Starting phenix.real_space_refine on Tue Aug 26 13:37:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8to5_41435/08_2025/8to5_41435_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8to5_41435/08_2025/8to5_41435.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8to5_41435/08_2025/8to5_41435_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8to5_41435/08_2025/8to5_41435_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8to5_41435/08_2025/8to5_41435.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8to5_41435/08_2025/8to5_41435.map" } resolution = 1.87 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.002 sd= 0.116 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 67 5.16 5 C 11403 2.51 5 N 3151 2.21 5 O 5478 1.98 5 H 17088 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37187 Number of models: 1 Model: "" Number of chains: 40 Chain: "M" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2446 Classifications: {'peptide': 162} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "N" Number of atoms: 2546 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 172, 2534 Classifications: {'peptide': 172} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 172, 2534 Classifications: {'peptide': 172} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2534 Chain: "O" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2446 Classifications: {'peptide': 162} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "P" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2534 Classifications: {'peptide': 172} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2446 Classifications: {'peptide': 162} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "R" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2534 Classifications: {'peptide': 172} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "S" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2446 Classifications: {'peptide': 162} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "T" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2534 Classifications: {'peptide': 172} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "U" Number of atoms: 2455 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 162, 2446 Classifications: {'peptide': 162} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Conformer: "B" Number of residues, atoms: 162, 2446 Classifications: {'peptide': 162} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} bond proxies already assigned to first conformer: 2456 Chain: "V" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2534 Classifications: {'peptide': 172} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "W" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 2446 Classifications: {'peptide': 162} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 157} Chain: "X" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 2534 Classifications: {'peptide': 172} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 167} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'MEN:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "b" Number of atoms: 3445 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 216, 3433 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 7, 'TRANS': 208} Conformer: "B" Number of residues, atoms: 216, 3433 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 7, 'TRANS': 208} bond proxies already assigned to first conformer: 3454 Chain: "c" Number of atoms: 1134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1134 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain breaks: 1 Chain: "M" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'CYC': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'CYC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 132 Classifications: {'water': 132} Link IDs: {None: 131} Chain: "N" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 168, 168 Classifications: {'water': 168} Link IDs: {None: 167} Chain: "O" Number of atoms: 134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 134 Classifications: {'water': 134} Link IDs: {None: 133} Chain: "P" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "Q" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 140 Classifications: {'water': 140} Link IDs: {None: 139} Chain: "R" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 152 Classifications: {'water': 152} Link IDs: {None: 151} Chain: "S" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 132 Classifications: {'water': 132} Link IDs: {None: 131} Chain: "T" Number of atoms: 164 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 164 Classifications: {'water': 164} Link IDs: {None: 163} Chain: "U" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 132 Classifications: {'water': 132} Link IDs: {None: 131} Chain: "V" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 143 Classifications: {'water': 143} Link IDs: {None: 142} Chain: "W" Number of atoms: 135 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 135 Classifications: {'water': 135} Link IDs: {None: 134} Chain: "X" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 147 Classifications: {'water': 147} Link IDs: {None: 146} Chain: "b" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 142 Classifications: {'water': 142} Link IDs: {None: 141} Chain: "c" Number of atoms: 69 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 69 Classifications: {'water': 69} Link IDs: {None: 68} Time building chain proxies: 10.29, per 1000 atoms: 0.28 Number of scatterers: 37187 At special positions: 0 Unit cell: (123.59, 122.863, 84.332, 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 67 16.00 O 5478 8.00 N 3151 7.00 C 11403 6.00 H 17088 1.00 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=18, symmetry=0 Number of additional bonds: simple=18, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.13 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 715.3 nanoseconds 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4230 