Starting phenix.real_space_refine on Thu Mar 5 09:47:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mqc_23942/03_2026/7mqc_23942.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mqc_23942/03_2026/7mqc_23942.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7mqc_23942/03_2026/7mqc_23942.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mqc_23942/03_2026/7mqc_23942.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mqc_23942/03_2026/7mqc_23942.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mqc_23942/03_2026/7mqc_23942.map" } resolution = 3.64 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11279 atoms to isotropic. 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 16 5.49 5 S 45 5.16 5 C 7949 2.51 5 N 2316 2.21 5 O 2230 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12556 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1512 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1512 Classifications: {'peptide': 205} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 90 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 10, 'ASN:plan1': 3, 'ARG:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 94 Chain: "B" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "C" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1530 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 128 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 8, 'ASN:plan1': 3, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 79 Chain: "D" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "E" Number of atoms: 1528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1528 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 8, 'ASN:plan1': 2, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 76 Chain: "F" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "G" Number of atoms: 1526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1526 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 107 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 81 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 7, 'ASN:plan1': 3, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 76 Chain: "H" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "I" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1527 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 106 Unresolved non-hydrogen angles: 133 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 9, 'ASN:plan1': 2, 'ARG:plan': 3, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 88 Chain: "J" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "K" Number of atoms: 1507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1507 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 157 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 10, 'ASN:plan1': 4, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 92 Chain: "L" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "M" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1520 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 113 Unresolved non-hydrogen angles: 141 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 9, 'ASN:plan1': 3, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 86 Chain: "N" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "O" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1530 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 103 Unresolved non-hydrogen angles: 130 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 9, 'ASN:plan1': 2, 'ARG:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 83 Chain: "P" Number of atoms: 47 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 47 Classifications: {'RNA': 2} Modifications used: {'p5*END': 1, 'rna3p_pur': 2} Link IDs: {'rna3p': 1} Time building chain proxies: 2.85, per 1000 atoms: 0.23 Number of scatterers: 12556 At special positions: 0 Unit cell: (111.6, 106.64, 91.76, 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 45 16.00 P 16 15.00 O 2230 8.00 N 2316 7.00 C 7949 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 1.05 Conformation dependent library (CDL) restraints added in 385.0 milliseconds 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3120 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 8 sheets defined 46.4% alpha, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 62 through 71 Processing helix chain 'A' and resid 80 through 93 removed outlier: 3.902A pdb=" N ASP A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA A 86 " --> pdb=" O ARG A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 110 Processing helix chain 'A' and resid 117 through 127 Processing helix chain 'A' and resid 145 through 157 removed outlier: 3.907A pdb=" N VAL A 156 " --> pdb=" O ALA A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 173 Processing helix chain 'A' and resid 175 through 196 Proline residue: A 187 - end of helix Processing helix chain 'C' and resid 62 through 71 Processing helix chain 'C' and resid 80 through 93 removed outlier: 3.879A pdb=" N ASP C 84 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA C 86 " --> pdb=" O ARG C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 110 Processing helix chain 'C' and resid 117 through 127 Processing helix chain 'C' and resid 145 through 157 removed outlier: 3.979A pdb=" N VAL C 156 " --> pdb=" O ALA C 152 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 173 Processing helix chain 'C' and resid 175 through 196 Proline residue: C 187 - end of helix Processing helix chain 'E' and resid 62 through 71 Processing helix chain 'E' and resid 80 through 93 removed outlier: 3.904A pdb=" N ASP E 84 " --> pdb=" O PHE E 80 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA E 86 " --> pdb=" O ARG E 82 " (cutoff:3.500A) Processing helix chain 'E' and resid 102 through 110 Processing helix chain 'E' and resid 117 through 127 Processing helix chain 'E' and resid 145 through 157 removed outlier: 3.970A pdb=" N VAL E 156 " --> pdb=" O ALA E 152 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 174 Processing helix chain 'E' and resid 175 through 196 Proline residue: E 187 - end of helix Processing helix chain 'G' and resid 62 through 71 Processing helix chain 'G' and resid 80 through 93 removed outlier: 3.758A pdb=" N ASP G 84 " --> pdb=" O PHE G 80 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA G 86 " --> pdb=" O ARG G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 110 Processing helix chain 'G' and resid 117 through 127 Processing helix chain 'G' and resid 145 through 155 Processing helix chain 'G' and resid 158 through 173 Processing helix chain 'G' and resid 175 through 196 Proline residue: G 187 - end of helix Processing helix chain 'I' and resid 62 through 70 Processing helix chain 'I' and resid 80 through 93 removed outlier: 3.943A pdb=" N ASP I 84 " --> pdb=" O PHE I 80 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA I 86 " --> pdb=" O ARG I 82 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 110 Processing helix chain 'I' and resid 117 through 127 Processing helix chain 'I' and resid 132 through 136 removed outlier: 4.172A pdb=" N SER I 136 " --> pdb=" O GLN I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 157 removed outlier: 3.771A pdb=" N VAL I 156 " --> pdb=" O ALA I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 158 through 173 Processing helix chain 'I' and resid 175 through 196 Proline residue: I 187 - end of helix Processing helix chain 'K' and resid 62 through 71 Processing helix chain 'K' and resid 80 through 93 removed outlier: 3.829A pdb=" N ASP K 84 " --> pdb=" O PHE K 80 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA K 86 " --> pdb=" O ARG K 82 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 110 Processing helix chain 'K' and resid 117 through 127 Processing helix chain 'K' and resid 145 through 155 Processing helix chain 'K' and resid 158 through 173 Processing helix chain 'K' and resid 175 through 196 Proline residue: K 187 - end of helix Processing helix chain 'M' and resid 62 through 71 Processing helix chain 'M' and resid 80 through 93 removed outlier: 3.860A pdb=" N ASP M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA M 86 " --> pdb=" O ARG M 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 102 through 110 Processing helix chain 'M' and resid 117 through 127 Processing helix chain 'M' and resid 145 through 157 removed outlier: 