Starting phenix.real_space_refine on Mon Oct 26 14:59:14 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7mqi_23948/10_2026/7mqi_23948.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mqi_23948/10_2026/7mqi_23948.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.21 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mqi_23948/10_2026/7mqi_23948.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mqi_23948/10_2026/7mqi_23948.map" model { file = "/net/cci-nas-00/data/ceres_data/7mqi_23948/10_2026/7mqi_23948.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mqi_23948/10_2026/7mqi_23948.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7mqi_23948/10_2026/7mqi_23948.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7mqi_23948/10_2026/7mqi_23948.cif" } resolution = 3.21 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= 0.001 sd= 0.017 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 11339 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 47 5.16 5 C 8025 2.51 5 N 2321 2.21 5 O 2287 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12696 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 1513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1513 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 145 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 2, 'GLU:plan': 9, 'ASN:plan1': 1, 'GLN:plan1': 4} Unresolved non-hydrogen planarities: 86 Chain: "C" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1551 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 82 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 66 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 5, 'ARG:plan': 2, 'GLN:plan1': 2, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 53 Chain: "E" Number of atoms: 1548 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1548 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 4, 'ARG:plan': 2, 'GLN:plan1': 4, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 58 Chain: "G" 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': 33} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 97 Unresolved non-hydrogen angles: 118 Unresolved non-hydrogen dihedrals: 76 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 8, 'ARG:plan': 1, 'GLN:plan1': 3, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 65 Chain: "I" 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: {'ASP:plan': 7, 'ASN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 6, 'GLN:plan1': 3} Unresolved non-hydrogen planarities: 65 Chain: "K" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1552 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 26} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 97 Unresolved non-hydrogen dihedrals: 65 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 1, 'GLN:plan1': 3, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 58 Chain: "M" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1545 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 71 Planarities with less than four sites: {'ASP:plan': 7, 'ARG:plan': 1, 'ASN:plan1': 1, 'GLN:plan1': 3, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 61 Chain: "O" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1545 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 5, 'TRANS': 199} Unresolved non-hydrogen bonds: 88 Unresolved non-hydrogen angles: 108 Unresolved non-hydrogen dihedrals: 68 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASP:plan': 8, 'ARG:plan': 1, 'GLN:plan1': 3, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 65 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: 2.81, per 1000 atoms: 0.22 Number of scatterers: 12696 At special positions: 0 Unit cell: (111.6, 114.08, 97.96, 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 47 16.00 P 16 15.00 O 2287 8.00 N 2321 7.00 C 8025 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: 0.76 Conformation dependent library (CDL) restraints added in 577.4 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, 13.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 62 through 71 Processing helix chain 'A' and resid 80 through 93 removed outlier: 3.968A pdb=" N ASP A 84 " --> pdb=" O PHE A 80 " (cutoff:3.500A) removed outlier: 3.600A 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: 3.657A 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: 3.979A pdb=" N ASP C 84 " --> pdb=" O PHE C 80 " (cutoff:3.500A) removed outlier: 3.627A 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: 3.948A pdb=" N ASP E 84 " --> pdb=" O PHE E 80 " (cutoff:3.500A) removed outlier: 3.656A 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: 3.884A 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: 4.009A pdb=" N ASP G 84 " --> pdb=" O PHE G 80 " (cutoff:3.500A) removed outlier: 3.573A 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: 3.690A 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: 3.956A pdb=" N ASP I 84 " --> pdb=" O PHE I 80 " (cutoff:3.500A) removed outlier: 3.574A 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: 3.550A 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: 3.965A pdb=" N ASP K 84 " --> pdb=" O PHE K 80 " (cutoff:3.500A) removed outlier: 3.597A 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: 3.744A 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: 4.029A pdb=" N ASP M 84 " --> pdb=" O PHE M 80 " (cutoff:3.500A) removed outlier: 3.597A 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: 3.571A 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: 3.985A pdb=" N ASP O 84 " --> pdb=" O PHE O 80 " (cutoff:3.500A) removed outlier: 3.566A 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 removed outlier: 6.521A pdb=" N GLU A 3 " --> pdb=" O ALA A 50 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL A 52 " --> pdb=" O GLU A 3 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ARG A 5 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N GLN A 54 " --> pdb=" O ARG A 5 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N HIS A 7 " --> pdb=" O GLN A 54 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU A 27 " --> pdb=" O CYS A 39 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N VAL A 41 " --> pdb=" O ASP A 25 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N ASP A 25 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A 43 " --> pdb=" O ALA A 23 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA A 23 " --> pdb=" O LEU A 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 