Starting phenix.real_space_refine on Thu Mar 14 13:27:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ct3_26979/03_2024/8ct3_26979_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ct3_26979/03_2024/8ct3_26979.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ct3_26979/03_2024/8ct3_26979_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ct3_26979/03_2024/8ct3_26979_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ct3_26979/03_2024/8ct3_26979_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ct3_26979/03_2024/8ct3_26979.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ct3_26979/03_2024/8ct3_26979.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ct3_26979/03_2024/8ct3_26979_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ct3_26979/03_2024/8ct3_26979_updated.pdb" } resolution = 3.3 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= 0.122 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 P 6 5.49 5 S 38 5.16 5 C 6006 2.51 5 N 1406 2.21 5 O 1508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 112": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 555": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 596": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 608": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 665": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 719": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8964 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 302 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 302 Classifications: {'peptide': 40} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 1, 'TRANS': 38} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4063 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 488} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 4063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4063 Classifications: {'peptide': 517} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PCIS': 1, 'PTRANS': 27, 'TRANS': 488} Chain breaks: 1 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 117 Unusual residues: {'CLR': 2, 'NAG': 1, 'PIO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 117 Unusual residues: {'CLR': 2, 'NAG': 1, 'PIO': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.24, per 1000 atoms: 0.58 Number of scatterers: 8964 At special positions: 0 Unit cell: (145.665, 79.68, 105.41, 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 38 16.00 P 6 15.00 O 1508 8.00 N 1406 7.00 C 6006 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 Links applied NAG-ASN " NAG C1002 " - " ASN C 642 " " NAG E1002 " - " ASN E 642 " Time building additional restraints: 3.40 Conformation dependent library (CDL) restraints added in 1.7 seconds 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2064 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 2 sheets defined 66.9% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.94 Creating SS restraints... Processing helix chain 'B' and resid 89 through 113 Processing helix chain 'D' and resid 89 through 113 Processing helix chain 'C' and resid 380 through 392 Proline residue: C 391 - end of helix Processing helix chain 'C' and resid 395 through 400 removed outlier: 5.119A pdb=" N ALA C 400 " --> pdb=" O ASP C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 430 removed outlier: 3.595A pdb=" N PHE C 414 " --> pdb=" O ILE C 410 " (cutoff:3.500A) Proline residue: C 419 - end of helix Processing helix chain 'C' and resid 437 through 454 Processing helix chain 'C' and resid 466 through 482 Processing helix chain 'C' and resid 486 through 506 removed outlier: 3.653A pdb=" N LEU C 499 " --> pdb=" O PHE C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 515 Processing helix chain 'C' and resid 518 through 546 removed outlier: 3.541A pdb=" N LEU C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 593 removed outlier: 3.551A pdb=" N ASN C 593 " --> pdb=" O ARG C 589 " (cutoff:3.500A) Processing helix chain 'C' and resid 599 through 607 Processing helix chain 'C' and resid 609 through 622 Processing helix chain 'C' and resid 661 through 689 removed outlier: 3.730A pdb=" N PHE C 665 " --> pdb=" O ILE C 661 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N ALA C 668 " --> pdb=" O MET C 664 