outlier: 3.878A pdb=" N VAL A 712 " --> pdb=" O LEU A 708 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS A 714 " --> pdb=" O LYS A 710 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU A 715 " --> pdb=" O ASN A 711 " (cutoff:3.500A) Processing helix chain 'A' and resid 738 through 742 Processing helix chain 'A' and resid 757 through 759 No H-bonds generated for 'chain 'A' and resid 757 through 759' Processing helix chain 'A' and resid 760 through 767 removed outlier: 3.640A pdb=" N LEU A 764 " --> pdb=" O ASP A 760 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N MET A 767 " --> pdb=" O ILE A 763 " (cutoff:3.500A) Processing helix chain 'A' and resid 832 through 838 Processing helix chain 'A' and resid 850 through 871 Processing helix chain 'B' and resid 157 through 170 Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 218 through 229 removed outlier: 3.575A pdb=" N LYS B 229 " --> pdb=" O ASN B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 238 removed outlier: 3.661A pdb=" N HIS B 238 " --> pdb=" O LYS B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 256 removed outlier: 3.559A pdb=" N GLY B 256 " --> pdb=" O PHE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 277 removed outlier: 3.520A pdb=" N TRP B 272 " --> pdb=" O SER B 268 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE B 277 " --> pdb=" O GLU B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 301 removed outlier: 4.288A pdb=" N ALA B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N CYS B 301 " --> pdb=" O VAL B 297 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 328 Processing helix chain 'B' and resid 334 through 348 removed outlier: 4.111A pdb=" N LEU B 339 " --> pdb=" O PRO B 335 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N SER B 340 " --> pdb=" O GLU B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 351 through 366 Processing helix chain 'B' and resid 368 through 382 Processing helix chain 'B' and resid 389 through 401 removed outlier: 3.763A pdb=" N ASN B 393 " --> pdb=" O PRO B 389 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LYS B 394 " --> pdb=" O GLU B 390 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU B 395 " --> pdb=" O ASN B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 415 removed outlier: 3.687A pdb=" N GLY B 415 " --> pdb=" O PHE B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 436 Processing helix chain 'B' and resid 445 through 460 Processing helix chain 'B' and resid 480 through 494 Processing helix chain 'B' and resid 511 through 516 Processing helix chain 'B' and resid 526 through 534 removed outlier: 3.533A pdb=" N LYS B 534 " --> pdb=" O PHE B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 565 Processing helix chain 'B' and resid 583 through 588 Processing helix chain 'B' and resid 605 through 611 Processing helix chain 'B' and resid 674 through 678 Processing helix chain 'B' and resid 679 through 685 Processing helix chain 'B' and resid 697 through 702 removed outlier: 3.861A pdb=" N LEU B 701 " --> pdb=" O LYS B 697 " (cutoff:3.500A) Processing helix chain 'B' and resid 708 through 715 removed outlier: 3.879A pdb=" N VAL B 712 " --> pdb=" O LEU B 708 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N LYS B 714 " --> pdb=" O LYS B 710 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 715 " --> pdb=" O ASN B 711 " (cutoff:3.500A) Processing helix chain 'B' and resid 738 through 742 Processing helix chain 'B' and resid 757 through 759 No H-bonds generated for 'chain 'B' and resid 757 through 759' Processing helix chain 'B' and resid 760 through 767 removed outlier: 3.640A pdb=" N LEU B 764 " --> pdb=" O ASP B 760 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N MET B 767 " --> pdb=" O ILE B 763 " (cutoff:3.500A) Processing helix chain 'B' and resid 832 through 838 Processing helix chain 'B' and resid 850 through 871 Processing sheet with id=AA1, first strand: chain 'A' and resid 207 through 212 removed outlier: 3.567A pdb=" N ILE A 209 " --> pdb=" O LEU A 260 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP A 265 " --> pdb=" O THR A 291 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLU A 176 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU A 290 " --> pdb=" O GLU A 176 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N VAL A 178 " --> pdb=" O LEU A 290 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR A 292 " --> pdb=" O VAL A 178 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N VAL A 180 " --> pdb=" O THR A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 423 through 424 removed outlier: 3.609A pdb=" N GLN A 467 " --> pdb=" O THR A 476 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG A 478 " --> pdb=" O VAL A 465 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N VAL A 465 " --> pdb=" O ARG A 478 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.818A pdb=" N PHE A 543 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N GLU A 574 " --> pdb=" O PHE A 543 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 520 through 522 removed outlier: 6.818A pdb=" N PHE A 543 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N GLU A 574 " --> pdb=" O PHE A 543 " (cutoff:3.500A) removed outlier: 10.309A pdb=" N TYR A 593 " --> pdb=" O ASP A 572 " (cutoff:3.500A) removed outlier: 9.393A pdb=" N GLU A 574 " --> pdb=" O TYR A 593 " (cutoff:3.500A) removed outlier: 8.766A pdb=" N ALA A 595 " --> pdb=" O GLU A 574 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ILE A 576 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE A 594 " --> pdb=" O ILE A 618 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ASN A 620 " --> pdb=" O ILE A 594 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N PHE A 596 " --> pdb=" O ASN A 620 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N LEU A 641 " --> pdb=" O SER A 671 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N ILE A 673 " --> pdb=" O LEU A 641 " (cutoff:3.500A) removed outlier: 9.614A pdb=" N THR A 643 " --> pdb=" O ILE A 673 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N THR A 669 " --> pdb=" O LYS A 691 " (cutoff:3.500A) removed outlier: 7.928A pdb=" N GLY A 693 " --> pdb=" O THR A 669 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N SER A 671 " --> pdb=" O GLY A 693 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N ARG A 695 " --> pdb=" O SER A 671 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N ILE A 673 " --> pdb=" O ARG A 695 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL A 752 " --> pdb=" O LEU A 723 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN A 725 " --> pdb=" O VAL A 752 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LEU A 749 " --> pdb=" O LYS A 774 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N LYS A 776 " --> pdb=" O LEU A 749 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU A 751 " --> pdb=" O LYS A 776 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU A 845 " --> pdb=" O LEU A 820 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU A 822 " --> pdb=" O GLU A 845 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 603 through 604 Processing sheet with id=AA6, first strand: chain 'A' and resid 784 through 786 removed outlier: 6.691A pdb=" N TRP A 785 " --> pdb=" O LYS A 808 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 207 through 212 removed outlier: 3.567A pdb=" N ILE B 209 " --> pdb=" O LEU B 260 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP B 265 " --> pdb=" O THR B 291 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLU B 176 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N LEU B 290 " --> pdb=" O GLU B 176 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL B 178 " --> pdb=" O LEU B 290 " (cutoff:3.500A) removed outlier: 7.282A pdb=" N THR B 292 " --> pdb=" O VAL B 178 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N VAL B 180 " --> pdb=" O THR B 292 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 423 through 424 removed outlier: 3.608A pdb=" N GLN B 467 " --> pdb=" O THR B 476 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N ARG B 478 " --> pdb=" O VAL B 465 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N VAL B 465 " --> pdb=" O ARG B 478 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 520 through 522 removed outlier: 6.819A pdb=" N PHE B 543 " --> pdb=" O ASP B 572 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N GLU B 574 " --> pdb=" O PHE B 543 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 520 through 522 removed outlier: 6.819A pdb=" N PHE B 543 " --> pdb=" O ASP B 572 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N GLU B 574 " --> pdb=" O PHE B 543 " (cutoff:3.500A) removed outlier: 10.308A pdb=" N TYR B 593 " --> pdb=" O ASP B 572 " (cutoff:3.500A) removed outlier: 9.393A pdb=" N GLU B 574 " --> pdb=" O TYR B 593 " (cutoff:3.500A) removed outlier: 8.767A pdb=" N ALA B 595 " --> pdb=" O GLU B 574 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE B 576 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N ILE B 594 " --> pdb=" O ILE B 618 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ASN B 620 " --> pdb=" O ILE B 594 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N PHE B 596 " --> pdb=" O ASN B 620 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU B 641 " --> pdb=" O SER B 671 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N ILE B 673 " --> pdb=" O LEU B 641 " (cutoff:3.500A) removed outlier: 9.821A pdb=" N THR B 643 " --> pdb=" O ILE B 673 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N THR B 672 " --> pdb=" O GLY B 693 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ARG B 695 " --> pdb=" O THR B 672 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N VAL B 752 " --> pdb=" O LEU B 723 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN B 725 " --> pdb=" O VAL B 752 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N LEU B 749 " --> pdb=" O LYS B 774 " (cutoff:3.500A) removed outlier: 8.103A pdb=" N LYS B 776 " --> pdb=" O LEU B 749 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N LEU B 751 " --> pdb=" O LYS B 776 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLU B 845 " --> pdb=" O LEU B 820 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 822 " --> pdb=" O GLU B 845 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 603 through 604 Processing sheet with id=AB3, first strand: chain 'B' and resid 784 through 786 removed outlier: 6.690A pdb=" N TRP B 785 " --> pdb=" O LYS B 808 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 458 hydrogen bonds defined for protein. 1254 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: 2.38 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3588 1.34 - 1.45: 1609 1.45 - 1.57: 6771 1.57 - 1.69: 6 1.69 - 1.81: 82 Bond restraints: 12056 Sorted by residual: bond pdb=" N THR A 315 " pdb=" CA THR A 315 " ideal model delta sigma weight residual 1.453 1.496 -0.043 1.31e-02 5.83e+03 1.08e+01 bond pdb=" N ILE A 673 " pdb=" CA ILE A 673 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.14e-02 7.69e+03 1.05e+01 bond pdb=" N THR B 315 " pdb=" CA THR B 315 " ideal model delta sigma weight residual 1.454 1.496 -0.042 1.34e-02 5.57e+03 9.89e+00 bond pdb=" N LEU A 314 " pdb=" CA LEU A 314 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.22e-02 6.72e+03 8.79e+00 bond pdb=" N ILE A 433 " pdb=" CA ILE A 433 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.21e-02 6.83e+03 8.15e+00 ... (remaining 12051 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.22: 15920 2.22 - 4.45: 277 4.45 - 6.67: 68 6.67 - 8.89: 14 8.89 - 11.12: 7 Bond angle restraints: 16286 Sorted by residual: angle pdb=" C SER A 671 " pdb=" N THR A 672 " pdb=" CA THR A 672 " ideal model delta sigma weight residual 122.30 114.12 8.18 1.35e+00 5.49e-01 3.67e+01 angle pdb=" C THR A 672 " pdb=" CA THR A 672 " pdb=" CB THR A 672 " ideal model delta