Starting phenix.real_space_refine on Thu Jul 2 23:22:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8c2i_16391/07_2026/8c2i_16391.cif Found real_map, /net/cci-nas-00/data/ceres_data/8c2i_16391/07_2026/8c2i_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 { model { file = "/net/cci-nas-00/data/ceres_data/8c2i_16391/07_2026/8c2i_16391.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8c2i_16391/07_2026/8c2i_16391.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8c2i_16391/07_2026/8c2i_16391.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8c2i_16391/07_2026/8c2i_16391.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8c2i_16391/07_2026/8c2i_16391.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8c2i_16391/07_2026/8c2i_16391.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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, 'TRP:plan': 1, 'ASP:plan': 1, 'ARG: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, 'TRP:plan': 1, 'ASP:plan': 1, 'ARG: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, 'TRP:plan': 1, 'ASP:plan': 1, 'ARG: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, 'TRP:plan': 1, 'ASP:plan': 1, 'ARG: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: 2.79, per 1000 atoms: 0.27 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: 1.01 Conformation dependent library (CDL) restraints added in 511.9 milliseconds 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: 0.18 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: 1.26 Time building geometry restraints manager: 1.36 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: 5516 23.89 - 47.77: 393 47.77 - 71.66: 85 71.66 - 95.54: 14 95.54 - 119.43: 2 Dihedral angle restraints: 6010 sinusoidal: 2373 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 6007 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 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 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: 0.760 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 10.470 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 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:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 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 : 17.038 119.430 3660 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.027 0.003 ARG G 102 TYR 0.041 0.009 TYR H 96 PHE 0.063 0.008 PHE D 567 TRP 0.045 0.010 TRP D 602 HIS 0.017 0.004 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00998 / 0.64 (10570) covalent geometry : angle 1.27441 / 0.82 (14227) SS BOND : bond 0.01891 / 0.97 ( 8) SS BOND : angle 2.81432 / 1.25 ( 16) hydrogen bonds : bond 0.13711 / 8.93 ( 795) hydrogen bonds : angle 5.50581 / 4.06 ( 2329) *********************** 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 : 0.299 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: 0.5064 time to fit residues: 112.7366 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 : 0.320 ------------------------------------------------------------------------------- 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 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 7.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** E 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 204 HIS F 204 HIS G 198 HIS G 204 HIS H 204 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.132479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.089675 restraints weight = 49262.435| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 6.05 r_work: 0.2571 rms_B_bonded: 5.08 restraints_weight: 2.0000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2573 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2573 r_free = 0.2573 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 = 0.2573 r_free = 0.2573 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2573 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10578 Z= 0.127 Angle : 0.488 6.273 14243 Z= 0.265 Chirality : 0.038 0.185 1577 Planarity : 0.004 0.031 1711 Dihedral : 13.359 114.639 1673 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.20 % Allowed : 9.99 % Favored : 86.