Starting phenix.real_space_refine on Sat Jan 18 08:16:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rfh_19121/01_2025/8rfh_19121.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rfh_19121/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8rfh_19121/01_2025/8rfh_19121.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rfh_19121/01_2025/8rfh_19121.map" model { file = "/net/cci-nas-00/data/ceres_data/8rfh_19121/01_2025/8rfh_19121.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rfh_19121/01_2025/8rfh_19121.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 6.98, per 1000 atoms: 0.59 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: 2.97 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.64 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: 4.23 Time building geometry restraints manager: 3.44 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: 0.06 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 29.010 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.340 ------------------------------------------------------------------------------- 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= 0.203 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 : 17.02 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (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 TRP 0.012 0.001 TRP B 798 HIS 0.004 0.001 HIS A 524 PHE 0.010 0.001 PHE B 571 TYR 0.006 0.001 TYR B 413 ARG 0.007 0.000 ARG A 478 *********************** 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 : 1.543 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: 0.2113 time to fit residues: 61.8735 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 : 1.532 ------------------------------------------------------------------------------- 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 123 optimal weight: 30.0000 chunk 110 optimal weight: 0.8980 chunk 61 optimal weight: 20.0000 chunk 37 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 114 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 85 optimal weight: 0.0060 chunk 132 optimal weight: 3.9990 overall best weight: 1.5800 ------------------------------------------------------------------------------- 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 = 0.4056 r_free = 0.4056 target = 0.107037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.079069 restraints weight = 33923.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.082231 restraints weight = 18655.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.084461 restraints weight = 12539.726| |-----------------------------------------------------------------------------| r_work (final): 0.3651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12056 Z= 0.199 Angle : 0.674 9.693 16286 Z= 0.325 Chirality : 0.045 0.157 1812 Planarity : 0.004 0.043 2060 Dihedral : 7.256 147.309 1586 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 12.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.96 % Allowed : 18.24 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.23), residues: 1452 helix: 0.59 (0.23), residues: 530 sheet: -0.08 (0.36), residues: 228 loop : 0.57 (0.25), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 432 HIS 0.004 0.001 HIS A 382 PHE 0.017 0.001 PHE A 585 TYR 0.012 0.001 TYR A 259 ARG 0.006 0.000 ARG B 478 *********************** 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 216 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 1.345 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 407 LEU cc_start: 0.9570 (tp) cc_final: 0.9367 (tp) REVERT: A 456 ASP cc_start: 0.8916 (m-30) cc_final: 0.8426 (t70) REVERT: A 671 SER cc_start: 0.7790 (OUTLIER) cc_final: 0.7356 (p) REVERT: A 722 LYS cc_start: 0.8762 (tptp) cc_final: 0.8254 (mttt) REVERT: B 407 LEU cc_start: 0.9524 (tp) cc_final: 0.9317 (tp) REVERT: B 432 TRP cc_start: 0.8465 (m-10) cc_final: 0.7995 (m-90) REVERT: B 456 ASP cc_start: 0.8895 (m-30) cc_final: 0.8412 (t70) REVERT: B 635 MET cc_start: 0.7618 (tpt) cc_final: 0.7415 (tpt) REVERT: B 671 SER cc_start: 0.8005 (t) cc_final: 0.7619 (p) REVERT: B 844 MET cc_start: 0.7426 (tmm) cc_final: 0.7205 (tmm) outliers start: 39 outliers final: 23 residues processed: 191 average time/residue: 0.1968 time to fit residues: 57.9415 Evaluate side-chains 190 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 1.423 ------------------------------------------------------------------------------- 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 570 VAL 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 579 SER 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 41 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 chunk 130 optimal weight: 0.0970 chunk 27 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 16 optimal weight: 6.9990 chunk 42 optimal weight: 7.9990 chunk 145 optimal weight: 8.9990 chunk 81 optimal weight: 5.9990 overall best weight: 2.5982 ------------------------------------------------------------------------------- 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 = 0.4021 r_free = 0.4021 target = 0.104374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.076299 restraints weight = 34864.