Starting phenix.real_space_refine on Wed Feb 14 08:40:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v19_26954/02_2024/7v19_26954_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v19_26954/02_2024/7v19_26954.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v19_26954/02_2024/7v19_26954_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/7v19_26954/02_2024/7v19_26954_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v19_26954/02_2024/7v19_26954_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v19_26954/02_2024/7v19_26954.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v19_26954/02_2024/7v19_26954.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v19_26954/02_2024/7v19_26954_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7v19_26954/02_2024/7v19_26954_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= 0.109 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 5968 2.51 5 N 1408 2.21 5 O 1516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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 TYR 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 824": "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 638": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 679": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 813": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 824": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 836": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 861": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8936 Number of models: 1 Model: "" Number of chains: 8 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: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "C" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'CLR': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 75 Unusual residues: {'CLR': 1, 'PIO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.50, per 1000 atoms: 0.62 Number of scatterers: 8936 At special positions: 0 Unit cell: (146.495, 91.3, 80.925, 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 1516 8.00 N 1408 7.00 C 5968 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 BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG F 1 " - " NAG F 2 " NAG-ASN " NAG A 1 " - " ASN C 642 " " NAG F 1 " - " ASN E 642 " Time building additional restraints: 3.67 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 3 sheets defined 66.1% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.82 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: 5.051A pdb=" N ALA C 400 " --> pdb=" O ASP C 396 " (cutoff:3.500A) Processing helix chain 'C' and resid 403 through 430 removed outlier: 3.758A 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: 3.596A pdb=" N LEU C 499 " --> pdb=" O PHE C 495 " (cutoff:3.500A) Processing helix chain 'C' and resid 509 through 515 removed outlier: 3.599A pdb=" N LEU C 512 " --> pdb=" O GLY C 509 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL C 513 " --> pdb=" O SER C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 518 through 546 removed outlier: 3.533A pdb=" N LEU C 540 " --> pdb=" O THR C 536 " (cutoff:3.500A) Processing helix chain 'C' and resid 570 through 593 removed outlier: 3.765A 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: 3.788A pdb=" N PHE C 665 " --> pdb=" O ILE C 661 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ALA C 668 " --> pdb=" O MET C 664 " (cutoff:3.500A) removed outlier: 5.200A 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 704 through 718 removed outlier: 3.533A 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: 4.441A pdb=" N ARG C 782 " --> pdb=" O PRO C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 785 through 798 Processing helix chain 'C' and resid 804 through 813 removed outlier: 4.184A 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 874 through 876 No H-bonds generated for 'chain 'C' and resid 874 through 876' 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: 5.357A pdb=" N ALA E 400 " --> pdb=" O ASP E 396 " (cutoff:3.500A) Processing helix chain 'E' and resid 403 through 430 removed outlier: 3.680A 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 481 Processing helix chain 'E' and resid 486 through 506 removed outlier: 3.789A pdb=" N LEU E 499 " --> pdb=" O PHE E 495 " (cutoff:3.500A) Processing helix chain 'E' and resid 509 through 515 removed outlier: 3.508A pdb=" N LEU E 512 " --> pdb=" O GLY E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 546 Processing helix chain 'E' and resid 570 through 593 removed outlier: 3.728A 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: 3.746A pdb=" N PHE E 665 " --> pdb=" O ILE E 661 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N ALA E 668 " --> pdb=" O