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU C 669 " --> pdb=" O PHE C 665 " (cutoff:3.500A) Proline residue: C 670 - end of helix Processing helix chain 'C' and resid 692 through 694 No H-bonds generated for 'chain 'C' and resid 692 through 694' Processing helix chain 'C' and resid 702 through 718 removed outlier: 3.524A pdb=" N LEU C 718 " --> pdb=" O GLY C 714 " (cutoff:3.500A) Processing helix chain 'C' and resid 728 through 737 Processing helix chain 'C' and resid 761 through 773 Processing helix chain 'C' and resid 777 through 782 removed outlier: 4.107A pdb=" N ARG C 782 " --> pdb=" O PRO C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 800 removed outlier: 4.008A pdb=" N LEU C 800 " --> pdb=" O GLY C 796 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 813 removed outlier: 4.159A pdb=" N PHE C 813 " --> pdb=" O ILE C 809 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 818 No H-bonds generated for 'chain 'C' and resid 816 through 818' Processing helix chain 'C' and resid 823 through 826 No H-bonds generated for 'chain 'C' and resid 823 through 826' Processing helix chain 'C' and resid 830 through 851 Processing helix chain 'C' and resid 856 through 871 Proline residue: C 860 - end of helix Proline residue: C 868 - end of helix Processing helix chain 'C' and resid 873 through 877 removed outlier: 3.803A pdb=" N ILE C 877 " --> pdb=" O LEU C 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 873 through 877' Processing helix chain 'C' and resid 880 through 886 Processing helix chain 'E' and resid 380 through 393 Proline residue: E 391 - end of helix Processing helix chain 'E' and resid 395 through 400 removed outlier: 5.118A pdb=" N ALA E 400 " --> pdb=" O ASP E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 430 removed outlier: 3.596A pdb=" N PHE E 414 " --> pdb=" O ILE E 410 " (cutoff:3.500A) Proline residue: E 419 - end of helix Processing helix chain 'E' and resid 437 through 454 Processing helix chain 'E' and resid 466 through 482 Processing helix chain 'E' and resid 486 through 506 removed outlier: 3.653A pdb=" N LEU E 499 " --> pdb=" O PHE E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 515 Processing helix chain 'E' and resid 518 through 546 removed outlier: 3.542A pdb=" N LEU E 540 " --> pdb=" O THR E 536 " (cutoff:3.500A) Processing helix chain 'E' and resid 570 through 593 removed outlier: 3.552A pdb=" N ASN E 593 " --> pdb=" O ARG E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 607 Processing helix chain 'E' and resid 609 through 622 Processing helix chain 'E' and resid 661 through 689 removed outlier: 3.730A pdb=" N PHE E 665 " --> pdb=" O ILE E 661 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ALA E 668 " --> pdb=" O MET E 664 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU E 669 " --> pdb=" O PHE E 665 " (cutoff:3.500A) Proline residue: E 670 - end of helix Processing helix chain 'E' and resid 692 through 694 No H-bonds generated for 'chain 'E' and resid 692 through 694' Processing helix chain 'E' and resid 702 through 718 removed outlier: 3.525A pdb=" N LEU E 718 " --> pdb=" O GLY E 714 " (cutoff:3.500A) Processing helix chain 'E' and resid 728 through 737 Processing helix chain 'E' and resid 761 through 773 Processing helix chain 'E' and resid 777 through 782 removed outlier: 4.107A pdb=" N ARG E 782 " --> pdb=" O PRO E 778 " (cutoff:3.500A) Processing helix chain 'E' and resid 785 through 800 removed outlier: 4.009A pdb=" N LEU E 800 " --> pdb=" O GLY E 796 " (cutoff:3.500A) Processing helix chain 'E' and resid 804 through 813 removed outlier: 4.160A pdb=" N PHE E 813 " --> pdb=" O ILE E 809 " (cutoff:3.500A) Processing helix chain 'E' and resid 816 through 818 No H-bonds generated for 'chain 'E' and resid 816 through 818' Processing helix chain 'E' and resid 823 through 826 No H-bonds generated for 'chain 'E' and resid 823 through 826' Processing helix chain 'E' and resid 830 through 851 Processing helix chain 'E' and resid 856 through 871 Proline residue: E 860 - end of helix Proline residue: E 868 - end of helix Processing helix chain 'E' and resid 873 through 877 removed outlier: 3.804A pdb=" N ILE E 877 " --> pdb=" O LEU E 873 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 873 through 877' Processing helix chain 'E' and resid 880 through 886 Processing sheet with id= A, first strand: chain 'C' and resid 739 through 742 removed outlier: 5.439A pdb=" N GLY C 742 " --> pdb=" O ILE C 753 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE C 753 " --> pdb=" O GLY C 742 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'E' and resid 739 through 742 removed outlier: 5.439A pdb=" N GLY E 742 " --> pdb=" O ILE E 753 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE E 753 " --> pdb=" O GLY E 742 " (cutoff:3.500A) 494 hydrogen bonds defined for protein. 