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.079297 restraints weight = 19281.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.081281 restraints weight = 13094.587| |-----------------------------------------------------------------------------| r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7599 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12056 Z= 0.238 Angle : 0.673 8.551 16286 Z= 0.324 Chirality : 0.045 0.197 1812 Planarity : 0.004 0.045 2060 Dihedral : 6.846 129.914 1583 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.95 % Allowed : 17.10 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.23), residues: 1452 helix: 0.75 (0.23), residues: 520 sheet: -0.31 (0.34), residues: 228 loop : 0.63 (0.25), residues: 704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP A 432 HIS 0.003 0.001 HIS B 480 PHE 0.013 0.002 PHE A 530 TYR 0.012 0.001 TYR A 413 ARG 0.004 0.000 ARG B 488 *********************** 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 224 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 172 time to evaluate : 1.431 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 522 CYS cc_start: 0.7587 (p) cc_final: 0.7297 (p) REVERT: A 671 SER cc_start: 0.7924 (OUTLIER) cc_final: 0.7555 (p) REVERT: A 722 LYS cc_start: 0.8815 (tptp) cc_final: 0.8392 (mttt) REVERT: B 313 PHE cc_start: 0.7744 (m-80) cc_final: 0.7404 (m-80) REVERT: B 432 TRP cc_start: 0.8507 (m-10) cc_final: 0.8071 (m-90) REVERT: B 522 CYS cc_start: 0.7599 (p) cc_final: 0.7271 (p) REVERT: B 671 SER cc_start: 0.8214 (t) cc_final: 0.7911 (p) REVERT: B 844 MET cc_start: 0.7545 (tmm) cc_final: 0.7308 (tmm) outliers start: 52 outliers final: 37 residues processed: 195 average time/residue: 0.2026 time to fit residues: 61.3371 Evaluate side-chains 206 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 168 time to evaluate : 1.478 ------------------------------------------------------------------------------- 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 395 LEU Chi-restraints excluded: chain A residue 457 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 570 VAL Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 594 ILE 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 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 240 MET Chi-restraints excluded: chain B residue 290 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 570 VAL Chi-restraints excluded: chain B residue 579 SER Chi-restraints excluded: chain B residue 594 ILE 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 69 optimal weight: 3.9990 chunk 132 optimal weight: 10.0000 chunk 25 optimal weight: 6.9990 chunk 20 optimal weight: 0.9990 chunk 80 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 7 optimal weight: 6.9990 chunk 54 optimal weight: 20.0000 chunk 43 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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 = 0.3982 r_free = 0.3982 target = 0.102236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.075437 restraints weight = 34183.325| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.078355 restraints weight = 18639.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.080267 restraints weight = 12597.763| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.2296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12056 Z= 0.275 Angle : 0.718 9.521 16286 Z= 0.349 Chirality : 0.046 0.167 1812 Planarity : 0.005 0.047 2060 Dihedral : 6.531 107.696 1582 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 17.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.33 % Allowed : 18.84 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.23), residues: 1452 helix: 0.68 (0.23), residues: 516 sheet: -0.51 (0.34), residues: 222 loop : 0.43 (0.25), residues: 714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.002 TRP A 432 HIS 0.004 0.001 HIS B 309 PHE 0.017 0.002 PHE A 530 TYR 0.014 0.002 TYR B 740 ARG 0.006 0.000 ARG A 488 *********************** 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 224 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 167 time to evaluate : 1.392 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: 0.8671 (tp) cc_final: 0.8286 (tt) REVERT: A 429 ILE cc_start: 0.9272 (pp) cc_final: 0.9069 (pp) REVERT: A 432 TRP cc_start: 0.8354 (m-90) cc_final: 0.7997 (m-90) REVERT: A 522 CYS cc_start: 0.7695 (p) cc_final: 0.7183 (p) REVERT: A 635 MET cc_start: 0.7867 (tpt) cc_final: 0.7665 (tpt) REVERT: A 671 SER cc_start: 0.7831 (OUTLIER) cc_final: 0.7601 (p) REVERT: A 722 LYS cc_start: 0.8840 (tptp) cc_final: 0.8476 (mttt) REVERT: B 313 PHE cc_start: 0.7849 (m-80) cc_final: 0.7462 (m-80) REVERT: B 432 TRP cc_start: 0.8490 (m-10) cc_final: 0.8093 (m-90) REVERT: B 522 CYS cc_start: 0.7581 (p) cc_final: 0.7090 (p) REVERT: B 671 SER cc_start: 0.8300 (t) cc_final: 0.8096 (p) REVERT: B 722 LYS cc_start: 0.8758 (tptp) cc_final: 0.8302 (mttt) REVERT: B 879 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8515 (tt) outliers start: 57 outliers final: 40 residues processed: 192 average time/residue: 0.1858 time to fit residues: 55.9038 Evaluate side-chains 203 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 161 time to evaluate : 1.