Starting phenix.real_space_refine on Mon Mar 11 06:37:16 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgj_7096/03_2024/6bgj_7096_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgj_7096/03_2024/6bgj_7096.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgj_7096/03_2024/6bgj_7096.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgj_7096/03_2024/6bgj_7096.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgj_7096/03_2024/6bgj_7096_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6bgj_7096/03_2024/6bgj_7096_neut.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 2 9.91 5 S 48 5.16 5 C 4892 2.51 5 N 1194 2.21 5 O 1282 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7418 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3708 Classifications: {'peptide': 490} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 19, 'TRANS': 470} Chain breaks: 3 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 234 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 171 Chain: "B" Number of atoms: 3708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 490, 3708 Classifications: {'peptide': 490} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 19, 'TRANS': 470} Chain breaks: 3 Unresolved non-hydrogen bonds: 273 Unresolved non-hydrogen angles: 348 Unresolved non-hydrogen dihedrals: 234 Unresolved non-hydrogen chiralities: 18 Planarities with less than four sites: {'GLN:plan1': 2, 'ASP:plan': 5, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 3, 'HIS:plan': 1, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 171 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.90, per 1000 atoms: 0.66 Number of scatterers: 7418 At special positions: 0 Unit cell: (103.02, 82.62, 99.96, 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) Ca 2 19.99 S 48 16.00 O 1282 8.00 N 1194 7.00 C 4892 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 - 3.50 Amino acid : False - 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: 2.93 Conformation dependent library (CDL) restraints added in 1.5 seconds 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1868 Finding SS restraints... Secondary structure from input PDB file: 48 helices and 0 sheets defined 74.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 292 through 303 removed outlier: 3.606A pdb=" N LEU A 300 " --> pdb=" O ASN A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 324 Processing helix chain 'A' and resid 325 through 362 removed outlier: 3.691A pdb=" N TYR A 331 " --> pdb=" O LYS A 327 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N PHE A 332 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE A 343 " --> pdb=" O THR A 339 " (cutoff:3.500A) Proline residue: A 344 - end of helix removed outlier: 3.534A pdb=" N VAL A 348 " --> pdb=" O PRO A 344 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR A 359 " --> pdb=" O TYR A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 375 Processing helix chain 'A' and resid 390 through 401 removed outlier: 3.847A pdb=" N ARG A 399 " --> pdb=" O CYS A 395 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA A 400 " --> pdb=" O ALA A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 404 No H-bonds generated for 'chain 'A' and resid 402 through 404' Processing helix chain 'A' and resid 407 through 442 removed outlier: 3.670A pdb=" N PHE A 412 " --> pdb=" O ALA A 408 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR A 436 " --> pdb=" O MET A 432 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 505 Processing helix chain 'A' and resid 508 through 522 removed outlier: 3.873A pdb=" N ALA A 519 " --> pdb=" O ALA A 515 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER A 522 " --> pdb=" O LEU A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 529 through 565 removed outlier: 3.584A pdb=" N VAL A 539 " --> pdb=" O THR A 535 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE A 547 " --> pdb=" O LEU A 543 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 552 " --> pdb=" O LEU A 548 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N TYR A 553 " --> pdb=" O LEU A 549 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY A 554 " --> pdb=" O ASP A 550 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS A 555 " --> pdb=" O GLU A 551 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP A 559 " --> pdb=" O CYS A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 589 removed outlier: 3.521A pdb=" N PHE A 578 " --> pdb=" O GLU A 574 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU A 582 " --> pdb=" O PHE A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 589 through 597 Processing helix chain 'A' and resid 627 through 642 removed outlier: 4.265A pdb=" N CYS A 631 " --> pdb=" O LEU A 627 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE A 636 " --> pdb=" O ILE A 632 " (cutoff:3.500A) Processing helix chain 'A' and resid 683 through 689 removed outlier: 3.684A pdb=" N PHE A 687 " --> pdb=" O GLU A 684 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU A 689 " --> pdb=" O ASP A 686 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 710 removed outlier: 3.615A pdb=" N GLN A 705 " --> pdb=" O GLU A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 718 through 740 removed outlier: 3.861A pdb=" N ASN A 726 " --> pdb=" O PHE A 722 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ILE A 729 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG A 732 " --> pdb=" O ILE A 728 