3 through 8 removed outlier: 6.586A pdb=" N GLU C 3 " --> pdb=" O ALA C 50 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N VAL C 52 " --> pdb=" O GLU C 3 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N ARG C 5 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N GLN C 54 " --> pdb=" O ARG C 5 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N HIS C 7 " --> pdb=" O GLN C 54 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLU C 27 " --> pdb=" O CYS C 39 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N VAL C 41 " --> pdb=" O ASP C 25 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ASP C 25 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N LEU C 43 " --> pdb=" O ALA C 23 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ALA C 23 " --> pdb=" O LEU C 43 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 4 through 8 removed outlier: 6.314A pdb=" N ARG E 5 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N GLN E 54 " --> pdb=" O ARG E 5 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N HIS E 7 " --> pdb=" O GLN E 54 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 4 through 8 removed outlier: 6.342A pdb=" N ARG G 5 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 7.561A pdb=" N GLN G 54 " --> pdb=" O ARG G 5 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N HIS G 7 " --> pdb=" O GLN G 54 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLU G 27 " --> pdb=" O CYS G 39 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N VAL G 41 " --> pdb=" O ASP G 25 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N ASP G 25 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N LEU G 43 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA G 23 " --> pdb=" O LEU G 43 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 4 through 8 removed outlier: 6.158A pdb=" N ARG I 5 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N GLN I 54 " --> pdb=" O ARG I 5 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N HIS I 7 " --> pdb=" O GLN I 54 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'K' and resid 4 through 8 removed outlier: 6.245A pdb=" N ARG K 5 " --> pdb=" O VAL K 52 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N GLN K 54 " --> pdb=" O ARG K 5 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N HIS K 7 " --> pdb=" O GLN K 54 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N GLU K 27 " --> pdb=" O CYS K 39 " (cutoff:3.500A) removed outlier: 4.786A pdb=" N VAL K 41 " --> pdb=" O ASP K 25 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ASP K 25 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LEU K 43 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N ALA K 23 " --> pdb=" O LEU K 43 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 3 through 8 removed outlier: 6.475A pdb=" N GLU M 3 " --> pdb=" O ALA M 50 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N VAL M 52 " --> pdb=" O GLU M 3 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N ARG M 5 " --> pdb=" O VAL M 52 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLN M 54 " --> pdb=" O ARG M 5 " (cutoff:3.500A) removed outlier: 6.687A 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: 6.720A pdb=" N GLU O 3 " --> pdb=" O ALA O 50 " (cutoff:3.500A) removed outlier: 7.752A pdb=" N VAL O 52 " --> pdb=" O GLU O 3 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ARG O 5 " --> pdb=" O VAL O 52 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N GLN O 54 " --> pdb=" O ARG O 5 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N HIS O 7 " --> pdb=" O GLN O 54 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N GLU O 27 " --> pdb=" O CYS O 39 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N VAL O 41 " --> pdb=" O ASP O 25 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N ASP O 25 " --> pdb=" O VAL O 41 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU O 43 " --> pdb=" O ALA O 23 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N ALA O 23 " --> pdb=" O LEU O 43 " (cutoff:3.500A) 568 hydrogen bonds defined for protein. 1704 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: 1.85 Time building geometry restraints manager: 1.05 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: 4082 1.34 - 1.45: 1805 1.45 - 1.57: 6986 1.57 - 1.69: 24 1.69 - 1.81: 63 Bond restraints: 12960 Sorted by residual: bond pdb=" N LEU C 126 " pdb=" CA LEU C 126 " ideal model delta sigma weight residual 1.457 1.494 -0.038 1.06e-02 8.90e+03 1.25e+01 bond pdb=" N ILE I 165 " pdb=" CA ILE I 165 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.17e-02 7.31e+03 9.44e+00 bond pdb=" N GLN E 42 " pdb=" CA GLN E 42 " ideal model delta sigma weight residual 1.455 1.491 -0.036 1.21e-02 6.83e+03 8.75e+00 bond pdb=" N GLN O 42 " pdb=" CA GLN O 42 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.21e-02 6.83e+03 7.20e+00 bond pdb=" N GLN K 42 " pdb=" CA GLN K 42 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.21e-02 6.83e+03 6.54e+00 ... (remaining 12955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.81: 16990 1.81 - 3.61: 619 3.61 - 5.42: 81 5.42 - 7.23: 13 7.23 - 9.04: 2 Bond angle restraints: 17705 Sorted by residual: angle pdb=" C SER I 137 " pdb=" N ASP I 138 " pdb=" CA ASP I 138 " ideal model delta sigma weight residual 122.32 129.36 -7.04 1.76e+00 3.23e-01 1.60e+01 angle pdb=" N LEU I 170 " pdb=" CA LEU I 170 " pdb=" C LEU I 170 " ideal model delta sigma weight residual 112.23 107.24 4.99 1.26e+00 6.30e-01 1.57e+01 angle pdb=" C SER A 137 " pdb=" N ASP A 138 " pdb=" CA ASP A 138 " ideal model delta sigma weight residual 122.32 128.91 -6.59 1.76e+00 3.23e-01 1.40e+01 angle pdb=" C ASP E 138 " pdb=" N TRP E 139 " pdb=" CA TRP E 139 " ideal model delta sigma weight residual 121.54 128.30 -6.76 1.91e+00 2.74e-01 1.25e+01 angle pdb=" N VAL O 41 " pdb=" CA VAL O 41 " pdb=" C VAL O 41 " ideal model delta sigma weight residual 108.11 112.92 -4.81 1.40e+00 5.10e-01 1.18e+01 ... (remaining 17700 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 7178 17.28 - 34.56: 372 34.56 - 51.85: 65 51.85 - 69.13: 22 69.13 - 86.41: 10 Dihedral angle restraints: 7647 sinusoidal: 2863 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 180.00 157.05 22.95 0 5.00e+00 4.00e-02 2.11e+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 180.00 157.07 22.93 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA PHE E 78 " pdb=" C PHE E 78 " pdb=" N HIS E 79 " pdb=" CA HIS E 