sigma weight residual 110.22 120.17 -9.95 1.67e+00 3.59e-01 3.55e+01 angle pdb=" N ASP B 317 " pdb=" CA ASP B 317 " pdb=" C ASP B 317 " ideal model delta sigma weight residual 111.28 105.88 5.40 1.09e+00 8.42e-01 2.46e+01 angle pdb=" N ASP A 317 " pdb=" CA ASP A 317 " pdb=" C ASP A 317 " ideal model delta sigma weight residual 111.28 106.71 4.57 1.09e+00 8.42e-01 1.76e+01 angle pdb=" C GLU A 316 " pdb=" CA GLU A 316 " pdb=" CB GLU A 316 " ideal model delta sigma weight residual 110.79 105.33 5.46 1.66e+00 3.63e-01 1.08e+01 ... (remaining 16281 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.69: 7135 34.69 - 69.38: 185 69.38 - 104.07: 12 104.07 - 138.76: 0 138.76 - 173.45: 2 Dihedral angle restraints: 7334 sinusoidal: 3096 harmonic: 4238 Sorted by residual: dihedral pdb=" C5' ADP B1001 " pdb=" O5' ADP B1001 " pdb=" PA ADP B1001 " pdb=" O2A ADP B1001 " ideal model delta sinusoidal sigma weight residual -60.00 113.45 -173.45 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" C5' ADP A1001 " pdb=" O5' ADP A1001 " pdb=" PA ADP A1001 " pdb=" O2A ADP A1001 " ideal model delta sinusoidal sigma weight residual -60.00 113.42 -173.42 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" CA SER A 671 " pdb=" C SER A 671 " pdb=" N THR A 672 " pdb=" CA THR A 672 " ideal model delta harmonic sigma weight residual -180.00 -150.32 -29.68 0 5.00e+00 4.00e-02 3.52e+01 ... (remaining 7331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1622 0.078 - 0.156: 182 0.156 - 0.234: 7 0.234 - 0.311: 0 0.311 - 0.389: 1 Chirality restraints: 1812 Sorted by residual: chirality pdb=" CA THR A 672 " pdb=" N THR A 672 " pdb=" C THR A 672 " pdb=" CB THR A 672 " both_signs ideal model delta sigma weight residual False 2.53 2.14 0.39 2.00e-01 2.50e+01 3.79e+00 chirality pdb=" CA GLU A 316 " pdb=" N GLU A 316 " pdb=" C GLU A 316 " pdb=" CB GLU A 316 " both_signs ideal model delta sigma weight residual False 2.51 2.73 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE B 673 " pdb=" N ILE B 673 " pdb=" C ILE B 673 " pdb=" CB ILE B 673 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1809 not shown) Planarity restraints: 2060 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 670 " 0.021 2.00e-02 2.50e+03 4.26e-02 1.82e+01 pdb=" C LEU A 670 " -0.074 2.00e-02 2.50e+03 pdb=" O LEU A 670 " 0.028 2.00e-02 2.50e+03 pdb=" N SER A 671 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 670 " -0.014 2.00e-02 2.50e+03 2.91e-02 8.49e+00 pdb=" C LEU B 670 " 0.050 2.00e-02 2.50e+03 pdb=" O LEU B 670 " -0.019 2.00e-02 2.50e+03 pdb=" N SER B 671 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 671 " 0.014 2.00e-02 2.50e+03 2.76e-02 7.61e+00 pdb=" C SER A 671 " -0.048 2.00e-02 2.50e+03 pdb=" O SER A 671 " 0.018 2.00e-02 2.50e+03 pdb=" N THR A 672 " 0.016 2.00e-02 2.50e+03 ... (remaining 2057 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 859 2.74 - 3.28: 12589 3.28 - 3.82: 20182 3.82 - 4.36: 23810 4.36 - 4.90: 38512 Nonbonded interactions: 95952 Sorted by model distance: nonbonded pdb=" OG1 THR B 469 " pdb=" OD1 ASP B 471 " model vdw 2.201 3.040 nonbonded pdb=" OG1 THR A 469 " pdb=" OD1 ASP A 471 " model vdw 2.201 3.040 nonbonded pdb=" OG SER A 268 " pdb=" OD1 ASP A 270 " model vdw 2.280 3.040 nonbonded pdb=" OG SER B 268 " pdb=" OD1 ASP B 270 " model vdw 2.280 3.040 nonbonded pdb=" O VAL A 653 " pdb=" NH2 ARG A 685 " model vdw 2.293 3.120 ... (remaining 95947 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.220 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 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 : 0.003 0.043 12056 Z= 0.190 Angle : 0.760 11.116 16286 Z= 0.383 Chirality : 0.048 0.389 1812 Planarity : 0.004 0.043 2060 Dihedral : 15.836 173.446 4582 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 17.06 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.69 % Favored : 97.18 % Rotamer: Outliers : 1.44 % Allowed : 21.35 % Favored : 77.20 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.23), residues: 1452 helix: 0.50 (0.23), residues: 518 sheet: 0.20 (0.37), residues: 212 loop : 0.67 (0.24), residues: 722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 478 TYR 0.006 0.001 TYR B 413 PHE 0.010 0.001 PHE B 571 TRP 0.012 0.001 TRP B 798 HIS 0.004 0.001 HIS A 524 Details of bonding type rmsd covalent geometry : bond 0.00311 (12056) covalent geometry : angle 0.75997 (16286) hydrogen bonds : bond 0.21346 ( 454) hydrogen bonds : angle 7.65969 ( 1254) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 184 time to evaluate : 0.526 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LEU cc_start: 0.7900 (tt) cc_final: 0.7248 (tp) REVERT: A 456 ASP cc_start: 0.8905 (m-30) cc_final: 0.8319 (t70) REVERT: A 692 LEU cc_start: 0.9270 (tp) cc_final: 0.9021 (tp) REVERT: A 844 MET cc_start: 0.7277 (tmm) cc_final: 0.7032 (tmm) REVERT: B 351 LEU cc_start: 0.7779 (tt) cc_final: 0.7215 (tp) REVERT: B 432 TRP cc_start: 0.8378 (m-10) cc_final: 0.8029 (m-90) REVERT: B 456 ASP cc_start: 0.8881 (m-30) cc_final: 0.8274 (t70) REVERT: B 671 SER cc_start: 0.7185 (OUTLIER) cc_final: 0.6842 (p) REVERT: B 672 THR cc_start: 0.6524 (OUTLIER) cc_final: 0.6154 (p) REVERT: B 692 LEU cc_start: 0.9234 (tp) cc_final: 0.9018 (tp) REVERT: B 844 MET cc_start: 0.7143 (tmm) cc_final: 0.6898 (tmm) outliers start: 19 outliers final: 3 residues processed: 194 average time/residue: 0.0970 time to fit residues: 28.6100 Evaluate side-chains 172 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 167 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 672 THR Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 671 SER Chi-restraints excluded: chain B residue 672 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.3980 chunk 103 optimal weight: 4.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.4980 chunk 91 optimal weight: 4.9990 chunk 55 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN A 668 GLN B 309 HIS B 349 ASN B 668 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.107390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.079395 restraints weight = 33878.