MET E 664 " (cutoff:3.500A) removed outlier: 5.504A 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: 3.772A 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: 4.193A pdb=" N ARG E 782 " --> pdb=" O PRO E 778 " (cutoff:3.500A) Processing helix chain 'E' and resid 785 through 800 removed outlier: 3.954A pdb=" N LEU E 800 " --> pdb=" O GLY E 796 " (cutoff:3.500A) Processing helix chain 'E' and resid 804 through 813 removed outlier: 3.502A pdb=" N LEU E 812 " --> pdb=" O ARG E 808 " (cutoff:3.500A) removed outlier: 4.158A 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 874 through 876 No H-bonds generated for 'chain 'E' and resid 874 through 876' Processing helix chain 'E' and resid 880 through 886 Processing sheet with id= A, first strand: chain 'C' and resid 461 through 463 removed outlier: 4.979A pdb=" N VAL C 461 " --> pdb=" O THR C 727 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 739 through 741 Processing sheet with id= C, first strand: chain 'E' and resid 739 through 741 490 hydrogen bonds defined for protein. 1410 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: 2.63 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1310 1.31 - 1.43: 2442 1.43 - 1.56: 5328 1.56 - 1.68: 8 1.68 - 1.81: 70 Bond restraints: 9158 Sorted by residual: bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.434 -0.028 2.00e-02 2.50e+03 1.91e+00 bond pdb=" C1 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.406 1.433 -0.027 2.00e-02 2.50e+03 1.88e+00 bond pdb=" C5 NAG F 1 " pdb=" O5 NAG F 1 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.29e+00 bond pdb=" C5 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.28e+00 bond pdb=" C VAL E 867 " pdb=" N PRO E 868 " ideal model delta sigma weight residual 1.335 1.348 -0.013 1.28e-02 6.10e+03 1.09e+00 ... (remaining 9153 not shown) Histogram of bond angle deviations from ideal: 98.67 - 105.73: 270 105.73 - 112.79: 5031 112.79 - 119.84: 2834 119.84 - 126.90: 4210 126.90 - 133.95: 117 Bond angle restraints: 12462 Sorted by residual: angle pdb=" C ARG E 389 " pdb=" N TYR E 390 " pdb=" CA TYR E 390 " ideal model delta sigma weight residual 120.06 123.35 -3.29 1.19e+00 7.06e-01 7.63e+00 angle pdb=" C ARG C 389 " pdb=" N TYR C 390 " pdb=" CA TYR C 390 " ideal model delta sigma weight residual 120.06 123.03 -2.97 1.19e+00 7.06e-01 6.21e+00 angle pdb=" C THR E 866 " pdb=" N VAL E 867 " pdb=" CA VAL E 867 " ideal model delta sigma weight residual 120.33 122.22 -1.89 8.00e-01 1.56e+00 5.61e+00 angle pdb=" N ASN E 569 " pdb=" CA ASN E 569 " pdb=" CB ASN E 569 " ideal model delta sigma weight residual 113.65 110.40 3.25 1.47e+00 4.63e-01 4.88e+00 angle pdb=" C TYR E 596 " pdb=" N PHE E 597 " pdb=" CA PHE E 597 " ideal model delta sigma weight residual 121.80 126.59 -4.79 2.44e+00 1.68e-01 3.85e+00 ... (remaining 12457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.14: 5282 21.14 - 42.28: 176 42.28 - 63.42: 40 63.42 - 84.56: 9 84.56 - 105.70: 23 Dihedral angle restraints: 5530 sinusoidal: 2328 harmonic: 3202 Sorted by residual: dihedral pdb=" C2 NAG F 2 " pdb=" C3 NAG F 2 " pdb=" C4 NAG F 2 " pdb=" C5 NAG F 2 " ideal model delta sinusoidal sigma weight residual 53.78 -51.92 105.70 1 3.00e+01 1.11e-03 1.36e+01 dihedral pdb=" C2 NAG F 2 " pdb=" C3 NAG F 2 " pdb=" C4 NAG F 2 " pdb=" O4 NAG F 2 " ideal model delta sinusoidal sigma weight residual 175.11 69.94 105.17 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" C2 NAG A 2 " pdb=" C3 NAG A 2 " pdb=" C4 NAG A 2 " pdb=" C5 NAG A 2 " ideal model delta sinusoidal sigma weight residual 53.78 -51.33 105.11 1 3.00e+01 1.11e-03 1.34e+01 ... (remaining 5527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 891 0.025 - 0.050: 333 0.050 - 0.075: 175 0.075 - 0.101: 65 0.101 - 0.126: 40 Chirality restraints: 1504 Sorted by residual: chirality pdb=" C1 NAG F 2 " pdb=" O4 NAG F 1 " pdb=" C2 NAG F 2 " pdb=" O5 NAG F 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.38 -0.02 2.00e-02 2.50e+03 6.21e-01 chirality pdb=" CA ILE E 516 " pdb=" N ILE E 516 " pdb=" C ILE E 516 " pdb=" CB ILE E 516 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.95e-01 chirality pdb=" CA VAL E 828 " pdb=" N VAL E 828 " pdb=" C VAL E 828 " pdb=" CB VAL E 828 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.71e-01 ... (remaining 1501 not shown) Planarity restraints: 1496 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR C 390 " -0.041 5.00e-02 4.00e+02 6.19e-02 6.14e+00 pdb=" N PRO C 391 " 0.107 5.00e-02 4.00e+02 pdb=" CA PRO C 391 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO C 391 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR E 390 " 0.040 5.00e-02 4.00e+02 6.09e-02 5.93e+00 pdb=" N PRO E 391 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO E 391 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO E 391 " 0.034 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 4.44e-02 3.16e+00 pdb=" N PRO C 467 " 0.077 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 1493 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 350 2.73 - 3.27: 9212 3.27 - 3.81: 15154 3.81 - 4.36: 18328 4.36 - 4.90: 31139 Nonbonded interactions: 74183 Sorted by model distance: nonbonded pdb=" OE1 GLU C 472 " pdb=" OH TYR C 486 " model vdw 2.186 2.440 nonbonded pdb=" OE1 GLU E 472 " pdb=" OH TYR E 486 " model vdw 2.228 2.440 nonbonded pdb=" O VAL C 850 " pdb=" OG1 THR C 853 " model vdw 2.283 2.440 nonbonded pdb=" O LEU C 427 " pdb=" OG1 THR C 431 " model vdw 2.287 2.440 nonbonded pdb=" O LEU E 427 " pdb=" OG1 THR E 431 " model vdw 2.324 2.440 ... (remaining 74178 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 'F' } 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: 3.230 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: 15.380 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 27.940 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 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:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 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 0.028 9158 Z= 0.149 Angle : 0.511 5.695 12462 Z= 0.274 Chirality : 0.039 0.126 1504 Planarity : 0.005 0.062 1494 Dihedral : 13.775 105.702 3466 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.16 % Allowed : 4.84 % Favored : 94.00 % 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: 1.59 (0.24), residues: 1102 helix: 1.56 (0.19), residues: 740 sheet: None (None), residues: 0 loop : 0.11 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 831 HIS 0.002 0.000 HIS E 734 PHE 0.008 0.001 PHE C 511 TYR 0.012 0.001 TYR E 519 ARG 0.002 0.000 ARG C 387 *********************** 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 199 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 188 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 435 MET cc_start: 0.7818 (mtm) cc_final: 0.7610 (mtp) REVERT: C 586 MET cc_start: 0.8580 (mmm) cc_final: 0.8374 (mmt) REVERT: C 622 PHE cc_start: 0.8271 (t80) cc_final: 0.8017 (t80) REVERT: C 626 ASP cc_start: 0.6111 (m-30) cc_final: 0.5832 (m-30) REVERT: C 646 ARG cc_start: 0.8702 (OUTLIER) cc_final: 0.7412 (ppp80) REVERT: C 676 ILE cc_start: 0.8210 (mt) cc_final: 0.7958 (pt) REVERT: C 812 LEU cc_start: 0.8865 (mt) cc_final: 0.8650 (mp) REVERT: C 885 CYS cc_start: 0.8219 (m) cc_final: 0.7875 (m) REVERT: E 454 LEU cc_start: 0.7955 (mt) cc_final: 0.7689 (mp) REVERT: E 646 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.5647 (ppp80) REVERT: E 650 ILE cc_start: 0.8147 (mp) cc_final: 0.7694 (mt) REVERT: E 759 GLN cc_start: 0.8260 (pp30) cc_final: 0.7957 (pp30) outliers start: 11 outliers final: 2 residues processed: 197 average time/residue: 0.2552 time to fit residues: 67.6042 Evaluate side-chains 150 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 146 time to evaluate : 0.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 511 PHE Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain E residue 473 GLU 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: 3.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 86 optimal weight: 0.3980 chunk 33 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 99 optimal weight: 2.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 HIS D 82 GLN C 377 GLN C 404 GLN C 630 GLN C 651 HIS C 683 GLN C 819 HIS E 377 GLN E 434 GLN E 457 GLN E 630 GLN ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 683 GLN E 804 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9158 Z= 0.256 Angle : 0.541 6.789 12462 Z= 0.263 Chirality : 0.043 0.213 1504 Planarity : 0.005 0.053 1494 Dihedral : 12.582 85.509 1469 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.11 % Allowed : 8.63 % Favored : 89.26 % 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: 1.88 (0.25), residues: 1102 helix: 1.80 (0.19), residues: 728 sheet: None (None), residues: 0 loop : 0.27 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 492 HIS 0.003 0.001 HIS E 547 PHE 0.013 0.002 PHE C 638 TYR 0.014 0.002 TYR C 824 ARG 0.004 0.001 ARG C 760 *********************** 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 174 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 154 time to evaluate : 1.019 Fit side-chains revert: symmetry clash REVERT: C 435 MET cc_start: 0.7937 (mtm) cc_final: 0.7617 (mtp) REVERT: C 586 MET cc_start: 0.8657 (mmm) cc_final: 0.8432 (mmt) REVERT: C 626 ASP cc_start: 0.6088 (m-30) cc_final: 0.5865 (m-30) REVERT: C 646 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.7152 (ppp80) REVERT: C 676 ILE cc_start: 