3.907A pdb=" N VAL M 156 " --> pdb=" O ALA M 152 " (cutoff:3.500A) Processing helix chain 'M' and resid 158 through 173 Processing helix chain 'M' and resid 175 through 196 Proline residue: M 187 - end of helix Processing helix chain 'O' and resid 62 through 71 Processing helix chain 'O' and resid 80 through 93 removed outlier: 3.837A pdb=" N ASP O 84 " --> pdb=" O PHE O 80 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA O 86 " --> pdb=" O ARG O 82 " (cutoff:3.500A) Processing helix chain 'O' and resid 102 through 110 Processing helix chain 'O' and resid 117 through 127 Processing helix chain 'O' and resid 145 through 157 removed outlier: 3.995A pdb=" N VAL O 156 " --> pdb=" O ALA O 152 " (cutoff:3.500A) Processing helix chain 'O' and resid 158 through 173 Processing helix chain 'O' and resid 175 through 196 Proline residue: O 187 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 8 removed outlier: 6.418A pdb=" N ARG A 5 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N GLN A 54 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N HIS A 7 " --> pdb=" O GLN A 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.275A pdb=" N ARG C 5 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N GLN C 54 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N HIS C 7 " --> pdb=" O GLN C 54 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL C 22 " --> pdb=" O ILE C 77 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 3 through 8 removed outlier: 6.414A pdb=" N GLU E 3 " --> pdb=" O ALA E 50 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL E 52 " --> pdb=" O GLU E 3 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ARG E 5 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N GLN E 54 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N HIS E 7 " --> pdb=" O GLN E 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 4 through 8 removed outlier: 6.362A pdb=" N ARG G 5 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N GLN G 54 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N HIS G 7 " --> pdb=" O GLN G 54 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N GLU G 27 " --> pdb=" O CYS G 39 " (cutoff:3.500A) removed outlier: 4.784A pdb=" N VAL G 41 " --> pdb=" O ASP G 25 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ASP G 25 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU G 43 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ALA G 23 " --> pdb=" O LEU G 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 3 through 8 removed outlier: 6.518A pdb=" N GLU I 3 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N VAL I 52 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N ARG I 5 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N GLN I 54 " --> pdb=" O ARG I 5 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N HIS I 7 " --> pdb=" O GLN I 54 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N GLU I 27 " --> pdb=" O CYS I 39 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N VAL I 41 " --> pdb=" O ASP I 25 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ASP I 25 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N LEU I 43 " --> pdb=" O ALA I 23 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA I 23 " --> pdb=" O LEU I 43 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 3 through 8 removed outlier: 6.464A pdb=" N GLU K 3 " --> pdb=" O ALA K 50 " (cutoff:3.500A) removed outlier: 7.640A pdb=" N VAL K 52 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG K 5 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLN K 54 " --> pdb=" O ARG K 5 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N HIS K 7 " --> pdb=" O GLN K 54 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 4 through 8 removed outlier: 6.377A pdb=" N ARG M 5 " --> pdb=" O VAL M 52 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N GLN M 54 " --> pdb=" O ARG M 5 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N HIS M 7 " --> pdb=" O GLN M 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'O' and resid 3 through 8 removed outlier: 6.475A pdb=" N GLU O 3 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N VAL O 52 " --> pdb=" O GLU O 3 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ARG O 5 " --> pdb=" O VAL O 52 " (cutoff:3.500A) removed outlier: 7.431A pdb=" N GLN O 54 " --> pdb=" O ARG O 5 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N HIS O 7 " --> pdb=" O GLN O 54 " (cutoff:3.500A) 594 hydrogen bonds defined for protein. 1779 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: 1.78 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4133 1.34 - 1.46: 2484 1.46 - 1.58: 6121 1.58 - 1.69: 24 1.69 - 1.81: 58 Bond restraints: 12820 Sorted by residual: bond pdb=" N GLU C 173 " pdb=" CA GLU C 173 " ideal model delta sigma weight residual 1.456 1.494 -0.038 1.32e-02 5.74e+03 8.28e+00 bond pdb=" N VAL O 178 " pdb=" CA VAL O 178 " ideal model delta sigma weight residual 1.460 1.493 -0.034 1.21e-02 6.83e+03 7.71e+00 bond pdb=" N MET E 95 " pdb=" CA MET E 95 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.21e-02 6.83e+03 7.60e+00 bond pdb=" C MET E 95 " pdb=" N PRO E 96 " ideal model delta sigma weight residual 1.332 1.368 -0.036 1.34e-02 5.57e+03 7.41e+00 bond pdb=" C MET A 95 " pdb=" N PRO A 96 " ideal model delta sigma weight residual 1.332 1.368 -0.036 1.34e-02 5.57e+03 7.33e+00 ... (remaining 12815 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.61: 16569 1.61 - 3.21: 802 3.21 - 4.82: 118 4.82 - 6.43: 17 6.43 - 8.03: 5 Bond angle restraints: 17511 Sorted by residual: angle pdb=" CA VAL O 178 " pdb=" C VAL O 178 " pdb=" O VAL O 178 " ideal model delta sigma weight residual 120.85 117.11 3.74 1.06e+00 8.90e-01 1.24e+01 angle pdb=" CA MET C 95 " pdb=" C MET C 95 " pdb=" O MET C 95 " ideal model delta sigma weight residual 119.36 116.40 2.96 8.40e-01 1.42e+00 1.24e+01 angle pdb=" CA MET A 95 " pdb=" C MET A 95 " pdb=" O MET A 95 " ideal model delta sigma weight residual 119.36 116.48 2.88 8.40e-01 1.42e+00 1.17e+01 angle pdb=" C THR K 28 " pdb=" CA THR K 28 " pdb=" CB THR K 28 " ideal model delta sigma weight residual 111.65 103.62 8.03 2.40e+00 1.74e-01 1.12e+01 angle pdb=" CA MET E 95 " pdb=" C MET E 95 " pdb=" O MET E 95 " ideal model delta sigma weight residual 119.36 116.57 2.79 8.40e-01 1.42e+00 1.10e+01 ... (remaining 17506 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7133 17.97 - 35.94: 360 35.94 - 53.91: 103 53.91 - 71.89: 53 71.89 - 89.86: 15 Dihedral angle restraints: 7664 sinusoidal: 2880 harmonic: 4784 Sorted by residual: dihedral pdb=" CA PHE I 78 " pdb=" C PHE I 78 " pdb=" N HIS I 79 " pdb=" CA HIS I 79 " ideal model delta harmonic sigma weight residual 180.00 157.85 22.15 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA PHE E 78 " pdb=" C PHE E 78 " pdb=" N HIS E 79 " pdb=" CA HIS E 79 " ideal model delta harmonic sigma weight residual 180.00 157.92 22.08 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA PHE K 78 " pdb=" C PHE K 78 " pdb=" N HIS K 79 " pdb=" CA HIS K 79 " ideal model delta harmonic sigma weight residual 180.00 158.01 21.99 0 5.00e+00 4.00e-02 1.93e+01 ... (remaining 7661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1494 0.059 - 0.117: 531 0.117 - 0.176: 65 0.176 - 0.235: 11 0.235 - 0.293: 2 Chirality restraints: 2103 Sorted by residual: chirality pdb=" CA THR K 28 " pdb=" N THR K 28 " pdb=" C THR K 28 " pdb=" CB THR K 28 " both_signs ideal model delta sigma weight residual False 2.53 2.82 -0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CA LEU K 38 " pdb=" N LEU K 38 " pdb=" C LEU K 38 " pdb=" CB LEU K 38 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.24 2.00e-01 2.50e+01 1.50e+00 chirality pdb=" CG LEU K 125 " pdb=" CB LEU K 125 " pdb=" CD1 LEU K 125 " pdb=" CD2 LEU K 125 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.24e+00 ... (remaining 2100 not shown) Planarity restraints: 2164 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU M 11 " -0.078 5.00e-02 4.00e+02 1.20e-01 2.29e+01 pdb=" N PRO M 12 " 0.207 5.00e-02 4.00e+02 pdb=" CA PRO M 12 " -0.064 5.00e-02 4.00e+02 pdb=" CD PRO M 12 " -0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 35 " 0.012 2.00e-02 2.50e+03 2.56e-02 6.57e+00 pdb=" C ARG A 35 " -0.044 2.00e-02 2.50e+03 pdb=" O ARG A 35 " 0.017 2.00e-02 2.50e+03 pdb=" N ASP A 36 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 