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.082494 restraints weight = 18598.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.084749 restraints weight = 12511.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.086329 restraints weight = 9507.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.087319 restraints weight = 7840.395| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7463 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12056 Z= 0.133 Angle : 0.673 9.979 16286 Z= 0.324 Chirality : 0.045 0.161 1812 Planarity : 0.004 0.043 2060 Dihedral : 7.272 148.131 1586 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.19 % Allowed : 17.86 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.23), residues: 1452 helix: 0.60 (0.23), residues: 530 sheet: -0.07 (0.34), residues: 254 loop : 0.72 (0.25), residues: 668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 478 TYR 0.013 0.001 TYR A 259 PHE 0.019 0.001 PHE A 585 TRP 0.020 0.001 TRP A 432 HIS 0.004 0.001 HIS B 539 Details of bonding type rmsd covalent geometry : bond 0.00295 (12056) covalent geometry : angle 0.67348 (16286) hydrogen bonds : bond 0.04379 ( 454) hydrogen bonds : angle 5.52616 ( 1254) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 179 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 456 ASP cc_start: 0.8888 (m-30) cc_final: 0.8409 (t70) REVERT: A 671 SER cc_start: 0.7682 (OUTLIER) cc_final: 0.7193 (p) REVERT: A 722 LYS cc_start: 0.8767 (tptp) cc_final: 0.8246 (mttt) REVERT: B 407 LEU cc_start: 0.9534 (tp) cc_final: 0.9329 (tp) REVERT: B 432 TRP cc_start: 0.8435 (m-10) cc_final: 0.8011 (m-90) REVERT: B 456 ASP cc_start: 0.8862 (m-30) cc_final: 0.8379 (t70) REVERT: B 635 MET cc_start: 0.7579 (tpt) cc_final: 0.7372 (tpt) REVERT: B 671 SER cc_start: 0.7913 (t) cc_final: 0.7555 (p) REVERT: B 844 MET cc_start: 0.7444 (tmm) cc_final: 0.7234 (tmm) outliers start: 42 outliers final: 21 residues processed: 196 average time/residue: 0.0801 time to fit residues: 24.5272 Evaluate side-chains 189 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 167 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 315 THR Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 751 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 33 optimal weight: 0.9990 chunk 109 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 chunk 129 optimal weight: 7.9990 chunk 15 optimal weight: 1.9990 chunk 119 optimal weight: 8.9990 chunk 42 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 124 optimal weight: 10.0000 chunk 18 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.106971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.078961 restraints weight = 34636.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.082126 restraints weight = 18836.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.084341 restraints weight = 12629.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.085843 restraints weight = 9617.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.086934 restraints weight = 7966.020| |-----------------------------------------------------------------------------| r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7475 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12056 Z= 0.119 Angle : 0.657 8.184 16286 Z= 0.309 Chirality : 0.045 0.200 1812 Planarity : 0.004 0.045 2060 Dihedral : 6.699 128.624 1583 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.27 % Allowed : 17.71 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.73 (0.23), residues: 1452 helix: 0.84 (0.24), residues: 506 sheet: -0.15 (0.34), residues: 228 loop : 0.65 (0.24), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 488 TYR 0.012 0.001 TYR B 740 PHE 0.012 0.001 PHE B 571 TRP 0.040 0.001 TRP A 432 HIS 0.004 0.001 HIS A 524 Details of bonding type rmsd covalent geometry : bond 0.00267 (12056) covalent geometry : angle 0.65704 (16286) hydrogen bonds : bond 0.03558 ( 454) hydrogen bonds : angle 5.27920 ( 1254) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 176 time to evaluate : 0.490 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 351 LEU cc_start: 0.7953 (tp) cc_final: 0.7375 (tt) REVERT: A 456 ASP cc_start: 0.8863 (m-30) cc_final: 0.8402 (t70) REVERT: A 722 LYS cc_start: 0.8806 (tptp) cc_final: 0.8353 (mttt) REVERT: B 313 PHE cc_start: 0.7775 (m-80) cc_final: 0.7514 (m-80) REVERT: B 432 TRP cc_start: 0.8489 (m-10) cc_final: 0.8114 (m-90) REVERT: B 456 ASP cc_start: 0.8865 (m-30) cc_final: 0.8400 (t70) REVERT: B 671 SER cc_start: 0.7979 (t) cc_final: 0.7606 (p) REVERT: B 722 LYS cc_start: 0.8744 (tptp) cc_final: 0.8156 (mttt) REVERT: B 844 MET cc_start: 0.7546 (tmm) cc_final: 0.7296 (tmm) outliers start: 43 outliers final: 29 residues processed: 192 average time/residue: 0.0875 time to fit residues: 26.2558 Evaluate side-chains 201 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 172 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 626 LEU Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 874 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 227 ILE Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 874 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 18 optimal weight: 20.0000 chunk 25 optimal weight: 0.5980 chunk 105 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 95 optimal weight: 0.6980 chunk 119 optimal weight: 8.9990 chunk 117 optimal weight: 6.9990 chunk 41 optimal weight: 0.8980 chunk 31 optimal weight: 0.0000 chunk 72 optimal weight: 8.9990 chunk 48 optimal weight: 6.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 875 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.105670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.077552 restraints weight = 34440.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.080683 restraints weight = 18853.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.082802 restraints weight = 12720.