Finding SS restraints... Secondary structure from input PDB file: 127 helices and 1 sheets defined 82.5% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'M' and resid 3 through 15 Processing helix chain 'M' and resid 20 through 47 removed outlier: 4.558A pdb=" N ASN M 35 " --> pdb=" O LEU M 31 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N ALA M 36 " --> pdb=" O ARG M 32 " (cutoff:3.500A) Processing helix chain 'M' and resid 47 through 63 Processing helix chain 'M' and resid 64 through 68 Processing helix chain 'M' and resid 77 through 102 Processing helix chain 'M' and resid 104 through 111 Processing helix chain 'M' and resid 114 through 122 Processing helix chain 'M' and resid 125 through 140 removed outlier: 3.978A pdb=" N TYR M 129 " --> pdb=" O SER M 125 " (cutoff:3.500A) Processing helix chain 'M' and resid 143 through 161 Processing helix chain 'N' and resid 3 through 15 removed outlier: 3.796A pdb=" N VAL N 8 " --> pdb=" O VAL N 4 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ARG N 15 " --> pdb=" O GLN N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 20 through 33 Processing helix chain 'N' and resid 33 through 47 Processing helix chain 'N' and resid 47 through 63 Processing helix chain 'N' and resid 64 through 67 Processing helix chain 'N' and resid 75 through 100 Processing helix chain 'N' and resid 102 through 109 Processing helix chain 'N' and resid 112 through 121 Processing helix chain 'N' and resid 123 through 144 Processing helix chain 'N' and resid 153 through 172 Processing helix chain 'O' and resid 3 through 15 Processing helix chain 'O' and resid 20 through 47 removed outlier: 4.503A pdb=" N ASN O 35 " --> pdb=" O LEU O 31 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N ALA O 36 " --> pdb=" O ARG O 32 " (cutoff:3.500A) Processing helix chain 'O' and resid 47 through 63 Processing helix chain 'O' and resid 64 through 69 removed outlier: 3.516A pdb=" N GLN O 68 " --> pdb=" O PRO O 64 " (cutoff:3.500A) Processing helix chain 'O' and resid 77 through 102 Processing helix chain 'O' and resid 104 through 111 Processing helix chain 'O' and resid 114 through 122 Processing helix chain 'O' and resid 125 through 140 removed outlier: 3.963A pdb=" N TYR O 129 " --> pdb=" O SER O 125 " (cutoff:3.500A) Processing helix chain 'O' and resid 143 through 161 Processing helix chain 'P' and resid 3 through 16 removed outlier: 4.049A pdb=" N VAL P 8 " --> pdb=" O VAL P 4 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ARG P 15 " --> pdb=" O GLN P 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 20 through 33 Processing helix chain 'P' and resid 33 through 47 Processing helix chain 'P' and resid 47 through 63 Processing helix chain 'P' and resid 64 through 67 Processing helix chain 'P' and resid 75 through 100 Processing helix chain 'P' and resid 102 through 109 Processing helix chain 'P' and resid 112 through 121 Processing helix chain 'P' and resid 123 through 144 Processing helix chain 'P' and resid 153 through 172 Processing helix chain 'Q' and resid 3 through 15 Processing helix chain 'Q' and resid 20 through 47 removed outlier: 4.542A pdb=" N ASN Q 35 " --> pdb=" O LEU Q 31 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ALA Q 36 " --> pdb=" O ARG Q 32 " (cutoff:3.500A) Processing helix chain 'Q' and resid 47 through 63 Processing helix chain 'Q' and resid 64 through 69 Processing helix chain 'Q' and resid 77 through 102 Processing helix chain 'Q' and resid 104 through 111 Processing helix chain 'Q' and resid 114 through 123 Processing helix chain 'Q' and resid 125 through 140 removed outlier: 4.002A pdb=" N TYR Q 129 " --> pdb=" O SER Q 125 " (cutoff:3.500A) Processing helix chain 'Q' and resid 143 through 162 Processing helix chain 'R' and resid 3 through 15 removed outlier: 3.910A pdb=" N VAL R 8 " --> pdb=" O VAL R 4 " (cutoff:3.500A) Processing helix chain 'R' and resid 20 through 33 Processing helix chain 'R' and resid 33 through 47 Processing helix chain 'R' and resid 47 through 63 Processing helix chain 'R' and resid 64 through 67 Processing helix chain 'R' and resid 75 through 100 Processing helix chain 'R' and resid 102 through 109 Processing helix chain 'R' and resid 112 through 121 Processing helix chain 'R' and resid 123 through 144 Processing helix chain 'R' and resid 153 through 172 Processing helix chain 'S' and resid 3 through 15 Processing helix chain 'S' and resid 20 through 47 removed outlier: 4.528A pdb=" N ASN S 35 " --> pdb=" O LEU S 31 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ALA S 36 " --> pdb=" O ARG S 32 " (cutoff:3.500A) Processing helix chain 'S' and resid 47 through 63 Processing helix chain 'S' and resid 64 through 68 Processing helix chain 'S' and resid 77 through 102 Processing helix chain 'S' and resid 104 through 111 Processing helix chain 'S' and resid 114 through 122 Processing helix chain 'S' and resid 125 through 140 removed outlier: 4.011A pdb=" N TYR S 129 " --> pdb=" O SER S 125 " (cutoff:3.500A) Processing helix chain 'S' and resid 143 through 162 Processing helix chain 'T' and resid 3 through 16 removed outlier: 3.829A pdb=" N VAL T 8 " --> pdb=" O VAL T 4 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG T 15 " --> pdb=" O GLN T 11 " (cutoff:3.500A) Processing helix chain 'T' and resid 20 through 33 Processing helix chain 'T' and resid 33 through 47 Processing helix chain 'T' and resid 47 through 63 Processing helix chain 'T' and resid 64 through 67 Processing helix chain 'T' and resid 75 through 100 Processing helix chain 'T' and resid 102 through 109 Processing helix chain 'T' and resid 112 through 121 Processing helix chain 'T' and resid 123 through 144 Processing helix chain 'T' and resid 153 through 172 removed outlier: 3.683A pdb=" N ALA T 172 " --> pdb=" O ALA T 168 " (cutoff:3.500A) Processing helix chain 'U' and resid 3 through 15 Processing helix chain 'U' and resid 20 through 47 removed outlier: 4.715A pdb=" N ASN U 35 " --> pdb=" O