79 " ideal model delta harmonic sigma weight residual 180.00 157.22 22.78 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 7644 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1636 0.065 - 0.129: 434 0.129 - 0.194: 35 0.194 - 0.258: 11 0.258 - 0.323: 8 Chirality restraints: 2124 Sorted by residual: 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 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" P G H 603 " pdb=" OP1 G H 603 " pdb=" OP2 G H 603 " pdb=" O5' G H 603 " both_signs ideal model delta sigma weight residual True 2.17 2.49 -0.32 2.00e-01 2.50e+01 2.57e+00 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 2.49 -0.32 2.00e-01 2.50e+01 2.56e+00 ... (remaining 2121 not shown) Planarity restraints: 2213 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA E 152 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.37e+00 pdb=" C ALA E 152 " -0.040 2.00e-02 2.50e+03 pdb=" O ALA E 152 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA E 153 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS K 122 " -0.009 2.00e-02 2.50e+03 1.78e-02 3.17e+00 pdb=" C CYS K 122 " 0.031 2.00e-02 2.50e+03 pdb=" O CYS K 122 " -0.012 2.00e-02 2.50e+03 pdb=" N GLY K 123 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS M 122 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C CYS M 122 " -0.029 2.00e-02 2.50e+03 pdb=" O CYS M 122 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY M 123 " 0.010 2.00e-02 2.50e+03 ... (remaining 2210 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1245 2.74 - 3.28: 11813 3.28 - 3.82: 20516 3.82 - 4.36: 26121 4.36 - 4.90: 43889 Nonbonded interactions: 103584 Sorted by model distance: nonbonded pdb=" OH TYR E 17 " pdb=" OD2 ASP E 51 " model vdw 2.202 3.040 nonbonded pdb=" OH TYR O 112 " pdb=" OE2 GLU O 124 " model vdw 2.298 3.040 nonbonded pdb=" O THR M 28 " pdb=" O2' G N 604 " model vdw 2.349 3.040 nonbonded pdb=" OD1 ASP M 25 " pdb=" N THR M 26 " model vdw 2.354 3.120 nonbonded pdb=" OE1 GLU I 173 " pdb=" NH1 ARG I 175 " model vdw 2.359 3.120 ... (remaining 103579 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 70 or (resid 71 through 73 and (name N or name CA or name C or name O or nam \ e CB )) or resid 74 through 129 or (resid 130 through 138 and (name N or name CA \ or name C or name O or name CB )) or resid 139 through 142 or (resid 143 and (n \ ame N or name CA or name C or name O or name CB )) or resid 144 through 153 or ( \ resid 154 through 155 and (name N or name CA or name C or name O or name CB )) o \ r resid 156 through 163 or (resid 164 and (name N or name CA or name C or name O \ or name CB )) or resid 165 through 176 or (resid 177 and (name N or name CA or \ name C or name O or name CB )) or resid 178 through 206)) selection = (chain 'C' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 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 38 or (resid 39 and (name N or na \ me CA or name C or name O or name CB )) or resid 40 through 46 or (resid 47 and \ (name N or name CA or name C or name O or name CB )) or resid 48 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 113 or (resid 114 and (name N or name CA or name C or name O or \ name CB )) or resid 115 through 118 or (resid 119 through 120 and (name N or na \ me CA or name C or name O or name CB )) or resid 121 through 128 or (resid 129 t \ hrough 138 and (name N or name CA or name C or name O or name CB )) or resid 139 \ through 153 or (resid 154 through 155 and (name N or name CA or name C or name \ O or name CB )) or resid 156 through 163 or (resid 164 and (name N or name CA or \ name C or name O or name CB )) or resid 165 through 166 or (resid 167 through 1 \ 68 and (name N or name CA or name C or name O or name CB )) or resid 169 through \ 172 or (resid 173 through 174 and (name N or name CA or name C or name O or nam \ e 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 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 \ (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 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 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 38 or (resid 39 and (name N or na \ me CA or name C or name O or name CB )) or resid 40 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 (name N or name CA or name C or name O or name CB )) or resid 58 th \ rough 60 or (resid 61 through 62 and (name N or name CA or name C or name O or n \ ame CB )) or resid 63 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 113 or (resid 114 and (nam \ e N or name CA or name C or name O or name CB )) or resid 115 through 118 or (re \ sid 119 through 120 and (name N or name CA or name C or name O or name CB )) or \ resid 121 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 through 155 and \ (name N or name CA or name C or name O or name CB )) or resid 156 through 163 or \ (resid 164 and (name N or name CA or name C or name O or name CB )) or resid 16 \ 5 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 throug \ h 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 38 or (re \ sid 39 and (name N or name CA or name C or name O or name CB )) or resid 40 thro \ ugh 56 or (resid 57 and (name N or name CA or name C or name O or name CB )) or \ resid 58 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 113 or (resid 114 and (name N or name C \ A or name C or name O or name CB )) or resid 115 through 119 or (resid 120 and ( \ name N or name CA or name C or name O or name CB )) or resid 121 through 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 142 or (resid 143 and (name N or name CA or name C or name \ O or name CB )) or resid 144 through 153 or (resid 154 through 155 and (name N o \ r name CA or name C or name O or name CB )) or resid 156 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 183 or (resid 184 and (name N or name CA or name C or name O or nam \ e 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 'I' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 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 (name N or name CA or name \ C or name O or name CB )) or resid 37 through 38 or (resid 39 and (name N or na \ me CA or name C or name O or name CB )) or resid 40 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 th \ rough 50 and (name N or name CA or name C or name O or name CB )) or resid 51 th \ rough 56 or (resid 57 and (name N or name CA or name C or name O or name CB )) o \ r resid 58 through 69 or (resid 70 through 73 and (name N or name CA or name C o \ r name O or name CB )) or resid 74 through 113 or (resid 114 and (name N or name \ CA or name C or name O or name CB )) or resid 115 through 128 or (resid 129 thr \ ough 138 and (name N or name CA or name C or name O or name CB )) or resid 139 t \ hrough 154 or (resid 155 and (name N or name CA or name C or name O or name CB ) \ ) or resid 156 through 166 or (resid 167 through 168 and (name N or name CA or n \ ame 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 1 \ 76 or (resid 177 and (name N or name CA or name C or name O or name CB )) or res \ id 178 through 183 or (resid 184 and (name N or name CA or name C or name O or n \ ame CB )) or resid 185 through 206)) selection = (chain 'K' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 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 (name N or na \ me CA or name C or name O or name CB )) or resid 37 through 38 or (resid 39 and \ (name N or name CA or name C or name O or name CB )) or resid 40 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 (name N or name CA or name C or name O or name CB )) o \ r resid 51 through 56 or (resid 57 and (name N or name CA or name C or name O or \ name CB )) or resid 58 through 60 or (resid 61 through 62 and (name N or name C \ A or name C or name O or name CB )) or resid 63 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 142 or (resid 143 and (name N or name CA or name \ C or name O or name CB )) or resid 144 through 153 or (resid 154 through 155 an \ d (name N or name CA or name C or name O or name CB )) or resid 156 through 163 \ or (resid 164 and (name N or name CA or name C or name O or name CB )) or resid \ 165 through 166 or (resid 167 through 168 and (name N or name CA or name C or na \ me 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 (resi \ d 177 and (name N or name CA or name C or name O or name CB )) or resid 178 thro \ ugh 183 or (resid 184 and (name N or name CA or name C or name O or name CB )) o \ r resid 185 through 206)) selection = (chain 'M' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 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 (name N or na \ me CA or name C or name O or name CB )) or resid 37 through 38 or (resid 39 and \ (name N or name CA or name C or name O or name CB )) or resid 40 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 (name N or name CA or name C or name O or name CB )) o \ r resid 51 through 56 or (resid 57 and (name N or name CA or name C or name O or \ name CB )) or resid 58 through 69 or (resid 70 through 73 and (name N or name C \ A or name C or name O or name CB )) or resid 74 through 119 or (resid 120 and (n \ ame N or name CA or name C or name O or name CB )) or resid 121 through 129 or ( \ resid 130 through 138 and (name N or name CA or name C or name O or name CB )) o \ r resid 139 through 142 or (resid 143 and (name N or name CA or name C or name O \ or name CB )) or resid 144 through 153 or (resid 154 through 155 and (name N or \ name CA or name C or name O or name CB )) or resid 156 through 166 or (resid 16 \ 7 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 na \ me 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 (n \ ame N or name CA or name C or name O or name CB )) or resid 185 through 206)) selection = (chain 'O' and ((resid 2 and (name N or name CA or name C or name O or name CB ) \ ) or resid 3 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 38 or (resid 39 and (name N or na \ me CA or name C or name O or name CB )) or resid 40 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 (name N or name CA or name C or name O or name CB )) or resid 58 th \ rough 60 or (resid 61 through 62 and (name N or name CA or name C or name O or n \ ame CB )) or resid 63 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 throug \ h 128 or (resid 129 through 138 and (name N or name CA or name C or name O or na \ me CB )) or resid 139 through 142 or (resid 143 and (name N or name CA or name C \ or name O or name CB )) or resid 144 through 153 or (resid 154 through 155 and \ (name N or name CA or name C or name O or name CB )) or resid 156 through 163 or \ (resid 164 and (name N or name CA or name C or name O or name CB )) or resid 16 \ 5 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 throug \ h 179 or (resid 180 through 181 and (name N or name CA or name C or name O or na \ me 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 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: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 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: 0.040 Process input model: 11.800 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:1.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 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 0.046 12960 Z= 0.281 Angle : 0.804 9.035 17705 Z= 0.483 Chirality : 0.060 0.323 2124 Planarity : 0.004 0.029 2213 Dihedral : 12.016 86.408 4527 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.59 % Allowed : 0.59 % Favored : 98.82 % 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: 0.80 (0.20), residues: 1624 helix: 0.50 (0.19), residues: 704 sheet: 0.59 (0.22), residues: 248 loop : 0.81 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG A 37 TYR 0.018 0.003 TYR G 151 PHE 0.023 0.002 PHE K 78 TRP 0.021 0.003 TRP A 139 HIS 0.008 0.001 HIS A 7 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.28 (12960) covalent geometry : angle 0.80369 / 0.48 (17705) hydrogen bonds : bond 0.11672 / 7.71 ( 568) hydrogen bonds : angle 7.46582 / 5.35 ( 1704) *********************** 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 210 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 203 time to evaluate : 0.441 Fit side-chains revert: symmetry clash REVERT: C 124 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7207 (tt0) REVERT: E 124 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.8050 (tm-30) REVERT: G 16 ASN cc_start: 0.7814 (m110) cc_final: 0.7550 (m110) REVERT: G 71 ASP cc_start: 0.8916 (t0) cc_final: 0.8687 (t0) REVERT: I 25 ASP cc_start: 0.7018 (t70) cc_final: 0.6530 (t70) REVERT: I 36 ASP cc_start: 0.7196 (m-30) cc_final: 0.6921 (m-30) REVERT: I 114 ASP cc_start: 0.7721 (t70) cc_final: 0.7511 (t0) REVERT: I 115 ARG cc_start: 0.7479 (mpp80) cc_final: 0.7120 (mtm-85) REVERT: K 28 THR cc_start: 0.8643 (p) cc_final: 0.8419 (p) REVERT: K 115 ARG cc_start: 0.7408 (mtt180) cc_final: 0.6589 (mmm160) REVERT: M 16 ASN