1416 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: 2.33 Time building geometry restraints manager: 3.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1308 1.31 - 1.43: 2420 1.43 - 1.56: 5386 1.56 - 1.68: 8 1.68 - 1.81: 70 Bond restraints: 9192 Sorted by residual: bond pdb=" C1 NAG C1002 " pdb=" O5 NAG C1002 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.39e+00 bond pdb=" C1 NAG E1002 " pdb=" O5 NAG E1002 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.29e+00 bond pdb=" C5 NAG E1002 " pdb=" O5 NAG E1002 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.30e+00 bond pdb=" C5 NAG C1002 " pdb=" O5 NAG C1002 " ideal model delta sigma weight residual 1.413 1.435 -0.022 2.00e-02 2.50e+03 1.26e+00 bond pdb=" C3 NAG E1002 " pdb=" O3 NAG E1002 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 1.04e+00 ... (remaining 9187 not shown) Histogram of bond angle deviations from ideal: 98.99 - 105.99: 285 105.99 - 112.98: 5125 112.98 - 119.97: 3087 119.97 - 126.97: 3911 126.97 - 133.96: 112 Bond angle restraints: 12520 Sorted by residual: angle pdb=" C THR E 866 " pdb=" N VAL E 867 " pdb=" CA VAL E 867 " ideal model delta sigma weight residual 120.33 122.56 -2.23 8.00e-01 1.56e+00 7.74e+00 angle pdb=" C THR C 866 " pdb=" N VAL C 867 " pdb=" CA VAL C 867 " ideal model delta sigma weight residual 120.33 122.52 -2.19 8.00e-01 1.56e+00 7.51e+00 angle pdb=" C ARG E 389 " pdb=" N TYR E 390 " pdb=" CA TYR E 390 " ideal model delta sigma weight residual 120.06 122.58 -2.52 1.19e+00 7.06e-01 4.49e+00 angle pdb=" C ARG C 389 " pdb=" N TYR C 390 " pdb=" CA TYR C 390 " ideal model delta sigma weight residual 120.06 122.57 -2.51 1.19e+00 7.06e-01 4.43e+00 angle pdb=" C TYR C 596 " pdb=" N PHE C 597 " pdb=" CA PHE C 597 " ideal model delta sigma weight residual 121.80 126.79 -4.99 2.44e+00 1.68e-01 4.18e+00 ... (remaining 12515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 5348 17.60 - 35.20: 184 35.20 - 52.80: 62 52.80 - 70.40: 16 70.40 - 88.00: 8 Dihedral angle restraints: 5618 sinusoidal: 2416 harmonic: 3202 Sorted by residual: dihedral pdb=" CB MET E 587 " pdb=" CG MET E 587 " pdb=" SD MET E 587 " pdb=" CE MET E 587 " ideal model delta sinusoidal sigma weight residual 60.00 108.67 -48.67 3 1.50e+01 4.44e-03 8.67e+00 dihedral pdb=" CB MET C 587 " pdb=" CG MET C 587 " pdb=" SD MET C 587 " pdb=" CE MET C 587 " ideal model delta sinusoidal sigma weight residual 60.00 108.63 -48.63 3 1.50e+01 4.44e-03 8.67e+00 dihedral pdb=" N GLU C 473 " pdb=" CA GLU C 473 " pdb=" CB GLU C 473 " pdb=" CG GLU C 473 " ideal model delta sinusoidal sigma weight residual -60.00 -108.31 48.31 3 1.50e+01 4.44e-03 8.62e+00 ... (remaining 5615 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 884 0.024 - 0.048: 307 0.048 - 0.072: 208 0.072 - 0.096: 54 0.096 - 0.119: 57 Chirality restraints: 1510 Sorted by residual: chirality pdb=" CA ILE C 783 " pdb=" N ILE C 783 " pdb=" C ILE C 783 " pdb=" CB ILE C 783 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.56e-01 chirality pdb=" CA ILE C 516 " pdb=" N ILE C 516 " pdb=" C ILE C 516 " pdb=" CB ILE C 516 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.49e-01 chirality pdb=" CA VAL C 828 " pdb=" N VAL C 828 " pdb=" C VAL C 828 " pdb=" CB VAL C 828 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.48e-01 ... (remaining 1507 not shown) Planarity restraints: 1494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 390 " -0.039 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO C 391 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 391 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 391 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 