LEU U 31 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ALA U 36 " --> pdb=" O ARG U 32 " (cutoff:3.500A) Processing helix chain 'U' and resid 47 through 63 Processing helix chain 'U' and resid 64 through 69 Processing helix chain 'U' and resid 77 through 102 Processing helix chain 'U' and resid 104 through 111 Processing helix chain 'U' and resid 114 through 122 Processing helix chain 'U' and resid 125 through 140 removed outlier: 3.990A pdb=" N TYR U 129 " --> pdb=" O SER U 125 " (cutoff:3.500A) Processing helix chain 'U' and resid 143 through 162 Processing helix chain 'V' and resid 3 through 16 removed outlier: 3.970A pdb=" N VAL V 8 " --> pdb=" O VAL V 4 " (cutoff:3.500A) Processing helix chain 'V' and resid 20 through 33 Processing helix chain 'V' and resid 33 through 47 Processing helix chain 'V' and resid 47 through 63 Processing helix chain 'V' and resid 64 through 67 Processing helix chain 'V' and resid 75 through 100 Processing helix chain 'V' and resid 102 through 108 Processing helix chain 'V' and resid 112 through 121 Processing helix chain 'V' and resid 123 through 144 Processing helix chain 'V' and resid 153 through 172 Processing helix chain 'W' and resid 3 through 16 Processing helix chain 'W' and resid 20 through 47 removed outlier: 4.520A pdb=" N ASN W 35 " --> pdb=" O LEU W 31 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ALA W 36 " --> pdb=" O ARG W 32 " (cutoff:3.500A) Processing helix chain 'W' and resid 47 through 63 Processing helix chain 'W' and resid 64 through 68 Processing helix chain 'W' and resid 77 through 102 Processing helix chain 'W' and resid 104 through 111 Processing helix chain 'W' and resid 114 through 122 Processing helix chain 'W' and resid 125 through 140 removed outlier: 3.998A pdb=" N TYR W 129 " --> pdb=" O SER W 125 " (cutoff:3.500A) Processing helix chain 'W' and resid 143 through 162 Processing helix chain 'X' and resid 3 through 16 removed outlier: 3.835A pdb=" N VAL X 8 " --> pdb=" O VAL X 4 " (cutoff:3.500A) Processing helix chain 'X' and resid 20 through 33 Processing helix chain 'X' and resid 33 through 47 Processing helix chain 'X' and resid 47 through 63 Processing helix chain 'X' and resid 64 through 67 Processing helix chain 'X' and resid 75 through 100 Processing helix chain 'X' and resid 102 through 109 Processing helix chain 'X' and resid 112 through 121 Processing helix chain 'X' and resid 123 through 143 Processing helix chain 'X' and resid 153 through 172 removed outlier: 3.574A pdb=" N VAL X 171 " --> pdb=" O ALA X 167 " (cutoff:3.500A) Processing helix chain 'b' and resid 12 through 17 Processing helix chain 'b' and resid 28 through 44 Processing helix chain 'b' and resid 50 through 54 Processing helix chain 'b' and resid 55 through 64 Processing helix chain 'b' and resid 68 through 79 Processing helix chain 'b' and resid 79 through 87 Processing helix chain 'b' and resid 91 through 105 Processing helix chain 'b' and resid 110 through 125 removed outlier: 3.835A pdb=" N VAL b 114 " --> pdb=" O SER b 110 " (cutoff:3.500A) Processing helix chain 'b' and resid 125 through 135 removed outlier: 3.528A pdb=" N TYR b 133 " --> pdb=" O ASP b 129 " (cutoff:3.500A) Processing helix chain 'b' and resid 136 through 143 Processing helix chain 'b' and resid 160 through 171 removed outlier: 3.921A pdb=" N PHE b 164 " --> pdb=" O ARG b 160 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N THR b 165 " --> pdb=" O THR b 161 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N PHE b 168 " --> pdb=" O PHE b 164 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG b 169 " --> pdb=" O THR b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 189 through 196 Processing helix chain 'c' and resid 250 through 263 removed outlier: 4.379A pdb=" N SER c 254 " --> pdb=" O TYR c 250 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N ALA c 255 " --> pdb=" O ASP c 251 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'c' and resid 243 through 249 removed outlier: 6.540A pdb=" N ILE c 228 " --> pdb=" O VAL c 267 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N VAL c 267 " --> pdb=" O ILE c 228 " (cutoff:3.500A) 1370 hydrogen bonds defined for protein. 4062 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: 9.67 Time building geometry restraints manager: 5.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17043 1.03 - 1.23: 178 1.23 - 1.42: 7803 1.42 - 1.62: 10434 1.62 - 1.81: 104 Bond restraints: 35562 Sorted by residual: bond pdb=" ND2 MEN N 72 " pdb=" HD2 MEN N 72 " ideal model delta sigma weight residual 0.860 1.015 -0.155 2.00e-02 2.50e+03 6.04e+01 bond pdb=" ND2 MEN V 72 " pdb=" HD2 MEN V 72 " ideal model delta sigma weight residual 0.860 1.015 -0.155 2.00e-02 2.50e+03 6.04e+01 bond pdb=" N MEN T 72 " pdb=" H MEN T 72 " ideal model delta sigma weight residual 0.860 1.015 -0.155 2.00e-02 2.50e+03 6.03e+01 bond pdb=" ND2 MEN X 72 " pdb=" HD2 MEN X 72 " ideal model delta sigma weight residual 0.860 1.015 -0.155 2.00e-02 2.50e+03 6.03e+01 bond pdb=" ND2 MEN R 72 " pdb=" HD2 MEN R 72 " ideal model delta sigma weight residual 0.860 1.015 -0.155 2.00e-02 2.50e+03 6.02e+01 ... (remaining 35557 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.25: 62941 2.25 - 4.49: 574 4.49 - 6.74: 72 6.74 - 8.99: 19 8.99 - 11.23: 3 Bond angle restraints: 63609 Sorted by residual: angle pdb=" C1B CYC X 201 " pdb=" CHB CYC X 201 " pdb=" C4A CYC X 201 " ideal model delta sigma weight residual 126.10 137.33 -11.23 3.00e+00 1.11e-01 1.40e+01 angle pdb=" CA GLN N 65 " pdb=" CB GLN N 65 " pdb=" CG GLN N 65 " ideal model delta sigma weight residual 114.10 120.47 -6.37 2.00e+00 2.50e-01 1.01e+01 angle pdb=" C1B CYC R 202 " pdb=" CHB CYC R 202 " pdb=" C4A CYC R 202 " ideal model delta sigma weight residual 126.10 135.65 -9.55 3.00e+00 1.11e-01 1.01e+01 angle pdb=" C4C CYC W 201 " pdb=" C3C CYC W 201 " pdb=" CAC CYC W 201 " ideal model delta sigma weight residual 113.00 122.05 -9.05 3.00e+00 1.11e-01 9.11e+00 angle