Starting phenix.real_space_refine on Tue May 13 18:52:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8c2i_16391/05_2025/8c2i_16391.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c2i_16391/05_2025/8c2i_16391.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8c2i_16391/05_2025/8c2i_16391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c2i_16391/05_2025/8c2i_16391.map" model { file = "/net/cci-nas-00/data/ceres_data/8c2i_16391/05_2025/8c2i_16391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c2i_16391/05_2025/8c2i_16391.cif" } resolution = 2.7 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 ------------------------------------------------------------------------------- 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= 0.002 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 8 5.49 5 S 63 5.16 5 C 6886 2.51 5 N 1591 2.21 5 O 1818 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 88 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10366 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1092 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 139, 1063 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 139, 1063 Classifications: {'peptide': 139} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 134} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 bond proxies already assigned to first conformer: 1059 Chain: "B" Number of atoms: 1102 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 137, 1055 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 137, 1055 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 1033 Chain: "C" Number of atoms: 1118 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 142, 1089 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 137} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 Conformer: "B" Number of residues, atoms: 142, 1089 Classifications: {'peptide': 142} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 137} Chain breaks: 2 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 36 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'TRP:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 28 bond proxies already assigned to first conformer: 1085 Chain: "D" Number of atoms: 1102 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 137, 1055 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Conformer: "B" Number of residues, atoms: 137, 1055 Classifications: {'peptide': 137} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 132} Chain breaks: 2 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 bond proxies already assigned to first conformer: 1033 Chain: "E" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1367 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Chain: "F" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1367 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Chain: "G" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1367 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Chain: "H" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1367 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 2, 'TRANS': 173} Chain breaks: 3 Chain: "A" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 113 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 32 Chain: "C" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 43 Unusual residues: {'OLC': 1, 'PLM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 113 Unusual residues: {'OLC': 1, 'PLM': 1, 'POV': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'POV:plan-1': 1} Unresolved non-hydrogen planarities: 2 Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Chain: "F" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "G" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 19 Chain: "H" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 39 Unusual residues: {'POV': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 13 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "C" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 20 residue: pdb=" N AGLY A 584 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 584 " occ=0.50 residue: pdb=" N ACYS A 585 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS A 585 " occ=0.50 residue: pdb=" N AASP A 586 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP A 586 " occ=0.50 residue: pdb=" N APHE A 619 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE A 619 " occ=0.50 residue: pdb=" N AGLN B 582 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 582 " occ=0.50 residue: pdb=" N AGLN B 583 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN B 583 " occ=0.50 residue: pdb=" N AGLY B 584 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 584 " occ=0.50 residue: pdb=" N ACYS B 585 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS B 585 " occ=0.50 residue: pdb=" N AASP B 586 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP B 586 " occ=0.50 residue: pdb=" N APHE B 619 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE B 619 " occ=0.50 residue: pdb=" N AGLY C 584 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY C 584 " occ=0.50 residue: pdb=" N ACYS C 585 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS C 585 " occ=0.50 ... (remaining 8 not shown) Time building chain proxies: 8.41, per 1000 atoms: 0.81 Number of scatterers: 10366 At special positions: 0 Unit cell: (97.52, 95.4, 87.98, 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 63 16.00 P 8 15.00 O 1818 8.00 N 1591 7.00 C 6886 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 40 " - pdb=" SG CYS E 68 " distance=2.01 Simple disulfide: pdb=" SG CYS E 67 " - pdb=" SG CYS E 77 " distance=2.06 Simple disulfide: pdb=" SG CYS F 40 " - pdb=" SG CYS F 68 " distance=2.04 Simple disulfide: pdb=" SG CYS F 67 " - pdb=" SG CYS F 77 " distance=2.03 Simple disulfide: pdb=" SG CYS G 40 " - pdb=" SG CYS G 68 " distance=2.02 Simple disulfide: pdb=" SG CYS G 67 " - pdb=" SG CYS G 77 " distance=2.06 Simple disulfide: pdb=" SG CYS H 40 " - pdb=" SG CYS H 68 " distance=2.04 Simple disulfide: pdb=" SG CYS H 67 " - pdb=" SG CYS H 77 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 1.8 seconds 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2326 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 6 sheets defined 74.5% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.00 Creating SS restraints... Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 518 through 542 Processing helix chain 'A' and resid 568 through 581 Processing helix chain 'A' and resid 591 through 622 Processing helix chain 'A' and resid 784 through 787 Processing helix chain 'A' and resid 788 through 814 removed outlier: 3.508A pdb=" N PHE A 792 " --> pdb=" O VAL A 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 515 Processing helix chain 'B' and resid 518 through 542 Processing helix chain 'B' and resid 568 through 581 Processing helix chain 'B' and resid 591 through 626 Processing helix chain 'B' and resid 784 through 787 Processing helix chain 'B' and resid 788 through 815 removed outlier: 3.597A pdb=" N PHE B 792 " --> pdb=" O VAL B 788 " (cutoff:3.500A) Processing helix chain 'C' and resid 511 through 515 Processing helix chain 'C' and resid 518 through 542 Processing helix chain 'C' and resid 568 through 581 Processing helix chain 'C' and resid 591 through 622 Processing helix chain 'C' and resid 784 through 787 Processing helix chain 'C' and resid 788 through 814 removed outlier: 3.521A pdb=" N PHE C 792 " --> pdb=" O VAL C 788 " (cutoff:3.500A) Processing helix chain 'D' and resid 511 through 515 Processing helix chain 'D' and resid 518 through 542 Processing helix chain 'D' and resid 568 through 581 Processing helix chain 'D' and resid 591 through 622 Processing helix chain 'D' and resid 784 through 787 Processing helix chain 'D' and resid 788 through 815 removed outlier: 3.575A pdb=" N PHE D 792 " --> pdb=" O VAL D 788 " (cutoff:3.500A) Processing helix chain 'E' and resid 6 through 30 Processing helix chain 'E' and resid 93 through 105 Processing helix chain 'E' and resid 105 through 128 removed outlier: 4.249A pdb=" N GLU E 126 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE E 127 " --> pdb=" O ALA E 123 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 162 removed outlier: 3.906A pdb=" N LEU E 136 " --> pdb=" O HIS E 132 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 209 removed outlier: 3.589A pdb=" N TYR E 180 " --> pdb=" O GLY E 176 " (cutoff:3.500A) Processing helix chain 'F' and resid 6 through 30 Processing helix chain 'F' and resid 93 through 105 Processing helix chain 'F' and resid 105 through 126 removed outlier: 3.835A pdb=" N GLU F 126 " --> pdb=" O VAL F 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 162 removed outlier: 3.799A pdb=" N LEU F 136 " --> pdb=" O HIS F 132 " (cutoff:3.500A) Processing helix chain 'F' and resid 176 through 209 removed outlier: 3.563A pdb=" N TYR F 180 " --> pdb=" O GLY F 176 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG F 208 " --> pdb=" O HIS F 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 30 Processing helix chain 'G' and resid 93 through 105 Processing helix chain 'G' and resid 105 through 128 removed outlier: 4.243A pdb=" N GLU G 126 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N PHE G 127 " --> pdb=" O ALA G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 132 through 162 removed outlier: 3.911A pdb=" N LEU G 136 " --> pdb=" O HIS G 132 " (cutoff:3.500A) Processing helix chain 'G' and resid 176 through 209 removed outlier: 3.592A pdb=" N TYR G 180 " --> pdb=" O GLY G 176 " (cutoff:3.500A) Processing helix chain 'H' and resid 6 through 30 Processing helix chain 'H' and resid 93 through 105 Processing helix chain 'H' and resid 105 through 126 removed outlier: 3.839A pdb=" N GLU H 126 " --> pdb=" O VAL H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 132 through 162 removed outlier: 3.798A pdb=" N LEU H 136 " --> pdb=" O HIS H 132 " (cutoff:3.500A) Processing helix chain 'H' and resid 176 through 209 removed outlier: 3.559A pdb=" N TYR H 180 " --> pdb=" O GLY H 176 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG H 208 " --> pdb=" O HIS H 204 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 34 through 35 Processing sheet with id=AA2, first strand: chain 'E' and resid 37 through 38 Processing sheet with id=AA3, first strand: chain 'F' and resid 77 through 79 Processing sheet with id=AA4, first strand: chain 'G' and resid 34 through 35 Processing sheet with id=AA5, first strand: chain 'G' and resid 37 through 38 Processing sheet with id=AA6, first strand: chain 'H' and resid 77 through 79 795 hydrogen bonds defined for protein. 2329 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: 3.37 Time building geometry restraints manager: 3.04 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: 1533 1.31 - 1.44: 3165 1.44 - 1.57: 5766 1.57 - 1.70: 16 1.70 - 1.83: 90 Bond restraints: 10570 Sorted by residual: bond pdb=" CA SER A 533 " pdb=" CB SER A 533 " ideal model delta sigma weight residual 1.528 1.473 0.055 1.56e-02 4.11e+03 1.24e+01 bond pdb=" C11 OLC B1002 " pdb=" C12 OLC B1002 " ideal model delta sigma weight residual 1.528 1.459 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" C SER B 540 " pdb=" N ARG B 541 " ideal model delta sigma weight residual 1.333 1.282 0.051 1.50e-02 4.44e+03 1.16e+01 bond pdb=" CA SER C 593 " pdb=" CB SER C 593 " ideal model delta sigma weight residual 1.528 1.478 0.050 1.59e-02 3.96e+03 1.00e+01 bond pdb=" CA SER A 593 " pdb=" CB SER A 593 " ideal model delta sigma weight residual 1.529 1.479 0.050 1.58e-02 4.01e+03 9.94e+00 ... (remaining 10565 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 13111 2.17 - 4.35: 1009 4.35 - 6.52: 78 6.52 - 8.70: 23 8.70 - 10.87: 6 Bond angle restraints: 14227 Sorted by residual: angle pdb=" CA BPHE B 619 " pdb=" CB BPHE B 619 " pdb=" CG BPHE B 619 " ideal model delta sigma weight residual 113.80 119.38 -5.58 1.00e+00 1.00e+00 3.11e+01 angle pdb=" C PHE D 542 " pdb=" CA PHE D 542 " pdb=" CB PHE D 542 " ideal model delta sigma weight residual 110.42 120.50 -10.08 1.99e+00 2.53e-01 2.57e+01 angle pdb=" C BASP B 586 " pdb=" N ILE B 587 " pdb=" CA ILE B 587 " ideal model delta sigma weight residual 122.71 115.49 7.22 1.44e+00 4.82e-01 2.51e+01 angle pdb=" C BASP D 586 " pdb=" N ILE D 587 " pdb=" CA ILE D 587 " ideal model delta sigma weight residual 122.71 115.49 7.22 1.44e+00 4.82e-01 2.51e+01 angle pdb=" CG ARG E 74 " pdb=" CD ARG E 74 " pdb=" NE ARG E 74 " ideal model delta sigma weight residual 112.00 101.13 10.87 2.20e+00 2.07e-01 2.44e+01 ... (remaining 14222 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.89: 5551 23.89 - 47.77: 413 47.77 - 71.66: 93 71.66 - 95.54: 22 95.54 - 119.43: 3 Dihedral angle restraints: 6082 sinusoidal: 2445 harmonic: 3637 Sorted by residual: dihedral pdb=" C ARG B 541 " pdb=" N ARG B 541 " pdb=" CA ARG B 541 " pdb=" CB ARG B 541 " ideal model delta harmonic sigma weight residual -122.60 -111.08 -11.52 0 2.50e+00 1.60e-01 2.12e+01 dihedral pdb=" CA ASN D 787 " pdb=" C ASN D 787 " pdb=" N VAL D 788 " pdb=" CA VAL D 788 " ideal model delta harmonic sigma weight residual 180.00 158.20 21.80 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA VAL E 39 " pdb=" C VAL E 39 " pdb=" N CYS E 40 " pdb=" CA CYS E 40 " ideal model delta harmonic sigma weight residual 180.00 158.39 21.61 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 6079 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 963 0.063 - 0.126: 473 0.126 - 0.189: 122 0.189 - 0.252: 14 0.252 - 0.315: 5 Chirality restraints: 1577 Sorted by residual: chirality pdb=" CA PHE C 511 " pdb=" N PHE C 511 " pdb=" C PHE C 511 " pdb=" CB PHE C 511 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.32 2.00e-01 2.50e+01 2.48e+00 chirality pdb=" CB VAL D 791 " pdb=" CA VAL D 791 " pdb=" CG1 VAL D 791 " pdb=" CG2 VAL D 791 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.43e+00 chirality pdb=" CB VAL B 791 " pdb=" CA VAL B 791 " pdb=" CG1 VAL B 791 " pdb=" CG2 