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 771 removed outlier: 3.747A pdb=" N TYR A 757 " --> pdb=" O ILE A 753 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE A 759 " --> pdb=" O ILE A 755 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL A 768 " --> pdb=" O GLY A 764 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE A 769 " --> pdb=" O LYS A 765 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 776 Processing helix chain 'A' and resid 781 through 790 removed outlier: 5.087A pdb=" N TYR A 787 " --> pdb=" O PRO A 783 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR A 789 " --> pdb=" O LEU A 785 " (cutoff:3.500A) Processing helix chain 'A' and resid 800 through 802 No H-bonds generated for 'chain 'A' and resid 800 through 802' Processing helix chain 'A' and resid 803 through 811 removed outlier: 3.938A pdb=" N SER A 807 " --> pdb=" O HIS A 803 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER A 811 " --> pdb=" O SER A 807 " (cutoff:3.500A) Processing helix chain 'A' and resid 820 through 825 Processing helix chain 'A' and resid 848 through 850 No H-bonds generated for 'chain 'A' and resid 848 through 850' Processing helix chain 'A' and resid 851 through 882 removed outlier: 3.738A pdb=" N ALA A 855 " --> pdb=" O LYS A 851 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL A 856 " --> pdb=" O ASP A 852 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ASN A 869 " --> pdb=" O ILE A 865 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N MET A 872 " --> pdb=" O GLN A 868 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TRP A 880 " --> pdb=" O ASP A 876 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N ILE A 882 " --> pdb=" O VAL A 878 " (cutoff:3.500A) Processing helix chain 'B' and resid 293 through 303 removed outlier: 3.606A pdb=" N LEU B 300 " --> pdb=" O ASN B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 316 through 324 Processing helix chain 'B' and resid 325 through 362 removed outlier: 3.690A pdb=" N TYR B 331 " --> pdb=" O LYS B 327 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE B 332 " --> pdb=" O VAL B 328 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE B 343 " --> pdb=" O THR B 339 " (cutoff:3.500A) Proline residue: B 344 - end of helix removed outlier: 3.535A pdb=" N VAL B 348 " --> pdb=" O PRO B 344 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N THR B 359 " --> pdb=" O TYR B 355 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 375 Processing helix chain 'B' and resid 390 through 401 removed outlier: 3.847A pdb=" N ARG B 399 " --> pdb=" O CYS B 395 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA B 400 " --> pdb=" O ALA B 396 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 404 No H-bonds generated for 'chain 'B' and resid 402 through 404' Processing helix chain 'B' and resid 407 through 442 removed outlier: 3.670A pdb=" N PHE B 412 " --> pdb=" O ALA B 408 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N TYR B 436 " --> pdb=" O MET B 432 " (cutoff:3.500A) Processing helix chain 'B' and resid 494 through 505 Processing helix chain 'B' and resid 508 through 522 removed outlier: 3.873A pdb=" N ALA B 519 " --> pdb=" O ALA B 515 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N SER B 522 " --> pdb=" O LEU B 518 " (cutoff:3.500A) Processing helix chain 'B' and resid 529 through 565 removed outlier: 3.584A pdb=" N VAL B 539 " --> pdb=" O THR B 535 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ILE B 547 " --> pdb=" O LEU B 543 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL B 552 " --> pdb=" O LEU B 548 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N TYR B 553 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY B 554 " --> pdb=" O ASP B 550 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N CYS B 555 " --> pdb=" O GLU B 551 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TRP B 559 " --> pdb=" O CYS B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 568 through 589 removed outlier: 3.521A pdb=" N PHE B 578 " --> pdb=" O GLU B 574 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU B 582 " --> pdb=" O PHE B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 589 through 597 Processing helix chain 'B' and resid 627 through 642 removed outlier: 4.265A pdb=" N CYS B 631 " --> pdb=" O LEU B 627 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE B 636 " --> pdb=" O ILE B 632 " (cutoff:3.500A) Processing helix chain 'B' and resid 683 through 689 removed outlier: 3.683A pdb=" N PHE B 687 " --> pdb=" O GLU B 684 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU B 689 " --> pdb=" O ASP B 686 " (cutoff:3.500A) Processing helix chain 'B' and resid 694 through 710 removed outlier: 3.614A pdb=" N GLN B 705 " --> pdb=" O GLU B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 718 through 740 removed outlier: 3.861A pdb=" N ASN B 726 " --> pdb=" O PHE B 722 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ILE B 729 " --> pdb=" O LEU B 725 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ARG B 732 " --> pdb=" O ILE B 728 " (cutoff:3.500A) Processing helix chain 'B' and resid 753 through 771 removed outlier: 3.748A pdb=" N TYR B 757 " --> pdb=" O ILE B 753 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE B 759 " --> pdb=" O ILE B 755 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N VAL B 768 " --> pdb=" O GLY B 764 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 769 " --> pdb=" O LYS B 765 " (cutoff:3.500A) Processing helix chain 'B' and resid 771 through 776 Processing helix chain 'B' and resid 781 through 790 removed outlier: 5.086A pdb=" N TYR B 787 " --> pdb=" O PRO B 783 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N TYR B 789 " --> pdb=" O LEU B 785 " (cutoff:3.500A) Processing helix chain 'B' and resid 800 through 802 No H-bonds generated for 'chain 'B' and resid 800 through 802' Processing helix chain 'B' and resid 803 through 811 removed outlier: 3.937A pdb=" N SER B 807 " --> pdb=" O HIS B 803 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N SER B 811 " --> pdb=" O SER B 807 " (cutoff:3.500A) Processing helix chain 'B' and resid 820 through 825 Processing helix chain 'B' and resid 848 through 850 No H-bonds generated for 'chain 'B' and resid 848 through 850' Processing helix chain 'B' and resid 851 through 882 removed outlier: 3.738A pdb=" N ALA B 855 " --> pdb=" O LYS B 851 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL B 856 " --> pdb=" O ASP B 852 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ASN B 869 " --> pdb=" O ILE B 865 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N MET B 872 " --> pdb=" O GLN B 868 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N TRP B 880 " --> pdb=" O ASP B 876 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ILE B 882 " --> pdb=" O VAL B 878 " (cutoff:3.500A) 453 hydrogen bonds defined for protein. 1347 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.06 Time building geometry restraints manager: 3.13 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: 2247 1.34 - 1.46: 1907 1.46 - 1.58: 3372 1.58 - 1.70: 0 1.70 - 1.82: 76 Bond restraints: 7602 Sorted by residual: bond pdb=" C ILE A 782 " pdb=" N PRO A 783 " ideal model delta sigma weight residual 1.334 1.382 -0.048 8.40e-03 1.42e+04 3.28e+01 bond pdb=" C ILE B 782 " pdb=" N PRO B 783 " ideal model delta sigma weight residual 1.334 1.381 -0.047 8.40e-03 1.42e+04 3.15e+01 bond pdb=" CG1 ILE A 775 " pdb=" CD1 ILE A 775 " ideal model delta sigma weight residual 1.513 1.408 0.105 3.90e-02 6.57e+02 7.30e+00 bond pdb=" CG1 ILE B 775 " pdb=" CD1 ILE B 775 " ideal model delta sigma weight residual 1.513 1.408 0.105 3.90e-02 6.57e+02 7.22e+00 bond pdb=" N SER A 811 " pdb=" CA SER A 811 " ideal model delta sigma weight residual 1.457 1.487 -0.029 1.29e-02 6.01e+03 5.18e+00 ... (remaining 7597 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.79: 227 106.79 - 113.61: 3990 113.61 - 120.42: 3365 120.42 - 127.24: 2696 127.24 - 134.05: 82 Bond angle restraints: 10360 Sorted by residual: angle pdb=" C ASN A 809 " pdb=" N VAL A 810 " pdb=" CA VAL A 810 " ideal model delta sigma weight residual 121.97 130.80 -8.83 1.80e+00 3.09e-01 2.41e+01 angle pdb=" C SER B 522 " pdb=" N SER B 523 " pdb=" CA SER B 523 " ideal model delta sigma weight residual 122.83 128.12 -5.29 1.08e+00 8.57e-01 2.40e+01 angle pdb=" C ASN B 809 " pdb=" N VAL B 810 " pdb=" CA VAL B 810 " ideal model delta sigma weight residual 121.97 130.77 -8.80 1.80e+00 3.09e-01 2.39e+01 angle pdb=" C SER A 522 " pdb=" N SER A 523 " pdb=" CA SER A 523 " ideal model delta sigma weight residual 122.83 128.10 -5.27 1.08e+00 8.57e-01 2.38e+01 angle pdb=" N ASP B 752 " pdb=" CA ASP B 752 " pdb=" C ASP B 752 " ideal model delta sigma weight residual 110.91 116.49 -5.58 1.17e+00 7.31e-01 2.28e+01 ... (remaining 10355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.03: 3780 11.03 - 22.06: 543 22.06 - 33.10: 59 33.10 - 44.13: 28 44.13 - 55.16: 10 Dihedral angle restraints: 4420 sinusoidal: 1538 harmonic: 2882 Sorted by residual: dihedral pdb=" CA GLN A 793 " pdb=" C GLN A 793 " pdb=" N ASN A 794 " pdb=" CA ASN A 794 " ideal model delta harmonic sigma weight residual 180.00 124.84 55.16 0 5.00e+00 4.00e-02 1.22e+02 dihedral pdb=" CA GLN B 793 " pdb=" C GLN B 793 " pdb=" N ASN B 794 " pdb=" CA ASN B 794 " ideal model delta harmonic sigma weight residual 180.00 124.90 55.10 0 5.00e+00 4.00e-02 1.21e+02 dihedral pdb=" CA ASN A 809 " pdb=" C ASN A 809 " pdb=" N VAL A 810 " pdb=" CA VAL A 810 " ideal model delta harmonic sigma weight residual 180.00 134.12 45.88 0 5.00e+00 4.00e-02 8.42e+01 ... (remaining 4417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 1014 0.081 - 0.161: 174 0.161 - 0.241: 14 0.241 - 0.322: 0 0.322 - 0.402: 2 Chirality restraints: 1204 Sorted by residual: chirality pdb=" CB ILE A 364 " pdb=" CA ILE A 364 " pdb=" CG1 ILE A 364 " pdb=" CG2 ILE A 364 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.04e+00 chirality pdb=" CB ILE B 364 " pdb=" CA ILE B 364 " pdb=" CG1 ILE B 364 " pdb=" CG2 ILE B 364 " both_signs ideal model delta sigma weight residual False 2.64 2.24 0.40 2.00e-01 2.50e+01 4.03e+00 chirality pdb=" CB VAL A 713 " pdb=" CA VAL A 713 " pdb=" CG1 VAL A 713 " pdb=" CG2 VAL A 713 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 1201 not shown) Planarity restraints: 1298 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS A 379 " -0.059 5.00e-02 4.00e+02 8.88e-02 1.26e+01 pdb=" N PRO A 380 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO A 380 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO A 380 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 379 " -0.059 5.00e-02 4.00e+02 8.87e-02 1.26e+01 pdb=" N PRO B 380 " 0.153 5.00e-02 4.00e+02 pdb=" CA PRO B 380 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO B 380 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 622 " 0.056 5.00e-02 4.00e+02 8.41e-02 1.13e+01 pdb=" N PRO