pdb=" C4C CYC U 201 " pdb=" C3C CYC U 201 " pdb=" CAC CYC U 201 " ideal model delta sigma weight residual 113.00 121.98 -8.98 3.00e+00 1.11e-01 8.95e+00 ... (remaining 63604 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 15393 17.90 - 35.80: 1241 35.80 - 53.71: 374 53.71 - 71.61: 139 71.61 - 89.51: 26 Dihedral angle restraints: 17173 sinusoidal: 9665 harmonic: 7508 Sorted by residual: dihedral pdb=" CA GLU b 145 " pdb=" C GLU b 145 " pdb=" N ASN b 146 " pdb=" CA ASN b 146 " ideal model delta harmonic sigma weight residual 180.00 -158.36 -21.64 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA GLN M 33 " pdb=" C GLN M 33 " pdb=" N ALA M 34 " pdb=" CA ALA M 34 " ideal model delta harmonic sigma weight residual -180.00 -159.11 -20.89 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA GLN Q 33 " pdb=" C GLN Q 33 " pdb=" N ALA Q 34 " pdb=" CA ALA Q 34 " ideal model delta harmonic sigma weight residual -180.00 -160.03 -19.97 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 17170 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 2537 0.069 - 0.138: 193 0.138 - 0.208: 10 0.208 - 0.277: 1 0.277 - 0.346: 5 Chirality restraints: 2746 Sorted by residual: chirality pdb=" C3C CYC U 201 " pdb=" C2C CYC U 201 " pdb=" C4C CYC U 201 " pdb=" CAC CYC U 201 " both_signs ideal model delta sigma weight residual False 2.62 2.27 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" C3C CYC W 201 " pdb=" C2C CYC W 201 " pdb=" C4C CYC W 201 " pdb=" CAC CYC W 201 " both_signs ideal model delta sigma weight residual False 2.62 2.28 0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" C3C CYC Q 201 " pdb=" C2C CYC Q 201 " pdb=" C4C CYC Q 201 " pdb=" CAC CYC Q 201 " both_signs ideal model delta sigma weight residual False 2.62 2.29 0.33 2.00e-01 2.50e+01 2.67e+00 ... (remaining 2743 not shown) Planarity restraints: 5517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" NB CYC U 201 " 0.008 2.00e-02 2.50e+03 1.06e-01 2.53e+02 pdb=" OB CYC U 201 " -0.048 2.00e-02 2.50e+03 pdb=" C1B CYC U 201 " 0.024 2.00e-02 2.50e+03 pdb=" C2B CYC U 201 " -0.062 2.00e-02 2.50e+03 pdb=" C3B CYC U 201 " -0.107 2.00e-02 2.50e+03 pdb=" C4B CYC U 201 " -0.055 2.00e-02 2.50e+03 pdb=" CAB CYC U 201 " 0.224 2.00e-02 2.50e+03 pdb=" CHB CYC U 201 " 0.129 2.00e-02 2.50e+03 pdb=" CMB CYC U 201 " -0.114 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CYC Q 201 " 0.003 2.00e-02 2.50e+03 1.05e-01 2.46e+02 pdb=" OB CYC Q 201 " -0.042 2.00e-02 2.50e+03 pdb=" C1B CYC Q 201 " 0.023 2.00e-02 2.50e+03 pdb=" C2B CYC Q 201 " -0.059 2.00e-02 2.50e+03 pdb=" C3B CYC Q 201 " -0.106 2.00e-02 2.50e+03 pdb=" C4B CYC Q 201 " -0.057 2.00e-02 2.50e+03 pdb=" CAB CYC Q 201 " 0.220 2.00e-02 2.50e+03 pdb=" CHB CYC Q 201 " 0.131 2.00e-02 2.50e+03 pdb=" CMB CYC Q 201 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" NB CYC M 201 " 0.001 2.00e-02 2.50e+03 1.00e-01 2.26e+02 pdb=" OB CYC M 201 " 0.038 2.00e-02 2.50e+03 pdb=" C1B CYC M 201 " -0.019 2.00e-02 2.50e+03 pdb=" C2B CYC M 201 " 0.056 2.00e-02 2.50e+03 pdb=" C3B CYC M 201 " 0.101 2.00e-02 2.50e+03 pdb=" C4B CYC M 201 " 0.055 2.00e-02 2.50e+03 pdb=" CAB CYC M 201 " -0.210 2.00e-02 2.50e+03 pdb=" CHB CYC M 201 " -0.128 2.00e-02 2.50e+03 pdb=" CMB CYC M 201 " 0.107 2.00e-02 2.50e+03 ... (remaining 5514 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.23: 3380 2.23 - 2.82: 79924 2.82 - 3.41: 113008 3.41 - 4.01: 154689 4.01 - 4.60: 234356 Nonbonded interactions: 585357 Sorted by model distance: nonbonded pdb="HH22 ARG S 79 " pdb=" O2D CYC S 201 " model vdw 1.633 2.450 nonbonded pdb="HH22 ARG O 79 " pdb=" O2D CYC O 201 " model vdw 1.636 2.450 nonbonded pdb="HH22 ARG U 79 " pdb=" O2D CYC U 201 " model vdw 1.653 2.450 nonbonded pdb="HH22 ARG M 79 " pdb=" O2D CYC M 201 " model vdw 1.667 2.450 nonbonded pdb="HH22 ARG Q 79 " pdb=" O2D CYC Q 201 " model vdw 1.678 2.450 ... (remaining 585352 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 'M' and (resid 1 through 46 or resid 48 through 201)) selection = (chain 'O' and (resid 1 through 46 or resid 48 through 201)) selection = (chain 'Q' and (resid 1 through 46 or resid 48 through 201)) selection = (chain 'S' and (resid 1 through 46 or resid 48 through 201)) selection = (chain 'U' and (resid 1 through 46 or resid 48 through 201)) selection = (chain 'W' and (resid 1 through 46 or resid 48 through 201)) } ncs_group { reference = (chain 'N' and (resid 1 through 85 or resid 87 through 202)) selection = (chain 'P' and (resid 1 through 85 or resid 87 through 202)) selection = (chain 'R' and (resid 1 through 85 or resid 87 through 202)) selection = (chain 'T' and (resid 1 through 85 or resid 87 through 202)) selection = (chain 'V' and (resid 1 through 85 or resid 87 through 202)) selection = (chain 'X' and (resid 1 through 85 or resid 87 through 202)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=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: 13.020 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.390 Extract box with map and model: 0.550 Check model and map are aligned: 0.140 Set scattering table: 0.120 Process input model: 42.280 Find NCS groups from input model: 0.800 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 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 0.059 18489 Z= 0.304 Angle : 0.703 11.233 25122 Z= 0.324 Chirality : 0.039 0.346 2746 Planarity : 0.009 0.124 3292 Dihedral : 14.676 89.510 7176 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Rotamer: Outliers : 0.23 % Allowed : 5.49 % Favored : 94.28 % 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 aren not related in a simple way. whole: 2.76 (0.17), residues: 2250 helix: 2.23 (0.12), residues: 1770 sheet: 2.13 (1.03), residues: 14 loop : 0.34 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG R 150 TYR 0.011 0.002 TYR b 15 PHE 0.016 0.002 PHE b 168 TRP 0.004 0.001 TRP S 128 HIS 0.004 0.002 HIS W 140 Details of bonding type rmsd covalent geometry : bond 0.00538 (18471) covalent geometry : angle 0.70280 (25122) hydrogen bonds : bond 0.15276 ( 1370) hydrogen bonds : angle 6.22361 ( 4062) Misc. bond : bond 0.05175 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 232 time to evaluate : 1.111 Fit side-chains revert: symmetry clash REVERT: Q 162 SER cc_start: 0.7285 (m) cc_final: 0.7081 (p) REVERT: W 39 GLN cc_start: 0.7849 (tm-30) cc_final: 0.7502 (tm-30) outliers start: 4 outliers final: 3 residues processed: 236 average time/residue: 2.4400 time to fit residues: 621.3446 Evaluate side-chains 231 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 228 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain b residue 47 ASP Chi-restraints excluded: chain c residue 218 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 216 optimal weight: 3.