Starting phenix.real_space_refine on Sun Sep 13 06:23:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mqg_23946/09_2026/7mqg_23946.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mqg_23946/09_2026/7mqg_23946.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7mqg_23946/09_2026/7mqg_23946.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mqg_23946/09_2026/7mqg_23946.cif" model { file = "/net/cci-nas-00/data/ceres_data/7mqg_23946/09_2026/7mqg_23946.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mqg_23946/09_2026/7mqg_23946.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7mqg_23946/09_2026/7mqg_23946.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mqg_23946/09_2026/7mqg_23946.map" } resolution = 3.25 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= 0.018 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 11321 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 48 5.16 5 C 8017 2.51 5 N 2313 2.21 5 O 2276 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 44 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12670 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1525 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 108 Unresolved non-hydrogen angles: 131 Unresolved non-hydrogen dihedrals: 85 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 9, 'ASP:plan': 6, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 79 Chain: "C" Number of atoms: 1538 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1538 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 114 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 7, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 65 Chain: "E" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1546 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 6, 'ARG:plan': 3, 'GLN:plan1': 2, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 61 Chain: "G" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1541 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 71 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 9, 'ARG:plan': 1, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 64 Chain: "I" Number of atoms: 1539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1539 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 94 Unresolved non-hydrogen angles: 113 Unresolved non-hydrogen dihedrals: 75 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 8, 'ASN:plan1': 1, 'ARG:plan': 2, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 69 Chain: "K" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1536 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 116 Unresolved non-hydrogen dihedrals: 78 Planarities with less than four sites: {'GLU:plan': 7, 'ASP:plan': 7, 'ARG:plan': 3, 'GLN:plan1': 2} Unresolved non-hydrogen planarities: 72 Chain: "M" Number of atoms: 1543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1543 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 90 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 72 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 2, 'ASN:plan1': 1, 'GLN:plan1': 3, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 66 Chain: "O" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1534 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 99 Unresolved non-hydrogen angles: 121 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 8, 'ASP:plan': 7, 'ARG:plan': 2, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 75 Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNAv2': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNAv2': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "F" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNAv2': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "H" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNAv2': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "J" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNAv2': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "L" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNAv2': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "N" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNAv2': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Chain: "P" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 46 Classifications: {'RNAv2': 2} Modifications used: {'rna3p_pur': 2} Link IDs: {'rna3p': 1} Time building chain proxies: 2.65, per 1000 atoms: 0.21 Number of scatterers: 12670 At special positions: 0 Unit cell: (105.4, 117.8, 110.36, 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 48 16.00 P 16 15.00 O 2276 8.00 N 2313 7.00 C 8017 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: 1.07 Conformation dependent library (CDL) restraints added in 496.9 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: 56 helices and 8 sheets defined 45.3% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 62 through 71 Processing helix chain 'A' and resid 80 through 93 removed outlier: 3.922A pdb=" N ASP A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 3.526A 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 155 removed outlier: 3.629A pdb=" N ASP A 155 " --> pdb=" O TYR A 151 " (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: 4.047A pdb=" N ASP C 84 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 3.549A 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 155 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: 4.003A pdb=" N ASP E 84 " --> pdb=" O PHE E 80 " (cutoff:3.500A) removed outlier: 3.625A 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 155 removed outlier: 3.554A pdb=" N ASP E 155 " --> pdb=" O TYR E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 158 through 173 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: 4.005A pdb=" N ASP G 84 " --> pdb=" O PHE G 80 " (cutoff:3.500A) removed outlier: 3.599A 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 removed outlier: 3.532A pdb=" N ASP G 155 " --> pdb=" O TYR G 151 " (cutoff:3.500A) 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: 3.973A pdb=" N ASP I 84 " --> pdb=" O PHE I 80 " (cutoff:3.500A) removed outlier: 3.614A 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 145 through 155 removed outlier: 3.619A pdb=" N ASP I 155 " --> pdb=" O TYR I 151 " (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: 3.969A pdb=" N ASP K 84 " --> pdb=" O PHE K 80 " (cutoff:3.500A) removed outlier: 