cc_start: 0.8363 (m110) cc_final: 0.7928 (m110) REVERT: M 18 ARG cc_start: 0.7624 (mmt180) cc_final: 0.7388 (mmt180) REVERT: M 25 ASP cc_start: 0.7803 (t0) cc_final: 0.6939 (t0) REVERT: M 188 MET cc_start: 0.7519 (mmt) cc_final: 0.7198 (tpt) outliers start: 7 outliers final: 0 residues processed: 206 average time/residue: 0.1138 time to fit residues: 33.9785 Evaluate side-chains 165 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 163 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 124 GLU Chi-restraints excluded: chain E residue 124 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [98, 107, 10, 66, 130, 124, 103, 77, 122, 91, 149] chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN A 191 ASN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 16 ASN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 8 GLN ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.111594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.096015 restraints weight = 15517.774| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.34 r_work: 0.2839 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2709 rms_B_bonded: 3.63 restraints_weight: 0.2500 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 12960 Z= 0.152 Angle : 0.506 7.459 17705 Z= 0.271 Chirality : 0.046 0.132 2124 Planarity : 0.003 0.029 2213 Dihedral : 5.457 52.993 1955 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.99 % Favored : 99.01 % Rotamer: Outliers : 0.84 % Allowed : 3.62 % Favored : 95.53 % 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: 1.58 (0.21), residues: 1624 helix: 1.60 (0.20), residues: 704 sheet: 0.95 (0.25), residues: 248 loop : 0.66 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 175 TYR 0.011 0.001 TYR O 17 PHE 0.017 0.002 PHE A 78 TRP 0.004 0.001 TRP C 197 HIS 0.005 0.001 HIS O 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 (12960) covalent geometry : angle 0.50575 / 0.27 (17705) hydrogen bonds : bond 0.04270 / 2.90 ( 568) hydrogen bonds : angle 5.94977 / 4.28 ( 1704) *********************** 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 187 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 177 time to evaluate : 0.430 Fit side-chains REVERT: A 25 ASP cc_start: 0.8897 (t0) cc_final: 0.8654 (t70) REVERT: C 120 GLU cc_start: 0.7969 (mp0) cc_final: 0.7729 (mp0) REVERT: C 124 GLU cc_start: 0.8071 (tt0) cc_final: 0.7758 (tt0) REVERT: E 115 ARG cc_start: 0.8264 (mtp180) cc_final: 0.7866 (mtm180) REVERT: E 146 ARG cc_start: 0.6963 (tpt170) cc_final: 0.6700 (tpt170) REVERT: G 16 ASN cc_start: 0.8029 (m110) cc_final: 0.7799 (m110) REVERT: G 71 ASP cc_start: 0.8927 (t0) cc_final: 0.8695 (t0) REVERT: I 25 ASP cc_start: 0.7670 (t70) cc_final: 0.7327 (t70) REVERT: I 114 ASP cc_start: 0.8176 (t70) cc_final: 0.7922 (t0) REVERT: K 28 THR cc_start: 0.8867 (p) cc_final: 0.8665 (p) REVERT: K 115 ARG cc_start: 0.8056 (mtt180) cc_final: 0.7354 (mmm160) REVERT: M 18 ARG cc_start: 0.7871 (mmt180) cc_final: 0.7551 (mmt180) REVERT: M 25 ASP cc_start: 0.8184 (t0) cc_final: 0.7628 (t0) outliers start: 10 outliers final: 7 residues processed: 184 average time/residue: 0.1130 time to fit residues: 30.2251 Evaluate side-chains 177 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 170 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain C residue 177 SER Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain K residue 61 SER Chi-restraints excluded: chain K residue 143 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [18, 26, 121, 91, 54, 5, 25, 131, 96, 132, 149] chunk 18 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 121 optimal weight: 8.9990 chunk 91 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 5 optimal weight: 6.9990 chunk 25 optimal weight: 0.4980 chunk 131 optimal weight: 8.9990 chunk 96 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 149 optimal weight: 5.9990 overall best weight: 2.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.110601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.095119 restraints weight = 15660.245| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.34 r_work: 0.2816 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 12960 Z= 0.153 Angle : 0.472 5.373 17705 Z= 0.253 Chirality : 0.045 0.127 2124 Planarity : 0.003 0.031 2213 Dihedral : 4.799 29.223 1949 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 0.93 % Allowed : 5.64 % Favored : 93.43 % 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: 1.40 (0.21), residues: 1624 helix: 1.58 (0.20), residues: 704 sheet: 1.00 (0.27), residues: 256 loop : 0.32 (0.26), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG O 175 TYR 0.015 0.002 TYR G 151 PHE 0.016 0.002 PHE A 78 TRP 0.005 0.001 TRP I 139 HIS 0.005 0.001 HIS O 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (12960) covalent geometry : angle 0.47226 / 0.25 (17705) hydrogen bonds : bond 0.04249 / 2.87 ( 568) hydrogen bonds : angle 5.76600 / 4.15 ( 1704) *********************** 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 184 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 173 time to evaluate : 0.465 Fit side-chains REVERT: A 25 ASP cc_start: 0.8906 (t0) cc_final: 0.8682 (t70) REVERT: A 36 ASP cc_start: 0.8508 (m-30) cc_final: 0.8191 (m-30) REVERT: C 120 GLU cc_start: 0.8017 (mp0) cc_final: 0.7776 (mp0) REVERT: C 124 GLU cc_start: 0.8055 (tt0) cc_final: 0.7740 (tt0) REVERT: E 115 ARG cc_start: 0.8248 (mtp180) cc_final: 0.7811 (mtm180) REVERT: G 16 ASN cc_start: 0.8181 (m110) cc_final: 0.7975 (m-40) REVERT: I 25 ASP cc_start: 0.7925 (t70) cc_final: 0.7607 (t70) REVERT: I 51 ASP cc_start: 0.8448 (m-30) cc_final: 0.7849 (m-30) REVERT: I 114 ASP cc_start: 0.8362 (t70) cc_final: 0.8120 (t0) REVERT: K 115 ARG cc_start: 0.8119 (mtt180) cc_final: 0.7273 (mmm160) REVERT: M 18 ARG cc_start: 0.7872 (mmt180) cc_final: 0.7519 (mmt180) REVERT: M 25 ASP cc_start: 0.8318 (t0) cc_final: 0.7823 (t0) REVERT: M 47 ASP cc_start: 0.7149 (p0) cc_final: 0.6864 (p0) outliers start: 11 outliers final: 7 residues processed: 179 average time/residue: 0.1075 time to fit residues: 28.3757 Evaluate side-chains 173 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 166 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain O residue 180 LYS Chi-restraints excluded: chain O residue 184 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [46, 18, 156, 159, 0, 88, 34, 83, 85, 52, 67] chunk 46 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 156 optimal weight: 3.9990 