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 4.9990 chunk 212 optimal weight: 3.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN O 68 GLN Q 68 GLN Q 139 ASN R 132 GLN S 49 GLN S 53 ASN U 68 GLN U 78 GLN W 70 GLN c 252 ASN ** c 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.109963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.102464 restraints weight = 43407.307| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 0.34 r_work: 0.2919 rms_B_bonded: 0.63 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 1.16 restraints_weight: 0.2500 r_work: 0.2622 rms_B_bonded: 3.27 restraints_weight: 0.1250 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2581 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2581 r_free = 0.2581 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2581 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9060 moved from start: 0.0838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18489 Z= 0.217 Angle : 0.677 7.951 25122 Z= 0.353 Chirality : 0.038 0.154 2746 Planarity : 0.006 0.052 3292 Dihedral : 9.935 77.373 3369 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.17 % Allowed : 5.21 % Favored : 94.62 % 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 aren not related in a simple way. whole: 2.51 (0.17), residues: 2250 helix: 2.03 (0.11), residues: 1777 sheet: 2.15 (1.04), residues: 14 loop : 0.29 (0.29), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 150 TYR 0.016 0.002 TYR b 15 PHE 0.024 0.002 PHE b 168 TRP 0.007 0.002 TRP M 128 HIS 0.004 0.001 HIS W 140 Details of bonding type rmsd covalent geometry : bond 0.00434 (18471) covalent geometry : angle 0.67684 (25122) hydrogen bonds : bond 0.06418 ( 1370) hydrogen bonds : angle 5.16915 ( 4062) Misc. bond : bond 0.00091 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 225 time to evaluate : 1.212 Fit side-chains REVERT: V 79 MET cc_start: 0.9342 (tpp) cc_final: 0.8959 (tpp) outliers start: 3 outliers final: 2 residues processed: 228 average time/residue: 2.3667 time to fit residues: 584.0389 Evaluate side-chains 220 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 218 time to evaluate : 1.111 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain b residue 47 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 117 optimal weight: 4.9990 chunk 141 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 69 optimal weight: 4.9990 chunk 217 optimal weight: 4.9990 chunk 198 optimal weight: 5.9990 chunk 177 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN O 39 GLN O 49 GLN O 68 GLN Q 39 GLN Q 68 GLN R 132 GLN U 68 GLN V 146 ASN W 70 GLN b 195 GLN c 263 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.109221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.101808 restraints weight = 42520.313| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 0.33 r_work: 0.2916 rms_B_bonded: 0.60 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 1.12 restraints_weight: 0.2500 r_work: 0.2616 rms_B_bonded: 3.18 restraints_weight: 0.1250 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2574 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2574 r_free = 0.2574 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2574 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18489 Z= 0.259 Angle : 0.727 7.554 25122 Z= 0.380 Chirality : 0.040 0.158 2746 Planarity : 0.006 0.060 3292 Dihedral : 10.053 75.304 3368 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.40 % Allowed : 4.87 % Favored : 94.74 % 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 aren not related in a simple way. whole: 1.99 (0.16), residues: 2250 helix: 1.65 (0.11), residues: 1777 sheet: 2.24 (1.05), residues: 14 loop : 0.16 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG R 150 TYR 0.019 0.003 TYR b 15 PHE 0.026 0.003 PHE b 168 TRP 0.008 0.003 TRP M 128 HIS 0.004 0.001 HIS W 140 Details of bonding type rmsd covalent geometry : bond 0.00519 (18471) covalent geometry : angle 0.72749 (25122) hydrogen bonds : bond 0.06758 ( 1370) hydrogen bonds : angle 5.27102 ( 4062) Misc. bond : bond 0.00104 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 222 time to evaluate : 1.071 Fit side-chains REVERT: V 79 MET cc_start: 0.9381 (tpp) cc_final: 0.9125 (tpp) outliers start: 7 outliers final: 5 residues processed: 226 average time/residue: 2.3964 time to fit residues: 585.3770 Evaluate side-chains 226 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 221 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain U residue 162 SER Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain b residue 47 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 92 optimal weight: 4.9990 chunk 118 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 174 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 218 optimal weight: 5.9990 chunk 94 optimal weight: 0.5980 chunk 219 optimal weight: 0.5980 chunk 178 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 140 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN O 39 GLN O 68 GLN Q 39 GLN S 139 ASN U 68 GLN V 146 ASN W 70 GLN W 139 ASN X 146 ASN b 195 GLN c 263 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.111073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.103092 