B 623 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO B 623 " 0.043 5.00e-02 4.00e+02 pdb=" CD PRO B 623 " 0.047 5.00e-02 4.00e+02 ... (remaining 1295 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 177 2.69 - 3.25: 7668 3.25 - 3.80: 11542 3.80 - 4.35: 15421 4.35 - 4.90: 24120 Nonbonded interactions: 58928 Sorted by model distance: nonbonded pdb=" OD2 ASP B 383 " pdb=" NH2 ARG B 614 " model vdw 2.142 2.520 nonbonded pdb=" OD2 ASP A 383 " pdb=" NH2 ARG A 614 " model vdw 2.142 2.520 nonbonded pdb=" NH2 ARG B 321 " pdb=" OE2 GLU B 326 " model vdw 2.195 2.520 nonbonded pdb=" NH2 ARG A 321 " pdb=" OE2 GLU A 326 " model vdw 2.195 2.520 nonbonded pdb=" OD2 ASP A 821 " pdb=" N LYS A 846 " model vdw 2.225 2.520 ... (remaining 58923 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.960 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 24.180 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5961 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 : 0.008 0.105 7602 Z= 0.515 Angle : 1.211 10.576 10360 Z= 0.673 Chirality : 0.060 0.402 1204 Planarity : 0.010 0.089 1298 Dihedral : 10.716 55.160 2552 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.62 % Allowed : 13.69 % Favored : 85.68 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 5.26 % Twisted General : 2.14 % 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: -5.82 (0.19), residues: 964 helix: -3.34 (0.14), residues: 582 sheet: None (None), residues: 0 loop : -4.63 (0.25), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP B 427 HIS 0.011 0.004 HIS A 803 PHE 0.044 0.004 PHE A 353 TYR 0.036 0.003 TYR A 338 ARG 0.006 0.001 ARG A 373 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 0.925 Fit side-chains REVERT: A 319 LEU cc_start: 0.8068 (tp) cc_final: 0.7828 (tp) REVERT: A 321 ARG cc_start: 0.5258 (tmt-80) cc_final: 0.4605 (ttm170) REVERT: A 618 MET cc_start: 0.3858 (tpt) cc_final: 0.3413 (mtt) REVERT: A 633 GLN cc_start: 0.5444 (mt0) cc_final: 0.5038 (mt0) REVERT: A 702 MET cc_start: 0.7551 (tpp) cc_final: 0.7304 (tpp) REVERT: B 319 LEU cc_start: 0.7988 (tp) cc_final: 0.7774 (tp) REVERT: B 574 GLU cc_start: 0.7249 (mm-30) cc_final: 0.7034 (mm-30) REVERT: B 618 MET cc_start: 0.3842 (tpt) cc_final: 0.3482 (mtm) REVERT: B 633 GLN cc_start: 0.5766 (mt0) cc_final: 0.5317 (mt0) REVERT: B 725 LEU cc_start: 0.7238 (mt) cc_final: 0.6899 (pp) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.1752 time to fit residues: 52.4163 Evaluate side-chains 158 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 158 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 0.0980 chunk 50 optimal weight: 0.8980 chunk 39 optimal weight: 0.7980 chunk 76 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 57 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** A 794 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 803 HIS A 809 ASN B 375 ASN B 645 GLN ** B 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 809 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5960 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7602 Z= 0.239 Angle : 0.859 10.612 10360 Z= 0.448 Chirality : 0.047 0.222 1204 Planarity : 0.007 0.056 1298 Dihedral : 8.350 47.304 1048 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.83 % Allowed : 12.14 % Favored : 87.03 % Rotamer: Outliers : 1.79 % Allowed : 10.19 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.28 % 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: -4.22 (0.22), residues: 964 helix: -1.88 (0.16), residues: 672 sheet: None (None), residues: 0 loop : -4.84 (0.29), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 419 HIS 0.007 0.003 HIS B 803 PHE 0.025 0.002 PHE B 873 TYR 0.020 0.002 TYR A 510 ARG 0.004 0.001 ARG B 860 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 172 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 318 ASP cc_start: 0.6562 (p0) cc_final: 0.6286 (p0) REVERT: A 321 ARG cc_start: 0.5024 (tmt-80) cc_final: 0.4288 (ttm170) REVERT: A 347 ILE cc_start: 0.8184 (mt) cc_final: 0.7956 (pt) REVERT: A 351 ILE cc_start: 0.8418 (mt) cc_final: 0.8115 (mm) REVERT: A 618 MET cc_start: 0.3888 (tpt) cc_final: 0.3506 (mtm) REVERT: A 633 GLN cc_start: 0.4664 (mt0) cc_final: 0.4364 (mt0) REVERT: A 702 MET cc_start: 0.7532 (tpp) cc_final: 0.7104 (mmp) REVERT: B 318 ASP cc_start: 0.6612 (p0) cc_final: 0.6159 (p0) REVERT: B 587 ASN cc_start: 0.7983 (t0) cc_final: 0.7745 (t0) REVERT: B 618 MET cc_start: 0.3962 (tpt) cc_final: 0.3717 (mtm) REVERT: B 633 GLN cc_start: 0.4985 (mt0) cc_final: 0.4623 (mt0) REVERT: B 718 LEU cc_start: 0.8468 (tt) cc_final: 0.7825 (pt) REVERT: B 725 LEU cc_start: 0.7191 (mt) cc_final: 0.6957 (pp) REVERT: B 790 MET cc_start: 0.4645 (mmt) cc_final: 0.4297 (mmt) outliers start: 13 outliers final: 3 residues processed: 174 average time/residue: 0.1678 time to fit residues: 40.6259 Evaluate side-chains 153 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 150 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 367 MET Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 728 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 10.0000 chunk 27 optimal weight: 0.5980 chunk 74 optimal weight: 0.0030 chunk 60 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 0.0970 chunk 96 optimal weight: 0.3980 chunk 79 optimal weight: 6.9990 chunk 88 optimal weight: 0.7980 chunk 30 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 overall best weight: 0.