158 " 0.017 2.00e-02 2.50e+03 1.36e-02 3.70e+00 pdb=" CG TYR E 158 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR E 158 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR E 158 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR E 158 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR E 158 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR E 158 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR E 158 " 0.003 2.00e-02 2.50e+03 ... (remaining 2161 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1646 2.75 - 3.29: 11543 3.29 - 3.83: 20561 3.83 - 4.36: 24958 4.36 - 4.90: 43071 Nonbonded interactions: 101779 Sorted by model distance: nonbonded pdb=" OH TYR I 17 " pdb=" OD1 ASP I 51 " model vdw 2.215 3.040 nonbonded pdb=" NE2 GLN G 135 " pdb=" OP2 G H 604 " model vdw 2.254 3.120 nonbonded pdb=" NE2 GLN I 135 " pdb=" OP2 G J 604 " model vdw 2.296 3.120 nonbonded pdb=" NZ LYS G 119 " pdb=" O ILE G 130 " model vdw 2.321 3.120 nonbonded pdb=" O GLU E 3 " pdb=" OG1 THR E 49 " model vdw 2.333 3.040 ... (remaining 101774 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 2 through 13 or (resid 14 through 16 and (name N or name C \ A or name C or name O or name CB )) or resid 17 through 27 or (resid 28 and (nam \ e N or name CA or name C or name O or name CB )) or resid 29 through 35 or (resi \ d 36 and (name N or name CA or name C or name O or name CB )) or resid 37 throug \ h 48 or (resid 49 through 51 and (name N or name CA or name C or name O or name \ CB )) or resid 52 through 60 or (resid 61 through 62 and (name N or name CA or n \ ame C or name O or name CB )) or resid 63 through 64 or (resid 65 through 67 and \ (name N or name CA or name C or name O or name CB )) or resid 68 through 112 or \ (resid 113 through 114 and (name N or name CA or name C or name O or name CB )) \ or resid 115 through 123 or (resid 124 and (name N or name CA or name C or name \ O or name CB )) or resid 125 through 126 or (resid 127 through 130 and (name N \ or name CA or name C or name O or name CB )) or resid 131 through 142 or (resid \ 143 and (name N or name CA or name C or name O or name CB )) or resid 144 throug \ h 145 or (resid 146 through 147 and (name N or name CA or name C or name O or na \ me CB )) or resid 148 or (resid 149 through 150 and (name N or name CA or name C \ or name O or name CB )) or resid 151 through 153 or (resid 154 and (name N or n \ ame CA or name C or name O or name CB )) or resid 155 through 156 or (resid 157 \ and (name N or name CA or name C or name O or name CB )) or resid 158 through 16 \ 3 or (resid 164 and (name N or name CA or name C or name O or name CB )) or resi \ d 165 through 170 or (resid 171 and (name N or name CA or name C or name O or na \ me CB )) or resid 172 or (resid 173 through 174 and (name N or name CA or name C \ or name O or name CB )) or resid 175 through 187 or (resid 188 and (name N or n \ ame CA or name C or name O or name CB )) or resid 189 through 192 or (resid 193 \ and (name N or name CA or name C or name O or name CB )) or resid 194 through 19 \ 9 or (resid 200 and (name N or name CA or name C or name O or name CB )) or resi \ d 201 through 206)) selection = (chain 'C' and (resid 2 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 through 16 and (nam \ e N or name CA or name C or name O or name CB )) or resid 17 through 27 or (resi \ d 28 and (name N or name CA or name C or name O or name CB )) or resid 29 throug \ h 35 or (resid 36 and (name N or name CA or name C or name O or name CB )) or re \ sid 37 through 48 or (resid 49 through 51 and (name N or name CA or name C or na \ me O or name CB )) or resid 52 through 60 or (resid 61 through 62 and (name N or \ name CA or name C or name O or name CB )) or resid 63 or (resid 64 through 67 a \ nd (name N or name CA or name C or name O or name CB )) or resid 68 through 93 o \ r (resid 94 and (name N or name CA or name C or name O or name CB )) or resid 95 \ through 123 or (resid 124 and (name N or name CA or name C or name O or name CB \ )) or resid 125 through 126 or (resid 127 through 130 and (name N or name CA or \ name C or name O or name CB )) or resid 131 through 137 or (resid 138 and (name \ N or name CA or name C or name O or name CB )) or resid 139 through 142 or (res \ id 143 and (name N or name CA or name C or name O or name CB )) or resid 144 thr \ ough 145 or (resid 146 through 147 and (name N or name CA or name C or name O or \ name CB )) or resid 148 or (resid 149 through 150 and (name N or name CA or nam \ e C or name O or name CB )) or resid 151 through 153 or (resid 154 and (name N o \ r name CA or name C or name O or name CB )) or resid 155 through 156 or (resid 1 \ 57 and (name N or name CA or name C or name O or name CB )) or resid 158 through \ 163 or (resid 164 and (name N or name CA or name C or name O or name CB )) or r \ esid 165 through 170 or (resid 171 and (name N or name CA or name C or name O or \ name CB )) or resid 172 or (resid 173 through 174 and (name N or name CA or nam \ e C or name O or name CB )) or resid 175 or (resid 176 and (name N or name CA or \ name C or name O or name CB )) or resid 177 through 192 or (resid 193 and (name \ N or name CA or name C or name O or name CB )) or resid 194 through 199 or (res \ id 200 and (name N or name CA or name C or name O or name CB )) or resid 201 thr \ ough 205 or (resid 206 and (name N or name CA or name C or name O or name CB ))) \ ) selection = (chain 'E' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 17 or (resid 18 through 21 and (name \ N or name CA or name C or name O or name CB )) or resid 22 through 27 or (resid \ 28 and (name N or name CA or name C or name O or name CB )) or resid 29 through \ 48 or (resid 49 through 51 and (name N or name CA or name C or name O or name C \ B )) or resid 52 through 63 or (resid 64 through 67 and (name N or name CA or na \ me C or name O or name CB )) or resid 68 through 93 or (resid 94 and (name N or \ name CA or name C or name O or name CB )) or resid 95 through 112 or (resid 113 \ through 114 and (name N or name CA or name C or name O or name CB )) or resid 11 \ 5 through 119 or (resid 120 and (name N or name CA or name C or name O or name C \ B )) or resid 121 through 123 or (resid 124 and (name N or name CA or name C or \ name O or name CB )) or resid 125 through 126 or (resid 127 through 130 and (nam \ e N or name CA or name C or name O or name CB )) or resid 131 through 137 or (re \ sid 138 and (name N or name CA or name C or name O or name CB )) or resid 139 th \ rough 142 or (resid 143 and (name N or name CA or name C or name O or name CB )) \ or resid 144 through 153 or (resid 154 and (name N or name CA or name C or name \ O or name CB )) or resid 155 through 156 or (resid 157 and (name N or name CA o \ r name C or name O or name CB )) or resid 158 through 163 or (resid 164 and (nam \ e N or name CA or name C or name O or name CB )) or resid 165 through 170 or (re \ sid 171 and (name N or name CA or name C or name O or name CB )) or resid 172 th \ rough 175 or (resid 176 and (name N or name CA or name C or name O or name CB )) \ or resid 177 through 187 or (resid 188 and (name N or name CA or name C or name \ O or name CB )) or resid 189 through 192 or (resid 193 and (name N or name CA o \ r name C or name O or name CB )) or resid 194 through 199 or (resid 200 and (nam \ e N or name CA or name C or name O or name CB )) or resid 201 through 205 or (re \ sid 206 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'G' and (resid 2 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 through 16 and (nam \ e N or name CA or name C or name O or name CB )) or resid 17 through 27 or (resi \ d 28 and (name N or name CA or name C or name O or name CB )) or resid 29 throug \ h 35 or (resid 36 and (name N or name CA or name C or name O or name CB )) or re \ sid 37 through 46 or (resid 47 and (name N or name CA or name C or name O or nam \ e CB )) or resid 48 or (resid 49 through 51 and (name N or name CA or name C or \ name O or name CB )) or resid 52 through 60 or (resid 61 through 62 and (name N \ or name CA or name C or name O or name CB )) or resid 63 or (resid 64 through 67 \ and (name N or name CA or name C or name O or name CB )) or resid 68 through 71 \ or (resid 72 through 73 and (name N or name CA or name C or name O or name CB ) \ ) or resid 74 through 