restraints weight = 48058.163| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 0.37 r_work: 0.2919 rms_B_bonded: 0.69 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 1.27 restraints_weight: 0.2500 r_work: 0.2628 rms_B_bonded: 3.42 restraints_weight: 0.1250 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2595 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2595 r_free = 0.2595 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2595 r_free = 0.2595 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2595 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9049 moved from start: 0.0978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18489 Z= 0.164 Angle : 0.600 6.845 25122 Z= 0.312 Chirality : 0.036 0.152 2746 Planarity : 0.005 0.050 3292 Dihedral : 9.778 75.669 3368 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.23 % Allowed : 5.09 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.54 (0.17), residues: 2250 helix: 2.08 (0.11), residues: 1765 sheet: 1.57 (0.90), residues: 18 loop : 0.24 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 150 TYR 0.013 0.002 TYR b 15 PHE 0.019 0.002 PHE b 168 TRP 0.005 0.001 TRP M 128 HIS 0.004 0.001 HIS W 140 Details of bonding type rmsd covalent geometry : bond 0.00321 (18471) covalent geometry : angle 0.59998 (25122) hydrogen bonds : bond 0.05604 ( 1370) hydrogen bonds : angle 4.93708 ( 4062) Misc. bond : bond 0.00066 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 222 time to evaluate : 1.054 Fit side-chains REVERT: V 79 MET cc_start: 0.9368 (tpp) cc_final: 0.8964 (tpp) REVERT: W 39 GLN cc_start: 0.8662 (tm-30) cc_final: 0.8396 (tm-30) outliers start: 4 outliers final: 2 residues processed: 224 average time/residue: 2.3880 time to fit residues: 577.8481 Evaluate side-chains 223 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 221 time to evaluate : 1.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain b residue 47 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 180 optimal weight: 2.9990 chunk 222 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 chunk 209 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 204 optimal weight: 5.9990 chunk 134 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 133 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN N 146 ASN O 39 GLN O 68 GLN Q 39 GLN R 132 GLN U 68 GLN W 70 GLN b 195 GLN c 263 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.109463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.101690 restraints weight = 45590.407| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 0.35 r_work: 0.2905 rms_B_bonded: 0.66 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 1.20 restraints_weight: 0.2500 r_work: 0.2614 rms_B_bonded: 3.25 restraints_weight: 0.1250 r_work (final): 0.2614 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2571 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2571 r_free = 0.2571 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2571 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9066 moved from start: 0.0953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 18489 Z= 0.249 Angle : 0.718 7.584 25122 Z= 0.374 Chirality : 0.039 0.160 2746 Planarity : 0.006 0.059 3292 Dihedral : 10.063 75.652 3368 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.51 % Allowed : 4.92 % Favored : 94.57 % 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 aren not related in a simple way. whole: 2.04 (0.16), residues: 2250 helix: 1.69 (0.11), residues: 1777 sheet: 2.13 (1.05), residues: 14 loop : 0.15 (0.28), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG b 9 TYR 0.019 0.003 TYR b 15 PHE 0.026 0.003 PHE b 168 TRP 0.008 0.003 TRP M 128 HIS 0.004 0.001 HIS W 140 Details of bonding type rmsd covalent geometry : bond 0.00499 (18471) covalent geometry : angle 0.71784 (25122) hydrogen bonds : bond 0.06608 ( 1370) hydrogen bonds : angle 5.22349 ( 4062) Misc. bond : bond 0.00098 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 231 time to evaluate : 0.860 Fit side-chains REVERT: V 79 MET cc_start: 0.9396 (tpp) cc_final: 0.8963 (tpp) outliers start: 9 outliers final: 6 residues processed: 237 average time/residue: 2.3061 time to fit residues: 592.4698 Evaluate side-chains 232 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 226 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain U residue 162 SER Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain W residue 118 ILE Chi-restraints excluded: chain b residue 47 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 40 optimal weight: 1.9990 chunk 89 optimal weight: 3.9990 chunk 197 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 95 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 97 optimal weight: 2.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN N 146 ASN O 39 GLN O 49 GLN O 68 GLN Q 39 GLN U 68 GLN W 70 GLN X 146 ASN b 195 GLN c 263 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.110127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.101956 restraints weight = 49612.431| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 0.39 r_work: 0.2900 rms_B_bonded: 0.73 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 1.31 restraints_weight: 0.2500 r_work: 0.2606 rms_B_bonded: 3.63 restraints_weight: 0.1250 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9072 moved from start: 0.0972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18489 Z= 0.205 Angle : 0.655 6.907 25122 Z= 0.341 Chirality : 0.038 0.152 2746 Planarity : 0.005 0.052 3292 Dihedral : 9.934 75.683 3368 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.34 % Allowed : 4.98 % Favored : 94.