3.600A 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 removed outlier: 3.823A pdb=" N ASP K 155 " --> pdb=" O TYR K 151 " (cutoff:3.500A) 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: 3.973A pdb=" N ASP M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) removed outlier: 3.613A 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 155 removed outlier: 3.612A pdb=" N ASP M 155 " --> pdb=" O TYR M 151 " (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: 3.992A pdb=" N ASP O 84 " --> pdb=" O PHE O 80 " (cutoff:3.500A) removed outlier: 3.562A 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 155 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 3 through 8 Processing sheet with id=AA2, first strand: chain 'C' and resid 4 through 8 removed outlier: 6.260A pdb=" N ARG C 5 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N GLN C 54 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N HIS C 7 " --> pdb=" O GLN C 54 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.318A pdb=" N ARG E 5 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N GLN E 54 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N HIS E 7 " --> pdb=" O GLN E 54 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU E 27 " --> pdb=" O CYS E 39 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL E 41 " --> pdb=" O ASP E 25 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ASP E 25 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LEU E 43 " --> pdb=" O ALA E 23 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ALA E 23 " --> pdb=" O LEU E 43 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 4 through 8 removed outlier: 6.303A pdb=" N ARG G 5 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N GLN G 54 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N HIS G 7 " --> pdb=" O GLN G 54 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N GLU G 27 " --> pdb=" O CYS G 39 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N VAL G 41 " --> pdb=" O ASP G 25 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASP G 25 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU G 43 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 6.644A 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: 6.701A pdb=" N GLU I 3 " --> pdb=" O ALA I 50 " (cutoff:3.500A) removed outlier: 7.770A pdb=" N VAL I 52 " --> pdb=" O GLU I 3 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ARG I 5 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N GLN I 54 " --> pdb=" O ARG I 5 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N HIS I 7 " --> pdb=" O GLN I 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 3 through 8 removed outlier: 6.666A pdb=" N GLU K 3 " --> pdb=" O ALA K 50 " (cutoff:3.500A) removed outlier: 7.698A pdb=" N VAL K 52 " --> pdb=" O GLU K 3 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N ARG K 5 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLN K 54 " --> pdb=" O ARG K 5 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N HIS K 7 " --> pdb=" O GLN K 54 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL K 22 " --> pdb=" O ILE K 77 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 3 through 8 removed outlier: 6.620A pdb=" N GLU M 3 " --> pdb=" O ALA M 50 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL M 52 " --> pdb=" O GLU M 3 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ARG M 5 " --> pdb=" O VAL M 52 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N GLN M 54 " --> pdb=" O ARG M 5 " (cutoff:3.500A) removed outlier: 6.764A 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: 6.580A pdb=" N GLU O 3 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL O 52 " --> pdb=" O GLU O 3 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ARG O 5 " --> pdb=" O VAL O 52 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLN O 54 " --> pdb=" O ARG O 5 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N HIS O 7 " --> pdb=" O GLN O 54 " (cutoff:3.500A) 585 hydrogen bonds defined for protein. 1755 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: 1.64 Time building geometry restraints manager: 1.43 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: 4206 1.34 - 1.46: 1958 1.46 - 1.57: 6682 1.57 - 1.69: 24 1.69 - 1.81: 64 Bond restraints: 12934 Sorted by residual: bond pdb=" N GLU O 27 " pdb=" CA GLU O 27 " ideal model delta sigma weight residual 1.457 1.491 -0.035 1.26e-02 6.30e+03 7.59e+00 bond pdb=" N TYR A 151 " pdb=" CA TYR A 151 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.23e-02 6.61e+03 5.64e+00 bond pdb=" CG LEU M 68 " pdb=" CD1 LEU M 68 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.58e+00 bond pdb=" CG ARG M 169 " pdb=" CD ARG M 169 " ideal model delta sigma weight residual 1.520 1.472 0.048 3.00e-02 1.11e+03 2.57e+00 bond pdb=" CA GLU O 27 " pdb=" C GLU O 27 " ideal model delta sigma weight residual 1.520 1.539 -0.019 1.20e-02 6.94e+03 2.43e+00 ... (remaining 12929 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.31: 17337 2.31 - 4.63: 295 4.63 - 6.94: 31 6.94 - 9.25: 6 9.25 - 11.57: 3 Bond angle restraints: 17672 Sorted by residual: angle pdb=" C LYS A 132 " pdb=" N GLN A 133 " pdb=" CA GLN A 133 " ideal model delta sigma weight residual 121.54 129.15 -7.61 1.91e+00 2.74e-01 1.59e+01 angle pdb=" CB MET E 188 " pdb=" CG MET E 188 " pdb=" SD MET E 188 " ideal model delta sigma weight residual 112.70 101.13 11.57 3.00e+00 1.11e-01 1.49e+01 angle pdb=" C ASP E 138 " pdb=" N TRP E 139 " pdb=" CA TRP E 139 " ideal model delta sigma weight residual 121.54 128.54 -7.00 1.91e+00 2.74e-01 1.34e+01 angle pdb=" CB LYS O 119 " pdb=" CG LYS O 119 " pdb=" CD LYS O 119 " ideal model delta sigma weight residual 111.30 119.03 -7.73 2.30e+00 1.89e-01 1.13e+01 angle pdb=" CB MET I 95 " pdb=" CG MET I 95 " pdb=" SD MET I 95 " ideal model delta sigma weight residual 112.70 122.37 -9.67 3.00e+00 1.11e-01 1.04e+01 ... (remaining 17667 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.19: 7146 17.19 - 34.39: 388 34.39 - 51.58: 66 51.58 - 68.78: 19 68.78 - 85.97: 9 Dihedral angle restraints: 7628 sinusoidal: 2844 harmonic: 4784 Sorted by residual: dihedral pdb=" CA PHE O 78 " pdb=" C PHE O 78 " pdb=" N HIS O 79 " pdb=" CA HIS O 79 " ideal model delta harmonic sigma weight residual 180.00 157.08 22.92 0 5.00e+00 4.00e-02 2.10e+01 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 180.00 