93 or (resid 94 and (name N or name CA or name C or name O \ or name CB )) or resid 95 through 112 or (resid 113 through 114 and (name N or \ name CA or name C or name O or name CB )) or resid 115 through 119 or (resid 120 \ and (name N or name CA or name C or name O or name CB )) or resid 121 through 1 \ 23 or (resid 124 and (name N or name CA or name C or name O or name CB )) or res \ id 125 through 137 or (resid 138 and (name N or name CA or name C or name O or n \ ame CB )) or resid 139 through 142 or (resid 143 and (name N or name CA or name \ C or name O or name CB )) or resid 144 through 148 or (resid 149 through 150 and \ (name N or name CA or name C or name O or name CB )) or resid 151 through 153 o \ r (resid 154 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 55 through 163 or (resid 164 and (name N or name CA or name C or name O or name \ CB )) or resid 165 through 175 or (resid 176 and (name N or name CA or name C or \ name O or name CB )) or resid 177 through 187 or (resid 188 and (name N or name \ CA or name C or name O or name CB )) or resid 189 through 192 or (resid 193 and \ (name N or name CA or name C or name O or name CB )) or resid 194 through 199 o \ r (resid 200 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 01 through 205 or (resid 206 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'I' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 through 16 and (name \ N or name CA or name C or name O or name CB )) or resid 17 through 35 or (resid \ 36 and (name N or name CA or name C or name O or name CB )) or resid 37 through \ 48 or (resid 49 through 51 and (name N or name CA or name C or name O or name C \ B )) or resid 52 through 60 or (resid 61 through 62 and (name N or name CA or na \ me C or name O or name CB )) or resid 63 or (resid 64 through 67 and (name N or \ name CA or name C or name O or name CB )) or resid 68 through 93 or (resid 94 an \ d (name N or name CA or name C or name O or name CB )) or resid 95 through 112 o \ r (resid 113 through 114 and (name N or name CA or name C or name O or name CB ) \ ) or resid 115 through 123 or (resid 124 and (name N or name CA or name C or nam \ e O or name CB )) or resid 125 through 127 or (resid 128 through 130 and (name N \ or name CA or name C or name O or name CB )) or resid 131 through 137 or (resid \ 138 and (name N or name CA or name C or name O or name CB )) or resid 139 throu \ gh 148 or (resid 149 through 150 and (name N or name CA or name C or name O or n \ ame CB )) or resid 151 through 153 or (resid 154 and (name N or name CA or name \ C or name O or name CB )) or resid 155 through 156 or (resid 157 and (name N or \ name CA or name C or name O or name CB )) or resid 158 through 170 or (resid 171 \ and (name N or name CA or name C or name O or name CB )) or resid 172 through 1 \ 75 or (resid 176 and (name N or name CA or name C or name O or name CB )) or res \ id 177 through 179 or (resid 180 through 181 and (name N or name CA or name C or \ name O or name CB )) or resid 182 through 187 or (resid 188 and (name N or name \ CA or name C or name O or name CB )) or resid 189 through 192 or (resid 193 and \ (name N or name CA or name C or name O or name CB )) or resid 194 through 199 o \ r (resid 200 and (name N or name CA or name C or name O or name CB )) or resid 2 \ 01 through 205 or (resid 206 and (name N or name CA or name C or name O or name \ CB )))) selection = (chain 'K' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 through 16 and (name \ N or name CA or name C or name O or name CB )) or resid 17 through 27 or (resid \ 28 and (name N or name CA or name C or name O or name CB )) or resid 29 through \ 50 or (resid 51 and (name N or name CA or name C or name O or name CB )) or res \ id 52 through 63 or (resid 64 through 67 and (name N or name CA or name C or nam \ e O or name CB )) or resid 68 through 112 or (resid 113 through 114 and (name N \ or name CA or name C or name O or name CB )) or resid 115 through 119 or (resid \ 120 and (name N or name CA or name C or name O or name CB )) or resid 121 throug \ h 127 or (resid 128 through 130 and (name N or name CA or name C or name O or na \ me CB )) or resid 131 through 137 or (resid 138 and (name N or name CA or name C \ or name O or name CB )) or resid 139 through 142 or (resid 143 and (name N or n \ ame CA or name C or name O or name CB )) or resid 144 through 145 or (resid 146 \ through 147 and (name N or name CA or name C or name O or name CB )) or resid 14 \ 8 or (resid 149 through 150 and (name N or name CA or name C or name O or name C \ B )) or resid 151 through 153 or (resid 154 and (name N or name CA or name C or \ name O or name CB )) or resid 155 through 156 or (resid 157 and (name N or name \ CA or name C or name O or name CB )) or resid 158 through 163 or (resid 164 and \ (name N or name CA or name C or name O or name CB )) or resid 165 through 166 or \ (resid 167 through 168 and (name N or name CA or name C or name O or name CB )) \ or resid 169 through 205 or (resid 206 and (name N or name CA or name C or name \ O or name CB )))) selection = (chain 'M' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 through 16 and (name \ N or name CA or name C or name O or name CB )) or resid 17 through 27 or (resid \ 28 and (name N or name CA or name C or name O or name CB )) or resid 29 through \ 48 or (resid 49 through 51 and (name N or name CA or name C or name O or name C \ B )) or resid 52 through 60 or (resid 61 through 62 and (name N or name CA or na \ me C or name O or name CB )) or resid 63 or (resid 64 through 67 and (name N or \ name CA or name C or name O or name CB )) or resid 68 through 123 or (resid 124 \ and (name N or name CA or name C or name O or name CB )) or resid 125 through 12 \ 9 or (resid 130 and (name N or name CA or name C or name O or name CB )) or resi \ d 131 through 137 or (resid 138 and (name N or name CA or name C or name O or na \ me CB )) or resid 139 through 142 or (resid 143 and (name N or name CA or name C \ or name O or name CB )) or resid 144 through 145 or (resid 146 through 147 and \ (name N or name CA or name C or name O or name CB )) or resid 148 or (resid 149 \ through 150 and (name N or name CA or name C or name O or name CB )) or resid 15 \ 1 through 156 or (resid 157 and (name N or name CA or name C or name O or name C \ B )) or resid 158 through 163 or (resid 164 and (name N or name CA or name C or \ name O or name CB )) or resid 165 through 170 or (resid 171 and (name N or name \ CA or name C or name O or name CB )) or resid 172 through 175 or (resid 176 and \ (name N or name CA or name C or name O or name CB )) or resid 177 through 192 or \ (resid 193 and (name N or name CA or name C or name O or name CB )) or resid 19 \ 4 through 199 or (resid 200 and (name N or name CA or name C or name O or name C \ B )) or resid 201 through 205 or (resid 206 and (name N or name CA or name C or \ name O or name CB )))) selection = (chain 'O' and (resid 2 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 13 or (resid 14 through 16 and (nam \ e N or name CA or name C or name O or name CB )) or resid 17 through 27 or (resi \ d 28 and (name N or name CA or name C or name O or name CB )) or resid 29 throug \ h 35 or (resid 36 and (name N or name CA or name C or name O or name CB )) or re \ sid 37 through 48 or (resid 49 through 51 and (name N or name CA or name C or na \ me O or name CB )) or resid 52 through 60 or (resid 61 through 62 and (name N or \ name CA or name C or name O or name CB )) or resid 63 or (resid 64 through 67 a \ nd (name N or name CA or name C or name O or name CB )) or resid 68 through 70 o \ r (resid 71 through 73 and (name N or name CA or name C or name O or name CB )) \ or resid 74 through 93 or (resid 94 and (name N or name CA or name C or name O o \ r name CB )) or resid 95 through 112 or (resid 113 through 114 and (name N or na \ me CA or name C or name O or name CB )) or resid 115 through 123 or (resid 124 a \ nd (name N or name CA or name C or name O or name CB )) or resid 125 through 126 \ or (resid 127 through 130 and (name N or name CA or name C or name O or name CB \ )) or resid 131 through 142 or (resid 143 and (name N or name CA or name C or n \ ame O or name CB )) or resid 144 through 145 or (resid 146 through 147 and (name \ N or name CA or name C or name O or name CB )) or resid 