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.19 (0.16), residues: 2250 helix: 1.81 (0.11), residues: 1777 sheet: 1.65 (0.88), residues: 18 loop : 0.17 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG R 150 TYR 0.015 0.002 TYR b 15 PHE 0.022 0.002 PHE b 168 TRP 0.006 0.002 TRP M 128 HIS 0.004 0.001 HIS W 140 Details of bonding type rmsd covalent geometry : bond 0.00405 (18471) covalent geometry : angle 0.65483 (25122) hydrogen bonds : bond 0.06119 ( 1370) hydrogen bonds : angle 5.08973 ( 4062) Misc. bond : bond 0.00082 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 223 time to evaluate : 1.113 Fit side-chains REVERT: V 79 MET cc_start: 0.9399 (tpp) cc_final: 0.8969 (tpp) outliers start: 6 outliers final: 3 residues processed: 226 average time/residue: 2.3729 time to fit residues: 580.9837 Evaluate side-chains 227 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 224 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain b residue 47 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 142 optimal weight: 4.9990 chunk 134 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 80 optimal weight: 4.9990 chunk 193 optimal weight: 0.5980 chunk 73 optimal weight: 2.9990 chunk 217 optimal weight: 3.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN N 146 ASN O 39 GLN O 49 GLN O 68 GLN Q 39 GLN R 132 GLN U 68 GLN W 70 GLN X 146 ASN b 195 GLN c 263 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.109878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.102053 restraints weight = 46366.746| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 0.36 r_work: 0.2907 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.2807 rms_B_bonded: 1.21 restraints_weight: 0.2500 r_work: 0.2608 rms_B_bonded: 3.43 restraints_weight: 0.1250 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9068 moved from start: 0.0965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 18489 Z= 0.216 Angle : 0.676 7.138 25122 Z= 0.351 Chirality : 0.038 0.152 2746 Planarity : 0.005 0.053 3292 Dihedral : 9.982 75.887 3368 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.45 % Allowed : 4.98 % Favored : 94.57 % 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 aren not related in a simple way. whole: 2.14 (0.16), residues: 2250 helix: 1.77 (0.11), residues: 1777 sheet: 1.65 (0.89), residues: 18 loop : 0.15 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG R 150 TYR 0.016 0.002 TYR b 15 PHE 0.023 0.002 PHE b 168 TRP 0.007 0.002 TRP M 128 HIS 0.004 0.001 HIS W 140 Details of bonding type rmsd covalent geometry : bond 0.00431 (18471) covalent geometry : angle 0.67611 (25122) hydrogen bonds : bond 0.06258 ( 1370) hydrogen bonds : angle 5.12490 ( 4062) Misc. bond : bond 0.00081 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 222 time to evaluate : 1.151 Fit side-chains REVERT: V 79 MET cc_start: 0.9401 (tpp) cc_final: 0.8961 (tpp) outliers start: 8 outliers final: 4 residues processed: 227 average time/residue: 2.3264 time to fit residues: 571.5850 Evaluate side-chains 225 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 221 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain U residue 162 SER Chi-restraints excluded: chain W residue 3 THR Chi-restraints excluded: chain b residue 47 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 79 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 141 optimal weight: 2.9990 chunk 158 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN N 146 ASN O 39 GLN O 49 GLN O 68 GLN Q 39 GLN U 68 GLN W 70 GLN X 146 ASN b 155 ASN b 195 GLN c 263 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.110633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.102844 restraints weight = 46231.491| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 0.36 r_work: 0.2921 rms_B_bonded: 0.67 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 1.21 restraints_weight: 0.2500 r_work: 0.2628 rms_B_bonded: 3.37 restraints_weight: 0.1250 r_work (final): 0.2628 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.0994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 18489 Z= 0.179 Angle : 0.625 6.795 25122 Z= 0.325 Chirality : 0.037 0.153 2746 Planarity : 0.005 0.059 3292 Dihedral : 9.867 75.756 3368 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.34 % Allowed : 5.32 % Favored : 94.34 % 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 aren not related in a simple way. whole: 2.36 (0.17), residues: 2250 helix: 1.94 (0.11), residues: 1777 sheet: 1.63 (0.89), residues: 18 loop : 0.17 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 150 TYR 0.014 0.002 TYR b 15 PHE 0.021 0.002 PHE b 168 TRP 0.005 0.002 TRP M 128 HIS 0.004 0.001 HIS W 140 Details of bonding type rmsd covalent geometry : bond 0.00352 (18471) covalent geometry : angle 0.62532 (25122) hydrogen bonds : bond 0.05844 ( 1370) hydrogen bonds : angle 4.99976 ( 4062) Misc. bond : bond 0.00065 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 224 time to evaluate : 1.101 Fit side-chains REVERT: V 79 MET cc_start: 0.9395 (tpp) cc_final: 0.8960 (tpp) outliers start: 6 outliers final: 3 residues processed: 226 average time/residue: 2.3548 time to fit residues: 575.5702 Evaluate side-chains 223 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 220 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain b residue 47 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 62 optimal weight: 4.9990 chunk 218 optimal weight: 7.9990 chunk 162 optimal weight: 0.7980 chunk 171 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 chunk 147 optimal weight: 2.9990 chunk 159 optimal weight: 3.9990 chunk 166 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN N 146 ASN O 39 GLN O 68 GLN Q 39 GLN U 68 GLN W 70 GLN b 195 GLN c 263 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.110899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.102849 restraints weight = 48103.107| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 0.38 r_work: 0.2919 rms_B_bonded: 0.71 restraints_weight: 0.5000 r_work: 0.2818 rms_B_bonded: 1.28 restraints_weight: 0.2500 r_work: 0.2630 rms_B_bonded: 3.45 restraints_weight: 0.1250 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2587 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2587 r_free = 0.2587 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2587 