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.084173 restraints weight = 9767.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.085230 restraints weight = 8167.888| |-----------------------------------------------------------------------------| r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12056 Z= 0.134 Angle : 0.666 9.897 16286 Z= 0.314 Chirality : 0.045 0.196 1812 Planarity : 0.004 0.046 2060 Dihedral : 6.349 110.216 1582 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 3.27 % Allowed : 18.01 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.61 (0.23), residues: 1452 helix: 0.79 (0.23), residues: 518 sheet: -0.33 (0.34), residues: 228 loop : 0.58 (0.25), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 402 TYR 0.014 0.001 TYR B 740 PHE 0.012 0.001 PHE B 841 TRP 0.054 0.002 TRP A 432 HIS 0.004 0.001 HIS A 819 Details of bonding type rmsd covalent geometry : bond 0.00302 (12056) covalent geometry : angle 0.66552 (16286) hydrogen bonds : bond 0.03294 ( 454) hydrogen bonds : angle 5.10524 ( 1254) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 166 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 403 LEU cc_start: 0.8572 (tp) cc_final: 0.8172 (tt) REVERT: A 428 LEU cc_start: 0.8894 (tp) cc_final: 0.8620 (tp) REVERT: A 522 CYS cc_start: 0.7515 (p) cc_final: 0.7262 (p) REVERT: A 671 SER cc_start: 0.7770 (OUTLIER) cc_final: 0.7447 (p) REVERT: A 722 LYS cc_start: 0.8819 (tptp) cc_final: 0.8421 (mttt) REVERT: B 313 PHE cc_start: 0.7758 (m-80) cc_final: 0.7495 (m-80) REVERT: B 351 LEU cc_start: 0.8015 (tt) cc_final: 0.7311 (tp) REVERT: B 432 TRP cc_start: 0.8466 (m-10) cc_final: 0.8049 (m-90) REVERT: B 522 CYS cc_start: 0.7536 (p) cc_final: 0.7214 (p) REVERT: B 671 SER cc_start: 0.8056 (t) cc_final: 0.7759 (p) REVERT: B 722 LYS cc_start: 0.8703 (tptp) cc_final: 0.8294 (mttt) REVERT: B 844 MET cc_start: 0.7615 (tmm) cc_final: 0.7384 (tmm) REVERT: B 879 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8423 (tt) outliers start: 43 outliers final: 31 residues processed: 184 average time/residue: 0.0861 time to fit residues: 24.8558 Evaluate side-chains 193 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 874 ASN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 626 LEU Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 874 ASN Chi-restraints excluded: chain B residue 879 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 28 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 86 optimal weight: 9.9990 chunk 121 optimal weight: 0.3980 chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 35 optimal weight: 0.9990 chunk 96 optimal weight: 7.9990 chunk 141 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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 = 0.4033 r_free = 0.4033 target = 0.105396 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.077399 restraints weight = 34293.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.080517 restraints weight = 18703.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.082590 restraints weight = 12601.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.083987 restraints weight = 9695.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.085004 restraints weight = 8100.809| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 12056 Z= 0.125 Angle : 0.678 10.359 16286 Z= 0.317 Chirality : 0.045 0.175 1812 Planarity : 0.004 0.048 2060 Dihedral : 5.999 93.073 1582 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.81 % Allowed : 19.53 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.67 (0.23), residues: 1452 helix: 0.82 (0.24), residues: 518 sheet: -0.36 (0.33), residues: 254 loop : 0.71 (0.26), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 488 TYR 0.016 0.001 TYR B 740 PHE 0.011 0.001 PHE B 571 TRP 0.078 0.002 TRP A 432 HIS 0.003 0.001 HIS A 819 Details of bonding type rmsd covalent geometry : bond 0.00285 (12056) covalent geometry : angle 0.67811 (16286) hydrogen bonds : bond 0.03168 ( 454) hydrogen bonds : angle 5.02454 ( 1254) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 171 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 GLU cc_start: 0.7498 (OUTLIER) cc_final: 0.7215 (mt-10) REVERT: A 428 LEU cc_start: 0.8839 (tp) cc_final: 0.8563 (tp) REVERT: A 522 CYS cc_start: 0.7583 (p) cc_final: 0.7219 (p) REVERT: A 671 SER cc_start: 0.7761 (OUTLIER) cc_final: 0.7440 (p) REVERT: A 722 LYS cc_start: 0.8802 (tptp) cc_final: 0.8453 (mttt) REVERT: A 879 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8480 (tt) REVERT: B 313 PHE cc_start: 0.7812 (m-80) cc_final: 0.7539 (m-80) REVERT: B 403 LEU cc_start: 0.8581 (tp) cc_final: 0.8211 (tt) REVERT: B 522 CYS cc_start: 0.7620 (p) cc_final: 0.7230 (p) REVERT: B 671 SER cc_start: 0.8041 (t) cc_final: 0.7758 (p) REVERT: B 722 LYS cc_start: 0.8713 (tptp) cc_final: 0.8343 (mttt) REVERT: B 844 MET cc_start: 0.7689 (tmm) cc_final: 0.7342 (tmm) REVERT: B 879 LEU cc_start: 0.8771 (OUTLIER) cc_final: 0.8474 (tt) outliers start: 37 outliers final: 28 residues processed: 187 average time/residue: 0.0906 time to fit residues: 26.4343 Evaluate side-chains 194 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 671 SER Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 874 ASN Chi-restraints excluded: chain A residue 879 LEU Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 570 VAL Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 874 ASN Chi-restraints excluded: chain B residue 879 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 27 optimal weight: 0.5980 chunk 25 optimal weight: 0.9980 chunk 69 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 41 optimal weight: 6.9990 chunk 94 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 40 optimal weight: 0.0040 chunk 84 optimal weight: 4.9990 chunk 2 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 overall best weight: 1.3194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 539 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.105527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.078088 restraints weight = 33370.