148 or (resid 149 throu \ gh 150 and (name N or name CA or name C or name O or name CB )) or resid 151 thr \ ough 153 or (resid 154 and (name N or name CA or name C or name O or name CB )) \ or resid 155 through 156 or (resid 157 and (name N or name CA or name C or name \ O or name CB )) or resid 158 through 163 or (resid 164 and (name N or name CA or \ name C or name O or name CB )) or resid 165 through 166 or (resid 167 through 1 \ 68 and (name N or name CA or name C or name O or name CB )) or resid 169 through \ 170 or (resid 171 and (name N or name CA or name C or name O or name CB )) or r \ esid 172 through 179 or (resid 180 through 181 and (name N or name CA or name C \ or name O or name CB )) or resid 182 through 187 or (resid 188 and (name N or na \ me CA or name C or name O or name CB )) or resid 189 through 192 or (resid 193 a \ nd (name N or name CA or name C or name O or name CB )) or resid 194 through 199 \ or (resid 200 and (name N or name CA or name C or name O or name CB )) or resid \ 201 through 205 or (resid 206 and (name N or name CA or name C or name O or nam \ e CB )))) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.450 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7586 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 : 0.007 0.050 12820 Z= 0.310 Angle : 0.806 8.034 17511 Z= 0.486 Chirality : 0.057 0.293 2103 Planarity : 0.005 0.120 2164 Dihedral : 14.358 89.857 4544 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 1.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % Rotamer: Outliers : 0.61 % Allowed : 1.13 % Favored : 98.26 % 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: 1.03 (0.20), residues: 1624 helix: 0.57 (0.18), residues: 704 sheet: 0.44 (0.24), residues: 248 loop : 1.22 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.002 ARG A 37 TYR 0.033 0.003 TYR E 158 PHE 0.020 0.002 PHE E 78 TRP 0.020 0.003 TRP E 197 HIS 0.006 0.002 HIS C 116 Details of bonding type rmsd covalent geometry : bond 0.00665 (12820) covalent geometry : angle 0.80606 (17511) hydrogen bonds : bond 0.12079 ( 594) hydrogen bonds : angle 7.74207 ( 1779) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 192 time to evaluate : 0.475 Fit side-chains REVERT: A 16 ASN cc_start: 0.7154 (m110) cc_final: 0.6902 (t0) REVERT: A 27 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7944 (mm-30) REVERT: C 51 ASP cc_start: 0.8345 (m-30) cc_final: 0.7941 (m-30) REVERT: C 57 LYS cc_start: 0.7387 (tttp) cc_final: 0.6882 (tptp) REVERT: C 157 LEU cc_start: 0.8142 (mt) cc_final: 0.7917 (mt) REVERT: E 95 MET cc_start: 0.7752 (tpp) cc_final: 0.7353 (tpt) REVERT: G 25 ASP cc_start: 0.7266 (t70) cc_final: 0.6548 (m-30) REVERT: G 26 THR cc_start: 0.8938 (p) cc_final: 0.8649 (p) REVERT: K 39 CYS cc_start: 0.8126 (m) cc_final: 0.7921 (m) REVERT: K 59 GLN cc_start: 0.6805 (tt0) cc_final: 0.6515 (tp40) REVERT: K 184 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.7901 (mm-40) REVERT: O 28 THR cc_start: 0.8692 (p) cc_final: 0.8388 (p) REVERT: O 37 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7617 (ptt90) REVERT: O 54 GLN cc_start: 0.7818 (mt0) cc_final: 0.7533 (mt0) REVERT: O 95 MET cc_start: 0.7503 (tpp) cc_final: 0.6956 (tpp) outliers start: 7 outliers final: 1 residues processed: 195 average time/residue: 0.1048 time to fit residues: 30.1504 Evaluate side-chains 150 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 147 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 184 GLN Chi-restraints excluded: chain O residue 37 ARG Chi-restraints excluded: chain O residue 178 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN A 54 GLN G 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.104527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.093103 restraints weight = 18389.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.094672 restraints weight = 12980.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.095586 restraints weight = 10059.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.096474 restraints weight = 8463.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.096994 restraints weight = 7386.909| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12820 Z= 0.125 Angle : 0.473 5.158 17511 Z= 0.257 Chirality : 0.045 0.138 2103 Planarity : 0.003 0.028 2164 Dihedral : 11.848 77.968 2045 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 0.96 % Allowed : 4.79 % Favored : 94.26 % 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: 1.92 (0.21), residues: 1624 helix: 1.81 (0.20), residues: 712 sheet: 0.84 (0.25), residues: 240 loop : 1.05 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 67 TYR 0.009 0.001 TYR O 17 PHE 0.013 0.001 PHE O 78 TRP 0.005 0.001 TRP O 197 HIS 0.004 0.001 HIS O 79 Details of bonding type rmsd covalent geometry : bond 0.00277 (12820) covalent geometry : angle 0.47280 (17511) hydrogen bonds : bond 0.03730 ( 594) hydrogen bonds : angle 5.76596 ( 1779) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 173 time to evaluate : 0.484 Fit side-chains REVERT: A 27 GLU cc_start: 0.8261 (mm-30) cc_final: 0.7934 (mm-30) REVERT: A 54 GLN cc_start: 0.6936 (OUTLIER) cc_final: 0.6641 (mt0) REVERT: A 127 ASN cc_start: 0.7752 (m110) cc_final: 0.6552 (t0) REVERT: A 194 LEU cc_start: 0.7832 (mt) cc_final: 0.7615 (tt) REVERT: C 191 ASN cc_start: 0.8429 (t0) cc_final: 0.8224 (t0) REVERT: E 193 ASP cc_start: 0.7463 (m-30) cc_final: 0.7031 (m-30) REVERT: G 25 ASP cc_start: 0.7046 (t70) cc_final: 0.6564 (m-30) REVERT: G 26 THR cc_start: 0.8376 (p) cc_final: 0.8031 (p) REVERT: G 51 ASP cc_start: 0.8428 (m-30) cc_final: 0.7703 (m-30) REVERT: I 200 ILE cc_start: 0.8099 (mm) cc_final: 0.7505 (tt) REVERT: K 184 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7899 (mm-40) REVERT: O 95 MET cc_start: 0.7301 (tpp) cc_final: 0.6951 (tpp) outliers start: 11 outliers final: 5 residues processed: 178 average time/residue: 0.0894 time to fit residues: 24.6553 Evaluate side-chains 153 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 146 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 GLN Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain K residue 184 GLN Chi-restraints excluded: chain M residue 137 SER Chi-restraints excluded: chain O residue 154 SER Chi-restraints excluded: chain O residue 206 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 54 optimal weight: 20.0000 chunk 126 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 9 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 140 optimal weight: 10.0000 chunk 35 optimal weight: 7.9990 chunk 142 optimal weight: 10.0000 chunk 68 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN A 32 GLN A 54 GLN G 54 GLN G 64 ASN M 135 GLN O 54 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.100683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.088999 restraints weight = 18915.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.090481 restraints weight = 13386.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.091633 restraints weight = 10423.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.092296 restraints weight = 8673.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.092910 restraints weight = 7643.135| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 12820 Z= 0.221 Angle : 0.554 5.873 17511 Z= 0.298 Chirality : 0.049 0.233 2103 Planarity : 0.004 0.040 2164 Dihedral : 12.225 85.187 2040 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 1.48 % Allowed : 7.40 % Favored : 91.12 % 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: 1.29 (0.21), residues: 1624 helix: 1.19 (0.19), residues: 752 sheet: 0.77 (0.26), residues: 248 loop : 0.69 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 169 TYR 0.012 0.002 TYR A 17 PHE 0.016 0.002 PHE C 78 TRP 0.006 0.001 TRP G 197 HIS 0.008 0.001 HIS O 79 Details of bonding type rmsd covalent geometry : bond 0.00522 (12820) covalent geometry : angle 0.55424 (17511) hydrogen bonds : bond 0.04555 ( 594) hydrogen bonds : angle 5.84278 ( 1779) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.452 Fit side-chains REVERT: A 42 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.8027 (pt0) REVERT: A 127 ASN cc_start: 0.7979 (m110) cc_final: 0.6543 (t0) REVERT: E 25 ASP cc_start: 0.7247 (t0) cc_final: 0.7005 (t70) REVERT: E 193 ASP cc_start: 0.7644 (m-30) cc_final: 0.7116 (m-30) REVERT: G 25 ASP cc_start: 0.7554 (t70) cc_final: 0.7282 (t70) REVERT: G 51 ASP cc_start: 0.8456 (m-30) cc_final: 0.7861 (m-30) REVERT: G 54 GLN cc_start: 0.8321 (mt0) cc_final: 0.8067 (mt0) REVERT: G 193 ASP cc_start: 0.7599 (OUTLIER) cc_final: 0.6931 (t0) REVERT: G 206 SER cc_start: 0.7261 (m) cc_final: 0.6933 (t) REVERT: I 200 ILE cc_start: 0.8124 (mm) cc_final: 0.7575 (tt) REVERT: K 134 GLN cc_start: 0.7341 (mm-40) cc_final: 0.6942 (mp10) REVERT: K 184 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.8058 (mm-40) REVERT: M 206 SER cc_start: 0.6691 (m) cc_final: 0.6282 (p) outliers start: 17 outliers final: 10 residues processed: 168 average time/residue: 0.0911 time to fit residues: 23.1917 Evaluate side-chains 161 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.489 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain K residue 184 GLN Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 39 CYS Chi-restraints excluded: chain O residue 128 VAL Chi-restraints excluded: chain O residue 154 SER Chi-restraints excluded: chain O residue 200 ILE Chi-restraints excluded: chain O residue 206 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 151 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 136 optimal weight: 3.9990 chunk 156 optimal weight: 5.9990 chunk 7 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 58 optimal weight: 0.9980 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN A 32 GLN G 32 GLN G 64 ASN O 54 GLN O 134 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.102233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.090602 restraints weight = 18605.392| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.092128 restraints weight = 13133.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.093284 restraints weight = 10217.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.094024 restraints weight = 8472.426| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.094502 restraints weight = 7399.044| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12820 Z= 0.144 Angle : 0.456 5.628 17511 Z= 0.247 Chirality : 0.045 0.132 2103 Planarity : 0.003 0.034 2164 Dihedral : 11.942 83.238 2040 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.22 % Allowed : 7.92 % Favored : 90.86 % 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: 1.29 (0.21), residues: 1624 helix: 1.26 (0.19), residues: 752 sheet: 0.92 (0.27), residues: 248 loop : 0.51 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 169 TYR 0.010 0.001 TYR M 151 PHE 0.011 0.001 PHE O 78 TRP 0.004 0.001 TRP C 197 HIS 0.005 0.001 HIS O 79 Details of bonding type rmsd covalent geometry : bond 0.00333 (12820) covalent geometry : angle 0.45596 (17511) hydrogen bonds : bond 0.03750 ( 594) hydrogen bonds : angle 5.50294 ( 1779) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 165 time to evaluate : 0.491 Fit side-chains REVERT: A 39 CYS cc_start: 0.8257 (m) cc_final: 0.8040 (m) REVERT: A 127 ASN cc_start: 0.7750 (m110) cc_final: 0.6472 (t0) REVERT: E 25 ASP cc_start: 0.7272 (t0) cc_final: 0.6890 (t70) REVERT: E 193 ASP cc_start: 0.7701 (m-30) cc_final: 0.7114 (m-30) REVERT: G 51 ASP cc_start: 0.8317 (m-30) cc_final: 0.7692 (m-30) REVERT: G 54 GLN cc_start: 0.8274 (mt0) cc_final: 0.8042 (mt0) REVERT: G 155 ASP cc_start: 0.8086 (t70) cc_final: 0.7629 (t0) REVERT: G 193 ASP cc_start: 0.7540 (OUTLIER) cc_final: 0.6961 (t0) REVERT: K 184 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7933 (mm-40) REVERT: M 206 SER cc_start: 0.7130 (m) cc_final: 0.6628 (p) outliers start: 14 outliers final: 10 residues processed: 172 average time/residue: 0.0866 time to fit residues: 23.4005 Evaluate side-chains 164 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 176 GLU Chi-restraints excluded: chain K residue 184 GLN Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain O residue 128 VAL Chi-restraints excluded: chain O residue 154 SER Chi-restraints excluded: chain O residue 206 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 56 optimal weight: 2.9990 chunk 14 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 57 optimal weight: 2.9990 chunk 111 optimal weight: 10.0000 chunk 101 optimal weight: 8.9990 chunk 90 optimal weight: 7.9990 chunk 126 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN G 64 ASN G 184 GLN O 54 GLN O 184 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.100847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.089179 restraints weight = 18801.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.090684 restraints weight = 13426.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.091764 restraints weight = 10522.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.092417 restraints weight = 8785.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.092846 restraints weight = 7764.653| |-----------------------------------------------------------------------------| r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 12820 Z= 0.200 Angle : 0.506 5.101 17511 Z= 0.272 Chirality : 0.047 0.166 2103 Planarity : 0.004 0.036 2164 Dihedral : 12.089 85.256 2040 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.74 % Allowed : 8.79 % Favored : 89.47 % 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: 0.90 (0.21), residues: 1624 helix: 0.95 (0.19), residues: 768 sheet: 0.73 (0.29), residues: 248 loop : 0.27 (0.28), residues: 608 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 169 TYR 0.012 0.002 TYR M 151 PHE 0.013 0.001 PHE A 78 TRP 0.005 0.001 TRP C 197 HIS 0.007 0.001 HIS O 79 Details of bonding type rmsd covalent geometry : bond 0.00471 (12820) covalent geometry : angle 0.50606 (17511) hydrogen bonds : bond 0.04233 ( 594) hydrogen bonds : angle 5.63696 ( 1779) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.452 Fit side-chains REVERT: A 32 GLN cc_start: 0.7897 (mt0) cc_final: 0.7568 (mm110) REVERT: A 39 CYS cc_start: 0.8311 (m) cc_final: 0.8084 (m) REVERT: A 127 ASN cc_start: 0.7831 (m110) cc_final: 0.6514 (t0) REVERT: A 155 ASP cc_start: 0.7695 (t0) cc_final: 0.7339 (t0) REVERT: E 25 ASP cc_start: 0.7433 (t0) cc_final: 0.6944 (t70) REVERT: E 27 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7200 (mp0) REVERT: E 193 ASP cc_start: 0.7683 (m-30) cc_final: 0.7088 (m-30) REVERT: G 51 ASP cc_start: 0.8353 (m-30) cc_final: 0.7758 (m-30) REVERT: G 155 ASP cc_start: 0.7852 (t70) cc_final: 0.7224 (t0) REVERT: G 193 ASP cc_start: 0.7587 (OUTLIER) cc_final: 0.6912 (t0) REVERT: G 206 SER cc_start: 0.7330 (m) cc_final: 0.6970 (t) REVERT: K 184 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.8007 (mm-40) REVERT: M 206 SER cc_start: 0.7433 (m) cc_final: 0.7019 (m) outliers start: 20 outliers final: 15 residues processed: 165 average time/residue: 0.0907 time to fit residues: 23.1897 Evaluate side-chains 171 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 153 time to evaluate : 0.472 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 184 GLN Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 176 GLU Chi-restraints excluded: chain K residue 184 GLN Chi-restraints excluded: chain M residue 49 THR Chi-restraints excluded: chain O residue 26 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 128 VAL Chi-restraints excluded: chain O residue 154 SER Chi-restraints excluded: chain O residue 200 ILE Chi-restraints excluded: chain O residue 206 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 35 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 57 optimal weight: 8.9990 chunk 138 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 118 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 52 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 132 optimal weight: 6.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 64 ASN G 184 GLN O 184 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.104497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.093074 restraints weight = 18491.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.094555 restraints weight = 13104.982| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.095670 restraints weight = 10184.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.096125 restraints weight = 8437.