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.24), residues: 1239 helix: 2.92 (0.17), residues: 933 sheet: 0.01 (1.20), residues: 20 loop : -1.62 (0.34), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 99 TYR 0.010 0.001 TYR C 519 PHE 0.018 0.001 PHE B 542 TRP 0.010 0.001 TRP C 574 HIS 0.004 0.001 HIS E 198 Details of bonding type rmsd/Z covalent geometry : bond 0.00270 / 0.13 (10570) covalent geometry : angle 0.48790 / 0.27 (14227) SS BOND : bond 0.00595 / 0.30 ( 8) SS BOND : angle 0.70216 / 0.35 ( 16) hydrogen bonds : bond 0.04375 / 2.84 ( 795) hydrogen bonds : angle 3.37222 / 2.48 ( 2329) *********************** 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 203 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.222 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7895 (mmm160) cc_final: 0.7609 (mmm-85) REVERT: A 566 GLU cc_start: 0.7528 (tt0) cc_final: 0.7172 (tp30) REVERT: A 590 ARG cc_start: 0.8672 (mtt180) cc_final: 0.8363 (mpp-170) REVERT: B 566 GLU cc_start: 0.8100 (pm20) cc_final: 0.7532 (pt0) REVERT: B 791 VAL cc_start: 0.8756 (OUTLIER) cc_final: 0.8425 (p) REVERT: B 809 GLU cc_start: 0.6923 (mm-30) cc_final: 0.6648 (pp20) REVERT: C 505 LYS cc_start: 0.7776 (tptp) cc_final: 0.7448 (tptp) REVERT: C 590 ARG cc_start: 0.8634 (mtt180) cc_final: 0.8181 (mtm-85) REVERT: C 623 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7702 (mt-10) REVERT: D 566 GLU cc_start: 0.7635 (pt0) cc_final: 0.6934 (pm20) REVERT: D 587 ILE cc_start: 0.8781 (pt) cc_final: 0.8553 (pt) REVERT: D 590 ARG cc_start: 0.8727 (mpt-90) cc_final: 0.8087 (mtt90) REVERT: D 623 GLU cc_start: 0.8688 (tt0) cc_final: 0.8434 (mm-30) REVERT: E 10 MET cc_start: 0.8185 (tpp) cc_final: 0.7824 (tpp) REVERT: E 37 ARG cc_start: 0.8262 (mtp-110) cc_final: 0.7866 (mtp85) REVERT: E 79 LYS cc_start: 0.7992 (mtmt) cc_final: 0.7660 (mptp) REVERT: E 81 ASP cc_start: 0.7565 (m-30) cc_final: 0.7240 (t0) REVERT: E 126 GLU cc_start: 0.6946 (OUTLIER) cc_final: 0.6562 (mp0) REVERT: E 160 ASN cc_start: 0.7738 (m-40) cc_final: 0.7421 (m110) REVERT: F 78 LYS cc_start: 0.7905 (ptmm) cc_final: 0.7676 (pttt) REVERT: F 150 ILE cc_start: 0.8579 (tt) cc_final: 0.8015 (pt) REVERT: G 24 MET cc_start: 0.8787 (tpt) cc_final: 0.8579 (tpt) REVERT: G 58 MET cc_start: 0.7815 (tpt) cc_final: 0.7569 (tpp) REVERT: G 65 ARG cc_start: 0.8145 (mtm-85) cc_final: 0.7904 (mtm-85) REVERT: G 76 VAL cc_start: 0.8079 (t) cc_final: 0.7864 (p) REVERT: G 79 LYS cc_start: 0.8441 (ttmm) cc_final: 0.7945 (mptt) REVERT: G 99 ARG cc_start: 0.8283 (tpp80) cc_final: 0.8069 (mtt90) REVERT: G 102 ARG cc_start: 0.8886 (tmt-80) cc_final: 0.8604 (tpt170) REVERT: G 184 PHE cc_start: 0.7938 (m-80) cc_final: 0.7597 (m-10) REVERT: G 202 GLU cc_start: 0.7747 (pp20) cc_final: 0.7523 (pp20) REVERT: H 58 MET cc_start: 0.7341 (OUTLIER) cc_final: 0.7140 (tpt) outliers start: 25 outliers final: 10 residues processed: 191 average time/residue: 0.5389 time to fit residues: 109.6743 Evaluate side-chains 178 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 164 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 58 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 56 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 52 optimal weight: 5.9990 chunk 111 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 44 optimal weight: 0.4980 chunk 101 optimal weight: 1.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 198 HIS G 160 ASN H 204 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.132475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.083198 restraints weight = 44787.811| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 3.61 r_work: 0.2647 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2642 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2642 r_free = 0.2642 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2642 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2641 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= 0.119 Angle : 0.444 6.871 14243 Z= 0.242 Chirality : 0.037 0.170 1577 Planarity : 0.004 0.031 1711 Dihedral : 11.722 87.604 1659 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.98 % Allowed : 10.57 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.49 (0.24), residues: 1239 helix: 3.30 (0.16), residues: 934 sheet: -0.11 (1.23), residues: 20 loop : -1.16 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 99 TYR 0.020 0.001 TYR C 812 PHE 0.023 0.001 PHE D 810 TRP 0.007 0.001 TRP C 574 HIS 0.002 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.12 (10570) covalent geometry : angle 0.44422 / 0.24 (14227) SS BOND : bond 0.00345 / 0.17 ( 8) SS BOND : angle 0.58343 / 0.31 ( 16) hydrogen bonds : bond 0.04147 / 2.67 ( 795) hydrogen bonds : angle 3.10833 / 2.29 ( 2329) *********************** 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 212 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 178 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7955 (mmm160) cc_final: 0.7694 (mmm-85) REVERT: A 566 GLU cc_start: 0.7494 (tt0) cc_final: 0.7225 (tp30) REVERT: A 590 ARG cc_start: 0.8639 (mtt180) cc_final: 0.8398 (mpp-170) REVERT: A 623 GLU cc_start: 0.8591 (mt-10) cc_final: 0.8360 (tt0) REVERT: B 566 GLU cc_start: 0.7690 (pm20) cc_final: 0.7294 (pt0) REVERT: B 791 VAL cc_start: 0.8722 (OUTLIER) cc_final: 0.8421 (p) REVERT: C 590 ARG cc_start: 0.8654 (mtt180) cc_final: 0.8427 (mmt90) REVERT: C 623 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7696 (tt0) REVERT: C 625 MET cc_start: 0.5917 (mmm) cc_final: 