390 " 0.039 5.00e-02 4.00e+02 5.83e-02 5.43e+00 pdb=" N PRO E 391 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO E 391 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 391 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 466 " -0.029 5.00e-02 4.00e+02 4.40e-02 3.10e+00 pdb=" N PRO C 467 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 467 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 467 " -0.025 5.00e-02 4.00e+02 ... (remaining 1491 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 979 2.75 - 3.29: 9147 3.29 - 3.83: 15334 3.83 - 4.36: 17910 4.36 - 4.90: 30950 Nonbonded interactions: 74320 Sorted by model distance: nonbonded pdb=" OE1 GLU C 472 " pdb=" OH TYR C 486 " model vdw 2.215 2.440 nonbonded pdb=" OE1 GLU E 472 " pdb=" OH TYR E 486 " model vdw 2.216 2.440 nonbonded pdb=" O LEU C 427 " pdb=" OG1 THR C 431 " model vdw 2.271 2.440 nonbonded pdb=" O LEU E 427 " pdb=" OG1 THR E 431 " model vdw 2.271 2.440 nonbonded pdb=" OG1 THR E 375 " pdb=" OE2 GLU E 508 " model vdw 2.279 2.440 ... (remaining 74315 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 'B' selection = chain 'D' } ncs_group { reference = chain 'C' selection = chain 'E' } 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 individual isotropic 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: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 13.980 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 27.610 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.050 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6985 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 : 0.002 0.031 9192 Z= 0.139 Angle : 0.482 5.552 12520 Z= 0.263 Chirality : 0.039 0.119 1510 Planarity : 0.005 0.058 1492 Dihedral : 11.155 87.999 3554 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 0.63 % Allowed : 3.37 % Favored : 96.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.87 (0.25), residues: 1102 helix: 1.71 (0.18), residues: 766 sheet: None (None), residues: 0 loop : 0.28 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 831 HIS 0.002 0.000 HIS C 734 PHE 0.008 0.001 PHE C 471 TYR 0.010 0.001 TYR E 519 ARG 0.001 0.000 ARG C 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 148 time to evaluate : 0.943 Fit side-chains revert: symmetry clash REVERT: D 100 MET cc_start: 0.4256 (ttm) cc_final: 0.3126 (tmm) REVERT: C 533 ILE cc_start: 0.7454 (mt) cc_final: 0.7233 (mt) REVERT: C 551 LYS cc_start: 0.5378 (tttt) cc_final: 0.4853 (mttt) REVERT: C 639 LYS cc_start: 0.5814 (pttp) cc_final: 0.5580 (pttt) REVERT: E 646 ARG cc_start: 0.6585 (OUTLIER) cc_final: 0.4799 (ppp80) outliers start: 6 outliers final: 3 residues processed: 154 average time/residue: 0.2335 time to fit residues: 48.4190 Evaluate side-chains 122 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain E residue 646 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 92 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 86 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 0.0060 chunk 64 optimal weight: 4.9990 chunk 99 optimal weight: 5.9990 overall best weight: 2.3402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 377 GLN C 457 GLN C 630 GLN C 651 HIS C 683 GLN E 377 GLN E 630 GLN E 683 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 9192 Z= 0.311 Angle : 0.618 7.563 12520 Z= 0.304 Chirality : 0.045 0.159 1510 Planarity : 0.005 0.050 1492 Dihedral : 9.928 77.370 1555 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer: Outliers : 2.53 % Allowed : 5.47 % Favored : 92.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.25), residues: 1102 helix: 1.38 (0.18), residues: 748 sheet: None (None), residues: 0 loop : 0.27 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 492 HIS 0.007 0.001 HIS C 734 PHE 0.019 0.002 PHE E 532 TYR 0.029 0.003 TYR E 519 ARG 0.005 0.001 ARG E 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 145 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: C 551 LYS cc_start: 0.5590 (tttt) cc_final: 0.4982 (mttt) REVERT: C 782 ARG cc_start: 0.6785 (mtp85) cc_final: 0.6523 (mtp180) REVERT: E 646 ARG cc_start: 0.7002 (OUTLIER) cc_final: 0.5195 (ppp80) REVERT: E 839 ILE cc_start: 0.7469 (tp) cc_final: 0.7224 (mt) outliers start: 24 outliers final: 