157.16 22.84 0 5.00e+00 4.00e-02 2.09e+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 180.00 157.38 22.62 0 5.00e+00 4.00e-02 2.05e+01 ... (remaining 7625 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1662 0.065 - 0.131: 420 0.131 - 0.196: 28 0.196 - 0.262: 9 0.262 - 0.327: 8 Chirality restraints: 2127 Sorted by residual: chirality pdb=" P G J 603 " pdb=" OP1 G J 603 " pdb=" OP2 G J 603 " pdb=" O5' G J 603 " both_signs ideal model delta sigma weight residual True 2.17 2.50 -0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" P G P 603 " pdb=" OP1 G P 603 " pdb=" OP2 G P 603 " pdb=" O5' G P 603 " both_signs ideal model delta sigma weight residual True 2.17 2.50 -0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" P G L 603 " pdb=" OP1 G L 603 " pdb=" OP2 G L 603 " pdb=" O5' G L 603 " both_signs ideal model delta sigma weight residual True 2.17 2.50 -0.33 2.00e-01 2.50e+01 2.64e+00 ... (remaining 2124 not shown) Planarity restraints: 2203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA M 153 " -0.010 2.00e-02 2.50e+03 1.99e-02 3.97e+00 pdb=" C ALA M 153 " 0.034 2.00e-02 2.50e+03 pdb=" O ALA M 153 " -0.013 2.00e-02 2.50e+03 pdb=" N SER M 154 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR O 26 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.67e+00 pdb=" C THR O 26 " 0.033 2.00e-02 2.50e+03 pdb=" O THR O 26 " -0.013 2.00e-02 2.50e+03 pdb=" N GLU O 27 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 83 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.04e+00 pdb=" C PHE C 83 " 0.030 2.00e-02 2.50e+03 pdb=" O PHE C 83 " -0.011 2.00e-02 2.50e+03 pdb=" N ASP C 84 " -0.010 2.00e-02 2.50e+03 ... (remaining 2200 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 875 2.73 - 3.27: 11929 3.27 - 3.82: 20435 3.82 - 4.36: 26259 4.36 - 4.90: 43967 Nonbonded interactions: 103465 Sorted by model distance: nonbonded pdb=" OH TYR M 112 " pdb=" OE2 GLU M 124 " model vdw 2.191 3.040 nonbonded pdb=" OD1 ASP A 25 " pdb=" N THR A 26 " model vdw 2.235 3.120 nonbonded pdb=" NZ LYS E 103 " pdb=" OP2 G F 603 " model vdw 2.247 3.120 nonbonded pdb=" OD1 ASP G 25 " pdb=" N THR G 26 " model vdw 2.248 3.120 nonbonded pdb=" OH TYR G 112 " pdb=" OE2 GLU G 124 " model vdw 2.254 3.040 ... (remaining 103460 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 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 46 or (resid 47 and (n \ ame N or name CA or name C or name O or name CB )) or resid 48 through 56 or (re \ sid 57 and (name N or name CA or name C or name O or name CB )) or resid 58 thro \ ugh 66 or (resid 67 and (name N or name CA or name C or name O or name CB )) or \ resid 68 through 70 or (resid 71 through 73 and (name N or name CA or name C or \ name O or name CB )) or resid 74 through 114 or (resid 115 and (name N or name C \ A or name C or name O or name CB )) or resid 116 through 118 or (resid 119 throu \ gh 120 and (name N or name CA or name C or name O or name CB )) or resid 121 thr \ ough 123 or (resid 124 and (name N or name CA or name C or name O or name CB )) \ or resid 125 through 129 or (resid 130 through 138 and (name N or name CA or nam \ e C or name O or name CB )) or resid 139 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 163 or (resid 1 \ 64 and (name N or name CA or name C or name O or name CB )) or resid 165 through \ 167 or (resid 168 and (name N or name CA or name C or name O or name CB )) or r \ esid 169 through 176 or (resid 177 and (name N or name CA or name C or name O or \ name CB )) or resid 178 through 183 or (resid 184 and (name N or name CA or nam \ e C or name O or name CB )) or resid 185 through 206)) selection = (chain 'C' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 46 or (resid 47 and (na \ me N or name CA or name C or name O or name CB )) or resid 48 through 66 or (res \ id 67 and (name N or name CA or name C or name O or name CB )) or resid 68 throu \ gh 70 or (resid 71 through 73 and (name N or name CA or name C or name O or name \ CB )) or resid 74 through 114 or (resid 115 and (name N or name CA or name C or \ name O or name CB )) or resid 116 through 119 or (resid 120 and (name N or name \ CA or name C or name O or name CB )) 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 129 o \ r (resid 130 through 138 and (name N or name CA or name C or name O or name CB ) \ ) or resid 139 through 153 or (resid 154 and (name N or name CA or name C or nam \ e O or name CB )) or resid 155 through 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 176 or (resid \ 177 and (name N or name CA or name C or name O or name CB )) or resid 178 throu \ gh 179 or (resid 180 through 181 and (name N or name CA or name C or name O or n \ ame CB )) or resid 182 through 183 or (resid 184 and (name N or name CA or name \ C or name O or name CB )) or resid 185 through 198 or (resid 199 and (name N or \ name CA or name C or name O or name CB )) or resid 200 through 206)) 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 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 56 or (resid 57 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 60 or (res \ id 61 through 62 and (name N or name CA or name C or name O or name CB )) or res \ id 63 through 66 or (resid 67 and (name N or name CA or name C or name O or name \ CB )) or resid 68 through 69 or (resid 70 through 73 and (name N or name CA or \ name C or name O or name CB )) or resid 74 through 118 or (resid 119 through 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 128 or (resid 129 through 138 and (name N or name CA or name C or \ name O or name CB )) or resid 139 through 153 or (resid 154 and (name N or name \ CA or name C or name O or name CB )) or resid 155 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 o \ r (resid 167 through 168 and (name N or name CA or name C or name O or name CB ) \ ) or resid 169 through 172 or (resid 173 through 174 and (name N or name CA or n \ ame C or name O or name CB )) or resid 175 through 176 or (resid 177 and (name N \ or name CA or name C or name O or name CB )) or resid 178 through 183 or (resid \ 184 and (name N or name CA or name C or name O or name CB )) or resid 185 throu \ gh 206)) selection = (chain 'G' and (resid 2 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 17 or (resid 18 and (name N or name \ CA or name C or name O or name CB )) or resid 19 through 35 or (resid 36 and (n \ ame N or