0.5529 (mmt) REVERT: D 587 ILE cc_start: 0.8800 (pt) cc_final: 0.8594 (pt) REVERT: D 590 ARG cc_start: 0.8689 (mpt-90) cc_final: 0.7968 (mtt90) REVERT: D 625 MET cc_start: 0.8964 (mtm) cc_final: 0.8764 (mtm) REVERT: E 10 MET cc_start: 0.8183 (tpp) cc_final: 0.7726 (tpp) REVERT: E 37 ARG cc_start: 0.8206 (mtp-110) cc_final: 0.7722 (mtp85) REVERT: E 81 ASP cc_start: 0.7772 (m-30) cc_final: 0.7462 (t0) REVERT: E 99 ARG cc_start: 0.8225 (OUTLIER) cc_final: 0.7932 (mtt90) REVERT: E 160 ASN cc_start: 0.7627 (m-40) cc_final: 0.7413 (m-40) REVERT: F 65 ARG cc_start: 0.7542 (mtm-85) cc_final: 0.6801 (mtp85) REVERT: F 150 ILE cc_start: 0.8584 (tt) cc_final: 0.7966 (pt) REVERT: G 58 MET cc_start: 0.7828 (tpt) cc_final: 0.7522 (tpp) REVERT: G 76 VAL cc_start: 0.8033 (t) cc_final: 0.7796 (p) REVERT: G 79 LYS cc_start: 0.8450 (ttmm) cc_final: 0.7942 (mptt) REVERT: G 99 ARG cc_start: 0.8211 (tpp80) cc_final: 0.7945 (mtt90) REVERT: G 184 PHE cc_start: 0.7874 (m-80) cc_final: 0.7532 (m-10) REVERT: G 202 GLU cc_start: 0.7856 (pp20) cc_final: 0.7622 (pp20) REVERT: G 205 GLN cc_start: 0.7291 (tt0) cc_final: 0.6970 (tt0) outliers start: 34 outliers final: 14 residues processed: 191 average time/residue: 0.5505 time to fit residues: 111.7158 Evaluate side-chains 179 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 162 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 791 VAL 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 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 14 optimal weight: 0.5980 chunk 75 optimal weight: 7.9990 chunk 109 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 88 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 115 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 198 HIS F 198 HIS 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 = 0.3638 r_free = 0.3638 target = 0.132543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.083560 restraints weight = 55890.424| |-----------------------------------------------------------------------------| r_work (start): 0.2882 rms_B_bonded: 4.05 r_work: 0.2609 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10578 Z= 0.116 Angle : 0.427 5.882 14243 Z= 0.234 Chirality : 0.036 0.121 1577 Planarity : 0.003 0.032 1711 Dihedral : 11.131 87.962 1659 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 3.69 % Allowed : 12.51 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.75 (0.24), residues: 1239 helix: 3.44 (0.16), residues: 934 sheet: 0.13 (1.30), residues: 20 loop : -0.91 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 99 TYR 0.013 0.001 TYR G 200 PHE 0.014 0.001 PHE B 542 TRP 0.006 0.001 TRP C 574 HIS 0.004 0.001 HIS H 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.12 (10570) covalent geometry : angle 0.42696 / 0.23 (14227) SS BOND : bond 0.00187 / 0.10 ( 8) SS BOND : angle 0.67034 / 0.36 ( 16) hydrogen bonds : bond 0.04067 / 2.62 ( 795) hydrogen bonds : angle 3.08414 / 2.27 ( 2329) *********************** 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 196 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7939 (mmm160) cc_final: 0.7664 (mmm-85) REVERT: A 566 GLU cc_start: 0.7566 (tt0) cc_final: 0.7271 (tp30) REVERT: A 590 ARG cc_start: 0.8643 (mtt180) cc_final: 0.8430 (mpp-170) REVERT: A 623 GLU cc_start: 0.8710 (mt-10) cc_final: 0.8454 (tt0) REVERT: B 566 GLU cc_start: 0.7738 (pm20) cc_final: 0.7326 (pt0) REVERT: B 791 VAL cc_start: 0.8769 (OUTLIER) cc_final: 0.8434 (p) REVERT: C 590 ARG cc_start: 0.8704 (mtt180) cc_final: 0.8481 (mmt90) REVERT: D 587 ILE cc_start: 0.8778 (pt) cc_final: 0.8560 (pt) REVERT: D 590 ARG cc_start: 0.8722 (mpt-90) cc_final: 0.8009 (mtt90) REVERT: D 625 MET cc_start: 0.8980 (mtm) cc_final: 0.8753 (mtm) REVERT: E 37 ARG cc_start: 0.8286 (mtp-110) cc_final: 0.7769 (mtp85) REVERT: E 81 ASP cc_start: 0.7639 (m-30) cc_final: 0.7391 (t0) REVERT: E 99 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7921 (mtt90) REVERT: E 160 ASN cc_start: 0.7584 (m-40) cc_final: 0.7365 (m-40) REVERT: F 65 ARG cc_start: 0.7533 (mtm-85) cc_final: 0.6763 (mtp85) REVERT: F 150 ILE cc_start: 0.8617 (tt) cc_final: 0.8031 (pt) REVERT: G 58 MET cc_start: 0.7760 (tpt) cc_final: 0.7520 (tpp) REVERT: G 65 ARG cc_start: 0.8096 (mtm-85) cc_final: 0.7886 (ptp90) REVERT: G 76 VAL cc_start: 0.8023 (t) cc_final: 0.7787 (p) REVERT: G 79 LYS cc_start: 0.8505 (ttmm) cc_final: 0.7998 (mptt) REVERT: G 99 ARG cc_start: 0.8277 (tpp80) cc_final: 0.8011 (mtt90) REVERT: G 184 PHE cc_start: 0.7882 (m-80) cc_final: 0.7534 (m-10) REVERT: G 202 GLU cc_start: 0.7850 (pp20) cc_final: 0.7639 (pp20) REVERT: G 205 GLN cc_start: 0.7258 (tt0) cc_final: 0.6966 (tt0) outliers start: 31 outliers final: 16 residues processed: 180 average time/residue: 0.5760 time to fit residues: 110.0189 Evaluate side-chains 179 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 115 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 48 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 70 optimal weight: 5.9990 chunk 58 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 105 optimal weight: 4.