chunk 159 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 34 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 85 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 67 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 42 GLN ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 GLN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.109584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.094209 restraints weight = 15761.241| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.33 r_work: 0.2807 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 12960 Z= 0.174 Angle : 0.480 5.111 17705 Z= 0.256 Chirality : 0.046 0.128 2124 Planarity : 0.003 0.034 2213 Dihedral : 4.766 26.012 1949 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.18 % Allowed : 5.90 % Favored : 92.92 % 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: 1.20 (0.21), residues: 1624 helix: 1.46 (0.20), residues: 704 sheet: 1.15 (0.27), residues: 248 loop : 0.04 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 169 TYR 0.015 0.002 TYR C 151 PHE 0.016 0.002 PHE C 78 TRP 0.005 0.001 TRP I 139 HIS 0.006 0.001 HIS O 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.17 (12960) covalent geometry : angle 0.48016 / 0.26 (17705) hydrogen bonds : bond 0.04420 / 2.99 ( 568) hydrogen bonds : angle 5.78574 / 4.17 ( 1704) *********************** 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 180 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 166 time to evaluate : 0.447 Fit side-chains REVERT: C 120 GLU cc_start: 0.8075 (mp0) cc_final: 0.7851 (mp0) REVERT: C 124 GLU cc_start: 0.8031 (tt0) cc_final: 0.7722 (tt0) REVERT: E 115 ARG cc_start: 0.8279 (mtp180) cc_final: 0.7788 (mtm180) REVERT: I 25 ASP cc_start: 0.7821 (t70) cc_final: 0.7580 (t70) REVERT: I 51 ASP cc_start: 0.8381 (m-30) cc_final: 0.7921 (m-30) REVERT: I 114 ASP cc_start: 0.8366 (t70) cc_final: 0.8165 (t0) REVERT: K 115 ARG cc_start: 0.8161 (mtt180) cc_final: 0.7381 (mmm160) outliers start: 14 outliers final: 10 residues processed: 174 average time/residue: 0.1083 time to fit residues: 27.6458 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 : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 180 LYS Chi-restraints excluded: chain O residue 184 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [32, 100, 80, 14, 75, 128, 106, 153, 34, 108, 40] chunk 32 optimal weight: 5.9990 chunk 100 optimal weight: 9.9990 chunk 80 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 75 optimal weight: 0.0770 chunk 128 optimal weight: 3.9990 chunk 106 optimal weight: 9.9990 chunk 153 optimal weight: 8.9990 chunk 34 optimal weight: 0.6980 chunk 108 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 overall best weight: 3.3544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.109362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.094023 restraints weight = 15664.617| |-----------------------------------------------------------------------------| r_work (start): 0.2914 rms_B_bonded: 1.32 r_work: 0.2801 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2670 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12960 Z= 0.180 Angle : 0.475 5.163 17705 Z= 0.254 Chirality : 0.046 0.128 2124 Planarity : 0.003 0.035 2213 Dihedral : 4.726 25.313 1949 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.35 % Allowed : 7.33 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.01 (0.21), residues: 1624 helix: 1.41 (0.20), residues: 704 sheet: 0.99 (0.28), residues: 248 loop : -0.18 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 169 TYR 0.016 0.002 TYR C 151 PHE 0.016 0.002 PHE C 78 TRP 0.005 0.001 TRP I 139 HIS 0.006 0.001 HIS O 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 (12960) covalent geometry : angle 0.47542 / 0.25 (17705) hydrogen bonds : bond 0.04432 / 3.00 ( 568) hydrogen bonds : angle 5.75801 / 4.15 ( 1704) *********************** 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 184 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.491 Fit side-chains revert: symmetry clash REVERT: C 120 GLU cc_start: 0.8100 (mp0) cc_final: 0.7831 (mp0) REVERT: C 124 GLU cc_start: 0.8036 (tt0) cc_final: 0.7737 (tt0) REVERT: C 199 GLU cc_start: 0.8367 (mm-30) cc_final: 0.8068 (mm-30) REVERT: E 115 ARG cc_start: 0.8322 (mtp180) cc_final: 0.7826 (mtm180) REVERT: I 25 ASP cc_start: 0.7981 (t70) cc_final: 0.7772 (t70) REVERT: I 114 ASP cc_start: 0.8297 (t70) cc_final: 0.8080 (t0) REVERT: K 115 ARG cc_start: 0.8173 (mtt180) cc_final: 0.7373 (mmm160) outliers start: 16 outliers final: 10 residues processed: 177 average time/residue: 0.1111 time to fit residues: 28.4006 Evaluate side-chains 178 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 168 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 180 LYS Chi-restraints excluded: chain O residue 184 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [9, 150, 54, 63, 83, 28, 40, 119, 74, 39, 47] chunk 9 optimal weight: 10.0000 chunk 150 optimal weight: 8.9990 chunk 54 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 40 optimal weight: 6.9990 chunk 119 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.109239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.093945 restraints weight = 15594.631| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 1.32 r_work: 0.2802 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2672 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8641 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 12960 Z= 0.182 Angle : 0.473 5.143 17705 Z= 0.253 Chirality : 0.046 0.128 2124 Planarity : 0.003 0.036 2213 Dihedral : 4.709 25.576 1949 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 1.26 % Allowed : 8.42 % Favored : 90.31 % 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: 0.87 (0.21), residues: 1624 helix: 1.38 (0.20), residues: 704 sheet: 0.89 (0.28), residues: 248 loop : -0.33 (0.25), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG O 115 TYR 0.017 0.002 TYR G 151 PHE 0.016 0.002 PHE C 78 TRP 0.006 0.001 TRP I 139 HIS 0.006 0.001 HIS O 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00439 / 0.18 (12960) covalent geometry : angle 0.47324 / 0.25 (17705) hydrogen bonds : bond 0.04429 / 3.00 ( 568) hydrogen bonds : angle 5.75056 / 4.15 ( 1704) *********************** 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 183 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 168 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: C 120 GLU cc_start: 