0.8251 (mt) cc_final: 0.7954 (pt) REVERT: C 885 CYS cc_start: 0.8337 (m) cc_final: 0.7958 (m) REVERT: E 430 LYS cc_start: 0.6629 (mttp) cc_final: 0.6069 (mttp) REVERT: E 473 GLU cc_start: 0.6791 (OUTLIER) cc_final: 0.6286 (mm-30) REVERT: E 646 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.5716 (ppp80) REVERT: E 759 GLN cc_start: 0.8508 (pp30) cc_final: 0.7977 (pp30) outliers start: 20 outliers final: 10 residues processed: 167 average time/residue: 0.2101 time to fit residues: 49.1381 Evaluate side-chains 154 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 141 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 682 SER Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 797 VAL Chi-restraints excluded: chain C residue 798 THR Chi-restraints excluded: chain C residue 856 SER Chi-restraints excluded: chain C residue 877 ILE Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 889 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 55 optimal weight: 0.7980 chunk 31 optimal weight: 0.0170 chunk 83 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 100 optimal weight: 0.6980 chunk 108 optimal weight: 0.0060 chunk 89 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 34 optimal weight: 4.9990 chunk 80 optimal weight: 0.9980 overall best weight: 0.4634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 404 GLN C 651 HIS ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 819 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 9158 Z= 0.117 Angle : 0.468 7.460 12462 Z= 0.225 Chirality : 0.039 0.151 1504 Planarity : 0.004 0.053 1494 Dihedral : 10.162 83.351 1467 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.37 % Allowed : 10.95 % Favored : 87.68 % 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: 2.18 (0.25), residues: 1102 helix: 2.06 (0.19), residues: 726 sheet: None (None), residues: 0 loop : 0.31 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 492 HIS 0.002 0.000 HIS C 651 PHE 0.017 0.001 PHE C 622 TYR 0.012 0.001 TYR C 486 ARG 0.002 0.000 ARG E 384 *********************** 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 160 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 435 MET cc_start: 0.7947 (mtm) cc_final: 0.7568 (mtp) REVERT: C 503 LEU cc_start: 0.8134 (mt) cc_final: 0.7213 (tt) REVERT: C 586 MET cc_start: 0.8598 (mmm) cc_final: 0.8390 (mmt) REVERT: C 646 ARG cc_start: 0.8699 (OUTLIER) cc_final: 0.7192 (ppp80) REVERT: C 676 ILE cc_start: 0.8248 (mt) cc_final: 0.8005 (pt) REVERT: C 885 CYS cc_start: 0.8297 (m) cc_final: 0.7922 (m) REVERT: E 646 ARG cc_start: 0.8271 (OUTLIER) cc_final: 0.5547 (ppp80) REVERT: E 650 ILE cc_start: 0.8222 (mp) cc_final: 0.7770 (mt) REVERT: E 759 GLN cc_start: 0.8439 (pp30) cc_final: 0.7950 (pp30) outliers start: 13 outliers final: 5 residues processed: 155 average time/residue: 0.2083 time to fit residues: 45.5198 Evaluate side-chains 151 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 144 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 634 VAL Chi-restraints excluded: chain E residue 646 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 chunk 67 optimal weight: 0.0030 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 chunk 52 optimal weight: 0.3980 chunk 95 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 GLN C 651 HIS ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 9158 Z= 0.124 Angle : 0.454 5.532 12462 Z= 0.221 Chirality : 0.039 0.170 1504 Planarity : 0.004 0.052 1494 Dihedral : 9.157 80.472 1467 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % Rotamer: Outliers : 2.21 % Allowed : 11.05 % Favored : 86.74 % 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: 2.29 (0.25), residues: 1102 helix: 2.16 (0.19), residues: 726 sheet: None (None), residues: 0 loop : 0.34 (0.31), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 492 HIS 0.002 0.000 HIS C 651 PHE 0.020 0.001 PHE C 622 TYR 0.010 0.001 TYR C 486 ARG 0.005 0.000 ARG C 760 *********************** 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: 21 poor density : 148 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 503 LEU cc_start: 0.8141 (mt) cc_final: 0.7168 (tt) REVERT: C 586 MET cc_start: 0.8599 (mmm) cc_final: 0.8392 (mmt) REVERT: C 646 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7199 (ppp80) REVERT: C 650 ILE cc_start: 0.8013 (OUTLIER) cc_final: 0.7754 (mp) REVERT: C 676 ILE cc_start: 0.8255 (mt) cc_final: 0.8004 (pt) REVERT: C 885 CYS cc_start: 0.8318 (m) cc_final: 0.7945 (m) REVERT: E 646 ARG cc_start: 0.8254 (OUTLIER) cc_final: 0.5416 (ppp80) REVERT: E 650 ILE cc_start: 0.8215 (OUTLIER) cc_final: 0.7771 (mt) REVERT: E 759 GLN cc_start: 0.8455 (pp30) cc_final: 0.7946 (pp30) outliers start: 21 outliers final: 10 residues processed: 