name CA or name C or name O or name CB )) or resid 37 through 56 or (re \ sid 57 and (name N or name CA or name C or name O or name CB )) or resid 58 thro \ ugh 66 or (resid 67 and (name N or name CA or name C or name O or name CB )) or \ resid 68 through 70 or (resid 71 through 73 and (name N or name CA or name C or \ name O or name CB )) or resid 74 through 114 or (resid 115 and (name N or name C \ A or name C or name O or name CB )) or resid 116 through 118 or (resid 119 throu \ gh 120 and (name N or name CA or name C or name O or name CB )) or resid 121 thr \ ough 123 or (resid 124 and (name N or name CA or name C or name O or name CB )) \ or resid 125 through 128 or (resid 129 through 138 and (name N or name CA or nam \ e C or name O or name CB )) or resid 139 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 166 or (resid 1 \ 67 through 168 and (name N or name CA or name C or name O or name CB )) or resid \ 169 through 172 or (resid 173 through 174 and (name N or name CA or name C or n \ ame O or name CB )) or resid 175 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 183 or (res \ id 184 and (name N or name CA or name C or name O or name CB )) or resid 185 thr \ ough 198 or (resid 199 and (name N or name CA or name C or name O or name CB )) \ or resid 200 through 206)) 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 35 or (resid 36 and (name N or name CA or name C \ or name O or name CB )) or resid 37 through 46 or (resid 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 or (resid 49 through 50 and (na \ me N or name CA or name C or name O or name CB )) or resid 51 through 56 or (res \ id 57 and (name N or name CA or name C or name O or name CB )) or resid 58 throu \ gh 66 or (resid 67 and (name N or name CA or name C or name O or name CB )) or r \ esid 68 through 69 or (resid 70 through 73 and (name N or name CA or name C or n \ ame O or name CB )) or resid 74 through 114 or (resid 115 and (name N or name CA \ or name C or name O or name CB )) or resid 116 through 118 or (resid 119 throug \ h 120 and (name N or name CA or name C or name O or name CB )) or resid 121 thro \ ugh 128 or (resid 129 through 138 and (name N or name CA or name C or name O or \ name CB )) or resid 139 through 166 or (resid 167 through 168 and (name N or nam \ e CA or name C or name O or name CB )) or resid 169 through 172 or (resid 173 th \ rough 174 and (name N or name CA or name C or name O or name CB )) or resid 175 \ or (resid 176 through 177 and (name N or name CA or name C or name O or name CB \ )) or resid 178 through 183 or (resid 184 and (name N or name CA or name C or na \ me O or name CB )) or resid 185 through 206)) 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 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 46 or (resid 47 and (na \ me N or name CA or name C or name O or name CB )) or resid 48 or (resid 49 throu \ gh 50 and (name N or name CA or name C or name O or name CB )) or resid 51 throu \ gh 56 or (resid 57 and (name N or name CA or name C or name O or name CB )) or r \ esid 58 through 60 or (resid 61 through 62 and (name N or name CA or name C or n \ ame O or name CB )) or resid 63 through 114 or (resid 115 and (name N or name CA \ or name C or name O or name CB )) or resid 116 through 118 or (resid 119 throug \ h 120 and (name N or name CA or name C or name O or name CB )) or resid 121 thro \ ugh 123 or (resid 124 and (name N or name CA or name C or name O or name CB )) o \ r resid 125 through 128 or (resid 129 through 138 and (name N or name CA or name \ C or name O or name CB )) or resid 139 through 153 or (resid 154 and (name N or \ name CA or name C or name O or name CB )) or resid 155 through 163 or (resid 16 \ 4 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 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 176 or (resid 177 and (n \ ame N or name CA or name C or name O or name CB )) or resid 178 through 183 or ( \ resid 184 and (name N or name CA or name C or name O or name CB )) or resid 185 \ through 206)) 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 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 35 or (resid 36 and (name N or name \ CA or name C or name O or name CB )) or resid 37 through 46 or (resid 47 and (na \ me N or name CA or name C or name O or name CB )) or resid 48 or (resid 49 throu \ gh 50 and (name N or name CA or name C or name O or name CB )) or resid 51 throu \ gh 56 or (resid 57 and (name N or name CA or name C or name O or name CB )) or r \ esid 58 through 66 or (resid 67 and (name N or name CA or name C or name O or na \ me CB )) or resid 68 through 69 or (resid 70 through 73 and (name N or name CA o \ r name C or name O or name CB )) or resid 74 through 114 or (resid 115 and (name \ N or name CA or name C or name O or name CB )) or resid 116 through 118 or (res \ id 119 through 120 and (name N or name CA or name C or name O or name CB )) or r \ esid 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 129 or (resid 130 through 138 and (name N or na \ me CA or name C or name O or name CB )) or resid 139 through 153 or (resid 154 a \ nd (name N or name CA or name C or name O or name CB )) or resid 155 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 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 176 or (resid 177 and (name \ N or name CA or name C or name O or name CB )) or resid 178 through 183 or (res \ id 184 and (name N or name CA or name C or name O or name CB )) or resid 185 thr \ ough 206)) selection = (chain 'O' and ((resid 2 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 12 or (resid 13 and (name N or name CA or name C \ or name O or name CB )) or resid 14 through 46 or (resid 47 and (name N or name \ CA or name C or name O or name CB )) or resid 48 through 56 or (resid 57 and (na \ me N or name CA or name C or name O or name CB )) or resid 58 through 60 or (res \ id 61 through 62 and (name N or name CA or name C or name O or name CB )) or res \ id 63 through 66 or (resid 67 and (name N or name CA or name C or name O or name \ CB )) or resid 68 through 69 or (resid 70 through 73 and (name N or name CA or \ name C or name O or name CB )) or resid 74 through 114 or (resid 115 and (name N \ or name CA or name C or name O or name CB )) or resid 116 through 118 or (resid \ 119 through 120 and (name N or name CA or name C or name O or name CB )) or res \ id 121 through 123 or (resid 124 and (name N or name CA or name C or name O or n \ ame CB )) or resid 125 through 128 or (resid 129 through 138 and (name N or name \ CA or name C or name O or name CB )) or resid 139 through 153 or (resid 154 and \ (name N or name CA or name C or name O or name CB )) or resid 155 through 163 o \ r (resid 164 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 65 through 166 or (resid 167 through 168 and (name N or name CA or name C or nam \ e O or name CB )) or resid 169 through 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 176 or (resid \ 177 and (name N or name CA or name C or name O or name CB )) or resid 178 throu \ gh 179 or (resid 180 through 181 and (name N or name CA or name C or name O or n \ ame CB )) or resid 182 through 206)) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.190 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.310 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 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 : 0.006 0.062 12934 Z= 0.260 Angle : 0.792 11.568 17672 Z= 0.460 Chirality : 0.059 0.327 2127 Planarity : 0.004 0.029 2203 Dihedral : 11.963 85.969 4508 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: 0.73 (0.20), residues: 1624 helix: 0.27 (0.18), residues: 752 sheet: 0.55 (0.22), residues: 248 loop : 1.07 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG E 37 TYR 0.030 0.003 TYR E 151 PHE 0.021 0.002 PHE G 78 TRP 0.019 0.002 TRP O 197 HIS 0.005 0.002 HIS K 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00605 / 0.26 (12934) covalent geometry : angle 0.79249 / 0.46 (17672) hydrogen bonds : bond 0.11216 / 7.58 ( 585) hydrogen bonds : angle 7.43095 / 5.13 ( 1755) *********************** 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 187 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 187 time to evaluate : 0.488 Fit side-chains REVERT: C 124 GLU cc_start: 0.8326 (tt0) cc_final: 0.8057 (tt0) REVERT: G 115 ARG cc_start: 0.7549 (mmt180) cc_final: 0.7251 (mtp180) REVERT: G 173 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7159 (mm-30) REVERT: I 36 ASP cc_start: 0.8467 (m-30) cc_final: 0.8231 (m-30) REVERT: K 25 ASP cc_start: 0.7604 (t70) cc_final: 0.7385 (t70) REVERT: O 95 MET cc_start: 0.9122 (tpt) cc_final: 0.8833 (tpt) REVERT: O 124 GLU cc_start: 0.7910 (tt0) cc_final: 0.7664 (tt0) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1191 time to fit residues: 32.0718 Evaluate side-chains 163 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 163 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 0.1980 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 10.0000 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 7.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 ASN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 16 ASN M 54 GLN M 184 GLN O 127 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.111038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.099762 restraints weight = 15166.623| |-----------------------------------------------------------------------------| r_work (start): 0.2956 rms_B_bonded: 1.06 r_work: 0.2838 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 3.17 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 12934 Z= 0.120 Angle : 0.474 5.828 17672 Z= 0.259 Chirality : 0.045 0.129 2127 Planarity : 0.003 0.023 2203 Dihedral : 5.117 37.544 1944 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.68 % Allowed : 2.87 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.22), residues: 1624 helix: 1.48 (0.20), residues: 752 sheet: 1.06 (0.24), residues: 248 loop : 0.99 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 169 TYR 0.012 0.001 TYR A 151 PHE 0.013 0.002 PHE E 78 TRP 0.007 0.001 TRP G 197 HIS 0.003 0.001 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (12934) covalent geometry : angle 0.47361 / 0.26 (17672) hydrogen bonds : bond 0.03945 / 2.69 ( 585) hydrogen bonds : angle 5.79268 / 3.99 ( 1755) *********************** 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 183 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 175 time to evaluate : 0.592 Fit side-chains REVERT: E 95 MET cc_start: 0.8652 (tpp) cc_final: 0.8381 (tpp) REVERT: G 27 GLU cc_start: 0.7968 (mm-30) cc_final: 0.7736 (mm-30) REVERT: G 115 ARG cc_start: 0.8540 (mmt180) cc_final: 0.7891 (mtp180) REVERT: I 36 ASP cc_start: 0.8666 (m-30) cc_final: 0.8422 (m-30) REVERT: K 8 GLN cc_start: 0.8269 (mp10) cc_final: 0.7875 (mm-40) REVERT: O 25 ASP cc_start: 0.8717 (t0) cc_final: 0.8469 (t0) outliers start: 8 outliers final: 5 residues processed: 181 average time/residue: 0.1316 time to fit residues: 33.5357 Evaluate side-chains 162 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 157 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain A residue 168 GLU Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain M residue 54 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 149 optimal weight: 4.9990 chunk 139 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 84 optimal weight: 8.9990 chunk 10 optimal weight: 0.5980 chunk 71 optimal weight: 6.9990 chunk 35 optimal weight: 7.9990 chunk 150 optimal weight: 5.9990 chunk 17 optimal weight: 8.9990 chunk 130 optimal weight: 8.9990 overall best weight: 4.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 13 ASN C 54 GLN G 34 HIS G 205 HIS ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 54 GLN I 184 GLN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 54 GLN M 184 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.106775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2923 r_free = 0.2923 target = 0.096301 restraints weight = 15782.029| |-----------------------------------------------------------------------------| r_work (start): 0.2916 rms_B_bonded: 0.85 r_work: 0.2806 rms_B_bonded: 1.52 restraints_weight: 0.5000 r_work: 0.2689 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 12934 Z= 0.246 Angle : 0.579 5.416 17672 Z= 0.307 Chirality : 0.049 0.145 2127 Planarity : 0.004 0.032 2203 Dihedral : 5.365 37.786 1944 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.01 % Allowed : 4.90 % Favored : 94.09 % 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: 1.01 (0.21), residues: 1624 helix: 0.98 (0.19), residues: 752 sheet: 0.96 (0.25), residues: 248 loop : 0.36 (0.28), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 175 