19 residues processed: 160 average time/residue: 0.1933 time to fit residues: 43.8764 Evaluate side-chains 152 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 132 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 498 ILE Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain E residue 378 LEU Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 551 LYS Chi-restraints excluded: chain E residue 593 ASN Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 761 ILE Chi-restraints excluded: chain E residue 842 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 5.9990 chunk 31 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 89 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 34 optimal weight: 0.0570 chunk 80 optimal weight: 0.7980 overall best weight: 0.6700 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 819 HIS E 433 ASN E 457 GLN E 819 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9192 Z= 0.141 Angle : 0.472 8.150 12520 Z= 0.229 Chirality : 0.040 0.205 1510 Planarity : 0.004 0.048 1492 Dihedral : 9.404 77.965 1554 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 2.53 % Allowed : 8.42 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.25), residues: 1102 helix: 1.82 (0.19), residues: 748 sheet: None (None), residues: 0 loop : 0.23 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 848 HIS 0.002 0.000 HIS C 651 PHE 0.023 0.001 PHE C 511 TYR 0.016 0.001 TYR E 519 ARG 0.002 0.000 ARG C 760 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 0.905 Fit side-chains revert: symmetry clash REVERT: C 551 LYS cc_start: 0.5492 (tttt) cc_final: 0.4927 (mttt) REVERT: C 639 LYS cc_start: 0.5936 (pttp) cc_final: 0.5708 (pttt) REVERT: C 782 ARG cc_start: 0.6730 (mtp85) cc_final: 0.6526 (mtp180) REVERT: E 426 LEU cc_start: 0.7198 (OUTLIER) cc_final: 0.6666 (mp) REVERT: E 646 ARG cc_start: 0.6908 (OUTLIER) cc_final: 0.5132 (ppp80) REVERT: E 700 SER cc_start: 0.8013 (p) cc_final: 0.7630 (m) outliers start: 24 outliers final: 17 residues processed: 146 average time/residue: 0.1997 time to fit residues: 41.0634 Evaluate side-chains 144 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 551 LYS Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 639 LYS Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 812 LEU Chi-restraints excluded: chain E residue 841 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 47 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 0.5980 chunk 52 optimal weight: 6.9990 chunk 95 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 GLN E 457 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9192 Z= 0.192 Angle : 0.505 5.428 12520 Z= 0.246 Chirality : 0.041 0.149 1510 Planarity : 0.004 0.045 1492 Dihedral : 9.193 80.906 1552 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 2.95 % Allowed : 10.53 % Favored : 86.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.25), residues: 1102 helix: 1.73 (0.19), residues: 746 sheet: None (None), residues: 0 loop : 0.13 (0.33), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 492 HIS 0.003 0.001 HIS C 651 PHE 0.014 0.001 PHE C 836 TYR 0.019 0.002 TYR E 519 ARG 0.002 0.000 ARG C 589 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 141 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: C 551 LYS cc_start: 0.5534 (tttt) cc_final: 0.4904 (mttt) REVERT: C 553 TYR cc_start: 0.7595 (m-80) cc_final: 0.6871 (m-80) REVERT: C 639 LYS cc_start: 0.6050 (pttp) cc_final: 0.5803 (pttt) REVERT: C 782 ARG cc_start: 0.6809 (mtp85) cc_final: 0.6550 (mtp180) REVERT: E 426 LEU cc_start: 0.7266 (OUTLIER) cc_final: 0.6752 (mp) REVERT: E 646 ARG cc_start: 0.7023 (OUTLIER) cc_final: 0.5193 (ppp80) outliers start: 28 outliers final: 20 residues processed: 157 average time/residue: 0.2069 time to fit residues: 45.3060 Evaluate side-chains 160 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 138 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 877 ILE Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 551 LYS Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 798 THR Chi-restraints excluded: chain E residue 812 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.6980 chunk 60 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 73 optimal weight: 0.7980 chunk 