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 227 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 570 VAL Chi-restraints excluded: chain A residue 579 SER Chi-restraints excluded: chain A residue 594 ILE Chi-restraints excluded: chain A residue 638 LEU Chi-restraints excluded: chain A residue 663 VAL 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 289 LEU Chi-restraints excluded: chain B residue 290 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 570 VAL Chi-restraints excluded: chain B residue 594 ILE Chi-restraints excluded: chain B residue 626 LEU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 55 optimal weight: 1.9990 chunk 9 optimal weight: 7.9990 chunk 82 optimal weight: 0.9990 chunk 71 optimal weight: 0.0470 chunk 129 optimal weight: 6.9990 chunk 135 optimal weight: 6.9990 chunk 119 optimal weight: 7.9990 chunk 49 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 overall best weight: 1.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 HIS A 539 HIS ** A 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 875 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.104656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.076664 restraints weight = 33762.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.079749 restraints weight = 18343.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.081804 restraints weight = 12401.330| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.2390 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= 0.171 Angle : 0.689 11.912 16286 Z= 0.321 Chirality : 0.045 0.250 1812 Planarity : 0.004 0.051 2060 Dihedral : 5.991 86.056 1582 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.58 % Allowed : 20.52 % Favored : 76.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.23), residues: 1452 helix: 0.77 (0.23), residues: 520 sheet: -0.46 (0.33), residues: 250 loop : 0.63 (0.26), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP A 432 HIS 0.006 0.001 HIS A 539 PHE 0.016 0.001 PHE B 571 TYR 0.009 0.001 TYR B 740 ARG 0.003 0.000 ARG A 488 *********************** 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: 34 poor density : 174 time to evaluate : 1.344 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 403 LEU cc_start: 0.8644 (tp) cc_final: 0.8321 (tt) REVERT: A 522 CYS cc_start: 0.7618 (p) cc_final: 0.7185 (p) REVERT: A 722 LYS cc_start: 0.8771 (tptp) cc_final: 0.8498 (mttt) REVERT: B 351 LEU cc_start: 0.7695 (tp) cc_final: 0.7057 (tt) REVERT: B 403 LEU cc_start: 0.8613 (tp) cc_final: 0.8252 (tt) REVERT: B 522 CYS cc_start: 0.7568 (p) cc_final: 0.7132 (p) REVERT: B 671 SER cc_start: 0.8262 (t) cc_final: 0.8033 (p) REVERT: B 722 LYS cc_start: 0.8782 (tptp) cc_final: 0.8421 (mttt) REVERT: B 841 PHE cc_start: 0.8704 (t80) cc_final: 0.8481 (t80) outliers start: 34 outliers final: 24 residues processed: 185 average time/residue: 0.2025 time to fit residues: 57.1489 Evaluate side-chains 182 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 158 time to evaluate : 1.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 579 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 A residue 775 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 521 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 81 optimal weight: 7.9990 chunk 144 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 145 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 122 optimal weight: 6.9990 chunk 127 optimal weight: 0.0170 chunk 102 optimal weight: 3.9990 chunk 23 optimal weight: 10.0000 chunk 63 optimal weight: 30.0000 chunk 70 optimal weight: 10.0000 overall best weight: 3.6026 ------------------------------------------------------------------------------- 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 = 0.3956 r_free = 0.3956 target = 0.100823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3443 r_free = 0.3443 target = 0.073238 restraints weight = 35444.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.076075 restraints weight = 19643.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.077981 restraints weight = 13455.714| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 12056 Z= 0.304 Angle : 0.751 15.025 16286 Z= 0.360 Chirality : 0.048 0.276 1812 Planarity : 0.005 0.049 2060 Dihedral : 6.159 86.811 1582 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.65 % Allowed : 21.35 % Favored : 75.