TYR 0.019 0.002 TYR G 17 PHE 0.018 0.002 PHE G 78 TRP 0.009 0.002 TRP I 139 HIS 0.008 0.002 HIS M 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00598 / 0.25 (12934) covalent geometry : angle 0.57921 / 0.31 (17672) hydrogen bonds : bond 0.05095 / 3.49 ( 585) hydrogen bonds : angle 6.01278 / 4.15 ( 1755) *********************** 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 171 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.497 Fit side-chains REVERT: I 36 ASP cc_start: 0.8537 (m-30) cc_final: 0.8330 (m-30) REVERT: I 47 ASP cc_start: 0.7195 (OUTLIER) cc_final: 0.6636 (m-30) outliers start: 12 outliers final: 8 residues processed: 166 average time/residue: 0.1204 time to fit residues: 29.0764 Evaluate side-chains 166 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 157 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain G residue 206 SER Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain O residue 61 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 159 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 52 optimal weight: 0.5980 chunk 63 optimal weight: 6.9990 chunk 113 optimal weight: 9.9990 chunk 28 optimal weight: 6.9990 chunk 143 optimal weight: 0.4980 chunk 153 optimal weight: 7.9990 chunk 48 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 91 optimal weight: 1.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 184 GLN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.108203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2952 r_free = 0.2952 target = 0.098292 restraints weight = 15633.816| |-----------------------------------------------------------------------------| r_work (start): 0.2945 rms_B_bonded: 0.78 r_work: 0.2804 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.2682 rms_B_bonded: 3.37 restraints_weight: 0.2500 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12934 Z= 0.165 Angle : 0.480 4.743 17672 Z= 0.259 Chirality : 0.045 0.134 2127 Planarity : 0.003 0.029 2203 Dihedral : 5.112 37.135 1944 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 0.84 % Allowed : 5.83 % Favored : 93.33 % 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: 0.92 (0.21), residues: 1624 helix: 1.02 (0.19), residues: 752 sheet: 0.94 (0.26), residues: 248 loop : 0.13 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 115 TYR 0.011 0.002 TYR E 17 PHE 0.016 0.002 PHE G 78 TRP 0.007 0.001 TRP I 139 HIS 0.005 0.001 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00394 / 0.17 (12934) covalent geometry : angle 0.47968 / 0.26 (17672) hydrogen bonds : bond 0.04250 / 2.92 ( 585) hydrogen bonds : angle 5.71627 / 3.94 ( 1755) *********************** 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 172 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 162 time to evaluate : 0.626 Fit side-chains REVERT: I 36 ASP cc_start: 0.8579 (m-30) cc_final: 0.8346 (m-30) REVERT: I 47 ASP cc_start: 0.7092 (OUTLIER) cc_final: 0.6557 (m-30) REVERT: K 115 ARG cc_start: 0.8589 (mmt-90) cc_final: 0.8223 (mtt90) REVERT: M 65 LEU cc_start: 0.7864 (tp) cc_final: 0.7581 (mt) REVERT: O 155 ASP cc_start: 0.7728 (OUTLIER) cc_final: 0.7473 (t0) outliers start: 10 outliers final: 6 residues processed: 169 average time/residue: 0.1154 time to fit residues: 28.5732 Evaluate side-chains 165 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 157 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 155 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 86 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 115 optimal weight: 10.0000 chunk 156 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 chunk 16 optimal weight: 6.9990 chunk 104 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 205 HIS ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 184 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.106897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.097007 restraints weight = 15812.994| |-----------------------------------------------------------------------------| r_work (start): 0.2932 rms_B_bonded: 0.74 r_work: 0.2780 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.2199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 12934 Z= 0.222 Angle : 0.535 5.044 17672 Z= 0.284 Chirality : 0.047 0.141 2127 Planarity : 0.004 0.031 2203 Dihedral : 5.260 39.879 1944 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.35 % Allowed : 6.17 % Favored : 92.48 % 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: 0.60 (0.21), residues: 1624 helix: 0.85 (0.19), residues: 752 sheet: 0.70 (0.26), residues: 248 loop : -0.13 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 172 TYR 0.016 0.002 TYR G 17 PHE 0.018 0.002 PHE G 78 TRP 0.007 0.002 TRP I 139 HIS 0.005 0.001 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00537 / 0.22 (12934) covalent geometry : angle 0.53524 / 0.28 (17672) hydrogen bonds : bond 0.04769 / 3.27 ( 585) hydrogen bonds : angle 5.84270 / 4.03 ( 1755) *********************** 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 176 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.483 Fit side-chains REVERT: I 36 ASP cc_start: 0.8574 (m-30) cc_final: 0.8316 (m-30) REVERT: I 47 ASP cc_start: 0.7207 (OUTLIER) cc_final: 0.6588 (m-30) REVERT: K 115 ARG cc_start: 0.8618 (mmt-90) cc_final: 0.8262 (mtt90) REVERT: M 65 LEU cc_start: 0.7960 (tp) cc_final: 0.7634 (mt) REVERT: O 155 ASP cc_start: 0.7736 (OUTLIER) cc_final: 0.7504 (t0) outliers start: 16 outliers final: 10 residues processed: 169 average time/residue: 0.1119 time to fit residues: 27.8393 Evaluate side-chains 172 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 160 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 119 LYS Chi-restraints excluded: chain O residue 155 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 122 optimal weight: 0.9990 chunk 72 optimal weight: 5.9990 chunk 157 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.109437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.099411 restraints weight = 15562.059| |-----------------------------------------------------------------------------| r_work (start): 0.2960 rms_B_bonded: 0.80 r_work: 0.2818 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 3.48 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 12934 Z= 0.119 Angle : 0.427 4.713 17672 Z= 0.234 Chirality : 0.044 0.128 2127 Planarity : 0.003 0.029 2203 Dihedral : 4.880 37.881 1944 