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 645 GLN ** B 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 375 ASN B 645 GLN ** B 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 803 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5909 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7602 Z= 0.202 Angle : 0.778 13.703 10360 Z= 0.406 Chirality : 0.045 0.221 1204 Planarity : 0.006 0.049 1298 Dihedral : 7.602 41.228 1048 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.52 % Allowed : 12.76 % Favored : 86.72 % Rotamer: Outliers : 1.65 % Allowed : 12.53 % Favored : 85.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.37 (0.24), residues: 964 helix: -1.22 (0.17), residues: 684 sheet: None (None), residues: 0 loop : -4.73 (0.29), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 334 HIS 0.007 0.003 HIS B 803 PHE 0.027 0.002 PHE A 873 TYR 0.015 0.001 TYR A 355 ARG 0.004 0.000 ARG B 373 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 164 time to evaluate : 0.993 Fit side-chains REVERT: A 341 MET cc_start: 0.7784 (mtt) cc_final: 0.7459 (mtm) REVERT: A 368 GLU cc_start: 0.7704 (pm20) cc_final: 0.7298 (pm20) REVERT: A 411 PHE cc_start: 0.7317 (t80) cc_final: 0.7084 (t80) REVERT: A 618 MET cc_start: 0.3841 (tpt) cc_final: 0.3597 (mtm) REVERT: A 633 GLN cc_start: 0.4662 (mt0) cc_final: 0.4341 (mt0) REVERT: A 642 GLN cc_start: 0.5750 (mt0) cc_final: 0.5476 (mm-40) REVERT: B 318 ASP cc_start: 0.6621 (p0) cc_final: 0.6383 (p0) REVERT: B 321 ARG cc_start: 0.5050 (tmt-80) cc_final: 0.4206 (ttm170) REVERT: B 353 PHE cc_start: 0.6754 (OUTLIER) cc_final: 0.6265 (m-80) REVERT: B 574 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6276 (mm-30) REVERT: B 587 ASN cc_start: 0.8057 (t0) cc_final: 0.7847 (t0) REVERT: B 633 GLN cc_start: 0.5036 (mt0) cc_final: 0.4673 (mt0) REVERT: B 790 MET cc_start: 0.4337 (mmt) cc_final: 0.3839 (mmt) REVERT: B 797 MET cc_start: 0.2083 (mpp) cc_final: 0.1559 (mmt) outliers start: 12 outliers final: 4 residues processed: 167 average time/residue: 0.1686 time to fit residues: 38.8820 Evaluate side-chains 146 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 141 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 870 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 0.7980 chunk 67 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 9 optimal weight: 9.9990 chunk 42 optimal weight: 0.0470 chunk 59 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 25 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 645 GLN ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 803 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5932 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7602 Z= 0.214 Angle : 0.765 12.402 10360 Z= 0.395 Chirality : 0.045 0.205 1204 Planarity : 0.005 0.046 1298 Dihedral : 7.198 40.227 1048 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.52 % Allowed : 12.86 % Favored : 86.62 % Rotamer: Outliers : 1.52 % Allowed : 14.19 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.96 % 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: -2.62 (0.25), residues: 964 helix: -0.60 (0.18), residues: 682 sheet: None (None), residues: 0 loop : -4.58 (0.29), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 305 HIS 0.006 0.001 HIS A 803 PHE 0.026 0.002 PHE B 708 TYR 0.015 0.001 TYR A 510 ARG 0.003 0.000 ARG B 373 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 149 time to evaluate : 0.865 Fit side-chains revert: symmetry clash REVERT: A 341 MET cc_start: 0.7840 (mtt) cc_final: 0.7571 (mtm) REVERT: A 633 GLN cc_start: 0.4733 (mt0) cc_final: 0.4456 (mt0) REVERT: A 642 GLN cc_start: 0.5722 (mt0) cc_final: 0.5436 (mm-40) REVERT: B 353 PHE cc_start: 0.6778 (OUTLIER) cc_final: 0.6316 (m-80) REVERT: B 368 GLU cc_start: 0.7818 (pm20) cc_final: 0.7523 (pm20) REVERT: B 391 MET cc_start: 0.4722 (mpp) cc_final: 0.3943 (mpp) REVERT: B 574 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6083 (mm-30) REVERT: B 618 MET cc_start: 0.4813 (mtm) cc_final: 0.4542 (mtt) REVERT: B 633 GLN cc_start: 0.5017 (mt0) cc_final: 0.4754 (mt0) REVERT: B 642 GLN cc_start: 0.6149 (mm-40) cc_final: 0.5908 (mm-40) REVERT: B 645 GLN cc_start: 0.6640 (mt0) cc_final: 0.6413 (pt0) REVERT: B 790 MET cc_start: 0.4347 (mmt) cc_final: 0.3821 (mmt) REVERT: B 797 MET cc_start: 0.2043 (mpp) cc_final: 0.1509 (mmt) outliers start: 11 outliers final: 6 residues processed: 152 average time/residue: 0.1528 time to fit residues: 33.2375 Evaluate side-chains 146 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 139 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 552 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 0.7980 chunk 1 optimal weight: 0.3980 chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 80 optimal weight: 0.4980 chunk 65 optimal weight: 0.7980 chunk 0 optimal weight: 9.9990 chunk 48 optimal weight: 2.9990 chunk 85 optimal weight: 0.0270 chunk 23 optimal weight: 0.7980 chunk 31 optimal weight: 0.0470 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5881 moved from start: 0.4830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 7602 Z= 0.196 Angle : 0.728 11.639 10360 Z= 0.375 Chirality : 0.043 0.195 1204 Planarity : 0.005 0.044 1298 Dihedral : 6.830 47.680 1048 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.24 % Favored : 87.45 % Rotamer: Outliers : 1.65 % Allowed : 14.05 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.75 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.93 (0.26), residues: 964 helix: -0.02 (0.20), residues: 