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3633 r_free = 0.3633 target = 0.132084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.090052 restraints weight = 50265.459| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 6.41 r_work: 0.2545 rms_B_bonded: 5.38 restraints_weight: 2.0000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2537 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2537 r_free = 0.2537 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 = 0.2537 r_free = 0.2537 target_work(ls_wunit_k1) = 0.061 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2537 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10578 Z= 0.120 Angle : 0.432 6.539 14243 Z= 0.235 Chirality : 0.036 0.122 1577 Planarity : 0.003 0.031 1711 Dihedral : 10.362 89.402 1656 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.88 % Allowed : 12.80 % Favored : 83.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.83 (0.24), residues: 1239 helix: 3.49 (0.16), residues: 934 sheet: 0.09 (1.23), residues: 20 loop : -0.82 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 99 TYR 0.013 0.001 TYR C 812 PHE 0.012 0.001 PHE B 580 TRP 0.006 0.001 TRP C 574 HIS 0.003 0.001 HIS E 128 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (10570) covalent geometry : angle 0.43187 / 0.23 (14227) SS BOND : bond 0.00103 / 0.06 ( 8) SS BOND : angle 0.65644 / 0.36 ( 16) hydrogen bonds : bond 0.04134 / 2.66 ( 795) hydrogen bonds : angle 3.08752 / 2.27 ( 2329) *********************** 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 202 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 169 time to evaluate : 0.249 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7887 (mmm160) cc_final: 0.7617 (mmm-85) REVERT: A 566 GLU cc_start: 0.7624 (tt0) cc_final: 0.7364 (tp30) REVERT: A 590 ARG cc_start: 0.8748 (mtt180) cc_final: 0.8471 (mpp-170) REVERT: A 623 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8576 (tt0) REVERT: B 566 GLU cc_start: 0.7785 (pm20) cc_final: 0.7360 (pt0) REVERT: B 791 VAL cc_start: 0.8792 (OUTLIER) cc_final: 0.8481 (p) REVERT: B 809 GLU cc_start: 0.7386 (mm-30) cc_final: 0.7111 (mt-10) REVERT: C 590 ARG cc_start: 0.8772 (mtt180) cc_final: 0.8542 (mmt90) REVERT: D 590 ARG cc_start: 0.8842 (mpt-90) cc_final: 0.8122 (mtt90) REVERT: D 625 MET cc_start: 0.9004 (mtm) cc_final: 0.8798 (mtm) REVERT: E 37 ARG cc_start: 0.8267 (mtp-110) cc_final: 0.7757 (mtp85) REVERT: E 81 ASP cc_start: 0.7721 (m-30) cc_final: 0.7435 (t0) REVERT: E 160 ASN cc_start: 0.7609 (m-40) cc_final: 0.7376 (m-40) REVERT: E 203 LYS cc_start: 0.7563 (OUTLIER) cc_final: 0.7358 (tttt) REVERT: F 41 ARG cc_start: 0.4466 (mtm180) cc_final: 0.4195 (mtt180) REVERT: F 65 ARG cc_start: 0.7588 (mtm-85) cc_final: 0.6895 (mtp85) REVERT: F 150 ILE cc_start: 0.8633 (tt) cc_final: 0.8042 (pt) REVERT: G 58 MET cc_start: 0.7723 (tpt) cc_final: 0.7506 (tpp) REVERT: G 65 ARG cc_start: 0.8398 (mtm-85) cc_final: 0.7893 (ptp90) REVERT: G 76 VAL cc_start: 0.8010 (t) cc_final: 0.7773 (p) REVERT: G 79 LYS cc_start: 0.8537 (ttmm) cc_final: 0.7997 (mptt) REVERT: G 99 ARG cc_start: 0.8309 (tpp80) cc_final: 0.8085 (mtt90) REVERT: G 184 PHE cc_start: 0.7973 (m-80) cc_final: 0.7654 (m-10) REVERT: G 202 GLU cc_start: 0.7928 (pp20) cc_final: 0.7643 (pp20) REVERT: G 205 GLN cc_start: 0.7074 (tt0) cc_final: 0.6815 (tt0) outliers start: 33 outliers final: 19 residues processed: 187 average time/residue: 0.5797 time to fit residues: 115.2495 Evaluate side-chains 185 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 588 SER Chi-restraints excluded: chain B residue 590 ARG Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain C residue 542 PHE Chi-restraints excluded: chain C residue 593 SER 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 14 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 99 optimal weight: 5.9990 chunk 112 optimal weight: 0.5980 chunk 36 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 102 optimal weight: 0.9980 chunk 96 optimal weight: 0.9990 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.132749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.090892 restraints weight = 52055.174| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 6.47 r_work: 0.2556 rms_B_bonded: 5.39 restraints_weight: 2.0000 r_work (final): 0.2556 ------------------------------------------------------------------------------- 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 = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 10578 Z= 0.114 Angle : 0.425 8.254 14243 Z= 0.231 Chirality : 0.036 0.119 1577 Planarity : 