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.096943 restraints weight = 7588.389| |-----------------------------------------------------------------------------| r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 12820 Z= 0.093 Angle : 0.401 4.880 17511 Z= 0.220 Chirality : 0.043 0.131 2103 Planarity : 0.003 0.033 2164 Dihedral : 11.641 82.555 2040 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.13 % Allowed : 9.75 % Favored : 89.12 % 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: 1.31 (0.22), residues: 1624 helix: 1.24 (0.19), residues: 776 sheet: 1.11 (0.29), residues: 248 loop : 0.45 (0.28), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 67 TYR 0.009 0.001 TYR E 158 PHE 0.011 0.001 PHE O 78 TRP 0.004 0.000 TRP C 197 HIS 0.002 0.000 HIS O 79 Details of bonding type rmsd covalent geometry : bond 0.00199 (12820) covalent geometry : angle 0.40107 (17511) hydrogen bonds : bond 0.03163 ( 594) hydrogen bonds : angle 5.21038 ( 1779) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 0.458 Fit side-chains REVERT: A 17 TYR cc_start: 0.7547 (m-80) cc_final: 0.7292 (m-80) REVERT: A 32 GLN cc_start: 0.8112 (mt0) cc_final: 0.7699 (mm110) REVERT: A 39 CYS cc_start: 0.8262 (m) cc_final: 0.8043 (m) REVERT: A 127 ASN cc_start: 0.7817 (m110) cc_final: 0.6317 (t0) REVERT: A 155 ASP cc_start: 0.7722 (t0) cc_final: 0.7512 (t0) REVERT: E 25 ASP cc_start: 0.7276 (t70) cc_final: 0.6881 (t70) REVERT: E 27 GLU cc_start: 0.7828 (mp0) cc_final: 0.7081 (mp0) REVERT: G 51 ASP cc_start: 0.8229 (m-30) cc_final: 0.7627 (m-30) REVERT: G 54 GLN cc_start: 0.8208 (mt0) cc_final: 0.7981 (mt0) REVERT: G 155 ASP cc_start: 0.7878 (t70) cc_final: 0.7315 (t0) REVERT: I 65 LEU cc_start: 0.7792 (tp) cc_final: 0.7570 (tp) REVERT: K 184 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7905 (mm-40) REVERT: M 206 SER cc_start: 0.7199 (m) cc_final: 0.6823 (m) outliers start: 13 outliers final: 10 residues processed: 171 average time/residue: 0.0893 time to fit residues: 23.8995 Evaluate side-chains 172 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 161 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 176 GLU Chi-restraints excluded: chain K residue 184 GLN Chi-restraints excluded: chain O residue 154 SER Chi-restraints excluded: chain O residue 206 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 72 optimal weight: 10.0000 chunk 106 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 120 optimal weight: 10.0000 chunk 143 optimal weight: 0.0070 chunk 141 optimal weight: 8.9990 chunk 17 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 148 optimal weight: 0.8980 chunk 129 optimal weight: 0.0670 overall best weight: 3.3940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 54 GLN G 32 GLN G 64 ASN O 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.101343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.089733 restraints weight = 18812.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.091243 restraints weight = 13399.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.092188 restraints weight = 10440.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.092851 restraints weight = 8861.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.093599 restraints weight = 7787.958| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12820 Z= 0.190 Angle : 0.488 5.140 17511 Z= 0.262 Chirality : 0.046 0.133 2103 Planarity : 0.004 0.036 2164 Dihedral : 11.966 85.686 2040 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.39 % Allowed : 10.44 % Favored : 88.16 % 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: 0.97 (0.21), residues: 1624 helix: 1.00 (0.19), residues: 776 sheet: 0.89 (0.30), residues: 248 loop : 0.25 (0.28), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 67 TYR 0.011 0.001 TYR A 17 PHE 0.012 0.001 PHE O 78 TRP 0.004 0.001 TRP O 197 HIS 0.007 0.001 HIS O 79 Details of bonding type rmsd covalent geometry : bond 0.00446 (12820) covalent geometry : angle 0.48849 (17511) hydrogen bonds : bond 0.04076 ( 594) hydrogen bonds : angle 5.52686 ( 1779) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.323 Fit side-chains REVERT: A 32 GLN cc_start: 0.7853 (mt0) cc_final: 0.7550 (mm110) REVERT: A 39 CYS cc_start: 0.8390 (m) cc_final: 0.8122 (m) REVERT: A 127 ASN cc_start: 0.7754 (m110) cc_final: 0.6451 (t0) REVERT: A 155 ASP cc_start: 0.7712 (t0) cc_final: 0.7423 (t0) REVERT: E 25 ASP cc_start: 0.7304 (t70) cc_final: 0.6773 (t70) REVERT: E 27 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7137 (mp0) REVERT: G 51 ASP cc_start: 0.8323 (m-30) cc_final: 0.7679 (m-30) REVERT: G 155 ASP cc_start: 0.7935 (t70) cc_final: 0.7238 (t0) REVERT: G 193 ASP cc_start: 0.7500 (OUTLIER) cc_final: 0.6850 (t0) REVERT: I 84 ASP cc_start: 0.8547 (m-30) cc_final: 0.8283 (m-30) REVERT: K 131 SER cc_start: 0.7014 (t) cc_final: 0.6768 (p) REVERT: K 184 GLN cc_start: 0.8211 (OUTLIER) cc_final: 0.8008 (mm-40) REVERT: M 206 SER cc_start: 0.7341 (m) cc_final: 0.7033 (m) outliers start: 16 outliers final: 13 residues processed: 161 average time/residue: 0.0836 time to fit residues: 20.9290 Evaluate side-chains 169 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 176 GLU Chi-restraints excluded: chain K residue 184 GLN Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 154 SER Chi-restraints excluded: chain O residue 206 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 131 optimal weight: 6.9990 chunk 67 optimal weight: 9.9990 chunk 147 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 chunk 78 optimal weight: 0.9980 chunk 117 optimal weight: 10.0000 chunk 73 optimal weight: 4.9990 chunk 136 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 110 optimal weight: 0.8980 chunk 135 optimal weight: 5.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 64 ASN M 135 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.102166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.090552 restraints weight = 18596.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.092084 restraints weight = 13190.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.093165 restraints weight = 10262.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.093787 restraints weight = 8585.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.094456 restraints weight = 7580.814| |-----------------------------------------------------------------------------| r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12820 Z= 0.142 Angle : 0.440 5.006 17511 Z= 0.238 Chirality : 0.045 0.128 2103 Planarity : 0.003 0.037 2164 Dihedral : 11.810 84.831 2040 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 1.91 % Allowed : 10.01 % Favored : 88.08 % 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: 0.99 (0.21), residues: 1624 helix: 1.05 (0.19), residues: 776 sheet: 0.94 (0.30), residues: 248 loop : 0.19 (0.28), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 67 TYR 0.010 0.001 TYR M 151 PHE 0.012 0.001 PHE O 78 TRP 0.003 0.001 TRP O 197 HIS 0.005 0.001 HIS O 79 Details of bonding type rmsd covalent geometry : bond 0.00329 (12820) covalent geometry : angle 0.44046 (17511) hydrogen bonds : bond 0.03657 ( 594) hydrogen bonds : angle 5.38388 ( 1779) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.471 Fit side-chains REVERT: A 17 TYR cc_start: 0.7644 (m-80) cc_final: 0.7277 (m-80) REVERT: A 32 GLN cc_start: 0.8066 (mt0) cc_final: 0.7733 (mm110) REVERT: A 39 CYS cc_start: 0.8260 (m) cc_final: 0.8001 (m) REVERT: A 42 GLN cc_start: 0.8554 (OUTLIER) cc_final: 0.8094 (pt0) REVERT: A 127 ASN cc_start: 0.7775 (m110) cc_final: 0.6530 (t0) REVERT: A 155 ASP cc_start: 0.7835 (t0) cc_final: 0.7583 (t0) REVERT: E 25 ASP cc_start: 0.7297 (t70) cc_final: 0.6803 (t70) REVERT: E 27 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7086 (mp0) REVERT: G 51 ASP cc_start: 0.8259 (m-30) cc_final: 0.7640 (m-30) REVERT: G 155 ASP cc_start: 0.7934 (t70) cc_final: 0.7277 (t0) REVERT: G 193 ASP cc_start: 0.7494 (OUTLIER) cc_final: 0.6871 (t0) REVERT: I 84 ASP cc_start: 0.8602 (m-30) cc_final: 0.8347 (m-30) REVERT: K 131 SER cc_start: 0.6999 (t) cc_final: 0.6760 (p) REVERT: K 184 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7961 (mm-40) REVERT: M 206 SER cc_start: 0.7345 (m) cc_final: 0.7047 (m) outliers start: 22 outliers final: 14 residues processed: 168 average time/residue: 0.0880 time to fit residues: 22.9215 Evaluate side-chains 173 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 155 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 176 GLU Chi-restraints excluded: chain K residue 184 GLN Chi-restraints excluded: chain O residue 26 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 154 SER Chi-restraints excluded: chain O residue 206 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 106 optimal weight: 0.6980 chunk 39 optimal weight: 8.9990 chunk 73 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 53 optimal weight: 0.2980 chunk 88 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 64 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.104774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.093256 restraints weight = 18494.