678 sheet: None (None), residues: 0 loop : -4.47 (0.30), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 305 HIS 0.006 0.001 HIS A 803 PHE 0.025 0.002 PHE B 708 TYR 0.012 0.001 TYR A 510 ARG 0.002 0.000 ARG B 373 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 158 time to evaluate : 0.839 Fit side-chains REVERT: A 341 MET cc_start: 0.7700 (mtt) cc_final: 0.7349 (mtm) REVERT: A 633 GLN cc_start: 0.4676 (mt0) cc_final: 0.4413 (mt0) REVERT: A 642 GLN cc_start: 0.5533 (mt0) cc_final: 0.5294 (mm-40) REVERT: A 702 MET cc_start: 0.7230 (mmm) cc_final: 0.6853 (mmp) REVERT: A 718 LEU cc_start: 0.8013 (tt) cc_final: 0.7495 (mt) REVERT: B 353 PHE cc_start: 0.6752 (OUTLIER) cc_final: 0.6364 (m-80) REVERT: B 574 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6181 (mm-30) REVERT: B 633 GLN cc_start: 0.4962 (mt0) cc_final: 0.4696 (mt0) REVERT: B 642 GLN cc_start: 0.5991 (mm-40) cc_final: 0.5556 (mm-40) REVERT: B 645 GLN cc_start: 0.6648 (mt0) cc_final: 0.6399 (pt0) REVERT: B 790 MET cc_start: 0.4362 (mmt) cc_final: 0.3858 (mmt) REVERT: B 797 MET cc_start: 0.2205 (mpp) cc_final: 0.1612 (mmt) REVERT: B 873 PHE cc_start: 0.6491 (t80) cc_final: 0.6181 (t80) outliers start: 12 outliers final: 5 residues processed: 162 average time/residue: 0.1671 time to fit residues: 37.8359 Evaluate side-chains 143 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 137 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain B residue 340 GLN Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 378 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 23 optimal weight: 8.9990 chunk 94 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5931 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7602 Z= 0.224 Angle : 0.741 11.186 10360 Z= 0.379 Chirality : 0.044 0.187 1204 Planarity : 0.005 0.044 1298 Dihedral : 6.714 44.935 1048 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 17.24 Ramachandran Plot: Outliers : 0.41 % Allowed : 13.17 % Favored : 86.41 % Rotamer: Outliers : 2.07 % Allowed : 15.56 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.64 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.27), residues: 964 helix: 0.23 (0.20), residues: 682 sheet: None (None), residues: 0 loop : -4.48 (0.30), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 427 HIS 0.005 0.001 HIS B 803 PHE 0.017 0.002 PHE B 708 TYR 0.016 0.001 TYR A 338 ARG 0.004 0.000 ARG B 860 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 147 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: A 321 ARG cc_start: 0.5452 (tmt-80) cc_final: 0.3755 (ttm170) REVERT: A 341 MET cc_start: 0.7694 (mtt) cc_final: 0.7283 (mtm) REVERT: A 633 GLN cc_start: 0.4745 (mt0) cc_final: 0.4481 (mt0) REVERT: A 642 GLN cc_start: 0.5496 (mt0) cc_final: 0.5281 (mm-40) REVERT: A 702 MET cc_start: 0.7218 (mmm) cc_final: 0.7002 (mmp) REVERT: A 790 MET cc_start: 0.1004 (ttm) cc_final: 0.0554 (mmm) REVERT: B 353 PHE cc_start: 0.6791 (OUTLIER) cc_final: 0.6345 (m-80) REVERT: B 574 GLU cc_start: 0.7131 (mm-30) cc_final: 0.6185 (mm-30) REVERT: B 633 GLN cc_start: 0.5038 (mt0) cc_final: 0.4767 (mt0) REVERT: B 642 GLN cc_start: 0.5828 (mm-40) cc_final: 0.5276 (mm-40) REVERT: B 643 LEU cc_start: 0.6887 (tp) cc_final: 0.6641 (tp) REVERT: B 645 GLN cc_start: 0.6669 (mt0) cc_final: 0.6438 (pt0) REVERT: B 755 ILE cc_start: 0.6529 (mm) cc_final: 0.5985 (mt) REVERT: B 797 MET cc_start: 0.2240 (mpp) cc_final: 0.1603 (mmt) outliers start: 15 outliers final: 7 residues processed: 152 average time/residue: 0.1681 time to fit residues: 36.3110 Evaluate side-chains 150 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 142 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain B residue 340 GLN Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 543 LEU Chi-restraints excluded: chain B residue 577 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 52 optimal weight: 0.8980 chunk 94 optimal weight: 0.1980 chunk 59 optimal weight: 3.9990 chunk 57 optimal weight: 4.9990 chunk 43 optimal weight: 0.0970 chunk 58 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5901 moved from start: 0.5244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 7602 Z= 0.204 Angle : 0.726 10.805 10360 Z= 0.371 Chirality : 0.043 0.192 1204 Planarity : 0.005 0.043 1298 Dihedral : 6.541 38.820 1048 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.41 % Allowed : 12.97 % Favored : 86.62 % Rotamer: Outliers : 2.20 % Allowed : 15.43 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.54 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.40 (0.27), residues: 964 helix: 0.45 (0.20), residues: 674 sheet: None (None), residues: 0 loop : -4.40 (0.29), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 305 HIS 0.005 0.001 HIS A 803 PHE 0.018 0.002 PHE B 708 TYR 0.011 0.001 TYR B 338 ARG 0.003 0.000 ARG B 373 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 149 time to evaluate : 0.831 Fit side-chains REVERT: A 321 ARG cc_start: 0.5483 (tmt-80) cc_final: 0.3447 (ttm170) REVERT: A 340 GLN cc_start: 0.6934 (OUTLIER) cc_final: 0.6641 (pm20) REVERT: A 341 MET cc_start: 0.7667 (mtt) cc_final: 0.7253 (mtm) REVERT: A 391 MET cc_start: 0.4955 (mpp) cc_final: 0.2435 (ttt) REVERT: A 577 THR cc_start: 0.7499 (m) cc_final: 0.7286 (m) REVERT: A 633 GLN cc_start: 0.4865 (mt0) cc_final: 0.4611 (mt0) REVERT: A 702 MET cc_start: 0.7224 (mmm) cc_final: 0.6971 (mmp) REVERT: B 353 PHE cc_start: 0.6821 (OUTLIER) cc_final: 0.6359 (m-80) REVERT: B 574 GLU cc_start: 0.7096 (mm-30) cc_final: 0.6170 (mm-30) REVERT: B 633 GLN cc_start: 0.5000 (mt0) cc_final: 0.4735 (mt0) REVERT: B 642 GLN cc_start: 0.5799 (mm-40) cc_final: 0.5283 (mm-40) REVERT: B 755 ILE cc_start: 0.6472 (mm) cc_final: 0.5997 (mt) REVERT: B 797 MET cc_start: 0.2189 (mpp) cc_final: 0.1574 (mmt) outliers start: 16 outliers final: 11 residues processed: 155 average time/residue: 0.1648 time to fit residues: 35.9003 Evaluate side-chains 151 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 138 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 GLN Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 340 GLN Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 847 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 0.4980 chunk 56 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 18 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.0010 chunk 74 optimal weight: 0.7980 chunk 85 optimal weight: 0.0370 chunk 90 optimal weight: 0.6980 overall best weight: 0.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 645 GLN ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 ASN ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 642 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5878 moved from start: 0.5512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7602 Z= 0.198 Angle : 0.748 10.622 10360 Z= 0.382 Chirality : 0.044 0.190 1204 Planarity : 0.004 0.045 1298 Dihedral : 6.444 48.549 1048 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.31 % Allowed : 13.49 % Favored : 86.20 % Rotamer: Outliers : 1.93 % Allowed : 16.94 % Favored : 81.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.28), residues: 964 helix: 0.55 (0.21), residues: 676 sheet: None (None), residues: 0 loop : -4.58 (0.28), residues: 288 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 427 HIS 0.005 0.001 HIS A 803 PHE 0.019 0.001 PHE B 708 TYR 0.012 0.001 TYR A 338 ARG 0.003 0.000 ARG B 373 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 146 time to evaluate : 0.967 Fit side-chains REVERT: A 321 ARG cc_start: 0.5534 (tmt-80) cc_final: 0.3551 (ttm170) REVERT: A 341 MET cc_start: 0.7620 (mtt) cc_final: 0.7188 (mtm) REVERT: A 391 MET cc_start: 0.4676 (mpp) cc_final: 0.2628 (ttt) REVERT: A 633 GLN cc_start: 0.4959 (mt0) cc_final: 0.4640 (mt0) REVERT: A 702 MET cc_start: 0.7221 (mmm) cc_final: 0.6977 (mmp) REVERT: B 323 TYR cc_start: 0.7301 (t80) cc_final: 0.7100 (t80) REVERT: B 353 PHE cc_start: 0.6808 (OUTLIER) cc_final: 0.6338 (m-10) REVERT: B 391 MET cc_start: 0.4307 (OUTLIER) cc_final: 0.2125 (ttt) REVERT: B 574 GLU cc_start: 0.7094 (mm-30) cc_final: 0.6223 (mm-30) REVERT: B 633 GLN cc_start: 0.4999 (mt0) cc_final: 0.4758 (mt0) REVERT: B 755 ILE cc_start: 0.6431 (mm) cc_final: 0.5966 (mt) REVERT: B 797 MET cc_start: 0.2395 (mpp) cc_final: 0.1690 (mmt) outliers start: 14 outliers final: 10 residues processed: 151 average time/residue: 0.1552 time to fit residues: 33.2427 Evaluate side-chains 148 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 136 time to evaluate : 0.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain B residue 303 GLU Chi-restraints excluded: chain B residue 340 GLN Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 369 MET Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 847 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 90 optimal weight: 0.6980 chunk 52 optimal weight: 0.3980 chunk 38 optimal weight: 0.6980 chunk 69 optimal weight: 0.8980 chunk 27 optimal weight: 0.2980 chunk 79 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 87 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 ASN ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 542 ASN ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5891 moved from start: 0.5653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7602 Z= 0.212 Angle : 0.748 10.666 10360 Z= 0.383 Chirality : 0.044 0.189 1204 Planarity : 0.004 0.048 1298 Dihedral : 6.371 45.698 1048 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.97 % Favored : 86.72 % Rotamer: Outliers : 2.34 % Allowed : 16.39 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.28), residues: 964 helix: 0.57 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -4.56 (0.29), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 427 HIS 0.004 0.001 HIS A 803 PHE 0.028 0.002 PHE A 708 TYR 0.015 0.001 TYR A 338 ARG 0.002 0.000 ARG B 373 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 321 ARG cc_start: 0.5505 (tmt-80) cc_final: 0.3562 (ttm170) REVERT: A 341 MET cc_start: 0.7571 (mtt) cc_final: 0.7319 (mtp) REVERT: A 378 MET cc_start: 0.1779 (ptm) cc_final: 0.1149 (ptp) REVERT: A 391 MET cc_start: 0.4489 (mpp) cc_final: 0.2921 (ttt) REVERT: A 633 GLN cc_start: 0.5009 (mt0) cc_final: 0.4683 (mt0) REVERT: A 702 MET cc_start: 0.7350 (mmm) cc_final: 0.7060 (mmp) REVERT: A 790 MET cc_start: -0.0609 (mtp) cc_final: -0.0875 (tpt) REVERT: A 797 MET cc_start: 0.0044 (mtt) cc_final: -0.0631 (mpp) REVERT: A 820 ASN cc_start: 0.5300 (t0) cc_final: 0.5026 (t0) REVERT: B 323 TYR cc_start: 0.7411 (t80) cc_final: 0.7211 (t80) REVERT: B 341 MET cc_start: 0.7232 (mtm) cc_final: 0.6699 (mtm) REVERT: B 353 PHE cc_start: 0.6793 (OUTLIER) cc_final: 0.6364 (m-10) REVERT: B 391 MET cc_start: 0.4432 (OUTLIER) cc_final: 0.2110 (ttt) REVERT: B 574 GLU cc_start: 0.7099 (mm-30) cc_final: 0.6210 (mm-30) REVERT: B 633 GLN cc_start: 0.4984 (mt0) cc_final: 0.4721 (mt0) REVERT: B 755 ILE cc_start: 0.6414 (mm) cc_final: 0.5954 (mt) REVERT: B 797 