0.8111 (mp0) cc_final: 0.7875 (mp0) REVERT: C 124 GLU cc_start: 0.8036 (tt0) cc_final: 0.7745 (tt0) REVERT: E 115 ARG cc_start: 0.8312 (mtp180) cc_final: 0.7809 (mtm180) REVERT: I 114 ASP cc_start: 0.8080 (t70) cc_final: 0.7875 (t0) REVERT: K 115 ARG cc_start: 0.8152 (mtt180) cc_final: 0.7357 (mmm160) outliers start: 15 outliers final: 11 residues processed: 176 average time/residue: 0.1127 time to fit residues: 28.6454 Evaluate side-chains 180 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 169 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain I residue 70 SER Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 180 LYS Chi-restraints excluded: chain O residue 184 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [96, 101, 124, 33, 148, 76, 93, 25, 94, 19, 95] chunk 96 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 124 optimal weight: 0.6980 chunk 33 optimal weight: 0.0030 chunk 148 optimal weight: 0.9980 chunk 76 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 25 optimal weight: 0.9990 chunk 94 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.113789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.098655 restraints weight = 15492.716| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 1.32 r_work: 0.2882 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 12960 Z= 0.080 Angle : 0.376 4.843 17705 Z= 0.207 Chirality : 0.042 0.125 2124 Planarity : 0.003 0.033 2213 Dihedral : 4.144 25.619 1949 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % Rotamer: Outliers : 0.51 % Allowed : 9.27 % Favored : 90.23 % 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: 1.34 (0.21), residues: 1624 helix: 1.79 (0.20), residues: 704 sheet: 1.16 (0.28), residues: 248 loop : -0.14 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 115 TYR 0.019 0.001 TYR G 151 PHE 0.011 0.001 PHE C 78 TRP 0.005 0.001 TRP A 139 HIS 0.001 0.000 HIS O 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00161 / 0.08 (12960) covalent geometry : angle 0.37626 / 0.21 (17705) hydrogen bonds : bond 0.03056 / 2.09 ( 568) hydrogen bonds : angle 5.20131 / 3.74 ( 1704) *********************** 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 198 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 192 time to evaluate : 0.462 Fit side-chains revert: symmetry clash REVERT: A 200 ILE cc_start: 0.8912 (mt) cc_final: 0.8640 (mp) REVERT: C 124 GLU cc_start: 0.8045 (tt0) cc_final: 0.7715 (tt0) REVERT: E 25 ASP cc_start: 0.7926 (t70) cc_final: 0.7556 (t70) REVERT: E 115 ARG cc_start: 0.8206 (mtp180) cc_final: 0.7788 (mtm180) REVERT: I 3 GLU cc_start: 0.7969 (tt0) cc_final: 0.7663 (tp30) REVERT: I 36 ASP cc_start: 0.7680 (m-30) cc_final: 0.7478 (m-30) REVERT: I 114 ASP cc_start: 0.8033 (t70) cc_final: 0.7821 (t0) REVERT: K 115 ARG cc_start: 0.8079 (mtt180) cc_final: 0.7377 (mmm160) REVERT: K 191 ASN cc_start: 0.8811 (t0) cc_final: 0.8593 (t0) outliers start: 6 outliers final: 3 residues processed: 196 average time/residue: 0.1118 time to fit residues: 31.9669 Evaluate side-chains 182 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 179 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 154 SER Chi-restraints excluded: chain K residue 19 ILE Chi-restraints excluded: chain O residue 180 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [136, 155, 125, 11, 18, 72, 131, 39, 67, 59, 28] chunk 136 optimal weight: 7.9990 chunk 155 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 18 optimal weight: 7.9990 chunk 72 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 chunk 39 optimal weight: 5.9990 chunk 67 optimal weight: 0.3980 chunk 59 optimal weight: 8.9990 chunk 28 optimal weight: 0.6980 overall best weight: 4.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.108466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.093218 restraints weight = 15546.863| |-----------------------------------------------------------------------------| r_work (start): 0.2898 rms_B_bonded: 1.31 r_work: 0.2791 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.2369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 12960 Z= 0.235 Angle : 0.519 5.305 17705 Z= 0.274 Chirality : 0.048 0.132 2124 Planarity : 0.004 0.037 2213 Dihedral : 4.715 25.357 1949 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.26 % Allowed : 9.10 % Favored : 89.64 % 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: 0.79 (0.21), residues: 1624 helix: 1.34 (0.20), residues: 712 sheet: 0.88 (0.29), residues: 248 loop : -0.46 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 115 TYR 0.016 0.002 TYR C 151 PHE 0.017 0.002 PHE C 78 TRP 0.005 0.001 TRP I 139 HIS 0.007 0.001 HIS O 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00575 / 0.23 (12960) covalent geometry : angle 0.51880 / 0.27 (17705) hydrogen bonds : bond 0.04902 / 3.31 ( 568) hydrogen bonds : angle 5.81390 / 4.20 ( 1704) *********************** 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 181 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: C 124 GLU cc_start: 0.7952 (tt0) cc_final: 0.7626 (tt0) REVERT: E 115 ARG cc_start: 0.8328 (mtp180) cc_final: 0.7814 (mtm180) REVERT: I 36 ASP cc_start: 0.7580 (m-30) cc_final: 0.7356 (m-30) REVERT: I 114 ASP cc_start: 0.8235 (t70) cc_final: 0.7984 (t0) REVERT: K 115 ARG cc_start: 0.8148 (mtt180) cc_final: 0.7358 (mmm160) outliers start: 15 outliers final: 9 residues processed: 174 average time/residue: 0.1143 time to fit residues: 28.5412 Evaluate side-chains 176 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 167 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain C residue 206 SER Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain G residue 200 ILE Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain K residue 177 SER Chi-restraints excluded: chain O residue 19 ILE Chi-restraints excluded: chain O residue 184 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [82, 3, 13, 131, 56, 143, 68, 74, 139, 102, 55] chunk 82 optimal weight: 1.