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.094781 restraints weight = 13134.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.095675 restraints weight = 10203.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.096634 restraints weight = 8630.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.097108 restraints weight = 7510.625| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 12820 Z= 0.094 Angle : 0.405 8.361 17511 Z= 0.219 Chirality : 0.043 0.271 2103 Planarity : 0.003 0.034 2164 Dihedral : 11.531 82.759 2040 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 1.48 % Allowed : 10.36 % Favored : 88.16 % 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: 1.36 (0.22), residues: 1624 helix: 1.25 (0.19), residues: 776 sheet: 1.25 (0.30), residues: 248 loop : 0.46 (0.29), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 5 TYR 0.011 0.001 TYR E 158 PHE 0.010 0.001 PHE O 78 TRP 0.002 0.000 TRP K 139 HIS 0.002 0.000 HIS G 79 Details of bonding type rmsd covalent geometry : bond 0.00205 (12820) covalent geometry : angle 0.40544 (17511) hydrogen bonds : bond 0.03102 ( 594) hydrogen bonds : angle 5.13450 ( 1779) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 167 time to evaluate : 0.417 Fit side-chains REVERT: A 39 CYS cc_start: 0.8222 (m) cc_final: 0.7985 (m) REVERT: A 42 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.8072 (pt0) REVERT: A 127 ASN cc_start: 0.7816 (m110) cc_final: 0.6341 (t0) REVERT: E 25 ASP cc_start: 0.7427 (t70) cc_final: 0.6980 (t70) REVERT: E 27 GLU cc_start: 0.7837 (OUTLIER) cc_final: 0.7011 (mp0) REVERT: G 51 ASP cc_start: 0.8147 (m-30) cc_final: 0.7605 (m-30) REVERT: G 155 ASP cc_start: 0.7912 (t70) cc_final: 0.7286 (t0) REVERT: G 193 ASP cc_start: 0.7537 (OUTLIER) cc_final: 0.6937 (t0) REVERT: I 84 ASP cc_start: 0.8597 (m-30) cc_final: 0.8362 (m-30) REVERT: I 171 LYS cc_start: 0.7223 (ttpp) cc_final: 0.6966 (ttpp) REVERT: K 5 ARG cc_start: 0.7741 (mtm-85) cc_final: 0.7535 (mtt180) REVERT: K 131 SER cc_start: 0.6893 (t) cc_final: 0.6600 (p) REVERT: K 184 GLN cc_start: 0.8103 (OUTLIER) cc_final: 0.7861 (mm-40) REVERT: M 206 SER cc_start: 0.7347 (m) cc_final: 0.7124 (m) outliers start: 17 outliers final: 12 residues processed: 174 average time/residue: 0.0920 time to fit residues: 24.4736 Evaluate side-chains 171 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain K residue 184 GLN Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 154 SER Chi-restraints excluded: chain O residue 206 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 1 optimal weight: 0.0770 chunk 54 optimal weight: 20.0000 chunk 90 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 30 optimal weight: 4.9990 chunk 120 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 chunk 157 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 127 ASN G 54 GLN G 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.100772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.089358 restraints weight = 18843.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.090805 restraints weight = 13419.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.091905 restraints weight = 10450.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.092603 restraints weight = 8751.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.092939 restraints weight = 7677.879| |-----------------------------------------------------------------------------| r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.2772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12820 Z= 0.219 Angle : 0.531 10.379 17511 Z= 0.280 Chirality : 0.048 0.212 2103 Planarity : 0.004 0.039 2164 Dihedral : 11.989 85.422 2040 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 1.91 % Allowed : 10.36 % Favored : 87.73 % 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: 0.82 (0.21), residues: 1624 helix: 0.92 (0.19), residues: 776 sheet: 0.87 (0.30), residues: 248 loop : 0.08 (0.28), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 67 TYR 0.011 0.002 TYR A 17 PHE 0.017 0.002 PHE A 78 TRP 0.004 0.001 TRP E 197 HIS 0.008 0.001 HIS O 79 Details of bonding type rmsd covalent geometry : bond 0.00521 (12820) covalent geometry : angle 0.53098 (17511) hydrogen bonds : bond 0.04340 ( 594) hydrogen bonds : angle 5.61343 ( 1779) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3248 Ramachandran restraints generated. 1624 Oldfield, 0 Emsley, 1624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 149 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 32 GLN cc_start: 0.7880 (mt0) cc_final: 0.7556 (mm110) REVERT: A 39 CYS cc_start: 0.8382 (m) cc_final: 0.8098 (m) REVERT: A 42 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8125 (pt0) REVERT: C 94 VAL cc_start: 0.7821 (t) cc_final: 0.7601 (m) REVERT: E 25 ASP cc_start: 0.7498 (t70) cc_final: 0.7002 (t70) REVERT: E 27 GLU cc_start: 0.7998 (OUTLIER) cc_final: 0.7062 (mp0) REVERT: G 155 ASP cc_start: 0.8134 (t70) cc_final: 0.7363 (t0) REVERT: G 193 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.6844 (t0) REVERT: G 206 SER cc_start: 0.7141 (m) cc_final: 0.6879 (t) REVERT: M 206 SER cc_start: 0.7367 (m) cc_final: 0.7127 (m) outliers start: 22 outliers final: 16 residues processed: 159 average time/residue: 0.0885 time to fit residues: 21.5132 Evaluate side-chains 166 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 147 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 GLN Chi-restraints excluded: chain A residue 131 SER Chi-restraints excluded: chain A residue 164 ASP Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain G residue 26 THR Chi-restraints excluded: chain G residue 44 SER Chi-restraints excluded: chain G residue 193 ASP Chi-restraints excluded: chain I residue 44 SER Chi-restraints excluded: chain I residue 131 SER Chi-restraints excluded: chain I residue 156 VAL Chi-restraints excluded: chain I residue 176 GLU Chi-restraints excluded: chain M residue 109 THR Chi-restraints excluded: chain O residue 28 THR Chi-restraints excluded: chain O residue 154 SER Chi-restraints excluded: chain O residue 206 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 118 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 chunk 37 optimal weight: 7.9990 chunk 117 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 109 optimal weight: 0.8980 chunk 101 optimal weight: 9.9990 chunk 105 optimal weight: 0.8980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 54 GLN G 64 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.102003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.090573 restraints weight = 18755.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.092012 restraints weight = 13364.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.092915 restraints weight = 10467.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.093715 restraints weight = 8852.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.094299 restraints weight = 7672.063| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12820 Z= 0.160 Angle : 0.468 7.094 17511 Z= 0.250 Chirality : 0.046 0.224 2103 Planarity : 0.003 0.039 2164 Dihedral : 11.628 73.648 2037 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.83 % Allowed : 10.44 % Favored : 87.73 % 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: 0.82 (0.21), residues: 1624 helix: 0.97 (0.19), residues: 776 sheet: 0.84 (0.30), residues: 248 loop : 0.02 (0.28), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 67 TYR 0.009 0.001 TYR A 158 PHE 0.013 0.001 PHE O 78 TRP 0.003 0.001 TRP G 139 HIS 0.005 0.001 HIS O 79 Details of bonding type rmsd covalent geometry : bond 0.00375 (12820) covalent geometry : angle 0.46813 (17511) hydrogen bonds : bond 0.03847 ( 594) hydrogen bonds : angle 5.45015 ( 1779) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1502.79 seconds wall clock time: 26 minutes 48.05 seconds (1608.05 seconds total)