0 optimal weight: 30.0000 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 457 GLN E 736 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.3521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 9192 Z= 0.265 Angle : 0.581 11.990 12520 Z= 0.280 Chirality : 0.043 0.172 1510 Planarity : 0.005 0.042 1492 Dihedral : 9.323 84.034 1552 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.26 % Allowed : 10.74 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.25), residues: 1102 helix: 1.36 (0.19), residues: 746 sheet: None (None), residues: 0 loop : -0.16 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 492 HIS 0.006 0.001 HIS C 651 PHE 0.017 0.002 PHE C 476 TYR 0.025 0.002 TYR E 519 ARG 0.004 0.000 ARG E 832 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 149 time to evaluate : 0.983 Fit side-chains revert: symmetry clash REVERT: C 553 TYR cc_start: 0.7650 (m-80) cc_final: 0.7175 (m-80) REVERT: C 782 ARG cc_start: 0.6926 (mtp85) cc_final: 0.6688 (mtp180) REVERT: E 426 LEU cc_start: 0.7339 (OUTLIER) cc_final: 0.6863 (mp) REVERT: E 646 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.5206 (ppp80) outliers start: 31 outliers final: 23 residues processed: 168 average time/residue: 0.2058 time to fit residues: 47.8690 Evaluate side-chains 164 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 139 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 877 ILE Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 551 LYS Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 731 SER Chi-restraints excluded: chain E residue 798 THR Chi-restraints excluded: chain E residue 812 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 21 optimal weight: 7.9990 chunk 62 optimal weight: 0.9990 chunk 26 optimal weight: 0.6980 chunk 106 optimal weight: 0.5980 chunk 88 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 457 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.079 9192 Z= 0.157 Angle : 0.495 9.360 12520 Z= 0.239 Chirality : 0.040 0.137 1510 Planarity : 0.004 0.043 1492 Dihedral : 8.832 83.702 1552 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.74 % Allowed : 12.21 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.25), residues: 1102 helix: 1.65 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -0.10 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 831 HIS 0.002 0.000 HIS C 651 PHE 0.017 0.001 PHE C 511 TYR 0.014 0.001 TYR E 519 ARG 0.002 0.000 ARG C 871 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 138 time to evaluate : 0.981 Fit side-chains revert: symmetry clash REVERT: C 553 TYR cc_start: 0.7658 (m-80) cc_final: 0.7264 (m-80) REVERT: C 782 ARG cc_start: 0.6874 (mtp85) cc_final: 0.6614 (mtp180) REVERT: E 426 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6824 (mp) REVERT: E 646 ARG cc_start: 0.7096 (OUTLIER) cc_final: 0.5222 (ppp80) outliers start: 26 outliers final: 21 residues processed: 154 average time/residue: 0.2059 time to fit residues: 44.7460 Evaluate side-chains 159 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 877 ILE Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 543 ILE Chi-restraints excluded: chain E residue 551 LYS Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 639 LYS Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 812 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 77 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 59 optimal weight: 9.9990 chunk 106 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 0.2980 chunk 65 optimal weight: 0.7980 chunk 42 optimal weight: 5.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 457 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7438 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9192 Z= 0.258 Angle : 0.563 8.584 12520 Z= 0.272 Chirality : 0.043 0.188 1510 Planarity : 0.004 0.041 1492 Dihedral : 8.880 85.824 1548 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 3.37 % Allowed : 11.26 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.25), residues: 1102 helix: 1.37 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -0.29 (0.31), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 492 HIS 0.004 0.001 HIS E 651 PHE 0.022 0.002 PHE C 476 TYR 0.022 0.002 TYR E 519 ARG 0.003 0.000 ARG E 832 