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.081187 restraints weight = 18019.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.083309 restraints weight = 12015.116| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.084782 restraints weight = 9129.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.085750 restraints weight = 7546.423| |-----------------------------------------------------------------------------| r_work (final): 0.3679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12056 Z= 0.117 Angle : 0.697 14.201 16286 Z= 0.321 Chirality : 0.045 0.219 1812 Planarity : 0.004 0.048 2060 Dihedral : 5.826 83.103 1582 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.04 % Allowed : 20.44 % Favored : 76.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.66 (0.23), residues: 1452 helix: 0.81 (0.23), residues: 520 sheet: -0.37 (0.33), residues: 254 loop : 0.70 (0.26), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 402 TYR 0.015 0.001 TYR B 740 PHE 0.015 0.001 PHE A 841 TRP 0.092 0.002 TRP A 432 HIS 0.005 0.001 HIS A 539 Details of bonding type rmsd covalent geometry : bond 0.00265 (12056) covalent geometry : angle 0.69718 (16286) hydrogen bonds : bond 0.03076 ( 454) hydrogen bonds : angle 4.93671 ( 1254) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 166 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 428 LEU cc_start: 0.8766 (tp) cc_final: 0.8559 (tp) REVERT: A 432 TRP cc_start: 0.8105 (m-90) cc_final: 0.7848 (m-90) REVERT: A 522 CYS cc_start: 0.7662 (p) cc_final: 0.7233 (p) REVERT: A 722 LYS cc_start: 0.8798 (tptp) cc_final: 0.8463 (mttt) REVERT: B 313 PHE cc_start: 0.7830 (m-80) cc_final: 0.7540 (m-80) REVERT: B 351 LEU cc_start: 0.7746 (tt) cc_final: 0.7516 (tp) REVERT: B 403 LEU cc_start: 0.8555 (tp) cc_final: 0.8215 (tt) REVERT: B 522 CYS cc_start: 0.7671 (p) cc_final: 0.7243 (p) REVERT: B 635 MET cc_start: 0.7751 (tpt) cc_final: 0.7550 (tpt) REVERT: B 671 SER cc_start: 0.8051 (t) cc_final: 0.7776 (p) REVERT: B 722 LYS cc_start: 0.8776 (tptp) cc_final: 0.8431 (mttt) REVERT: B 841 PHE cc_start: 0.8612 (t80) cc_final: 0.8402 (t80) REVERT: B 844 MET cc_start: 0.7733 (tmm) cc_final: 0.7374 (tmm) REVERT: B 879 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8482 (tt) outliers start: 40 outliers final: 31 residues processed: 183 average time/residue: 0.0892 time to fit residues: 25.6376 Evaluate side-chains 195 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 163 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 874 ASN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 874 ASN Chi-restraints excluded: chain B residue 879 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 68 optimal weight: 6.9990 chunk 136 optimal weight: 20.0000 chunk 12 optimal weight: 0.0870 chunk 57 optimal weight: 6.9990 chunk 141 optimal weight: 9.9990 chunk 144 optimal weight: 7.9990 chunk 129 optimal weight: 5.9990 chunk 119 optimal weight: 7.9990 chunk 116 optimal weight: 0.5980 chunk 78 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 overall best weight: 3.1364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 778 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.101750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.073801 restraints weight = 34823.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.076735 restraints weight = 19448.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.078669 restraints weight = 13384.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.079908 restraints weight = 10421.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.080602 restraints weight = 8821.607| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12056 Z= 0.189 Angle : 0.751 14.486 16286 Z= 0.356 Chirality : 0.048 0.295 1812 Planarity : 0.005 0.047 2060 Dihedral : 6.011 82.529 1582 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 17.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.04 % Allowed : 21.35 % Favored : 75.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.42 (0.23), residues: 1452 helix: 0.80 (0.23), residues: 520 sheet: -0.60 (0.34), residues: 222 loop : 0.37 (0.25), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 430 TYR 0.014 0.002 TYR A 518 PHE 0.017 0.002 PHE A 530 TRP 0.069 0.002 TRP A 432 HIS 0.008 0.001 HIS A 539 Details of bonding type rmsd covalent geometry : bond 0.00420 (12056) covalent geometry : angle 0.75077 (16286) hydrogen bonds : bond 0.03550 ( 454) hydrogen bonds : angle 5.08903 ( 1254) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 163 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 TRP cc_start: 0.8260 (m-90) cc_final: 0.7750 (m-90) REVERT: A 522 CYS cc_start: 0.7668 (p) cc_final: 0.7119 (p) REVERT: A 722 LYS cc_start: 0.8836 (tptp) cc_final: 0.8502 (mttt) REVERT: B 403 LEU cc_start: 0.8518 (tp) cc_final: 0.8195 (tt) REVERT: B 522 CYS cc_start: 0.7596 (p) cc_final: 0.7080 (p) REVERT: B 671 SER cc_start: 0.8245 (t) cc_final: 0.8045 (p) REVERT: B 722 LYS cc_start: 0.8781 (tptp) cc_final: 0.8429 (mttt) REVERT: B 844 MET cc_start: 0.7728 (tmm) cc_final: 0.7380 (tmm) REVERT: B 879 LEU cc_start: 0.8768 (OUTLIER) cc_final: 0.8471 (tt) outliers start: 40 outliers final: 36 residues processed: 180 average time/residue: 0.0875 time to fit residues: 24.6426 Evaluate side-chains 191 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 154 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 874 ASN Chi-restraints excluded: chain B residue 186 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 314 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 548 LEU Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 874 ASN Chi-restraints excluded: chain B residue 879 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 107 optimal weight: 3.9990 chunk 20 optimal weight: 0.1980 chunk 7 optimal weight: 4.9990 chunk 61 optimal weight: 8.9990 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 20.0000 chunk 88 optimal weight: 20.0000 chunk 40 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 49 optimal weight: 5.9990 chunk 9 optimal weight: 1.