161 average time/residue: 0.2118 time to fit residues: 47.1335 Evaluate side-chains 156 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 142 time to evaluate : 1.010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 650 ILE Chi-restraints excluded: chain C residue 682 SER Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 594 SER Chi-restraints excluded: chain E residue 634 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 650 ILE Chi-restraints excluded: chain E residue 831 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.9980 chunk 60 optimal weight: 9.9990 chunk 1 optimal weight: 0.7980 chunk 79 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 90 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 0 optimal weight: 30.0000 chunk 54 optimal weight: 0.6980 chunk 95 optimal weight: 4.9990 chunk 26 optimal weight: 0.4980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 651 HIS ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7874 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9158 Z= 0.163 Angle : 0.466 5.714 12462 Z= 0.229 Chirality : 0.039 0.131 1504 Planarity : 0.004 0.051 1494 Dihedral : 8.915 82.764 1467 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.21 % Allowed : 11.79 % 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: 2.19 (0.25), residues: 1102 helix: 2.08 (0.19), residues: 728 sheet: None (None), residues: 0 loop : 0.29 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 492 HIS 0.003 0.001 HIS C 651 PHE 0.012 0.001 PHE E 471 TYR 0.010 0.001 TYR E 519 ARG 0.005 0.000 ARG C 760 *********************** 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 168 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 147 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: C 384 ARG cc_start: 0.7443 (mmm160) cc_final: 0.7222 (mmm160) REVERT: C 503 LEU cc_start: 0.8138 (mt) cc_final: 0.7240 (tt) REVERT: C 586 MET cc_start: 0.8609 (mmm) cc_final: 0.8406 (mmt) REVERT: C 646 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.7264 (ppp80) REVERT: C 651 HIS cc_start: 0.5599 (OUTLIER) cc_final: 0.5031 (t70) REVERT: C 676 ILE cc_start: 0.8244 (mt) cc_final: 0.7990 (pt) REVERT: C 755 GLU cc_start: 0.7438 (pt0) cc_final: 0.7157 (pt0) REVERT: C 885 CYS cc_start: 0.8328 (m) cc_final: 0.7946 (m) REVERT: E 430 LYS cc_start: 0.6518 (OUTLIER) cc_final: 0.5005 (tptt) REVERT: E 473 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6487 (mm-30) REVERT: E 646 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.5497 (ppp80) REVERT: E 650 ILE cc_start: 0.8250 (OUTLIER) cc_final: 0.7764 (mt) REVERT: E 759 GLN cc_start: 0.8479 (pp30) cc_final: 0.7921 (pp30) REVERT: E 777 GLU cc_start: 0.6856 (tm-30) cc_final: 0.6522 (tm-30) REVERT: E 859 LEU cc_start: 0.8050 (tp) cc_final: 0.7841 (tp) outliers start: 21 outliers final: 12 residues processed: 162 average time/residue: 0.2048 time to fit residues: 46.3939 Evaluate side-chains 164 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 146 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain C residue 682 SER Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 797 VAL Chi-restraints excluded: chain C residue 798 THR Chi-restraints excluded: chain C residue 877 ILE Chi-restraints excluded: chain E residue 430 LYS Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 634 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 650 ILE Chi-restraints excluded: chain E residue 831 TRP Chi-restraints excluded: chain E residue 889 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 35 optimal weight: 7.9990 chunk 95 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 62 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 106 optimal weight: 0.0980 chunk 88 optimal weight: 0.2980 chunk 49 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 102 optimal weight: 0.0000 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 404 GLN C 550 GLN C 651 HIS ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 9158 Z= 0.134 Angle : 0.450 5.565 12462 Z= 0.222 Chirality : 0.039 0.136 1504 Planarity : 0.004 0.051 1494 Dihedral : 8.771 83.393 1467 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 2.21 % Allowed : 12.32 % Favored : 85.47 % 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: 2.24 (0.25), residues: 1102 helix: 2.11 (0.19), residues: 728 sheet: None (None), residues: 0 loop : 0.32 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 492 HIS 0.004 0.001 HIS C 651 PHE 0.012 0.001 PHE E 471 TYR 0.010 0.001 TYR C 486 ARG 0.005 0.000 ARG C 760 *********************** 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 167 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 146 time to evaluate : 1.041 Fit side-chains revert: symmetry clash REVERT: C 435 