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 133 time to evaluate : 0.972 Fit side-chains REVERT: C 553 TYR cc_start: 0.7682 (m-80) cc_final: 0.7348 (m-80) REVERT: C 782 ARG cc_start: 0.6961 (mtp85) cc_final: 0.6751 (mtp180) REVERT: E 426 LEU cc_start: 0.7324 (OUTLIER) cc_final: 0.6857 (mp) REVERT: E 646 ARG cc_start: 0.7216 (OUTLIER) cc_final: 0.5210 (ppp80) REVERT: E 700 SER cc_start: 0.8172 (OUTLIER) cc_final: 0.7850 (m) outliers start: 32 outliers final: 25 residues processed: 151 average time/residue: 0.2025 time to fit residues: 42.7582 Evaluate side-chains 163 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 135 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 877 ILE Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 551 LYS Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 700 SER Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 731 SER Chi-restraints excluded: chain E residue 812 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 67 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 0.3980 chunk 9 optimal weight: 4.9990 chunk 83 optimal weight: 0.7980 chunk 96 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 457 GLN E 736 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.052 9192 Z= 0.152 Angle : 0.495 8.370 12520 Z= 0.236 Chirality : 0.040 0.158 1510 Planarity : 0.004 0.042 1492 Dihedral : 8.445 84.884 1548 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.84 % Allowed : 12.11 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.25), residues: 1102 helix: 1.71 (0.19), residues: 750 sheet: None (None), residues: 0 loop : -0.09 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 831 HIS 0.003 0.001 HIS C 834 PHE 0.022 0.001 PHE C 476 TYR 0.013 0.001 TYR E 519 ARG 0.002 0.000 ARG C 490 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 132 time to evaluate : 0.870 Fit side-chains revert: symmetry clash REVERT: C 553 TYR cc_start: 0.7681 (m-80) cc_final: 0.7331 (m-80) REVERT: C 765 LEU cc_start: 0.8801 (mp) cc_final: 0.8598 (mt) REVERT: C 782 ARG cc_start: 0.6925 (mtp85) cc_final: 0.6720 (mtp180) REVERT: E 426 LEU cc_start: 0.7279 (OUTLIER) cc_final: 0.6825 (mp) REVERT: E 646 ARG cc_start: 0.7124 (OUTLIER) cc_final: 0.5231 (ppp80) outliers start: 27 outliers final: 22 residues processed: 149 average time/residue: 0.1999 time to fit residues: 42.2943 Evaluate side-chains 156 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 132 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain C residue 877 ILE Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 435 MET Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 551 LYS Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 657 SER Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 731 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 6.9990 chunk 101 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 30 optimal weight: 0.0980 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 64 optimal weight: 5.9990 chunk 104 optimal weight: 8.9990 chunk 63 optimal weight: 0.5980 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 457 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 9192 Z= 0.146 Angle : 0.488 8.175 12520 Z= 0.232 Chirality : 0.040 0.161 1510 Planarity : 0.004 0.040 1492 Dihedral : 8.174 84.371 1548 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.63 % Allowed : 12.84 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.25), residues: 1102 helix: 1.81 (0.19), residues: 752 sheet: None (None), residues: 0 loop : -0.05 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 831 HIS 0.004 0.001 HIS C 834 PHE 0.021 0.001 PHE C 476 TYR 0.012 0.001 TYR E 519 ARG 0.002 0.000 ARG E 808 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 137 time to evaluate : 0.897 Fit side-chains revert: symmetry clash REVERT: C 553 TYR cc_start: 0.7675 (m-80) cc_final: 0.7295 (m-80) REVERT: C 693 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7124 (pt0) REVERT: E 426 LEU cc_start: 0.7255 (OUTLIER) cc_final: 0.6813 (mp) REVERT: E 646 ARG cc_start: 0.7090 (OUTLIER) cc_final: 0.5220 (ppp80) outliers start: 25 outliers final: 20 residues processed: 153 average time/residue: 0.2079 time to fit residues: 44.5619 Evaluate side-chains 159 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 731 SER Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 551 LYS Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 639 LYS Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 729 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 49 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 109 optimal weight: 0.0970 chunk 100 optimal weight: 0.9990 chunk 87 optimal weight: 0.0000 chunk 9 optimal weight: 5.9990 chunk 67 optimal weight: 0.6980 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 92 optimal weight: 2.9990 chunk 26 optimal weight: 8.9990 overall best weight: 0.