VAL B 791 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.33e+00 ... (remaining 1574 not shown) Planarity restraints: 1711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C28 POV D1003 " 0.047 2.00e-02 2.50e+03 8.88e-02 7.89e+01 pdb=" C29 POV D1003 " -0.116 2.00e-02 2.50e+03 pdb="C210 POV D1003 " 0.117 2.00e-02 2.50e+03 pdb="C211 POV D1003 " -0.047 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 OLC B1002 " 0.067 2.00e-02 2.50e+03 5.10e-02 2.60e+01 pdb=" C11 OLC B1002 " -0.026 2.00e-02 2.50e+03 pdb=" C8 OLC B1002 " 0.027 2.00e-02 2.50e+03 pdb=" C9 OLC B1002 " -0.068 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C28 POV B1003 " -0.051 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" C29 POV B1003 " 0.054 2.00e-02 2.50e+03 pdb="C210 POV B1003 " 0.047 2.00e-02 2.50e+03 pdb="C211 POV B1003 " -0.050 2.00e-02 2.50e+03 ... (remaining 1708 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1352 2.76 - 3.29: 10740 3.29 - 3.83: 17633 3.83 - 4.36: 20441 4.36 - 4.90: 35773 Nonbonded interactions: 85939 Sorted by model distance: nonbonded pdb=" O BGLN B 583 " pdb=" O BGLY B 584 " model vdw 2.222 3.040 nonbonded pdb=" O21 POV E1201 " pdb=" O31 POV E1201 " model vdw 2.330 2.432 nonbonded pdb=" N GLU G 55 " pdb=" OE1 GLU G 55 " model vdw 2.351 3.120 nonbonded pdb=" N GLU E 55 " pdb=" OE1 GLU E 55 " model vdw 2.354 3.120 nonbonded pdb=" N BASP B 586 " pdb=" OD1BASP B 586 " model vdw 2.354 3.120 ... (remaining 85934 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 506 through 546 or resid 567 through 581 or resid 587 thro \ ugh 618 or resid 620 through 624 or resid 780 through 815 or resid 1001 through \ 1002)) selection = (chain 'B' and (resid 506 through 545 or (resid 566 and (name N or name CA or na \ me C or name O or name CB )) or resid 567 through 581 or resid 587 through 618 o \ r resid 620 through 624 or resid 780 through 813 or (resid 814 through 815 and ( \ name N or name CA or name C or name O or name CB )) or resid 1001 through 1002)) \ selection = (chain 'C' and (resid 506 through 546 or resid 567 through 581 or resid 587 thro \ ugh 618 or resid 620 through 624 or resid 780 through 815 or resid 1001 through \ 1002)) selection = (chain 'D' and (resid 506 through 545 or (resid 566 and (name N or name CA or na \ me C or name O or name CB )) or resid 567 through 581 or resid 587 through 618 o \ r resid 620 through 624 or resid 780 through 813 or (resid 814 through 815 and ( \ name N or name CA or name C or name O or name CB )) or resid 1001 through 1002)) \ } ncs_group { reference = (chain 'E' and (resid 5 through 209 or (resid 1201 and (name C1 or name C2 or na \ me C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 o \ r name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or name C3 \ 4 or name C35 or name C36 or name O11 or name O12 or name O13 or name O14 or nam \ e O21 or name O22 or name O31 or name O32 or name P or name C210 or name C211))) \ ) selection = (chain 'F' and (resid 5 through 209 or (resid 1301 and (name C1 or name C2 or na \ me C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 o \ r name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or name C3 \ 4 or name C35 or name C36 or name O11 or name O12 or name O13 or name O14 or nam \ e O21 or name O22 or name O31 or name O32 or name P or name C210 or name C211))) \ ) selection = (chain 'G' and (resid 5 through 209 or (resid 1201 and (name C1 or name C2 or na \ me C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 o \ r name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or name C3 \ 4 or name C35 or name C36 or name O11 or name O12 or name O13 or name O14 or nam \ e O21 or name O22 or name O31 or name O32 or name P or name C210 or name C211))) \ ) selection = (chain 'H' and (resid 5 through 209 or (resid 1301 and (name C1 or name C2 or na \ me C21 or name C22 or name C23 or name C24 or name C25 or name C26 or name C27 o \ r name C28 or name C29 or name C3 or name C31 or name C32 or name C33 or name C3 \ 4 or name C35 or name C36 or name O11 or name O12 or name O13 or name O14 or nam \ e O21 or name O22 or name O31 or name O32 or name P or name C210 or name C211))) \ ) } 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=0.50 max=1.00 mean=0.99 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: 0.830 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: 0.340 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 28.670 Find NCS groups from input model: 0.560 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:11.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 : 0.010 0.069 10578 Z= 0.638 Angle : 1.277 10.874 14243 Z= 0.821 Chirality : 0.075 0.315 1577 Planarity : 0.013 0.143 1711 Dihedral : 17.793 119.430 3732 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.83 % Favored : 97.09 % Rotamer: Outliers : 4.07 % Allowed : 3.30 % Favored : 92.63 % Cbeta Deviations : 0.26 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.22), residues: 1239 helix: 1.04 (0.16), residues: 934 sheet: -0.79 (1.05), residues: 20 loop : -2.66 (0.29), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.010 TRP D 602 HIS 0.017 0.004 HIS E 60 PHE 0.063 0.008 PHE D 567 TYR 0.041 0.009 TYR H 96 ARG 0.027 0.003 ARG G 102 Details of bonding type rmsd hydrogen bonds : bond 0.13711 ( 795) hydrogen bonds : angle 5.50581 ( 2329) SS BOND : bond 0.01891 ( 8) SS BOND : angle 2.81432 ( 16) covalent geometry : bond 0.00998 (10570) covalent geometry : angle 1.27441 (14227) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 1.079 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 566 GLU cc_start: 0.7287 (tt0) cc_final: 0.7014 (tp30) REVERT: A 588 SER cc_start: 0.9410 (OUTLIER) cc_final: 0.9064 (p) REVERT: A 590 ARG cc_start: 0.8927 (mtt180) cc_final: 0.8472 (mpp-170) REVERT: A 781 SER cc_start: 0.8635 (OUTLIER) cc_final: 0.8426 (p) REVERT: C 590 ARG cc_start: 0.8698 (mtt180) cc_final: 0.8168 (mtm-85) REVERT: C 623 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8047 (mt-10) REVERT: D 566 GLU cc_start: 0.7343 (pt0) cc_final: 0.6638 (pm20) REVERT: D 590 ARG cc_start: 0.8852 (mpt-90) cc_final: 0.8229 (mtt90) REVERT: D 623 GLU cc_start: 0.8771 (tt0) cc_final: 0.8437 (mm-30) REVERT: E 37 ARG cc_start: 0.8015 (mtp-110) cc_final: 0.7791 (mtp85) REVERT: E 79 LYS cc_start: 0.8193 (mtmt) cc_final: 0.7640 (mptp) REVERT: E 81 ASP cc_start: 0.7544 (m-30) cc_final: 0.7220 (t0) REVERT: E 160 ASN cc_start: 0.7976 (m-40) cc_final: 0.7644 (m110) REVERT: F 58 MET cc_start: 0.7849 (tpp) cc_final: 0.7645 (mmm) REVERT: F 65 ARG cc_start: 0.8099 (mpp-170) cc_final: 0.7441 (mtm-85) REVERT: F 78 LYS cc_start: 0.8089 (ptmm) cc_final: 0.7761 (pttt) REVERT: G 24 MET cc_start: 0.8743 (tpt) cc_final: 0.8382 (tpt) REVERT: G 79 LYS cc_start: 0.8364 (ttmm) cc_final: 0.7906 (mptt) REVERT: G 99 ARG cc_start: 0.8270 (tpp80) cc_final: 0.7982 (mmt-90) REVERT: G 184 PHE cc_start: 0.7804 (m-80) cc_final: 0.7537 (m-10) outliers start: 31 outliers final: 8 residues processed: 208 average time/residue: 1.2605 time to fit residues: 280.5543 Evaluate side-chains 168 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 157 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain A residue 781 SER Chi-restraints excluded: chain B residue 623 GLU Chi-restraints excluded: chain B residue 781 SER Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 626 VAL Chi-restraints excluded: chain D residue 810 PHE Chi-restraints excluded: chain E residue 76 VAL Chi-restraints excluded: chain E residue 174 SER Chi-restraints excluded: chain G residue 174 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 0.9990 chunk 91 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 48 optimal weight: 0.9990 chunk 94 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 109 optimal weight: 8.