0.003 0.031 1711 Dihedral : 10.013 89.360 1656 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 3.69 % Allowed : 13.87 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.98 (0.24), residues: 1239 helix: 3.59 (0.16), residues: 934 sheet: 0.36 (1.27), residues: 20 loop : -0.74 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 129 TYR 0.015 0.001 TYR C 812 PHE 0.012 0.001 PHE B 580 TRP 0.006 0.001 TRP C 574 HIS 0.002 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.11 (10570) covalent geometry : angle 0.42511 / 0.23 (14227) SS BOND : bond 0.00231 / 0.11 ( 8) SS BOND : angle 0.67366 / 0.38 ( 16) hydrogen bonds : bond 0.03943 / 2.54 ( 795) hydrogen bonds : angle 3.02553 / 2.23 ( 2329) *********************** 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 197 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 166 time to evaluate : 0.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7848 (mmm160) cc_final: 0.7604 (mmm-85) REVERT: A 566 GLU cc_start: 0.7554 (tt0) cc_final: 0.7304 (tp30) REVERT: A 590 ARG cc_start: 0.8718 (mtt180) cc_final: 0.8425 (mpp-170) REVERT: A 623 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8624 (tt0) REVERT: B 566 GLU cc_start: 0.7711 (pm20) cc_final: 0.7323 (pt0) REVERT: B 791 VAL cc_start: 0.8771 (OUTLIER) cc_final: 0.8425 (p) REVERT: B 809 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6998 (mt-10) REVERT: C 590 ARG cc_start: 0.8749 (mtt180) cc_final: 0.8521 (mmt90) REVERT: D 590 ARG cc_start: 0.8830 (mpt-90) cc_final: 0.8104 (mtt90) REVERT: E 37 ARG cc_start: 0.8276 (mtp-110) cc_final: 0.7861 (mtp85) REVERT: E 56 GLU cc_start: 0.7961 (mt-10) cc_final: 0.7531 (mm-30) REVERT: E 81 ASP cc_start: 0.7724 (m-30) cc_final: 0.7425 (t0) REVERT: E 99 ARG cc_start: 0.8155 (mpt-90) cc_final: 0.7939 (mtt90) REVERT: E 203 LYS cc_start: 0.7621 (tppt) cc_final: 0.7404 (tttt) REVERT: F 65 ARG cc_start: 0.7593 (mtm-85) cc_final: 0.6892 (mtp85) REVERT: F 150 ILE cc_start: 0.8587 (tt) cc_final: 0.8033 (pt) REVERT: G 31 ASP cc_start: 0.8487 (OUTLIER) cc_final: 0.7562 (p0) REVERT: G 58 MET cc_start: 0.7721 (tpt) cc_final: 0.7477 (tpp) REVERT: G 65 ARG cc_start: 0.8416 (mtm-85) cc_final: 0.8009 (ptp90) REVERT: G 76 VAL cc_start: 0.8003 (t) cc_final: 0.7756 (p) REVERT: G 79 LYS cc_start: 0.8543 (ttmm) cc_final: 0.8013 (mptt) REVERT: G 99 ARG cc_start: 0.8294 (tpp80) cc_final: 0.8010 (mmt-90) REVERT: G 184 PHE cc_start: 0.7958 (m-80) cc_final: 0.7643 (m-10) REVERT: G 202 GLU cc_start: 0.7906 (pp20) cc_final: 0.7605 (pp20) REVERT: G 205 GLN cc_start: 0.6974 (tt0) cc_final: 0.6696 (tt0) REVERT: H 203 LYS cc_start: 0.7435 (ttmm) cc_final: 0.6916 (ttmt) outliers start: 31 outliers final: 18 residues processed: 185 average time/residue: 0.5476 time to fit residues: 107.6376 Evaluate side-chains 182 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 C residue 542 PHE Chi-restraints excluded: chain C residue 593 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 4 optimal weight: 5.9990 chunk 52 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 8 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 115 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 108 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3610 r_free = 0.3610 target = 0.130127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.089490 restraints weight = 59780.232| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 6.90 r_work: 0.2505 rms_B_bonded: 5.51 restraints_weight: 2.0000 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2479 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2479 r_free = 0.2479 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2479 r_free = 0.2479 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2479 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10578 Z= 0.161 Angle : 0.481 8.435 14243 Z= 0.258 Chirality : 0.038 0.130 1577 Planarity : 0.004 0.031 1711 Dihedral : 10.539 88.835 1656 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 4.07 % Allowed : 14.26 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.74 (0.24), residues: 1239 helix: 3.39 (0.16), residues: 934 sheet: 0.87 (1.34), residues: 20 loop : -0.76 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 129 TYR 0.014 0.002 TYR G 200 PHE 0.027 0.002 PHE D 810 TRP 0.007 0.001 TRP D 574 HIS 0.003 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 (10570) covalent geometry : angle 0.48062 / 0.26 (14227) SS BOND : bond 0.00249 / 0.12 ( 8) SS BOND : angle 0.93345 / 0.54 ( 16) hydrogen bonds : bond 0.04649 / 2.99 ( 795) hydrogen bonds : angle 3.23852 / 2.37 ( 2329) *********************** 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 199 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 164 time to evaluate : 0.