MET cc_start: 0.2239 (mpp) cc_final: 0.1511 (mmt) outliers start: 17 outliers final: 10 residues processed: 143 average time/residue: 0.1668 time to fit residues: 33.2805 Evaluate side-chains 142 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 130 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain B residue 340 GLN Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 373 ARG Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 847 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 0.0050 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 64 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 77 optimal weight: 0.0980 chunk 8 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 47 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 727 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5876 moved from start: 0.5789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7602 Z= 0.209 Angle : 0.761 10.700 10360 Z= 0.392 Chirality : 0.045 0.228 1204 Planarity : 0.005 0.044 1298 Dihedral : 6.335 45.222 1048 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.31 % Allowed : 12.76 % Favored : 86.93 % Rotamer: Outliers : 1.52 % Allowed : 17.08 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.28), residues: 964 helix: 0.60 (0.21), residues: 680 sheet: None (None), residues: 0 loop : -4.58 (0.28), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 427 HIS 0.004 0.001 HIS A 803 PHE 0.030 0.002 PHE A 708 TYR 0.014 0.001 TYR A 338 ARG 0.002 0.000 ARG B 373 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1928 Ramachandran restraints generated. 964 Oldfield, 0 Emsley, 964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 139 time to evaluate : 0.837 Fit side-chains REVERT: A 321 ARG cc_start: 0.5414 (tmt-80) cc_final: 0.3259 (ttm170) REVERT: A 341 MET cc_start: 0.7573 (mtt) cc_final: 0.7136 (mtm) REVERT: A 378 MET cc_start: 0.1907 (ptm) cc_final: 0.1306 (ptp) REVERT: A 391 MET cc_start: 0.4315 (mpp) cc_final: 0.2739 (ttt) REVERT: A 633 GLN cc_start: 0.4998 (mt0) cc_final: 0.4669 (mt0) REVERT: A 702 MET cc_start: 0.7354 (mmm) cc_final: 0.7074 (mmp) REVERT: A 797 MET cc_start: 0.0036 (mtt) cc_final: -0.0358 (mpp) REVERT: A 820 ASN cc_start: 0.5181 (t0) cc_final: 0.4889 (t0) REVERT: B 321 ARG cc_start: 0.5419 (tmt-80) cc_final: 0.3582 (ttm170) REVERT: B 323 TYR cc_start: 0.7447 (t80) cc_final: 0.7231 (t80) REVERT: B 341 MET cc_start: 0.7292 (mtm) cc_final: 0.6755 (mtm) REVERT: B 353 PHE cc_start: 0.6789 (OUTLIER) cc_final: 0.6335 (m-10) REVERT: B 391 MET cc_start: 0.4263 (OUTLIER) cc_final: 0.2063 (ttt) REVERT: B 574 GLU cc_start: 0.7138 (mm-30) cc_final: 0.6281 (mm-30) REVERT: B 633 GLN cc_start: 0.4952 (mt0) cc_final: 0.4682 (mt0) REVERT: B 755 ILE cc_start: 0.6335 (mm) cc_final: 0.5904 (mt) REVERT: B 797 MET cc_start: 0.2184 (mpp) cc_final: 0.1443 (mmt) outliers start: 11 outliers final: 9 residues processed: 140 average time/residue: 0.1668 time to fit residues: 32.6851 Evaluate side-chains 146 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 135 time to evaluate : 0.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 369 MET Chi-restraints excluded: chain A residue 552 VAL Chi-restraints excluded: chain A residue 643 LEU Chi-restraints excluded: chain A residue 782 ILE Chi-restraints excluded: chain B residue 340 GLN Chi-restraints excluded: chain B residue 353 PHE Chi-restraints excluded: chain B residue 378 MET Chi-restraints excluded: chain B residue 391 MET Chi-restraints excluded: chain B residue 552 VAL Chi-restraints excluded: chain B residue 704 ILE Chi-restraints excluded: chain B residue 847 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.0980 chunk 23 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 77 optimal weight: 0.0470 chunk 32 optimal weight: 2.9990 chunk 79 optimal weight: 9.9990 chunk 9 optimal weight: 0.4980 chunk 14 optimal weight: 0.6980 chunk 68 optimal weight: 0.4980 overall best weight: 0.3678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 798 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 727 ASN ** B 802 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 869 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.236826 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.199148 restraints weight = 10329.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.202622 restraints weight = 6971.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.205366 restraints weight = 5517.235| |-----------------------------------------------------------------------------| r_work (final): 0.4598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6024 moved from start: 0.6011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7602 Z= 0.199 Angle : 0.747 10.456 10360 Z= 0.385 Chirality : 0.044 0.243 1204 Planarity : 0.004 0.040 1298 Dihedral : 6.295 48.203 1048 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.21 % Allowed : 12.97 % Favored : 86.83 % Rotamer: Outliers : 2.07 % Allowed : 16.67 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.43 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.28), residues: 964 helix: 0.65 (0.20), residues: 680 sheet: None (None), residues: 0 loop : -4.52 (0.28), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 427 HIS 0.005 0.001 HIS A 803 PHE 0.032 0.002 PHE A 708 TYR 0.011 0.001 TYR A 338 ARG 0.003 0.000 ARG B 373 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1748.41 seconds wall clock time: 32 minutes 17.80 seconds (1937.80 seconds total)