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 198 HIS E 204 HIS F 204 HIS G 198 HIS G 204 HIS H 204 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.132138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.088784 restraints weight = 45934.628| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 5.65 r_work: 0.2576 rms_B_bonded: 4.94 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2572 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2572 r_free = 0.2572 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2572 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10578 Z= 0.135 Angle : 0.495 6.231 14243 Z= 0.268 Chirality : 0.038 0.179 1577 Planarity : 0.004 0.031 1711 Dihedral : 14.359 116.967 1745 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.39 % Allowed : 9.89 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 2.85 (0.24), residues: 1239 helix: 2.90 (0.17), residues: 933 sheet: -0.05 (1.19), residues: 20 loop : -1.63 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 574 HIS 0.003 0.001 HIS E 198 PHE 0.018 0.001 PHE B 542 TYR 0.009 0.001 TYR A 519 ARG 0.007 0.000 ARG F 99 Details of bonding type rmsd hydrogen bonds : bond 0.04423 ( 795) hydrogen bonds : angle 3.38279 ( 2329) SS BOND : bond 0.00970 ( 8) SS BOND : angle 0.70237 ( 16) covalent geometry : bond 0.00288 (10570) covalent geometry : angle 0.49444 (14227) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 1.119 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7891 (mmm160) cc_final: 0.7604 (mmm-85) REVERT: A 566 GLU cc_start: 0.7519 (tt0) cc_final: 0.7182 (tp30) REVERT: A 590 ARG cc_start: 0.8662 (mtt180) cc_final: 0.8352 (mpp-170) REVERT: B 566 GLU cc_start: 0.8103 (pm20) cc_final: 0.7526 (pt0) REVERT: B 791 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8419 (p) REVERT: B 809 GLU cc_start: 0.6880 (mm-30) cc_final: 0.6601 (pp20) REVERT: C 505 LYS cc_start: 0.7793 (tptp) cc_final: 0.7424 (tptp) REVERT: C 590 ARG cc_start: 0.8629 (mtt180) cc_final: 0.8179 (mtm-85) REVERT: C 623 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7684 (mt-10) REVERT: D 566 GLU cc_start: 0.7637 (pt0) cc_final: 0.6928 (pm20) REVERT: D 587 ILE cc_start: 0.8741 (pt) cc_final: 0.8515 (pt) REVERT: D 590 ARG cc_start: 0.8722 (mpt-90) cc_final: 0.8074 (mtt90) REVERT: D 623 GLU cc_start: 0.8654 (tt0) cc_final: 0.8400 (mm-30) REVERT: E 10 MET cc_start: 0.8177 (tpp) cc_final: 0.7816 (tpp) REVERT: E 37 ARG cc_start: 0.8241 (mtp-110) cc_final: 0.7826 (mtp85) REVERT: E 79 LYS cc_start: 0.7995 (mtmt) cc_final: 0.7658 (mptp) REVERT: E 81 ASP cc_start: 0.7562 (m-30) cc_final: 0.7242 (t0) REVERT: E 126 GLU cc_start: 0.6949 (OUTLIER) cc_final: 0.6561 (mp0) REVERT: E 160 ASN cc_start: 0.7734 (m-40) cc_final: 0.7486 (m-40) REVERT: F 150 ILE cc_start: 0.8584 (tt) cc_final: 0.8015 (pt) REVERT: G 24 MET cc_start: 0.8783 (tpt) cc_final: 0.8555 (tpt) REVERT: G 58 MET cc_start: 0.7813 (tpt) cc_final: 0.7573 (tpp) REVERT: G 65 ARG cc_start: 0.8130 (mtm-85) cc_final: 0.7891 (mtm-85) REVERT: G 76 VAL cc_start: 0.8082 (t) cc_final: 0.7870 (p) REVERT: G 79 LYS cc_start: 0.8436 (ttmm) cc_final: 0.7939 (mptt) REVERT: G 99 ARG cc_start: 0.8281 (tpp80) cc_final: 0.7897 (mmt-90) REVERT: G 102 ARG cc_start: 0.8883 (tmt-80) cc_final: 0.8583 (tpt170) REVERT: G 184 PHE cc_start: 0.7923 (m-80) cc_final: 0.7583 (m-10) REVERT: G 202 GLU cc_start: 0.7745 (pp20) cc_final: 0.7519 (pp20) outliers start: 27 outliers final: 10 residues processed: 190 average time/residue: 1.4260 time to fit residues: 288.1000 Evaluate side-chains 175 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain C residue 593 SER Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 126 GLU Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 31 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 8 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 4 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 120 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 71 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 10 optimal weight: 0.0170 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 198 HIS G 160 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.129371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.085967 restraints weight = 43430.606| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 5.63 r_work: 0.2531 rms_B_bonded: 4.91 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10578 Z= 0.171 Angle : 0.510 6.711 14243 Z= 0.275 Chirality : 0.039 0.175 1577 Planarity : 0.004 0.036 1711 Dihedral : 13.405 89.170 1731 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 4.07 % Allowed : 11.25 % Favored : 84.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.12 (0.24), residues: 1239 helix: 3.01 (0.16), residues: 933 sheet: -0.06 (1.28), residues: 20 loop : -1.19 (0.35), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 574 HIS 0.003 0.001 HIS E 60 PHE 0.023 0.002 PHE D 810 TYR 0.020 0.002 TYR C 812 ARG 0.008 0.001 ARG F 99 Details of bonding type rmsd hydrogen bonds : bond 0.04973 ( 795) hydrogen bonds : angle 3.36343 ( 2329) SS BOND : bond 0.00461 ( 8) SS BOND : angle 0.67101 ( 16) covalent geometry : bond 0.00394 (10570) covalent geometry : angle 0.50933 (14227) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 1.083 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7903 (mmm160) cc_final: 0.7636 (mmm-85) REVERT: A 566 GLU cc_start: 0.7626 (tt0) cc_final: 0.7383 (tp30) REVERT: A 590 ARG cc_start: 0.8723 (mtt180) cc_final: 0.8432 (mpp-170) REVERT: A 623 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8572 (tt0) REVERT: B 566 GLU cc_start: 0.7999 (pm20) cc_final: 0.7457 (pt0) REVERT: B 791 VAL cc_start: 0.8785 (OUTLIER) cc_final: 0.8521 (p) REVERT: C 590 ARG cc_start: 0.8795 (mtt180) cc_final: 0.8563 (mmt90) REVERT: C 623 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7783 (mt-10) REVERT: D 590 ARG cc_start: 0.8793 (mpt-90) cc_final: 0.8044 (mtt90) REVERT: D 623 GLU cc_start: 0.8636 (tt0) cc_final: 0.8424 (mm-30) REVERT: D 625 MET cc_start: 0.8995 (mtm) cc_final: 0.8759 (mtm) REVERT: E 10 MET cc_start: 0.8273 (tpp) cc_final: 0.7914 (tpp) REVERT: E 37 ARG cc_start: 0.8283 (mtp-110) cc_final: 0.7858 (mtp85) REVERT: E 81 ASP cc_start: 0.7704 (m-30) cc_final: 