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7798 (mmm160) cc_final: 0.7538 (mmm-85) REVERT: A 566 GLU cc_start: 0.7570 (tt0) cc_final: 0.7344 (tp30) REVERT: A 590 ARG cc_start: 0.8750 (mtt180) cc_final: 0.8404 (mpp-170) REVERT: A 623 GLU cc_start: 0.8914 (mt-10) cc_final: 0.8607 (tt0) REVERT: B 566 GLU cc_start: 0.7941 (pm20) cc_final: 0.7518 (pt0) REVERT: B 791 VAL cc_start: 0.8776 (OUTLIER) cc_final: 0.8479 (p) REVERT: B 809 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7235 (mt-10) REVERT: C 590 ARG cc_start: 0.8777 (mtt180) cc_final: 0.8546 (mmt90) REVERT: D 590 ARG cc_start: 0.8761 (mpt-90) cc_final: 0.7976 (mtt90) REVERT: E 37 ARG cc_start: 0.8265 (mtp-110) cc_final: 0.7846 (mtp85) REVERT: E 56 GLU cc_start: 0.8002 (mt-10) cc_final: 0.7557 (mm-30) REVERT: E 81 ASP cc_start: 0.7741 (m-30) cc_final: 0.7436 (t0) REVERT: E 99 ARG cc_start: 0.8179 (mpt-90) cc_final: 0.7950 (mtt90) REVERT: F 65 ARG cc_start: 0.7587 (mtm-85) cc_final: 0.6889 (mtp85) REVERT: F 150 ILE cc_start: 0.8611 (tt) cc_final: 0.8003 (pt) REVERT: G 58 MET cc_start: 0.7753 (tpt) cc_final: 0.7515 (tpp) REVERT: G 65 ARG cc_start: 0.8401 (mtm-85) cc_final: 0.7903 (ptp90) REVERT: G 79 LYS cc_start: 0.8540 (ttmm) cc_final: 0.8000 (mptt) REVERT: G 99 ARG cc_start: 0.8304 (tpp80) cc_final: 0.8032 (mmt-90) REVERT: G 184 PHE cc_start: 0.8017 (m-80) cc_final: 0.7740 (m-10) REVERT: G 202 GLU cc_start: 0.7891 (pp20) cc_final: 0.7591 (pp20) REVERT: G 205 GLN cc_start: 0.6980 (tt0) cc_final: 0.6689 (tt0) REVERT: H 126 GLU cc_start: 0.6373 (OUTLIER) cc_final: 0.5778 (mm-30) outliers start: 35 outliers final: 20 residues processed: 185 average time/residue: 0.6820 time to fit residues: 134.2110 Evaluate side-chains 183 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 161 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 590 ARG 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 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 31 ASP Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 204 HIS Chi-restraints excluded: chain H residue 205 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 23 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 63 optimal weight: 0.8980 chunk 120 optimal weight: 2.9990 chunk 104 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 132 HIS 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.132968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.091434 restraints weight = 52546.916| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 6.37 r_work: 0.2567 rms_B_bonded: 5.37 restraints_weight: 2.0000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.3304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 10578 Z= 0.110 Angle : 0.434 9.262 14243 Z= 0.233 Chirality : 0.036 0.117 1577 Planarity : 0.003 0.031 1711 Dihedral : 9.971 89.380 1656 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 3.49 % Allowed : 15.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.05 (0.24), residues: 1239 helix: 3.62 (0.16), residues: 934 sheet: 0.69 (1.34), residues: 20 loop : -0.68 (0.35), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 129 TYR 0.017 0.001 TYR C 812 PHE 0.019 0.001 PHE B 542 TRP 0.007 0.001 TRP E 177 HIS 0.003 0.001 HIS E 60 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 (10570) covalent geometry : angle 0.43301 / 0.23 (14227) SS BOND : bond 0.00146 / 0.07 ( 8) SS BOND : angle 0.92777 / 0.54 ( 16) hydrogen bonds : bond 0.03879 / 2.50 ( 795) hydrogen bonds : angle 3.02412 / 2.22 ( 2329) *********************** 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 192 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 163 time to evaluate : 0.365 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7806 (mmm160) cc_final: 0.7551 (mmm-85) REVERT: A 566 GLU cc_start: 0.7551 (tt0) cc_final: 0.7318 (tp30) REVERT: A 590 ARG cc_start: 0.8719 (mtt180) cc_final: 0.8409 (mpp-170) REVERT: B 566 GLU cc_start: 0.7708 (pm20) cc_final: 0.7307 (pt0) REVERT: B 791 VAL cc_start: 0.8766 (OUTLIER) cc_final: 0.8433 (p) REVERT: B 809 GLU cc_start: 0.7465 (mm-30) cc_final: 0.6995 (mt-10) REVERT: C 590 ARG cc_start: 0.8752 (mtt180) cc_final: 0.8538 (mmt90) REVERT: D 590 ARG cc_start: 0.8742 (mpt-90) cc_final: 0.8002 (mtt90) REVERT: E 37 ARG cc_start: 0.8268 (mtp-110) cc_final: 0.7853 (mtp85) REVERT: E 56 GLU cc_start: 0.8058 (mt-10) cc_final: 0.7581 (mm-30) REVERT: E 81 ASP cc_start: 0.7720 (m-30) cc_final: 0.7425 (t0) REVERT: E 99 ARG cc_start: 0.8106 (mpt-90) cc_final: 0.7879 (mtt90) REVERT: E 207 LEU cc_start: 0.7643 (tp) cc_final: 0.7341 (tp) REVERT: F 65 ARG cc_start: 0.7542 (mtm-85) cc_final: 0.6910 (mtp85) REVERT: F 150 ILE cc_start: 0.8593 (tt) cc_final: 0.8058 (pt) REVERT: G 58 MET cc_start: 0.7697 (tpt) cc_final: 0.7447 (tpp) REVERT: G 65 ARG cc_start: 0.8405 (mtm-85) cc_final: 0.7988 (ptp90) REVERT: G 79 LYS cc_start: 0.8514 (ttmm) cc_final: 0.7990 (mptt) REVERT: G 99 ARG