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.102655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.074699 restraints weight = 34401.913| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.077691 restraints weight = 19026.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.079751 restraints weight = 12970.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.081036 restraints weight = 9979.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.082021 restraints weight = 8409.830| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12056 Z= 0.148 Angle : 0.739 15.686 16286 Z= 0.342 Chirality : 0.046 0.378 1812 Planarity : 0.004 0.049 2060 Dihedral : 5.827 70.755 1582 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.74 % Allowed : 21.81 % Favored : 75.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.23), residues: 1452 helix: 0.85 (0.23), residues: 522 sheet: -0.64 (0.34), residues: 222 loop : 0.41 (0.25), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 488 TYR 0.012 0.001 TYR A 212 PHE 0.017 0.001 PHE A 841 TRP 0.064 0.002 TRP A 432 HIS 0.005 0.001 HIS A 539 Details of bonding type rmsd covalent geometry : bond 0.00336 (12056) covalent geometry : angle 0.73922 (16286) hydrogen bonds : bond 0.03198 ( 454) hydrogen bonds : angle 5.03470 ( 1254) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 167 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 432 TRP cc_start: 0.8254 (m-90) cc_final: 0.7889 (m-90) REVERT: A 522 CYS cc_start: 0.7664 (p) cc_final: 0.7084 (p) REVERT: A 584 GLU cc_start: 0.8937 (mp0) cc_final: 0.8581 (tm-30) REVERT: A 722 LYS cc_start: 0.8867 (tptp) cc_final: 0.8548 (mttt) REVERT: A 844 MET cc_start: 0.7088 (tmm) cc_final: 0.6650 (tmm) REVERT: B 277 ILE cc_start: 0.8437 (OUTLIER) cc_final: 0.7929 (tp) REVERT: B 403 LEU cc_start: 0.8539 (tp) cc_final: 0.8225 (tt) REVERT: B 522 CYS cc_start: 0.7576 (p) cc_final: 0.7036 (p) REVERT: B 671 SER cc_start: 0.8204 (t) cc_final: 0.7982 (p) REVERT: B 722 LYS cc_start: 0.8803 (tptp) cc_final: 0.8506 (mttt) REVERT: B 844 MET cc_start: 0.7729 (tmm) cc_final: 0.7457 (tmm) REVERT: B 879 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8454 (tt) outliers start: 36 outliers final: 30 residues processed: 180 average time/residue: 0.0899 time to fit residues: 25.2196 Evaluate side-chains 194 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 466 MET Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 874 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 277 ILE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 874 ASN Chi-restraints excluded: chain B residue 879 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 111 optimal weight: 6.9990 chunk 97 optimal weight: 5.9990 chunk 94 optimal weight: 5.9990 chunk 20 optimal weight: 0.1980 chunk 78 optimal weight: 7.9990 chunk 74 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 52 optimal weight: 0.0060 chunk 38 optimal weight: 5.9990 chunk 116 optimal weight: 6.9990 chunk 138 optimal weight: 40.0000 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.103379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.075365 restraints weight = 34226.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.078380 restraints weight = 18811.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.080413 restraints weight = 12776.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.081846 restraints weight = 9890.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.082522 restraints weight = 8259.186| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 12056 Z= 0.127 Angle : 0.756 16.079 16286 Z= 0.342 Chirality : 0.046 0.377 1812 Planarity : 0.004 0.048 2060 Dihedral : 5.700 62.531 1580 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.89 % Allowed : 21.96 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.23), residues: 1452 helix: 0.84 (0.23), residues: 518 sheet: -0.48 (0.34), residues: 240 loop : 0.48 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 488 TYR 0.008 0.001 TYR B 196 PHE 0.019 0.001 PHE B 841 TRP 0.060 0.002 TRP A 432 HIS 0.005 0.001 HIS A 539 Details of bonding type rmsd covalent geometry : bond 0.00292 (12056) covalent geometry : angle 0.75627 (16286) hydrogen bonds : bond 0.03111 ( 454) hydrogen bonds : angle 4.94769 ( 1254) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 169 time to evaluate : 0.542 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8735 (pp) REVERT: A 351 LEU cc_start: 0.7759 (tt) cc_final: 0.7221 (tp) REVERT: A 522 CYS cc_start: 0.7642 (p) cc_final: 0.7067 (p) REVERT: A 584 GLU cc_start: 0.8917 (mp0) cc_final: 0.8532 (tm-30) REVERT: A 722 LYS cc_start: 0.8835 (tptp) cc_final: 0.8544 (mttt) REVERT: A 844 MET cc_start: 0.7192 (tmm) cc_final: 0.6753 (tmm) REVERT: B 351 LEU cc_start: 0.7708 (tt) cc_final: 0.7281 (tp) REVERT: B 403 LEU cc_start: 0.8592 (tp) cc_final: 0.8289 (tt) REVERT: B 522 CYS cc_start: 0.7623 (p) cc_final: 0.7071 (p) REVERT: B 671 SER cc_start: 0.8143 (t) cc_final: 0.7893 (p) REVERT: B 722 LYS cc_start: 0.8784 (tptp) cc_final: 0.8502 (mttt) REVERT: B 844 MET cc_start: 0.7765 (tmm) cc_final: 0.7346 (tmm) REVERT: B 879 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8475 (tt) outliers start: 38 outliers final: 29 residues processed: 181 average time/residue: 0.0899 time to fit residues: 25.7804 Evaluate side-chains 195 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 164 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 315 THR Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 548 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 686 THR Chi-restraints excluded: chain A residue 692 LEU Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 874 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 289 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 531 ILE Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 686 THR Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 874 ASN Chi-restraints excluded: chain B residue 879 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 14 optimal weight: 8.9990 chunk 128 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 82 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 110 optimal weight: 0.0970 chunk 6 optimal weight: 0.0010 chunk 97 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 127 optimal weight: 0.0980 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 640 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 = 0.105701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.077674 restraints weight = 34361.