0.7445 (t0) REVERT: E 99 ARG cc_start: 0.8199 (OUTLIER) cc_final: 0.7986 (mtt90) REVERT: E 160 ASN cc_start: 0.7780 (m-40) cc_final: 0.7523 (m-40) REVERT: F 65 ARG cc_start: 0.7632 (mtm-85) cc_final: 0.6782 (mtp85) REVERT: F 150 ILE cc_start: 0.8647 (tt) cc_final: 0.8003 (pt) REVERT: G 24 MET cc_start: 0.8877 (tpt) cc_final: 0.8671 (tpt) REVERT: G 58 MET cc_start: 0.7843 (tpt) cc_final: 0.7567 (tpp) REVERT: G 79 LYS cc_start: 0.8529 (ttmm) cc_final: 0.7991 (mptt) REVERT: G 99 ARG cc_start: 0.8362 (tpp80) cc_final: 0.8096 (mtt90) REVERT: G 102 ARG cc_start: 0.8883 (tmt-80) cc_final: 0.8621 (tpt90) REVERT: G 184 PHE cc_start: 0.8005 (m-80) cc_final: 0.7722 (m-10) REVERT: G 202 GLU cc_start: 0.7857 (pp20) cc_final: 0.7633 (pp20) REVERT: G 205 GLN cc_start: 0.7035 (tt0) cc_final: 0.6818 (tt0) outliers start: 35 outliers final: 18 residues processed: 186 average time/residue: 1.4630 time to fit residues: 289.9517 Evaluate side-chains 179 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 623 GLU Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 15 VAL Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 82 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 198 HIS G 160 ASN H 160 ASN H 204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.132387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.090308 restraints weight = 48728.179| |-----------------------------------------------------------------------------| r_work (start): 0.3015 rms_B_bonded: 5.94 r_work: 0.2570 rms_B_bonded: 5.24 restraints_weight: 2.0000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2564 r_free = 0.2564 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2564 r_free = 0.2564 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 10578 Z= 0.113 Angle : 0.427 6.609 14243 Z= 0.234 Chirality : 0.036 0.118 1577 Planarity : 0.003 0.031 1711 Dihedral : 12.173 88.328 1731 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 3.69 % Allowed : 12.42 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.71 (0.24), residues: 1239 helix: 3.46 (0.16), residues: 928 sheet: 0.22 (1.27), residues: 20 loop : -1.01 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 177 HIS 0.002 0.001 HIS G 128 PHE 0.029 0.001 PHE G 127 TYR 0.015 0.001 TYR C 812 ARG 0.008 0.000 ARG F 99 Details of bonding type rmsd hydrogen bonds : bond 0.03940 ( 795) hydrogen bonds : angle 3.05110 ( 2329) SS BOND : bond 0.00294 ( 8) SS BOND : angle 0.63407 ( 16) covalent geometry : bond 0.00242 (10570) covalent geometry : angle 0.42633 (14227) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7881 (mmm160) cc_final: 0.7599 (mmm-85) REVERT: A 566 GLU cc_start: 0.7605 (tt0) cc_final: 0.7362 (tp30) REVERT: A 590 ARG cc_start: 0.8708 (mtt180) cc_final: 0.8442 (mpp-170) REVERT: A 623 GLU cc_start: 0.8822 (mt-10) cc_final: 0.8543 (tt0) REVERT: B 566 GLU cc_start: 0.7735 (pm20) cc_final: 0.7347 (pt0) REVERT: B 791 VAL cc_start: 0.8773 (OUTLIER) cc_final: 0.8444 (p) REVERT: C 590 ARG cc_start: 0.8795 (mtt180) cc_final: 0.8584 (mmt90) REVERT: D 587 ILE cc_start: 0.8791 (pt) cc_final: 0.8566 (pt) REVERT: D 590 ARG cc_start: 0.8849 (mpt-90) cc_final: 0.8139 (mtt90) REVERT: D 623 GLU cc_start: 0.8645 (tt0) cc_final: 0.8378 (mm-30) REVERT: D 625 MET cc_start: 0.8979 (mtm) cc_final: 0.8771 (mtm) REVERT: E 37 ARG cc_start: 0.8324 (mtp-110) cc_final: 0.7905 (mtp85) REVERT: E 56 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7227 (mm-30) REVERT: E 81 ASP cc_start: 0.7680 (m-30) cc_final: 0.7419 (t0) REVERT: E 99 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7840 (mtt90) REVERT: E 160 ASN cc_start: 0.7578 (m-40) cc_final: 0.7308 (m-40) REVERT: F 65 ARG cc_start: 0.7513 (mtm-85) cc_final: 0.6866 (mtp85) REVERT: F 150 ILE cc_start: 0.8574 (tt) cc_final: 0.8023 (pt) REVERT: G 58 MET cc_start: 0.7755 (tpt) cc_final: 0.7517 (tpp) REVERT: G 65 ARG cc_start: 0.8156 (mtm-85) cc_final: 0.7939 (ptp90) REVERT: G 76 VAL cc_start: 0.7903 (t) cc_final: 0.7630 (p) REVERT: G 79 LYS cc_start: 0.8524 (ttmm) cc_final: 0.8014 (mptt) REVERT: G 99 ARG cc_start: 0.8385 (tpp80) cc_final: 0.8108 (mtt90) REVERT: G 184 PHE cc_start: 0.7938 (m-80) cc_final: 0.7622 (m-10) REVERT: G 205 GLN cc_start: 0.6984 (tt0) cc_final: 0.6775 (tt0) outliers start: 31 outliers final: 18 residues processed: 185 average time/residue: 1.4402 time to fit residues: 283.3753 Evaluate side-chains 180 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 160 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain D residue 791 VAL Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 99 ARG Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 204 HIS Chi-restraints excluded: chain H residue 205 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 22 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 105 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 114 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 100 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 198 HIS F 160 ASN G 160 ASN H 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.130613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.087536 restraints weight = 47102.620| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 6.12 r_work: 0.2533 rms_B_bonded: 5.17 restraints_weight: 2.0000 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2529 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2529 r_free = 0.2529 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2529 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10578 Z= 0.143 Angle : 0.466 7.779 14243 Z= 0.252 Chirality : 0.037 0.125 1577 Planarity : 0.004 0.032 1711 Dihedral : 11.941 89.770 1728 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.88 % Allowed : 14.06 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.64 (0.24), residues: 1239 helix: 3.39 (0.16), residues: 927 sheet: 0.28 (1.27), residues: 20 loop : -0.95 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 574 HIS 0.007 0.001 HIS H 204 PHE 0.025 0.001 PHE D 810 TYR 0.014 0.001 TYR C 812 ARG 0.007 0.001 ARG F 99 Details of bonding type rmsd hydrogen bonds : bond 0.04479 ( 795) hydrogen bonds : angle 3.19192 ( 2329) SS BOND : bond 0.00257 ( 8) SS BOND : angle 0.71745 ( 16) covalent geometry : bond 0.00327 (10570) covalent geometry : angle 0.46528 (14227) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 161 time to evaluate : 1.