cc_start: 0.8339 (tpp80) cc_final: 0.8133 (mtt90) REVERT: G 173 TYR cc_start: 0.8889 (p90) cc_final: 0.8605 (p90) REVERT: G 184 PHE cc_start: 0.7957 (m-80) cc_final: 0.7652 (m-10) REVERT: G 202 GLU cc_start: 0.7838 (pp20) cc_final: 0.7531 (pp20) REVERT: G 205 GLN cc_start: 0.7021 (tt0) cc_final: 0.6793 (tt0) REVERT: H 149 ASN cc_start: 0.8750 (t0) cc_final: 0.8440 (t160) outliers start: 29 outliers final: 17 residues processed: 182 average time/residue: 0.6107 time to fit residues: 118.3012 Evaluate side-chains 179 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 C residue 593 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 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 64 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 101 optimal weight: 0.9980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3618 r_free = 0.3618 target = 0.130759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.089564 restraints weight = 53872.440| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 6.58 r_work: 0.2523 rms_B_bonded: 5.40 restraints_weight: 2.0000 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2515 r_free = 0.2515 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 = 0.2515 r_free = 0.2515 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 10578 Z= 0.154 Angle : 0.493 8.873 14243 Z= 0.264 Chirality : 0.038 0.145 1577 Planarity : 0.004 0.033 1711 Dihedral : 10.395 88.765 1656 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 3.88 % Allowed : 15.52 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.78 (0.23), residues: 1239 helix: 3.42 (0.16), residues: 934 sheet: None (None), residues: 0 loop : -0.68 (0.32), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 129 TYR 0.015 0.001 TYR G 200 PHE 0.017 0.001 PHE B 542 TRP 0.007 0.001 TRP D 574 HIS 0.003 0.001 HIS H 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.15 (10570) covalent geometry : angle 0.48730 / 0.26 (14227) SS BOND : bond 0.00685 / 0.33 ( 8) SS BOND : angle 2.37326 / 1.24 ( 16) hydrogen bonds : bond 0.04546 / 2.92 ( 795) hydrogen bonds : angle 3.21314 / 2.35 ( 2329) *********************** 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 193 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7799 (mmm160) cc_final: 0.7443 (mmm-85) REVERT: A 566 GLU cc_start: 0.7536 (tt0) cc_final: 0.7311 (tp30) REVERT: A 590 ARG cc_start: 0.8742 (mtt180) cc_final: 0.8420 (mpp-170) REVERT: B 566 GLU cc_start: 0.7932 (pm20) cc_final: 0.7500 (pt0) REVERT: B 791 VAL cc_start: 0.8785 (OUTLIER) cc_final: 0.8503 (p) REVERT: B 809 GLU cc_start: 0.7519 (mm-30) cc_final: 0.6985 (mt-10) REVERT: C 590 ARG cc_start: 0.8754 (mtt180) cc_final: 0.8529 (mmt90) REVERT: D 590 ARG cc_start: 0.8775 (mpt-90) cc_final: 0.7988 (mtt90) REVERT: E 37 ARG cc_start: 0.8301 (mtp-110) cc_final: 0.7872 (mtp85) REVERT: E 56 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7641 (mm-30) REVERT: E 81 ASP cc_start: 0.7738 (m-30) cc_final: 0.7456 (t0) REVERT: E 99 ARG cc_start: 0.8105 (mpt-90) cc_final: 0.7866 (mtt90) REVERT: E 207 LEU cc_start: 0.7714 (tp) cc_final: 0.7386 (tp) REVERT: F 65 ARG cc_start: 0.7607 (mtm-85) cc_final: 0.6918 (mtp85) REVERT: F 150 ILE cc_start: 0.8630 (tt) cc_final: 0.8024 (pt) REVERT: G 58 MET cc_start: 0.7740 (tpt) cc_final: 0.7496 (tpp) REVERT: G 65 ARG cc_start: 0.8409 (mtm-85) cc_final: 0.7953 (ptp90) REVERT: G 79 LYS cc_start: 0.8533 (ttmm) cc_final: 0.8000 (mptt) REVERT: G 99 ARG cc_start: 0.8352 (tpp80) cc_final: 0.8035 (mmt-90) REVERT: G 184 PHE cc_start: 0.8006 (m-80) cc_final: 0.7756 (m-10) REVERT: G 202 GLU cc_start: 0.7910 (pp20) cc_final: 0.7618 (pp20) REVERT: G 205 GLN cc_start: 0.6975 (tt0) cc_final: 0.6750 (tt0) REVERT: H 126 GLU cc_start: 0.6349 (OUTLIER) cc_final: 0.5789 (mm-30) REVERT: H 149 ASN cc_start: 0.8742 (t0) cc_final: 0.8444 (t160) outliers start: 33 outliers final: 20 residues processed: 180 average time/residue: 0.6353 time to fit residues: 121.8118 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 : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 587 ILE Chi-restraints excluded: chain B residue 542 PHE Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 590 ARG Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain C residue 542 PHE 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 31 ASP Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 204 HIS Chi-restraints excluded: chain H residue 205 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 46 optimal weight: 0.9980 chunk 87 optimal weight: 0.0010 chunk 41 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3655 r_free = 0.3655 target = 0.133945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.092336 restraints weight = 51250.646| |-----------------------------------------------------------------------------| r_work (start): 0.3043 rms_B_bonded: 6.28 r_work: 0.2581 rms_B_bonded: 5.37 restraints_weight: 2.0000 r_work (final): 0.2581 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.065 10578 Z= 0.108 Angle : 0.452 10.025 14243 Z= 0.240 Chirality : 0.036 0.131 1577 Planarity : 0.003 0.032 1711 Dihedral : 9.767 88.911 1656 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 3.10 % Allowed : 16.00 % Favored : 80.