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.080842 restraints weight = 18641.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.082961 restraints weight = 12530.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.084427 restraints weight = 9610.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.085317 restraints weight = 7991.830| |-----------------------------------------------------------------------------| r_work (final): 0.3660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.3062 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12056 Z= 0.114 Angle : 0.775 16.730 16286 Z= 0.345 Chirality : 0.046 0.390 1812 Planarity : 0.004 0.052 2060 Dihedral : 5.353 48.472 1580 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 1.75 % Allowed : 23.78 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.62 (0.23), residues: 1452 helix: 0.84 (0.23), residues: 524 sheet: -0.39 (0.34), residues: 250 loop : 0.60 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 488 TYR 0.035 0.001 TYR A 212 PHE 0.020 0.001 PHE A 841 TRP 0.059 0.002 TRP A 432 HIS 0.005 0.001 HIS A 524 Details of bonding type rmsd covalent geometry : bond 0.00254 (12056) covalent geometry : angle 0.77465 (16286) hydrogen bonds : bond 0.02958 ( 454) hydrogen bonds : angle 4.86818 ( 1254) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2904 Ramachandran restraints generated. 1452 Oldfield, 0 Emsley, 1452 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 0.525 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8723 (pp) REVERT: A 351 LEU cc_start: 0.7767 (tt) cc_final: 0.7541 (tp) REVERT: A 432 TRP cc_start: 0.8200 (m-90) cc_final: 0.7860 (m-90) REVERT: A 522 CYS cc_start: 0.7623 (p) cc_final: 0.7181 (p) REVERT: A 584 GLU cc_start: 0.8858 (mp0) cc_final: 0.8577 (tm-30) REVERT: A 635 MET cc_start: 0.7674 (tpt) cc_final: 0.7458 (tpt) REVERT: A 722 LYS cc_start: 0.8802 (tptp) cc_final: 0.8543 (mttt) REVERT: A 844 MET cc_start: 0.7178 (tmm) cc_final: 0.6784 (tmm) REVERT: B 351 LEU cc_start: 0.7708 (tt) cc_final: 0.7453 (tp) REVERT: B 403 LEU cc_start: 0.8583 (tp) cc_final: 0.8288 (tt) REVERT: B 522 CYS cc_start: 0.7653 (p) cc_final: 0.7159 (p) REVERT: B 671 SER cc_start: 0.8103 (t) cc_final: 0.7837 (p) REVERT: B 722 LYS cc_start: 0.8783 (tptp) cc_final: 0.8519 (mttt) REVERT: B 844 MET cc_start: 0.7795 (tmm) cc_final: 0.7358 (tmm) REVERT: B 879 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8524 (tt) outliers start: 23 outliers final: 17 residues processed: 188 average time/residue: 0.0823 time to fit residues: 24.3715 Evaluate side-chains 185 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 166 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 721 LEU Chi-restraints excluded: chain A residue 751 LEU Chi-restraints excluded: chain A residue 874 ASN Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 466 MET Chi-restraints excluded: chain B residue 553 MET Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 692 LEU Chi-restraints excluded: chain B residue 721 LEU Chi-restraints excluded: chain B residue 751 LEU Chi-restraints excluded: chain B residue 874 ASN Chi-restraints excluded: chain B residue 879 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 78 optimal weight: 0.9990 chunk 47 optimal weight: 7.9990 chunk 141 optimal weight: 0.0040 chunk 105 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 107 optimal weight: 0.1980 chunk 10 optimal weight: 9.9990 chunk 56 optimal weight: 6.9990 chunk 89 optimal weight: 9.9990 chunk 35 optimal weight: 0.1980 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.4037 r_free = 0.4037 target = 0.105952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.077783 restraints weight = 34029.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.080989 restraints weight = 18433.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.083197 restraints weight = 12356.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.084550 restraints weight = 9418.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.085620 restraints weight = 7859.168| |-----------------------------------------------------------------------------| r_work (final): 0.3669 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.3153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 12056 Z= 0.109 Angle : 0.763 16.679 16286 Z= 0.342 Chirality : 0.046 0.377 1812 Planarity : 0.004 0.060 2060 Dihedral : 4.949 46.550 1580 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.60 % Allowed : 24.24 % Favored : 74.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.23), residues: 1452 helix: 0.82 (0.23), residues: 520 sheet: -0.41 (0.33), residues: 254 loop : 0.61 (0.25), residues: 678 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 488 TYR 0.032 0.001 TYR A 212 PHE 0.020 0.001 PHE B 841 TRP 0.055 0.002 TRP A 432 HIS 0.005 0.001 HIS A 539 Details of bonding type rmsd covalent geometry : bond 0.00246 (12056) covalent geometry : angle 0.76294 (16286) hydrogen bonds : bond 0.02857 ( 454) hydrogen bonds : angle 4.84201 ( 1254) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2277.02 seconds wall clock time: 40 minutes 10.18 seconds (2410.18 seconds total)