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9053 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18489 Z= 0.171 Angle : 0.617 6.795 25122 Z= 0.320 Chirality : 0.036 0.152 2746 Planarity : 0.005 0.069 3292 Dihedral : 9.841 75.793 3368 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.23 % Allowed : 5.60 % Favored : 94.17 % 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 aren not related in a simple way. whole: 2.44 (0.17), residues: 2250 helix: 2.00 (0.11), residues: 1777 sheet: 1.57 (0.87), residues: 18 loop : 0.18 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG T 150 TYR 0.014 0.002 TYR b 15 PHE 0.020 0.002 PHE b 168 TRP 0.005 0.002 TRP M 128 HIS 0.004 0.001 HIS W 140 Details of bonding type rmsd covalent geometry : bond 0.00335 (18471) covalent geometry : angle 0.61697 (25122) hydrogen bonds : bond 0.05738 ( 1370) hydrogen bonds : angle 4.95912 ( 4062) Misc. bond : bond 0.00060 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 221 time to evaluate : 1.127 Fit side-chains REVERT: V 79 MET cc_start: 0.9391 (tpp) cc_final: 0.8961 (tpp) outliers start: 4 outliers final: 3 residues processed: 223 average time/residue: 2.3271 time to fit residues: 562.8359 Evaluate side-chains 222 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 219 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain b residue 47 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 29 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 172 optimal weight: 1.9990 chunk 191 optimal weight: 4.9990 chunk 70 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 chunk 177 optimal weight: 2.9990 chunk 190 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 85 optimal weight: 3.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN N 146 ASN O 39 GLN O 68 GLN Q 39 GLN U 68 GLN V 146 ASN W 70 GLN X 146 ASN b 195 GLN c 263 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.111031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.103624 restraints weight = 42752.772| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 0.33 r_work: 0.2940 rms_B_bonded: 0.63 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 1.13 restraints_weight: 0.2500 r_work: 0.2644 rms_B_bonded: 3.26 restraints_weight: 0.1250 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18489 Z= 0.168 Angle : 0.615 6.803 25122 Z= 0.319 Chirality : 0.036 0.152 2746 Planarity : 0.005 0.068 3292 Dihedral : 9.824 75.915 3368 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.34 % Allowed : 5.55 % Favored : 94.11 % 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 aren not related in a simple way. whole: 2.47 (0.17), residues: 2250 helix: 2.03 (0.11), residues: 1777 sheet: 1.56 (0.86), residues: 18 loop : 0.17 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 150 TYR 0.013 0.002 TYR b 15 PHE 0.020 0.002 PHE b 168 TRP 0.005 0.002 TRP M 128 HIS 0.004 0.001 HIS W 140 Details of bonding type rmsd covalent geometry : bond 0.00330 (18471) covalent geometry : angle 0.61529 (25122) hydrogen bonds : bond 0.05688 ( 1370) hydrogen bonds : angle 4.94278 ( 4062) Misc. bond : bond 0.00056 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4500 Ramachandran restraints generated. 2250 Oldfield, 0 Emsley, 2250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 222 time to evaluate : 1.162 Fit side-chains REVERT: V 79 MET cc_start: 0.9387 (tpp) cc_final: 0.8960 (tpp) outliers start: 6 outliers final: 3 residues processed: 224 average time/residue: 2.3599 time to fit residues: 571.9258 Evaluate side-chains 224 residues out of total 1761 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 221 time to evaluate : 1.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain R residue 1 MET Chi-restraints excluded: chain b residue 47 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 226 random chunks: chunk 20 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 200 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 154 optimal weight: 0.4980 chunk 45 optimal weight: 1.9990 chunk 94 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 155 optimal weight: 1.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 68 GLN N 146 ASN O 39 GLN O 49 GLN O 68 GLN Q 39 GLN U 68 GLN V 146 ASN W 70 GLN X 146 ASN b 195 GLN c 263 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.111496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.104121 restraints weight = 42872.127| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 0.33 r_work: 0.2950 rms_B_bonded: 0.62 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 1.14 restraints_weight: 0.2500 r_work: 0.2658 rms_B_bonded: 3.17 restraints_weight: 0.1250 r_work (final): 0.2658 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2620 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2620 r_free = 0.2620 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2620 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9033 moved from start: 0.1060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 18489 Z= 0.155 Angle : 0.594 6.847 25122 Z= 0.308 Chirality : 0.036 0.151 2746 Planarity : 0.005 0.066 3292 Dihedral : 9.756 75.844 3368 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.34 % Allowed : 5.66 % Favored : 94.00 % 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 aren not related in a simple way. whole: 2.60 (0.17), residues: 2250 helix: 2.12 (0.11), residues: 1777 sheet: 1.53 (0.86), residues: 18 loop : 0.19 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG R 150 TYR 0.012 0.002 TYR b 15 PHE 0.018 0.002 PHE b 168 TRP 0.004 0.001 TRP S 128 HIS 0.004 0.001 HIS W 140 Details of bonding type rmsd covalent geometry : bond 0.00301 (18471) covalent geometry : angle 0.59389 (25122) hydrogen bonds : bond 0.05488 ( 1370) hydrogen bonds : angle 4.87446 ( 4062) Misc. bond : bond 0.00055 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19276.94 seconds wall clock time: 327 minutes 15.70 seconds (19635.70 seconds total)