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.23), residues: 1452 helix: 0.69 (0.23), residues: 518 sheet: -0.64 (0.34), residues: 218 loop : 0.29 (0.25), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 432 HIS 0.007 0.001 HIS A 539 PHE 0.017 0.002 PHE A 530 TYR 0.013 0.002 TYR B 593 ARG 0.004 0.000 ARG B 488 *********************** 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 215 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 167 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 323 LEU cc_start: 0.8938 (OUTLIER) cc_final: 0.8712 (pp) REVERT: A 432 TRP cc_start: 0.8365 (m-10) cc_final: 0.8156 (m-90) REVERT: A 522 CYS cc_start: 0.7709 (p) cc_final: 0.7158 (p) REVERT: A 722 LYS cc_start: 0.8812 (tptp) cc_final: 0.8482 (mttt) REVERT: B 403 LEU cc_start: 0.8583 (tp) cc_final: 0.8247 (tt) REVERT: B 522 CYS cc_start: 0.7598 (p) cc_final: 0.7029 (p) REVERT: B 722 LYS cc_start: 0.8817 (tptp) cc_final: 0.8421 (mttt) outliers start: 48 outliers final: 37 residues processed: 189 average time/residue: 0.2140 time to fit residues: 61.0965 Evaluate side-chains 196 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 158 time to evaluate : 1.491 ------------------------------------------------------------------------------- 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 289 LEU 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 531 ILE 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 638 LEU 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 314 LEU Chi-restraints excluded: chain B residue 348 CYS Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 521 LEU Chi-restraints excluded: chain B residue 531 ILE 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 120 optimal weight: 0.1980 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 9.9990 chunk 9 optimal weight: 2.9990 chunk 134 optimal weight: 20.0000 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 5 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- 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 875 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.102584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.074481 restraints weight = 34955.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.077476 restraints weight = 19111.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.079427 restraints weight = 13017.871| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12056 Z= 0.199 Angle : 0.745 15.251 16286 Z= 0.342 Chirality : 0.047 0.326 1812 Planarity : 0.005 0.076 2060 Dihedral : 5.915 74.228 1582 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.58 % Allowed : 22.87 % Favored : 74.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.23), residues: 1452 helix: 0.77 (0.23), residues: 514 sheet: -0.55 (0.34), residues: 218 loop : 0.30 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 432 HIS 0.004 0.001 HIS A 524 PHE 0.026 0.001 PHE B 841 TYR 0.013 0.001 TYR A 212 ARG 0.010 0.000 ARG B 478 *********************** 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 207 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 1.388 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: 0.8945 (OUTLIER) cc_final: 0.8718 (pp) REVERT: A 351 LEU cc_start: 0.7975 (tt) cc_final: 0.7772 (tp) REVERT: A 522 CYS cc_start: 0.7609 (p) cc_final: 0.7077 (p) REVERT: A 722 LYS cc_start: 0.8818 (tptp) cc_final: 0.8520 (mttt) REVERT: A 844 MET cc_start: 0.7247 (tmm) cc_final: 0.7047 (tmm) REVERT: B 403 LEU cc_start: 0.8570 (tp) cc_final: 0.8228 (tt) REVERT: B 522 CYS cc_start: 0.7611 (p) cc_final: 0.7167 (p) REVERT: B 722 LYS cc_start: 0.8845 (tptp) cc_final: 0.8526 (mttt) outliers start: 34 outliers final: 24 residues processed: 188 average time/residue: 0.2159 time to fit residues: 60.9225 Evaluate side-chains 188 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 227 ILE Chi-restraints excluded: chain A residue 240 MET Chi-restraints excluded: chain A residue 323 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 553 MET Chi-restraints excluded: chain A residue 579 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 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 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 12 optimal weight: 0.0070 chunk 60 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 105 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 46 optimal weight: 6.9990 chunk 137 optimal weight: 8.9990 chunk 132 optimal weight: 10.0000 chunk 73 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- 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 = 0.3959 r_free = 0.3959 target = 0.101253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.073599 restraints weight = 35080.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.076474 restraints weight = 19464.