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 457 GLN E 521 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9192 Z= 0.136 Angle : 0.485 8.799 12520 Z= 0.229 Chirality : 0.039 0.157 1510 Planarity : 0.004 0.039 1492 Dihedral : 7.983 83.701 1548 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.53 % Allowed : 12.95 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.25), residues: 1102 helix: 1.86 (0.19), residues: 756 sheet: None (None), residues: 0 loop : 0.01 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 831 HIS 0.002 0.000 HIS C 834 PHE 0.019 0.001 PHE C 476 TYR 0.010 0.001 TYR E 519 ARG 0.001 0.000 ARG E 389 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2204 Ramachandran restraints generated. 1102 Oldfield, 0 Emsley, 1102 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 0.877 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 553 TYR cc_start: 0.7683 (m-80) cc_final: 0.7232 (m-80) REVERT: C 693 GLU cc_start: 0.7437 (OUTLIER) cc_final: 0.7109 (pt0) REVERT: E 426 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.6787 (mp) REVERT: E 646 ARG cc_start: 0.7099 (OUTLIER) cc_final: 0.5293 (ppp80) outliers start: 24 outliers final: 18 residues processed: 149 average time/residue: 0.2044 time to fit residues: 42.8998 Evaluate side-chains 154 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 133 time to evaluate : 0.763 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 107 ILE Chi-restraints excluded: chain D residue 108 LEU Chi-restraints excluded: chain C residue 462 VAL Chi-restraints excluded: chain C residue 500 LEU Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 640 VAL Chi-restraints excluded: chain C residue 644 SER Chi-restraints excluded: chain C residue 673 LEU Chi-restraints excluded: chain C residue 680 LEU Chi-restraints excluded: chain C residue 693 GLU Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 864 ILE Chi-restraints excluded: chain E residue 426 LEU Chi-restraints excluded: chain E residue 528 ILE Chi-restraints excluded: chain E residue 551 LYS Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 595 SER Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 680 LEU Chi-restraints excluded: chain E residue 729 VAL Chi-restraints excluded: chain E residue 731 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 2.9990 chunk 12 optimal weight: 0.0570 chunk 24 optimal weight: 0.2980 chunk 87 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 89 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 overall best weight: 0.4898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 457 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.171325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.148229 restraints weight = 10022.857| |-----------------------------------------------------------------------------| r_work (start): 0.3605 rms_B_bonded: 1.33 r_work: 0.3501 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 9192 Z= 0.132 Angle : 0.478 8.102 12520 Z= 0.226 Chirality : 0.039 0.150 1510 Planarity : 0.004 0.039 1492 Dihedral : 7.854 83.354 1548 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.63 % Allowed : 12.74 % Favored : 84.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 2.00 (0.25), residues: 1102 helix: 1.92 (0.19), residues: 756 sheet: None (None), residues: 0 loop : 0.08 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 831 HIS 0.003 0.000 HIS C 834 PHE 0.018 0.001 PHE C 476 TYR 0.010 0.001 TYR E 519 ARG 0.001 0.000 ARG E 432 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2653.22 seconds wall clock time: 47 minutes 51.31 seconds (2871.31 seconds total)