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 131 optimal weight: 9.9990 chunk 56 optimal weight: 0.6980 chunk 143 optimal weight: 4.9990 chunk 68 optimal weight: 6.9990 chunk 74 optimal weight: 5.9990 chunk 139 optimal weight: 6.9990 chunk 102 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.109683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.094455 restraints weight = 15538.684| |-----------------------------------------------------------------------------| r_work (start): 0.2917 rms_B_bonded: 1.31 r_work: 0.2807 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 12960 Z= 0.162 Angle : 0.452 5.073 17705 Z= 0.242 Chirality : 0.045 0.128 2124 Planarity : 0.003 0.035 2213 Dihedral : 4.578 25.777 1949 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.93 % Allowed : 9.52 % Favored : 89.55 % 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: 0.79 (0.21), residues: 1624 helix: 1.37 (0.20), residues: 712 sheet: 0.83 (0.28), residues: 248 loop : -0.48 (0.25), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 115 TYR 0.017 0.002 TYR C 151 PHE 0.016 0.002 PHE C 78 TRP 0.005 0.001 TRP I 139 HIS 0.005 0.001 HIS O 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.16 (12960) covalent geometry : angle 0.45185 / 0.24 (17705) hydrogen bonds : bond 0.04183 / 2.83 ( 568) hydrogen bonds : angle 5.64170 / 4.08 ( 1704) *********************** 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 178 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 167 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: C 124 GLU cc_start: 0.7967 (tt0) cc_final: 0.7661 (tt0) REVERT: E 115 ARG cc_start: 0.8342 (mtp180) cc_final: 0.7818 (mtm180) REVERT: I 36 ASP cc_start: 0.7776 (m-30) cc_final: 0.7525 (m-30) REVERT: I 114 ASP cc_start: 0.8124 (t70) cc_final: 0.7890 (t0) REVERT: K 115 ARG cc_start: 0.8074 (mtt180) cc_final: 0.7338 (mmm160) outliers start: 11 outliers final: 9 residues processed: 170 average time/residue: 0.1127 time to fit residues: 28.0507 Evaluate side-chains 177 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 168 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 SER Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain G residue 120 GLU Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain K residue 143 THR Chi-restraints excluded: chain M residue 47 ASP Chi-restraints excluded: chain O residue 143 THR Chi-restraints excluded: chain O residue 184 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [28, 61, 63, 106, 39, 2, 126, 32, 6, 27, 114] chunk 28 optimal weight: 5.9990 chunk 61 optimal weight: 0.2980 chunk 63 optimal weight: 0.9980 chunk 106 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 2 optimal weight: 6.9990 chunk 126 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 114 optimal weight: 4.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN ** G 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 42 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.112772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.097686 restraints weight = 15557.567| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 1.31 r_work: 0.2859 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.2730 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 12960 Z= 0.089 Angle : 0.385 4.864 17705 Z= 0.211 Chirality : 0.042 0.125 2124 Planarity : 0.003 0.035 2213 Dihedral : 4.177 24.616 1949 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.76 % Allowed : 9.86 % Favored : 89.39 % 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: 1.13 (0.21), residues: 1624 helix: 1.66 (0.20), residues: 712 sheet: 1.05 (0.28), residues: 248 loop : -0.33 (0.26), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 115 TYR 0.018 0.001 TYR C 151 PHE 0.012 0.001 PHE C 78 TRP 0.006 0.001 TRP M 139 HIS 0.002 0.000 HIS C 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00189 / 0.09 (12960) covalent geometry : angle 0.38526 / 0.21 (17705) hydrogen bonds : bond 0.03234 / 2.20 ( 568) hydrogen bonds : angle 5.24638 / 3.78 ( 1704) ********************** 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 186 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 177 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 200 ILE cc_start: 0.8906 (mt) cc_final: 0.8656 (mp) REVERT: C 124 GLU cc_start: 0.8019 (tt0) cc_final: 0.7715 (tt0) REVERT: E 115 ARG cc_start: 0.8235 (mtp180) cc_final: 0.7776 (mtm180) REVERT: I 3 GLU cc_start: 0.8005 (tt0) cc_final: 0.7683 (tp30) REVERT: I 36 ASP cc_start: 0.7699 (m-30) cc_final: 0.7488 (m-30) REVERT: I 114 ASP cc_start: 0.8118 (t70) cc_final: 0.7895 (t0) REVERT: K 115 ARG cc_start: 0.8047 (mtt180) cc_final: 0.7321 (mmm160) REVERT: K 191 ASN cc_start: 0.8844 (t0) cc_final: 0.8628 (t0) outliers start: 9 outliers final: 7 residues processed: 181 average time/residue: 0.1129 time to fit residues: 29.5067 Evaluate side-chains 181 residues out of total 1424 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 174 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 198 SER Chi-restraints excluded: chain E residue 114 ASP Chi-restraints excluded: chain G residue 154 SER Chi-restraints excluded: chain I residue 168 GLU Chi-restraints excluded: chain M residue 47 ASP Chi-restraints excluded: chain O residue 19 ILE Chi-restraints excluded: chain O residue 143 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: [116, 2, 7, 79, 142, 38, 30, 23, 5, 133, 126] chunk 116 optimal weight: 7.9990 chunk 2 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 38 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 5 optimal weight: 6.9990 chunk 133 optimal weight: 0.0980 chunk 126 optimal weight: 0.8980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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** ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.113565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.098532 restraints weight = 15490.652| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 1.31 r_work: 0.2875 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 12960 Z= 0.087 Angle : 0.383 4.855 17705 Z= 0.209 Chirality : 0.042 0.124 2124 Planarity : 0.003 0.034 2213 Dihedral : 4.047 24.583 1949 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.51 % Allowed : 9.94 % Favored : 89.55 % 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: 1.33 (0.21), residues: 1624 helix: 1.84 (0.20), residues: 704 sheet: 1.25 (0.29), residues: 248 loop : -0.26 (0.26), residues: 672 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG O 115 TYR 0.017 0.001 TYR C 151 PHE 0.012 0.001 PHE C 78 TRP 0.005 0.001 TRP M 139 HIS 0.002 0.000 HIS O 79 Details of bonding type rmsd/Z covalent geometry : bond 0.00184 / 0.09 (12960) covalent geometry : angle 0.38293 / 0.21 (17705) hydrogen bonds : bond 0.03170 / 2.16 ( 568) hydrogen bonds : angle 5.15754 / 3.72 ( 1704) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2615.61 seconds wall clock time: 45 minutes 22.92 seconds (2722.92 seconds total)