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.078441 restraints weight = 13348.733| |-----------------------------------------------------------------------------| r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12056 Z= 0.244 Angle : 0.767 15.684 16286 Z= 0.355 Chirality : 0.047 0.318 1812 Planarity : 0.005 0.084 2060 Dihedral : 5.900 70.682 1580 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.34 % Allowed : 22.26 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.23), residues: 1452 helix: 0.73 (0.23), residues: 514 sheet: -0.69 (0.34), residues: 218 loop : 0.27 (0.25), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 432 HIS 0.005 0.001 HIS A 309 PHE 0.018 0.002 PHE A 841 TYR 0.016 0.002 TYR B 740 ARG 0.013 0.000 ARG B 488 *********************** 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 211 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 1.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.8250 (OUTLIER) cc_final: 0.8019 (mp) REVERT: A 323 LEU cc_start: 0.8943 (OUTLIER) cc_final: 0.8715 (pp) REVERT: A 522 CYS cc_start: 0.7634 (p) cc_final: 0.6993 (p) REVERT: A 722 LYS cc_start: 0.8841 (tptp) cc_final: 0.8555 (mttt) REVERT: B 175 LEU cc_start: 0.8115 (OUTLIER) cc_final: 0.7888 (mp) REVERT: B 351 LEU cc_start: 0.7704 (tt) cc_final: 0.7264 (tp) REVERT: B 403 LEU cc_start: 0.8579 (tp) cc_final: 0.8254 (tt) REVERT: B 522 CYS cc_start: 0.7539 (p) cc_final: 0.6929 (p) REVERT: B 722 LYS cc_start: 0.8839 (tptp) cc_final: 0.8516 (mttt) outliers start: 44 outliers final: 31 residues processed: 186 average time/residue: 0.2032 time to fit residues: 57.9309 Evaluate side-chains 195 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU 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 395 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 544 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 175 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 433 ILE 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 570 VAL 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 130 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 131 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 chunk 141 optimal weight: 3.9990 chunk 133 optimal weight: 4.9990 chunk 129 optimal weight: 6.9990 chunk 102 optimal weight: 5.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.101948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.073945 restraints weight = 34685.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.076893 restraints weight = 19271.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.078870 restraints weight = 13192.396| |-----------------------------------------------------------------------------| r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.3344 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= 0.217 Angle : 0.770 15.717 16286 Z= 0.350 Chirality : 0.047 0.364 1812 Planarity : 0.004 0.085 2060 Dihedral : 5.819 58.428 1580 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.96 % Allowed : 22.72 % Favored : 74.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.23), residues: 1452 helix: 0.78 (0.23), residues: 516 sheet: -0.63 (0.34), residues: 218 loop : 0.28 (0.25), residues: 718 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 432 HIS 0.004 0.001 HIS A 309 PHE 0.018 0.001 PHE B 841 TYR 0.009 0.001 TYR A 518 ARG 0.009 0.000 ARG A 478 *********************** 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 205 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 166 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 LEU cc_start: 0.8212 (OUTLIER) cc_final: 0.7994 (mp) REVERT: A 318 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7097 (mp0) REVERT: A 522 CYS cc_start: 0.7597 (p) cc_final: 0.7043 (p) REVERT: A 722 LYS cc_start: 0.8823 (tptp) cc_final: 0.8558 (mttt) REVERT: A 844 MET cc_start: 0.7211 (tmm) cc_final: 0.6644 (tmm) REVERT: B 175 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7853 (mp) REVERT: B 323 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8694 (pp) REVERT: B 351 LEU cc_start: 0.7779 (tt) cc_final: 0.7573 (tp) REVERT: B 403 LEU cc_start: 0.8577 (tp) cc_final: 0.8266 (tt) REVERT: B 522 CYS cc_start: 0.7578 (p) cc_final: 0.7095 (p) REVERT: B 722 LYS cc_start: 0.8843 (tptp) cc_final: 0.8513 (mttt) outliers start: 39 outliers final: 30 residues processed: 180 average time/residue: 0.2024 time to fit residues: 55.6887 Evaluate side-chains 197 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 163 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 318 GLU Chi-restraints excluded: chain A residue 395 LEU Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 544 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 775 LEU Chi-restraints excluded: chain A residue 874 ASN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 433 ILE 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 570 VAL 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 54 optimal weight: 0.8980 chunk 144 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 93 optimal weight: 4.9990 chunk 90 optimal weight: 0.0170 chunk 64 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 89 optimal weight: 3.9990 chunk 126 optimal weight: 9.9990 chunk 116 optimal weight: 6.9990 overall best weight: 1.3620 ------------------------------------------------------------------------------- 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 = 0.3983 r_free = 0.3983 target = 0.102750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.075355 restraints weight = 33600.