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7892 (mmm160) cc_final: 0.7613 (mmm-85) REVERT: A 566 GLU cc_start: 0.7638 (tt0) cc_final: 0.7365 (tp30) REVERT: A 590 ARG cc_start: 0.8752 (mtt180) cc_final: 0.8433 (mpp-170) REVERT: A 623 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8531 (tt0) REVERT: B 566 GLU cc_start: 0.7988 (pm20) cc_final: 0.7553 (pt0) REVERT: B 791 VAL cc_start: 0.8793 (OUTLIER) cc_final: 0.8506 (p) REVERT: C 590 ARG cc_start: 0.8833 (mtt180) cc_final: 0.8594 (mmt90) REVERT: D 587 ILE cc_start: 0.8782 (pt) cc_final: 0.8565 (pt) REVERT: D 590 ARG cc_start: 0.8840 (mpt-90) cc_final: 0.8090 (mtt90) REVERT: D 623 GLU cc_start: 0.8669 (tt0) cc_final: 0.8421 (mm-30) REVERT: D 625 MET cc_start: 0.8918 (mtm) cc_final: 0.8710 (mtm) REVERT: E 37 ARG cc_start: 0.8285 (mtp-110) cc_final: 0.7845 (mtp85) REVERT: E 56 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7200 (mm-30) REVERT: E 81 ASP cc_start: 0.7720 (m-30) cc_final: 0.7432 (t0) REVERT: E 160 ASN cc_start: 0.7634 (m-40) cc_final: 0.7376 (m-40) REVERT: F 65 ARG cc_start: 0.7615 (mtm-85) cc_final: 0.6892 (mtp85) REVERT: F 150 ILE cc_start: 0.8637 (tt) cc_final: 0.8039 (pt) REVERT: G 58 MET cc_start: 0.7742 (tpt) cc_final: 0.7518 (tpp) REVERT: G 65 ARG cc_start: 0.8419 (mtm-85) cc_final: 0.7865 (ptp90) REVERT: G 79 LYS cc_start: 0.8526 (ttmm) cc_final: 0.8007 (mptt) REVERT: G 99 ARG cc_start: 0.8387 (tpp80) cc_final: 0.7937 (mmt-90) REVERT: G 184 PHE cc_start: 0.7958 (m-80) cc_final: 0.7651 (m-10) REVERT: G 202 GLU cc_start: 0.7703 (pp20) cc_final: 0.7463 (pp20) REVERT: G 205 GLN cc_start: 0.6968 (tt0) cc_final: 0.6744 (tt0) outliers start: 33 outliers final: 22 residues processed: 180 average time/residue: 1.4304 time to fit residues: 274.2086 Evaluate side-chains 183 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 203 LYS Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 31 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 86 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 36 optimal weight: 9.9990 chunk 72 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 160 ASN G 160 ASN H 160 ASN H 204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.130765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.088509 restraints weight = 52774.709| |-----------------------------------------------------------------------------| r_work (start): 0.2987 rms_B_bonded: 6.08 r_work: 0.2528 rms_B_bonded: 5.25 restraints_weight: 2.0000 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2517 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2517 r_free = 0.2517 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2517 r_free = 0.2517 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10578 Z= 0.143 Angle : 0.463 7.691 14243 Z= 0.250 Chirality : 0.037 0.126 1577 Planarity : 0.004 0.032 1711 Dihedral : 11.768 89.548 1728 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 4.07 % Allowed : 13.97 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.72 (0.24), residues: 1239 helix: 3.42 (0.16), residues: 927 sheet: 0.71 (1.33), residues: 20 loop : -0.87 (0.34), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 574 HIS 0.002 0.001 HIS E 60 PHE 0.014 0.001 PHE D 542 TYR 0.015 0.001 TYR C 812 ARG 0.009 0.001 ARG F 99 Details of bonding type rmsd hydrogen bonds : bond 0.04398 ( 795) hydrogen bonds : angle 3.18016 ( 2329) SS BOND : bond 0.00252 ( 8) SS BOND : angle 0.76282 ( 16) covalent geometry : bond 0.00328 (10570) covalent geometry : angle 0.46230 (14227) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 0.988 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7812 (mmm160) cc_final: 0.7561 (mmm-85) REVERT: A 566 GLU cc_start: 0.7566 (tt0) cc_final: 0.7365 (tp30) REVERT: A 590 ARG cc_start: 0.8751 (mtt180) cc_final: 0.8407 (mpp-170) REVERT: A 623 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8597 (tt0) REVERT: B 566 GLU cc_start: 0.7968 (pm20) cc_final: 0.7598 (pt0) REVERT: B 791 VAL cc_start: 0.8776 (OUTLIER) cc_final: 0.8488 (p) REVERT: B 809 GLU cc_start: 0.7468 (mm-30) cc_final: 0.7233 (mt-10) REVERT: D 587 ILE cc_start: 0.8761 (pt) cc_final: 0.8547 (pt) REVERT: D 590 ARG cc_start: 0.8833 (mpt-90) cc_final: 0.8049 (mtt90) REVERT: D 623 GLU cc_start: 0.8611 (tt0) cc_final: 0.8310 (mm-30) REVERT: D 625 MET cc_start: 0.8902 (mtm) cc_final: 0.8675 (mtm) REVERT: E 37 ARG cc_start: 0.8281 (mtp-110) cc_final: 0.7832 (mtp85) REVERT: E 56 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7587 (mm-30) REVERT: E 81 ASP cc_start: 0.7707 (m-30) cc_final: 0.7420 (t0) REVERT: E 160 ASN cc_start: 0.7650 (m-40) cc_final: 0.7428 (m-40) REVERT: F 65 ARG cc_start: 0.7547 (mtm-85) cc_final: 0.6870 (mtp85) REVERT: F 150 ILE cc_start: 0.8617 (tt) cc_final: 0.8020 (pt) REVERT: G 58 MET cc_start: 0.7745 (tpt) cc_final: 0.7543 (tpp) REVERT: G 79 LYS cc_start: 0.8547 (ttmm) cc_final: 0.8000 (mptt) REVERT: G 99 ARG cc_start: 0.8359 (tpp80) cc_final: 0.8043 (mmt-90) REVERT: G 184 PHE cc_start: 0.7934 (m-80) cc_final: 0.7723 (m-10) REVERT: G 202 GLU cc_start: 0.7735 (pp20) cc_final: 0.7531 (pp20) REVERT: H 126 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.5796 (mm-30) outliers start: 35 outliers final: 22 residues processed: 181 average time/residue: 1.4200 time to fit residues: 273.2668 Evaluate side-chains 187 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 8 ILE Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 89 optimal weight: 1.9990 chunk 95 optimal weight: 0.5980 chunk 52 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 198 HIS F 160 ASN G 160 ASN H 160 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.132338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.090640 restraints weight = 55327.238| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 6.55 r_work: 0.2548 rms_B_bonded: 5.43 restraints_weight: 2.0000 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2541 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2541 r_free = 0.2541 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2541 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.3294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 10578 Z= 0.114 Angle : 0.434 7.879 14243 Z= 0.235 Chirality : 0.036 0.119 1577 Planarity : 0.003 0.038 1711 Dihedral : 11.323 89.735 1728 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.49 % Allowed : 15.13 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.96 (0.24), residues: 1239 helix: 3.59 (0.16), residues: 928 sheet: 0.97 (1.37), residues: 20 loop : -0.76 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 177 HIS 0.002 0.001 HIS E 60 PHE 0.026 0.001 PHE D 810 TYR 0.016 0.001 TYR C 812 ARG 0.009 0.000 ARG F 99 Details of bonding type rmsd hydrogen bonds : bond 0.04000 ( 795) hydrogen bonds : angle 3.05921 ( 2329) SS BOND : bond 0.00198 ( 8) SS BOND : angle 0.74319 ( 16) covalent geometry : bond 0.00248 (10570) covalent geometry : angle 0.43331 (14227) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7833 (mmm160) cc_final: 0.7575 (mmm-85) REVERT: A 590 ARG cc_start: 0.8770 (mtt180) cc_final: 0.8442 (mpp-170) REVERT: A 623 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8638 (tt0) REVERT: B 566 GLU cc_start: 0.8001 (pm20) cc_final: 0.7539 (pt0) REVERT: B 791 VAL cc_start: 0.8769 (OUTLIER) cc_final: 0.8465 (p) REVERT: B 809 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7227 (mt-10) REVERT: D 587 ILE cc_start: 0.8729 (pt) cc_final: 0.8510 (pt) REVERT: D 590 ARG cc_start: 0.8851 (mpt-90) cc_final: 0.8092 (mtt90) REVERT: D 623 GLU cc_start: 0.8628 (tt0) cc_final: 0.8287 (tp30) REVERT: D 625 MET cc_start: 0.8927 (mtm) cc_final: 0.8704 (mtm) REVERT: E 37 ARG cc_start: 0.8304 (mtp-110) cc_final: 0.7850 (mtp85) REVERT: E 56 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7640 (mm-30) REVERT: E 81 ASP cc_start: 0.7711 (m-30) cc_final: 0.7411 (t0) REVERT: F 65 ARG cc_start: 0.7534 (mtm-85) cc_final: 0.6891 (mtp85) REVERT: F 150 ILE cc_start: 0.8629 (tt) cc_final: 0.8045 (pt) REVERT: G 31 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.7572 (p0) REVERT: G 58 MET cc_start: 0.7712 (tpt) cc_final: 0.7489 (tpp) REVERT: G 65 ARG cc_start: 0.8404 (mtm-85) cc_final: 0.7853 (ptp90) REVERT: G 79 LYS cc_start: 0.8542 (ttmm) cc_final: 0.8011 (mptt) REVERT: G 99 ARG cc_start: 0.8377 (tpp80) cc_final: 0.8166 (mtt90) REVERT: G 184 PHE cc_start: 0.7937 (m-10) cc_final: 0.7718 (m-10) REVERT: G 202 GLU cc_start: 0.7732 (pp20) cc_final: 0.7505 (pp20) outliers start: 29 outliers final: 19 residues processed: 182 average time/residue: 1.3811 time to fit residues: 267.6562 Evaluate side-chains 180 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 159 time to evaluate : 1.044 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 31 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 37 optimal weight: 3.9990 chunk 104 optimal weight: 0.7980 chunk 90 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 116 optimal weight: 1.9990 chunk 108 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 198 HIS F 160 ASN G 160 ASN H 160 ASN H 204 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.132004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.090159 restraints weight = 55899.051| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 6.47 r_work: 0.2542 rms_B_bonded: 5.41 restraints_weight: 2.0000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2538 r_free = 0.2538 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2538 r_free = 0.2538 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10578 Z= 0.119 Angle : 0.440 7.929 14243 Z= 0.238 Chirality : 0.036 0.121 1577 Planarity : 0.003 0.034 1711 Dihedral : 11.103 88.970 1728 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.78 % Allowed : 14.84 % Favored : 81.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.00 (0.24), residues: 1239 helix: 3.61 (0.16), residues: 928 sheet: 0.93 (1.37), residues: 20 loop : -0.69 (0.35), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 574 HIS 0.003 0.001 HIS E 60 PHE 0.014 0.001 PHE D 542 TYR 0.016 0.001 TYR C 812 ARG 0.008 0.000 ARG F 99 Details of bonding type rmsd hydrogen bonds : bond 0.04075 ( 795) hydrogen bonds : angle 3.06749 ( 2329) SS BOND : bond 0.00189 ( 8) SS BOND : angle 0.99571 ( 16) covalent geometry : bond 0.00262 (10570) covalent geometry : angle 0.43914 (14227) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 162 time to evaluate : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7817 (mmm160) cc_final: 0.7560 (mmm-85) REVERT: A 590 ARG cc_start: 0.8747 (mtt180) cc_final: 0.8473 (mpp-170) REVERT: A 623 GLU cc_start: 0.8873 (mt-10) cc_final: 0.8656 (tt0) REVERT: B 566 GLU cc_start: 0.7954 (pm20) cc_final: 0.7529 (pt0) REVERT: B 791 VAL cc_start: 0.8777 (OUTLIER) cc_final: 0.8490 (p) REVERT: B 809 GLU cc_start: 0.7471 (mm-30) cc_final: 0.7192 (mt-10) REVERT: D 587 ILE cc_start: 0.8762 (pt) cc_final: 0.8532 (pt) REVERT: D 590 ARG cc_start: 0.8879 (mpt-90) cc_final: 0.8105 (mtt90) REVERT: D 623 GLU cc_start: 0.8643 (tt0) cc_final: 0.8285 (tp30) REVERT: D 625 MET cc_start: 0.8917 (mtm) cc_final: 0.8691 (mtm) REVERT: E 37 ARG cc_start: 0.8296 (mtp-110) cc_final: 0.7895 (mtp85) REVERT: E 56 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7642 (mm-30) REVERT: E 81 ASP cc_start: 0.7707 (m-30) cc_final: 0.7410 (t0) REVERT: F 65 ARG cc_start: 0.7517 (mtm-85) cc_final: 0.6900 (mtp85) REVERT: F 150 ILE cc_start: 0.8641 (tt) cc_final: 0.8055 (pt) REVERT: G 31 ASP cc_start: 0.8576 (OUTLIER) cc_final: 0.7609 (p0) REVERT: G 58 MET cc_start: 0.7708 (tpt) cc_final: 0.7484 (tpp) REVERT: G 65 ARG cc_start: 0.8418 (mtm-85) cc_final: 0.7950 (ptp90) REVERT: G 79 LYS cc_start: 0.8542 (ttmm) cc_final: 0.7997 (mptt) REVERT: G 99 ARG cc_start: 0.8382 (tpp80) cc_final: 0.8166 (mtt90) REVERT: G 173 TYR cc_start: 0.8883 (p90) cc_final: 0.8660 (p90) REVERT: G 184 PHE cc_start: 0.7946 (m-10) cc_final: 0.7721 (m-10) REVERT: G 202 GLU cc_start: 0.7738 (pp20) cc_final: 0.7496 (pp20) outliers start: 32 outliers final: 20 residues processed: 182 average time/residue: 1.3636 time to fit residues: 264.6064 Evaluate side-chains 181 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 159 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 8 ILE Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 56 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 36 optimal weight: 0.3980 chunk 54 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 83 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 198 HIS F 160 ASN F 198 HIS G 160 ASN H 160 ASN H 204 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.132977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.090883 restraints weight = 52035.374| |-----------------------------------------------------------------------------| r_work (start): 0.3023 rms_B_bonded: 6.15 r_work: 0.2565 rms_B_bonded: 5.34 restraints_weight: 2.0000 r_work (final): 0.2565 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2550 r_free = 0.2550 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2550 r_free = 0.2550 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10578 Z= 0.115 Angle : 0.453 8.915 14243 Z= 0.243 Chirality : 0.036 0.146 1577 Planarity : 0.003 0.040 1711 Dihedral : 10.871 88.051 1728 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 3.98 % Allowed : 15.03 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.06 (0.24), residues: 1239 helix: 3.68 (0.16), residues: 928 sheet: None (None), residues: 0 loop : -0.68 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 177 HIS 0.003 0.001 HIS H 204 PHE 0.027 0.001 PHE D 810 TYR 0.026 0.001 TYR C 812 ARG 0.010 0.000 ARG F 99 Details of bonding type rmsd hydrogen bonds : bond 0.03898 ( 795) hydrogen bonds : angle 3.02430 ( 2329) SS BOND : bond 0.00690 ( 8) SS BOND : angle 2.36332 ( 16) covalent geometry : bond 0.00252 (10570) covalent geometry : angle 0.44601 (14227) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 161 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7805 (mmm160) cc_final: 0.7545 (mmm-85) REVERT: A 590 ARG cc_start: 0.8732 (mtt180) cc_final: 0.8480 (mpp-170) REVERT: B 566 GLU cc_start: 0.7810 (pm20) cc_final: 0.7388 (pt0) REVERT: B 791 VAL cc_start: 0.8770 (OUTLIER) cc_final: 0.8479 (p) REVERT: B 809 GLU cc_start: 0.7456 (mm-30) cc_final: 0.7169 (mt-10) REVERT: D 587 ILE cc_start: 0.8728 (pt) cc_final: 0.8509 (pt) REVERT: D 590 ARG cc_start: 0.8875 (mpt-90) cc_final: 0.8103 (mtt90) REVERT: D 623 GLU cc_start: 0.8604 (tt0) cc_final: 0.8266 (tp30) REVERT: D 625 MET cc_start: 0.8923 (mtm) cc_final: 0.8693 (mtm) REVERT: E 37 ARG cc_start: 0.8293 (mtp-110) cc_final: 0.7885 (mtp85) REVERT: E 56 GLU cc_start: 0.8021 (mt-10) cc_final: 0.7652 (mm-30) REVERT: E 81 ASP cc_start: 0.7695 (m-30) cc_final: 0.7399 (t0) REVERT: E 203 LYS cc_start: 0.7482 (ttpt) cc_final: 0.7203 (tttt) REVERT: F 65 ARG cc_start: 0.7524 (mtm-85) cc_final: 0.6909 (mtp85) REVERT: F 150 ILE cc_start: 0.8596 (tt) cc_final: 0.8048 (pt) REVERT: G 58 MET cc_start: 0.7714 (tpt) cc_final: 0.7474 (tpp) REVERT: G 65 ARG cc_start: 0.8416 (mtm-85) cc_final: 0.7920 (ptp90) REVERT: G 79 LYS cc_start: 0.8526 (ttmm) cc_final: 0.7989 (mptt) REVERT: G 99 ARG cc_start: 0.8376 (tpp80) cc_final: 0.8158 (mtt90) REVERT: G 184 PHE cc_start: 0.7932 (m-10) cc_final: 0.7716 (m-10) REVERT: G 202 GLU cc_start: 0.7733 (pp20) cc_final: 0.7487 (pp20) outliers start: 34 outliers final: 20 residues processed: 182 average time/residue: 1.4012 time to fit residues: 271.1202 Evaluate side-chains 178 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 157 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 542 PHE Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 31 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 34 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 109 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 114 optimal weight: 9.9990 chunk 92 optimal weight: 5.9990 chunk 19 optimal weight: 0.4980 chunk 102 optimal weight: 0.7980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 198 HIS F 160 ASN F 198 HIS G 160 ASN H 160 ASN H 204 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.132531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.089622 restraints weight = 50817.064| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 5.82 r_work: 0.2566 rms_B_bonded: 5.18 restraints_weight: 2.0000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2554 r_free = 0.2554 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2554 r_free = 0.2554 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 10578 Z= 0.120 Angle : 0.475 10.840 14243 Z= 0.250 Chirality : 0.036 0.130 1577 Planarity : 0.003 0.040 1711 Dihedral : 10.834 87.460 1728 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.49 % Allowed : 15.81 % Favored : 80.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.01 (0.24), residues: 1239 helix: 3.65 (0.16), residues: 928 sheet: None (None), residues: 0 loop : -0.71 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 574 HIS 0.003 0.001 HIS F 204 PHE 0.014 0.001 PHE D 542 TYR 0.026 0.001 TYR C 812 ARG 0.010 0.000 ARG F 99 Details of bonding type rmsd hydrogen bonds : bond 0.03989 ( 795) hydrogen bonds : angle 3.04666 ( 2329) SS BOND : bond 0.00755 ( 8) SS BOND : angle 2.94532 ( 16) covalent geometry : bond 0.00268 (10570) covalent geometry : angle 0.46452 (14227) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2478 Ramachandran restraints generated. 1239 Oldfield, 0 Emsley, 1239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 155 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7838 (mmm160) cc_final: 0.7581 (mmm-85) REVERT: A 590 ARG cc_start: 0.8741 (mtt180) cc_final: 0.8487 (mpp-170) REVERT: B 566 GLU cc_start: 0.7805 (pm20) cc_final: 0.7410 (pt0) REVERT: B 791 VAL cc_start: 0.8784 (OUTLIER) cc_final: 0.8505 (p) REVERT: B 809 GLU cc_start: 0.7466 (mm-30) cc_final: 0.7033 (mt-10) REVERT: D 587 ILE cc_start: 0.8754 (pt) cc_final: 0.8533 (pt) REVERT: D 590 ARG cc_start: 0.8869 (mpt-90) cc_final: 0.8102 (mtt90) REVERT: D 623 GLU cc_start: 0.8582 (tt0) cc_final: 0.8325 (mm-30) REVERT: D 625 MET cc_start: 0.8925 (mtm) cc_final: 0.8719 (mtm) REVERT: E 37 ARG cc_start: 0.8317 (mtp-110) cc_final: 0.7896 (mtp85) REVERT: E 56 GLU cc_start: 0.8020 (mt-10) cc_final: 0.7667 (mm-30) REVERT: E 81 ASP cc_start: 0.7726 (m-30) cc_final: 0.7439 (t0) REVERT: F 65 ARG cc_start: 0.7525 (mtm-85) cc_final: 0.6914 (mtp85) REVERT: F 150 ILE cc_start: 0.8643 (tt) cc_final: 0.8053 (pt) REVERT: G 31 ASP cc_start: 0.8564 (OUTLIER) cc_final: 0.7581 (p0) REVERT: G 65 ARG cc_start: 0.8412 (mtm-85) cc_final: 0.7993 (ptp90) REVERT: G 79 LYS cc_start: 0.8521 (ttmm) cc_final: 0.8004 (mptt) REVERT: G 99 ARG cc_start: 0.8384 (tpp80) cc_final: 0.8161 (mtt90) REVERT: G 184 PHE cc_start: 0.7953 (m-10) cc_final: 0.7732 (m-10) REVERT: G 202 GLU cc_start: 0.7751 (pp20) cc_final: 0.7499 (pp20) outliers start: 29 outliers final: 21 residues processed: 174 average time/residue: 1.3835 time to fit residues: 256.1429 Evaluate side-chains 177 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 154 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 542 PHE Chi-restraints excluded: chain A residue 588 SER Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain D residue 588 SER Chi-restraints excluded: chain E residue 66 THR Chi-restraints excluded: chain E residue 204 HIS Chi-restraints excluded: chain F residue 8 ILE Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain F residue 61 SER Chi-restraints excluded: chain F residue 66 THR Chi-restraints excluded: chain F residue 120 LEU Chi-restraints excluded: chain F residue 148 SER Chi-restraints excluded: chain F residue 204 HIS Chi-restraints excluded: chain G residue 31 ASP Chi-restraints excluded: chain G residue 66 THR Chi-restraints excluded: chain G residue 70 GLU Chi-restraints excluded: chain G residue 204 HIS Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 204 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 113 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 115 optimal weight: 1.9990 chunk 63 optimal weight: 0.0870 chunk 89 optimal weight: 0.8980 overall best weight: 0.8960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 198 HIS F 160 ASN F 198 HIS G 160 ASN H 160 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.132442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.089715 restraints weight = 53132.748| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 5.90 r_work: 0.2562 rms_B_bonded: 5.22 restraints_weight: 2.0000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2559 r_free = 0.2559 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2559 r_free = 0.2559 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 10578 Z= 0.122 Angle : 0.476 10.528 14243 Z= 0.250 Chirality : 0.036 0.130 1577 Planarity : 0.003 0.039 1711 Dihedral : 10.837 87.070 1728 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 3.69 % Allowed : 15.71 % Favored : 80.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 4.01 (0.24), residues: 1239 helix: 3.65 (0.16), residues: 928 sheet: None (None), residues: 0 loop : -0.74 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 574 HIS 0.003 0.001 HIS F 204 PHE 0.031 0.001 PHE D 810 TYR 0.026 0.001 TYR C 812 ARG 0.009 0.000 ARG F 99 Details of bonding type rmsd hydrogen bonds : bond 0.04018 ( 795) hydrogen bonds : angle 3.05048 ( 2329) SS BOND : bond 0.00749 ( 8) SS BOND : angle 2.92005 ( 16) covalent geometry : bond 0.00274 (10570) covalent geometry : angle 0.46559 (14227) =============================================================================== Job complete usr+sys time: 8331.52 seconds wall clock time: 143 minutes 54.72 seconds (8634.72 seconds total)