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7597 (mtp) REVERT: C 503 LEU cc_start: 0.8116 (mt) cc_final: 0.7245 (tt) REVERT: C 586 MET cc_start: 0.8599 (mmm) cc_final: 0.8397 (mmt) REVERT: C 646 ARG cc_start: 0.8714 (OUTLIER) cc_final: 0.7290 (ppp80) REVERT: C 651 HIS cc_start: 0.5439 (OUTLIER) cc_final: 0.4854 (t70) REVERT: C 676 ILE cc_start: 0.8250 (mt) cc_final: 0.7995 (pt) REVERT: C 755 GLU cc_start: 0.7469 (pt0) cc_final: 0.7172 (pt0) REVERT: C 885 CYS cc_start: 0.8329 (m) cc_final: 0.7950 (m) REVERT: E 430 LYS cc_start: 0.6546 (OUTLIER) cc_final: 0.5067 (tptt) REVERT: E 473 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6445 (mm-30) REVERT: E 646 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.5473 (ppp80) REVERT: E 650 ILE cc_start: 0.8245 (OUTLIER) cc_final: 0.7782 (mt) REVERT: E 759 GLN cc_start: 0.8460 (OUTLIER) cc_final: 0.7913 (pp30) REVERT: E 777 GLU cc_start: 0.6840 (tm-30) cc_final: 0.6514 (tm-30) outliers start: 21 outliers final: 11 residues processed: 160 average time/residue: 0.2148 time to fit residues: 48.1526 Evaluate side-chains 162 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain C residue 682 SER Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain E residue 430 LYS Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 634 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 650 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 759 GLN Chi-restraints excluded: chain E residue 831 TRP Chi-restraints excluded: chain E residue 889 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 59 optimal weight: 9.9990 chunk 106 optimal weight: 2.9990 chunk 66 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 651 HIS ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9158 Z= 0.199 Angle : 0.479 5.991 12462 Z= 0.237 Chirality : 0.040 0.182 1504 Planarity : 0.004 0.051 1494 Dihedral : 8.732 84.712 1467 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.42 % Allowed : 12.32 % Favored : 85.26 % 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: 2.11 (0.25), residues: 1102 helix: 2.00 (0.19), residues: 730 sheet: None (None), residues: 0 loop : 0.29 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 492 HIS 0.014 0.001 HIS C 651 PHE 0.013 0.001 PHE E 471 TYR 0.010 0.001 TYR C 824 ARG 0.006 0.000 ARG C 760 *********************** 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 170 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 147 time to evaluate : 1.075 Fit side-chains revert: symmetry clash REVERT: C 384 ARG cc_start: 0.7458 (mmm160) cc_final: 0.7214 (mmm160) REVERT: C 503 LEU cc_start: 0.8128 (mt) cc_final: 0.7159 (tt) REVERT: C 586 MET cc_start: 0.8631 (mmm) cc_final: 0.8419 (mmt) REVERT: C 646 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.7287 (ppp80) REVERT: C 651 HIS cc_start: 0.5358 (OUTLIER) cc_final: 0.4774 (t70) REVERT: C 755 GLU cc_start: 0.7524 (pt0) cc_final: 0.7220 (pt0) REVERT: C 885 CYS cc_start: 0.8348 (m) cc_final: 0.7964 (m) REVERT: E 430 LYS cc_start: 0.6642 (OUTLIER) cc_final: 0.5707 (tptt) REVERT: E 646 ARG cc_start: 0.8299 (OUTLIER) cc_final: 0.5442 (ppp80) REVERT: E 650 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7816 (mt) REVERT: E 672 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7621 (tt) REVERT: E 759 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.7925 (pp30) REVERT: E 777 GLU cc_start: 0.6882 (tm-30) cc_final: 0.6528 (tm-30) outliers start: 23 outliers final: 12 residues processed: 163 average time/residue: 0.2077 time to fit residues: 47.4384 Evaluate side-chains 164 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 145 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain C residue 682 SER Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain E residue 430 LYS Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 634 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 650 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 759 GLN Chi-restraints excluded: chain E residue 831 TRP Chi-restraints excluded: chain E residue 889 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 63 optimal weight: 0.6980 chunk 31 optimal weight: 5.9990 chunk 20 optimal weight: 2.9990 chunk 67 optimal weight: 0.8980 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 83 optimal weight: 0.5980 chunk 96 optimal weight: 8.9990 chunk 101 optimal weight: 0.0770 chunk 92 optimal weight: 0.9980 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 GLN C 651 HIS C 884 GLN ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 9158 Z= 0.136 Angle : 0.459 5.741 12462 Z= 0.226 Chirality : 0.040 0.263 1504 Planarity : 0.004 0.051 1494 Dihedral : 8.602 84.934 1467 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.21 % Allowed : 12.74 % 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: 2.20 (0.25), residues: 1102 helix: 2.11 (0.19), residues: 728 sheet: None (None), residues: 0 loop : 0.24 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 492 HIS 0.007 0.001 HIS C 651 PHE 0.012 0.001 PHE E 471 TYR 0.010 0.001 TYR C 486 ARG 0.003 0.000 ARG C 760 *********************** 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 165 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 144 time to evaluate : 1.002 Fit side-chains revert: symmetry clash REVERT: C 586 MET cc_start: 0.8601 (mmm) cc_final: 0.8396 (mmt) REVERT: C 646 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.7294 (ppp80) REVERT: C 651 HIS cc_start: 0.5362 (OUTLIER) cc_final: 0.4760 (t70) REVERT: C 755 GLU cc_start: 0.7503 (pt0) cc_final: 0.7194 (pt0) REVERT: C 885 CYS cc_start: 0.8331 (m) cc_final: 0.7942 (m) REVERT: E 430 LYS cc_start: 0.6647 (OUTLIER) cc_final: 0.5694 (tptt) REVERT: E 646 ARG cc_start: 0.8282 (OUTLIER) cc_final: 0.5459 (ppp80) REVERT: E 650 ILE cc_start: 0.8265 (OUTLIER) cc_final: 0.7835 (mt) REVERT: E 672 LEU cc_start: 0.7806 (OUTLIER) cc_final: 0.7590 (tt) REVERT: E 759 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.7909 (pp30) REVERT: E 777 GLU cc_start: 0.6885 (tm-30) cc_final: 0.6564 (tm-30) outliers start: 21 outliers final: 14 residues processed: 157 average time/residue: 0.2060 time to fit residues: 45.6091 Evaluate side-chains 164 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 143 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain C residue 682 SER Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain E residue 430 LYS Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 634 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 650 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 759 GLN Chi-restraints excluded: chain E residue 831 TRP Chi-restraints excluded: chain E residue 889 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 98 optimal weight: 2.9990 chunk 101 optimal weight: 0.0470 chunk 59 optimal weight: 10.0000 chunk 43 optimal weight: 0.8980 chunk 77 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 104 optimal weight: 7.9990 chunk 63 optimal weight: 0.7980 overall best weight: 1.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 GLN C 651 HIS ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.2194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9158 Z= 0.201 Angle : 0.484 5.794 12462 Z= 0.238 Chirality : 0.040 0.186 1504 Planarity : 0.004 0.051 1494 Dihedral : 8.603 86.011 1467 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.42 % Allowed : 12.84 % Favored : 84.74 % 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: 2.10 (0.25), residues: 1102 helix: 2.01 (0.19), residues: 728 sheet: None (None), residues: 0 loop : 0.23 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 492 HIS 0.007 0.001 HIS C 651 PHE 0.013 0.001 PHE E 471 TYR 0.010 0.001 TYR E 519 ARG 0.004 0.000 ARG C 760 *********************** 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 167 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 144 time to evaluate : 0.859 Fit side-chains revert: symmetry clash REVERT: C 384 ARG cc_start: 0.7468 (mmm160) cc_final: 0.7266 (mmm160) REVERT: C 586 MET cc_start: 0.8632 (mmm) cc_final: 0.8419 (mmt) REVERT: C 646 ARG cc_start: 0.8728 (OUTLIER) cc_final: 0.7289 (ppp80) REVERT: C 651 HIS cc_start: 0.5257 (OUTLIER) cc_final: 0.4723 (t70) REVERT: C 755 GLU cc_start: 0.7555 (pt0) cc_final: 0.7247 (pt0) REVERT: C 885 CYS cc_start: 0.8331 (m) cc_final: 0.7943 (m) REVERT: E 430 LYS cc_start: 0.6709 (OUTLIER) cc_final: 0.6167 (ptmt) REVERT: E 433 ASN cc_start: 0.8051 (m-40) cc_final: 0.7758 (t0) REVERT: E 646 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.5475 (ppp80) REVERT: E 650 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.7857 (mt) REVERT: E 672 LEU cc_start: 0.7851 (OUTLIER) cc_final: 0.7637 (tt) REVERT: E 759 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7944 (pp30) REVERT: E 777 GLU cc_start: 0.6933 (tm-30) cc_final: 0.6582 (tm-30) outliers start: 23 outliers final: 16 residues processed: 158 average time/residue: 0.2096 time to fit residues: 45.7127 Evaluate side-chains 165 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 142 time to evaluate : 1.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 435 MET Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain C residue 682 SER Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 791 ILE Chi-restraints excluded: chain C residue 797 VAL Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain E residue 430 LYS Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 634 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 650 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 759 GLN Chi-restraints excluded: chain E residue 831 TRP Chi-restraints excluded: chain E residue 889 ASP 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: 3.9990 chunk 109 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 87 optimal weight: 0.1980 chunk 9 optimal weight: 4.9990 chunk 67 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 26 optimal weight: 3.