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.078305 restraints weight = 18303.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.080324 restraints weight = 12395.725| |-----------------------------------------------------------------------------| r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 12056 Z= 0.184 Angle : 0.776 16.291 16286 Z= 0.348 Chirality : 0.047 0.370 1812 Planarity : 0.004 0.062 2060 Dihedral : 5.400 47.688 1580 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.36 % Allowed : 23.40 % Favored : 74.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.23), residues: 1452 helix: 0.84 (0.23), residues: 522 sheet: -0.52 (0.34), residues: 240 loop : 0.41 (0.26), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 432 HIS 0.006 0.001 HIS A 524 PHE 0.016 0.001 PHE A 841 TYR 0.037 0.002 TYR A 212 ARG 0.008 0.000 ARG B 488 ********************** 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 205 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 1.454 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 175 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.8012 (mp) REVERT: A 522 CYS cc_start: 0.7693 (p) cc_final: 0.7089 (p) REVERT: A 584 GLU cc_start: 0.8888 (mp0) cc_final: 0.8512 (tm-30) REVERT: A 722 LYS cc_start: 0.8826 (tptp) cc_final: 0.8566 (mttt) REVERT: A 844 MET cc_start: 0.7230 (tmm) cc_final: 0.6656 (tmm) REVERT: B 175 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7856 (mp) REVERT: B 323 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8699 (pp) REVERT: B 351 LEU cc_start: 0.7748 (tt) cc_final: 0.7377 (tp) REVERT: B 403 LEU cc_start: 0.8647 (tp) cc_final: 0.8371 (tt) REVERT: B 522 CYS cc_start: 0.7621 (p) cc_final: 0.7071 (p) REVERT: B 722 LYS cc_start: 0.8828 (tptp) cc_final: 0.8543 (mttt) outliers start: 31 outliers final: 28 residues processed: 185 average time/residue: 0.2013 time to fit residues: 57.2165 Evaluate side-chains 196 residues out of total 1316 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 1.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 LEU Chi-restraints excluded: chain A residue 186 LEU Chi-restraints excluded: chain A residue 201 ILE Chi-restraints excluded: chain A residue 521 LEU Chi-restraints excluded: chain A residue 531 ILE Chi-restraints excluded: chain A residue 544 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 775 LEU Chi-restraints excluded: chain A residue 874 ASN Chi-restraints excluded: chain B residue 175 LEU Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 240 MET Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 395 LEU Chi-restraints excluded: chain B residue 433 ILE 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 570 VAL Chi-restraints excluded: chain B residue 579 SER 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 146 random chunks: chunk 93 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 118 optimal weight: 0.3980 chunk 107 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 96 optimal weight: 20.0000 chunk 92 optimal weight: 0.7980 chunk 103 optimal weight: 1.9990 chunk 119 optimal weight: 3.9990 chunk 84 optimal weight: 9.9990 chunk 54 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.104116 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.076225 restraints weight = 34956.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.079209 restraints weight = 19322.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.081250 restraints weight = 13216.402| |-----------------------------------------------------------------------------| r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12056 Z= 0.176 Angle : 0.773 16.275 16286 Z= 0.345 Chirality : 0.047 0.375 1812 Planarity : 0.004 0.054 2060 Dihedral : 5.084 47.040 1580 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.51 % Allowed : 23.94 % Favored : 73.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.23), residues: 1452 helix: 0.80 (0.23), residues: 516 sheet: -0.30 (0.34), residues: 236 loop : 0.45 (0.25), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 432 HIS 0.005 0.001 HIS A 524 PHE 0.025 0.001 PHE B 841 TYR 0.040 0.001 TYR A 212 ARG 0.008 0.000 ARG B 488 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3804.30 seconds wall clock time: 69 minutes 21.78 seconds (4161.78 seconds total)