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.93 % Allowed : 7.09 % Favored : 91.98 % 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: 0.84 (0.21), residues: 1624 helix: 1.06 (0.20), residues: 760 sheet: 0.78 (0.26), residues: 248 loop : -0.04 (0.28), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 115 TYR 0.012 0.001 TYR E 151 PHE 0.014 0.001 PHE G 78 TRP 0.006 0.001 TRP I 139 HIS 0.004 0.001 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (12934) covalent geometry : angle 0.42706 / 0.23 (17672) hydrogen bonds : bond 0.03734 / 2.57 ( 585) hydrogen bonds : angle 5.47918 / 3.78 ( 1755) *********************** 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 177 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 166 time to evaluate : 0.478 Fit side-chains REVERT: A 206 SER cc_start: 0.7127 (p) cc_final: 0.6923 (t) REVERT: I 36 ASP cc_start: 0.8538 (m-30) cc_final: 0.8311 (m-30) REVERT: I 47 ASP cc_start: 0.7101 (OUTLIER) cc_final: 0.6536 (m-30) REVERT: I 51 ASP cc_start: 0.8568 (m-30) cc_final: 0.8191 (m-30) REVERT: K 115 ARG cc_start: 0.8634 (mmt-90) cc_final: 0.8242 (mtt90) outliers start: 11 outliers final: 7 residues processed: 175 average time/residue: 0.1175 time to fit residues: 29.8501 Evaluate side-chains 169 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 161 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain G residue 42 GLN Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain O residue 61 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 158 optimal weight: 0.8980 chunk 14 optimal weight: 0.0050 chunk 32 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 16 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 46 optimal weight: 6.9990 chunk 111 optimal weight: 7.9990 chunk 138 optimal weight: 3.9990 chunk 154 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 overall best weight: 1.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 8 GLN O 13 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.109558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.099707 restraints weight = 15473.918| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 0.71 r_work: 0.2809 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12934 Z= 0.119 Angle : 0.422 4.710 17672 Z= 0.230 Chirality : 0.044 0.128 2127 Planarity : 0.003 0.028 2203 Dihedral : 4.762 35.241 1944 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.01 % Allowed : 7.26 % Favored : 91.72 % 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: 0.93 (0.21), residues: 1624 helix: 1.14 (0.20), residues: 760 sheet: 0.84 (0.27), residues: 248 loop : 0.00 (0.28), residues: 616 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 115 TYR 0.010 0.001 TYR G 17 PHE 0.015 0.001 PHE G 78 TRP 0.004 0.001 TRP I 139 HIS 0.003 0.001 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (12934) covalent geometry : angle 0.42205 / 0.23 (17672) hydrogen bonds : bond 0.03719 / 2.56 ( 585) hydrogen bonds : angle 5.40516 / 3.73 ( 1755) *********************** 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 180 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 168 time to evaluate : 0.431 Fit side-chains REVERT: A 206 SER cc_start: 0.7165 (p) cc_final: 0.6953 (t) REVERT: I 47 ASP cc_start: 0.7146 (OUTLIER) cc_final: 0.6566 (m-30) REVERT: I 51 ASP cc_start: 0.8542 (m-30) cc_final: 0.8276 (m-30) REVERT: K 115 ARG cc_start: 0.8640 (mmt-90) cc_final: 0.8254 (mtt90) REVERT: O 13 ASN cc_start: 0.8339 (p0) cc_final: 0.7861 (p0) outliers start: 12 outliers final: 10 residues processed: 176 average time/residue: 0.1143 time to fit residues: 29.4552 Evaluate side-chains 176 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 165 time to evaluate : 0.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain G residue 42 GLN Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 206 SER Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain O residue 61 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 3 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 154 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 109 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 10.0000 chunk 136 optimal weight: 6.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 184 GLN C 59 GLN G 42 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 184 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.105421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.094507 restraints weight = 15649.775| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 0.96 r_work: 0.2779 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2658 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.053 12934 Z= 0.355 Angle : 0.660 7.038 17672 Z= 0.343 Chirality : 0.053 0.192 2127 Planarity : 0.005 0.035 2203 Dihedral : 5.523 45.334 1944 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.27 % Allowed : 7.26 % Favored : 91.47 % 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: 0.30 (0.21), residues: 1624 helix: 0.71 (0.19), residues: 736 sheet: 0.52 (0.27), residues: 256 loop : -0.40 (0.26), residues: 632 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 172 TYR 0.021 0.003 TYR G 17 PHE 0.022 0.003 PHE G 78 TRP 0.009 0.002 TRP I 139 HIS 0.007 0.002 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00873 / 0.36 (12934) covalent geometry : angle 0.66017 / 0.34 (17672) hydrogen bonds : bond 0.05756 / 3.95 ( 585) hydrogen bonds : angle 6.06184 / 4.18 ( 1755) *********************** 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 176 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 161 time to evaluate : 0.595 Fit side-chains REVERT: I 47 ASP cc_start: 0.7005 (OUTLIER) cc_final: 0.6366 (m-30) REVERT: K 115 ARG cc_start: 0.8535 (mmt-90) cc_final: 0.8200 (mtt90) outliers start: 15 outliers final: 12 residues processed: 170 average time/residue: 0.1168 time to fit residues: 29.1769 Evaluate side-chains 170 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 157 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain G residue 42 GLN Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 206 SER Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain O residue 61 SER Chi-restraints excluded: chain O residue 119 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 20 optimal weight: 9.9990 chunk 79 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 3 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 