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.12 (0.24), residues: 1239 helix: 3.70 (0.16), residues: 932 sheet: None (None), residues: 0 loop : -0.65 (0.32), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 129 TYR 0.018 0.001 TYR C 812 PHE 0.017 0.001 PHE B 542 TRP 0.008 0.001 TRP E 177 HIS 0.003 0.001 HIS H 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (10570) covalent geometry : angle 0.44267 / 0.24 (14227) SS BOND : bond 0.00783 / 0.38 ( 8) SS BOND : angle 2.74908 / 1.39 ( 16) hydrogen bonds : bond 0.03757 / 2.42 ( 795) hydrogen bonds : angle 2.97741 / 2.18 ( 2329) ********************** 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 187 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 541 ARG cc_start: 0.7791 (mmm160) cc_final: 0.7459 (mmm-85) REVERT: A 590 ARG cc_start: 0.8726 (mtt180) cc_final: 0.8419 (mpp-170) REVERT: B 566 GLU cc_start: 0.7686 (pm20) cc_final: 0.7299 (pt0) REVERT: B 791 VAL cc_start: 0.8744 (OUTLIER) cc_final: 0.8424 (p) REVERT: B 809 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7004 (mt-10) REVERT: C 590 ARG cc_start: 0.8727 (mtt180) cc_final: 0.8513 (mmt90) REVERT: D 590 ARG cc_start: 0.8769 (mpt-90) cc_final: 0.8018 (mtt90) REVERT: E 37 ARG cc_start: 0.8313 (mtp-110) cc_final: 0.7893 (mtp85) REVERT: E 56 GLU cc_start: 0.8135 (mt-10) cc_final: 0.7621 (mm-30) REVERT: E 81 ASP cc_start: 0.7734 (m-30) cc_final: 0.7463 (t0) REVERT: E 99 ARG cc_start: 0.8099 (mpt-90) cc_final: 0.7868 (mtt90) REVERT: E 203 LYS cc_start: 0.7366 (ttpt) cc_final: 0.7089 (tttt) REVERT: E 207 LEU cc_start: 0.7679 (tp) cc_final: 0.7356 (tp) REVERT: F 65 ARG cc_start: 0.7543 (mtm-85) cc_final: 0.6947 (mtp85) REVERT: F 150 ILE cc_start: 0.8589 (tt) cc_final: 0.8054 (pt) REVERT: G 65 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.7993 (ptp90) REVERT: G 79 LYS cc_start: 0.8516 (ttmm) cc_final: 0.7988 (mptt) REVERT: G 99 ARG cc_start: 0.8341 (tpp80) cc_final: 0.8123 (mtt90) REVERT: G 184 PHE cc_start: 0.7952 (m-80) cc_final: 0.7659 (m-10) REVERT: G 202 GLU cc_start: 0.7843 (pp20) cc_final: 0.7606 (pp20) REVERT: H 149 ASN cc_start: 0.8599 (t0) cc_final: 0.8277 (t160) outliers start: 25 outliers final: 17 residues processed: 177 average time/residue: 0.6459 time to fit residues: 121.6014 Evaluate side-chains 177 residues out of total 1019 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 543 SER Chi-restraints excluded: chain B residue 590 ARG Chi-restraints excluded: chain B residue 791 VAL Chi-restraints excluded: chain C residue 542 PHE 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 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 31 ASP Chi-restraints excluded: chain H residue 204 HIS Chi-restraints excluded: chain H residue 205 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 26 optimal weight: 4.9990 chunk 55 optimal weight: 0.6980 chunk 54 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 105 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 2 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 6.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3641 r_free = 0.3641 target = 0.132776 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.090633 restraints weight = 51957.545| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 6.01 r_work: 0.2569 rms_B_bonded: 5.27 restraints_weight: 2.0000 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 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 0.062 10578 Z= 0.120 Angle : 0.457 10.105 14243 Z= 0.244 Chirality : 0.036 0.129 1577 Planarity : 0.003 0.033 1711 Dihedral : 9.779 89.113 1656 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 3.10 % Allowed : 16.29 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.03 (0.24), residues: 1239 helix: 3.63 (0.16), residues: 934 sheet: None (None), residues: 0 loop : -0.70 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 129 TYR 0.020 0.001 TYR C 812 PHE 0.018 0.001 PHE B 542 TRP 0.006 0.001 TRP C 574 HIS 0.003 0.001 HIS F 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (10570) covalent geometry : angle 0.44738 / 0.24 (14227) SS BOND : bond 0.00766 / 0.37 ( 8) SS BOND : angle 2.83547 / 1.44 ( 16) hydrogen bonds : bond 0.03953 / 2.54 ( 795) hydrogen bonds : angle 3.03889 / 2.23 ( 2329) =============================================================================== Job complete usr+sys time: 3661.58 seconds wall clock time: 62 minutes 52.96 seconds (3772.96 seconds total)