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 GLN C 651 HIS C 884 GLN ** E 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 9158 Z= 0.145 Angle : 0.462 5.685 12462 Z= 0.227 Chirality : 0.039 0.141 1504 Planarity : 0.004 0.052 1494 Dihedral : 8.496 86.030 1467 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 2.42 % Allowed : 12.95 % 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: 2.17 (0.25), residues: 1102 helix: 2.10 (0.19), residues: 728 sheet: None (None), residues: 0 loop : 0.19 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 492 HIS 0.004 0.001 HIS C 651 PHE 0.013 0.001 PHE E 471 TYR 0.010 0.001 TYR E 519 ARG 0.004 0.000 ARG C 760 ********************** 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 160 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 137 time to evaluate : 1.015 Fit side-chains revert: symmetry clash REVERT: C 586 MET cc_start: 0.8608 (mmm) cc_final: 0.8400 (mmt) REVERT: C 646 ARG cc_start: 0.8721 (OUTLIER) cc_final: 0.7308 (ppp80) REVERT: C 651 HIS cc_start: 0.5264 (OUTLIER) cc_final: 0.4737 (t70) REVERT: C 755 GLU cc_start: 0.7550 (pt0) cc_final: 0.7237 (pt0) REVERT: C 885 CYS cc_start: 0.8313 (m) cc_final: 0.7925 (m) REVERT: E 430 LYS cc_start: 0.6697 (OUTLIER) cc_final: 0.6115 (ptmt) REVERT: E 433 ASN cc_start: 0.8043 (m-40) cc_final: 0.7765 (t0) REVERT: E 646 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.5507 (ppp80) REVERT: E 650 ILE cc_start: 0.8282 (OUTLIER) cc_final: 0.7861 (mt) REVERT: E 672 LEU cc_start: 0.7815 (OUTLIER) cc_final: 0.7610 (tt) REVERT: E 759 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.7934 (pp30) REVERT: E 777 GLU cc_start: 0.6927 (tm-30) cc_final: 0.6600 (tm-30) REVERT: E 842 ILE cc_start: 0.7892 (tt) cc_final: 0.7618 (pt) outliers start: 23 outliers final: 13 residues processed: 151 average time/residue: 0.2070 time to fit residues: 43.8652 Evaluate side-chains 155 residues out of total 964 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 112 TYR Chi-restraints excluded: chain C residue 418 SER Chi-restraints excluded: chain C residue 528 ILE Chi-restraints excluded: chain C residue 543 ILE Chi-restraints excluded: chain C residue 643 SER Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 651 HIS Chi-restraints excluded: chain C residue 682 SER Chi-restraints excluded: chain C residue 727 THR Chi-restraints excluded: chain C residue 873 LEU Chi-restraints excluded: chain E residue 430 LYS Chi-restraints excluded: chain E residue 473 GLU Chi-restraints excluded: chain E residue 560 VAL Chi-restraints excluded: chain E residue 634 VAL Chi-restraints excluded: chain E residue 646 ARG Chi-restraints excluded: chain E residue 650 ILE Chi-restraints excluded: chain E residue 672 LEU Chi-restraints excluded: chain E residue 759 GLN Chi-restraints excluded: chain E residue 831 TRP Chi-restraints excluded: chain E residue 889 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.0770 chunk 76 optimal weight: 0.6980 chunk 4 optimal weight: 10.0000 chunk 63 optimal weight: 0.6980 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 550 GLN ** C 651 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 651 HIS ** 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 = 0.3693 r_free = 0.3693 target = 0.160911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.136806 restraints weight = 10265.007| |-----------------------------------------------------------------------------| r_work (start): 0.3426 rms_B_bonded: 1.58 r_work: 0.3322 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3197 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 9158 Z= 0.137 Angle : 0.460 5.626 12462 Z= 0.227 Chirality : 0.039 0.130 1504 Planarity : 0.004 0.051 1494 Dihedral : 8.417 86.107 1467 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 2.00 % Allowed : 13.05 % Favored : 84.95 % 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: 2.21 (0.25), residues: 1102 helix: 2.13 (0.19), residues: 728 sheet: None (None), residues: 0 loop : 0.21 (0.32), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 492 HIS 0.007 0.001 HIS C 651 PHE 0.012 0.001 PHE E 471 TYR 0.010 0.001 TYR C 486 ARG 0.005 0.000 ARG C 760 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3387.77 seconds wall clock time: 61 minutes 27.17 seconds (3687.17 seconds total)