chunk 137 optimal weight: 6.9990 chunk 71 optimal weight: 3.9990 chunk 136 optimal weight: 2.9990 chunk 130 optimal weight: 0.6980 chunk 123 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.108444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.097861 restraints weight = 15597.611| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 0.87 r_work: 0.2831 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2715 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12934 Z= 0.146 Angle : 0.452 4.713 17672 Z= 0.245 Chirality : 0.044 0.130 2127 Planarity : 0.003 0.033 2203 Dihedral : 5.050 40.809 1944 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.10 % Allowed : 7.77 % Favored : 91.13 % 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: 0.48 (0.21), residues: 1624 helix: 0.92 (0.19), residues: 752 sheet: 0.50 (0.27), residues: 248 loop : -0.37 (0.27), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 115 TYR 0.013 0.001 TYR G 17 PHE 0.017 0.002 PHE G 78 TRP 0.006 0.001 TRP I 139 HIS 0.004 0.001 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 (12934) covalent geometry : angle 0.45233 / 0.25 (17672) hydrogen bonds : bond 0.04006 / 2.76 ( 585) hydrogen bonds : angle 5.61008 / 3.87 ( 1755) *********************** 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 176 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.479 Fit side-chains REVERT: I 47 ASP cc_start: 0.7028 (OUTLIER) cc_final: 0.6429 (m-30) REVERT: I 51 ASP cc_start: 0.8567 (m-30) cc_final: 0.8158 (m-30) REVERT: K 49 THR cc_start: 0.8578 (p) cc_final: 0.8306 (p) REVERT: K 115 ARG cc_start: 0.8507 (mmt-90) cc_final: 0.8191 (mtt90) REVERT: O 188 MET cc_start: 0.8616 (tpt) cc_final: 0.8415 (mmt) outliers start: 13 outliers final: 12 residues processed: 171 average time/residue: 0.1179 time to fit residues: 29.2372 Evaluate side-chains 175 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 162 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain G residue 42 GLN Chi-restraints excluded: chain G residue 149 ILE Chi-restraints excluded: chain G residue 206 SER Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain O residue 61 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 81 optimal weight: 0.0470 chunk 37 optimal weight: 10.0000 chunk 46 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 109 optimal weight: 10.0000 chunk 19 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 chunk 124 optimal weight: 10.0000 chunk 43 optimal weight: 2.9990 overall best weight: 3.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.107598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.096499 restraints weight = 15737.123| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 0.94 r_work: 0.2812 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 2.87 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 12934 Z= 0.193 Angle : 0.496 4.815 17672 Z= 0.265 Chirality : 0.046 0.135 2127 Planarity : 0.004 0.032 2203 Dihedral : 5.109 40.916 1944 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.10 % Allowed : 8.02 % Favored : 90.88 % 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: 0.41 (0.21), residues: 1624 helix: 0.88 (0.19), residues: 752 sheet: 0.47 (0.28), residues: 248 loop : -0.44 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 115 TYR 0.017 0.002 TYR G 17 PHE 0.018 0.002 PHE G 78 TRP 0.006 0.001 TRP I 139 HIS 0.004 0.001 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.19 (12934) covalent geometry : angle 0.49629 / 0.26 (17672) hydrogen bonds : bond 0.04435 / 3.06 ( 585) hydrogen bonds : angle 5.68869 / 3.92 ( 1755) ********************** 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 176 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.373 Fit side-chains REVERT: I 47 ASP cc_start: 0.6968 (OUTLIER) cc_final: 0.6379 (m-30) REVERT: I 51 ASP cc_start: 0.8593 (m-30) cc_final: 0.8212 (m-30) REVERT: K 115 ARG cc_start: 0.8521 (mmt-90) cc_final: 0.8190 (mtt90) outliers start: 13 outliers final: 12 residues processed: 172 average time/residue: 0.1119 time to fit residues: 28.0103 Evaluate side-chains 176 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 143 THR Chi-restraints excluded: chain A residue 154 SER Chi-restraints excluded: chain E residue 19 ILE Chi-restraints excluded: chain G residue 42 GLN Chi-restraints excluded: chain G residue 206 SER Chi-restraints excluded: chain I residue 47 ASP Chi-restraints excluded: chain I residue 198 SER Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 198 SER Chi-restraints excluded: chain M residue 68 LEU Chi-restraints excluded: chain O residue 22 VAL Chi-restraints excluded: chain O residue 61 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 111 optimal weight: 4.9990 chunk 153 optimal weight: 7.9990 chunk 159 optimal weight: 5.9990 chunk 57 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 102 optimal weight: 5.9990 chunk 61 optimal weight: 0.6980 chunk 132 optimal weight: 5.9990 chunk 95 optimal weight: 9.9990 chunk 59 optimal weight: 3.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** I 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.107727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.097088 restraints weight = 15595.618| |-----------------------------------------------------------------------------| r_work (start): 0.2921 rms_B_bonded: 0.90 r_work: 0.2815 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 12934 Z= 0.199 Angle : 0.501 4.869 17672 Z= 0.267 Chirality : 0.046 0.135 2127 Planarity : 0.004 0.033 2203 Dihedral : 5.131 41.253 1944 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 2.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.10 % Allowed : 7.94 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.37 (0.21), residues: 1624 helix: 0.85 (0.19), residues: 752 sheet: 0.46 (0.28), residues: 248 loop : -0.47 (0.26), residues: 624 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 115 TYR 0.016 0.002 TYR G 17 PHE 0.018 0.002 PHE G 78 TRP 0.006 0.001 TRP I 139 HIS 0.005 0.001 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00481 / 0.20 (12934) covalent geometry : angle 0.50148 / 0.27 (17672) hydrogen bonds : bond 0.04490 / 3.09 ( 585) hydrogen bonds : angle 5.70503 / 3.93 ( 1755) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2830.12 seconds wall clock time: 49 minutes 17.91 seconds (2957.91 seconds total)