Starting phenix.real_space_refine on Thu Aug 6 10:02:57 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qyy_18766/08_2026/8qyy_18766.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qyy_18766/08_2026/8qyy_18766.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qyy_18766/08_2026/8qyy_18766.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qyy_18766/08_2026/8qyy_18766.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qyy_18766/08_2026/8qyy_18766.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qyy_18766/08_2026/8qyy_18766.map" } resolution = 2.56 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= 0.065 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: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 P 15 5.49 5 S 44 5.16 5 C 9497 2.51 5 N 2282 2.21 5 O 2986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14829 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 1969 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 245, 1960 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 8, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 245, 1960 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 8, 'TRANS': 236} bond proxies already assigned to first conformer: 1997 Chain: "B" Number of atoms: 1960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1960 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 8, 'TRANS': 236} Chain: "C" Number of atoms: 1960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1960 Classifications: {'peptide': 245} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 235} Chain: "D" Number of atoms: 1960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1960 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 8, 'TRANS': 236} Chain: "E" Number of atoms: 1967 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 245, 1960 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 8, 'TRANS': 236} Conformer: "B" Number of residues, atoms: 245, 1960 Classifications: {'peptide': 245} Link IDs: {'PTRANS': 8, 'TRANS': 236} bond proxies already assigned to first conformer: 1999 Chain: "F" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1970 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 6, 'TRANS': 239} Chain: "G" Number of atoms: 1970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 246, 1970 Classifications: {'peptide': 246} Link IDs: {'PTRANS': 6, 'TRANS': 239} Chain: "A" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {' CA': 1, 'CDL': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 203 Unusual residues: {' CA': 1, 'CDL': 1, 'PEE': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {' CA': 1, 'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {' CA': 1, 'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {' CA': 1, 'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Classifications: {'water': 51} Link IDs: {None: 50} Chain: "B" Number of atoms: 65 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 65 Classifications: {'water': 65} Link IDs: {None: 64} Chain: "C" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 78 Classifications: {'water': 78} Link IDs: {None: 77} Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 60 Classifications: {'water': 60} Link IDs: {None: 59} Chain: "E" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 52 Classifications: {'water': 52} Link IDs: {None: 51} Chain: "F" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Time building chain proxies: 3.32, per 1000 atoms: 0.22 Number of scatterers: 14829 At special positions: 0 Unit cell: (84.032, 80.704, 197.184, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 S 44 16.00 P 15 15.00 O 2986 8.00 N 2282 7.00 C 9497 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS F 68 " - pdb=" SG CYS F 86 " distance=2.03 Simple disulfide: pdb=" SG CYS F 165 " - pdb=" SG CYS F 240 " distance=2.03 Simple disulfide: pdb=" SG CYS G 68 " - pdb=" SG CYS G 86 " distance=2.03 Simple disulfide: pdb=" SG CYS G 165 " - pdb=" SG CYS G 240 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 598.5 milliseconds 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3276 Finding SS restraints... Secondary structure from input PDB file: 80 helices and 7 sheets defined 76.6% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 1 through 13 Processing helix chain 'A' and resid 17 through 38 Processing helix chain 'A' and resid 38 through 58 Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 77 through 91 Processing helix chain 'A' and resid 112 through 116 Processing helix chain 'A' and resid 118 through 123 Processing helix chain 'A' and resid 128 through 133 Processing helix chain 'A' and resid 134 through 158 Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 165 through 218 Processing helix chain 'A' and resid 223 through 245 removed outlier: 3.667A pdb=" N GLU A 227 " --> pdb=" O GLY A 223 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 12 Processing helix chain 'B' and resid 13 through 14 No H-bonds generated for 'chain 'B' and resid 13 through 14' Processing helix chain 'B' and resid 15 through 16 No H-bonds generated for 'chain 'B' and resid 15 through 16' Processing helix chain 'B' and resid 17 through 38 Processing helix chain 'B' and resid 38 through 57 Processing helix chain 'B' and resid 63 through 75 Processing helix chain 'B' and resid 77 through 90 Processing helix chain 'B' and resid 112 through 116 Processing helix chain 'B' and resid 118 through 123 Processing helix chain 'B' and resid 128 through 133 Processing helix chain 'B' and resid 134 through 158 Processing helix chain 'B' and resid 162 through 164 No H-bonds generated for 'chain 'B' and resid 162 through 164' Processing helix chain 'B' and resid 165 through 220 removed outlier: 3.761A pdb=" N LEU B 219 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYR B 220 " --> pdb=" O LEU B 216 " (cutoff:3.500A) Processing helix chain 'B' and resid 223 through 245 removed outlier: 3.780A pdb=" N THR B 241 " --> pdb=" O ASN B 237 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 13 Processing helix chain 'C' and resid 17 through 38 Processing helix chain 'C' and resid 38 through 59 Processing helix chain 'C' and resid 63 through 75 Processing helix chain 'C' and resid 77 through 90 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'C' and resid 118 through 123 Processing helix chain 'C' and resid 123 through 128 Processing helix chain 'C' and resid 128 through 133 Processing helix chain 'C' and resid 134 through 157 Processing helix chain 'C' and resid 162 through 218 Processing helix chain 'C' and resid 223 through 245 Processing helix chain 'D' and resid 2 through 13 Processing helix chain 'D' and resid 17 through 38 removed outlier: 3.511A pdb=" N VAL D 21 " --> pdb=" O TYR D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 58 Processing helix chain 'D' and resid 63 through 77 removed outlier: 4.278A pdb=" N ARG D 77 " --> pdb=" O SER D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 90 Processing helix chain 'D' and resid 112 through 116 Processing helix chain 'D' and resid 118 through 123 Processing helix chain 'D' and resid 123 through 128 Processing helix chain 'D' and resid 128 through 133 Processing helix chain 'D' and resid 134 through 158 Processing helix chain 'D' and resid 162 through 164 No H-bonds generated for 'chain 'D' and resid 162 through 164' Processing helix chain 'D' and resid 165 through 218 Processing helix chain 'D' and resid 223 through 245 Processing helix chain 'E' and resid 2 through 12 Processing helix chain 'E' and resid 13 through 14 No H-bonds generated for 'chain 'E' and resid 13 through 14' Processing helix chain 'E' and resid 15 through 16 No H-bonds generated for 'chain 'E' and resid 15 through 16' Processing helix chain 'E' and resid 17 through 38 Processing helix chain 'E' and resid 38 through 58 Processing helix chain 'E' and resid 63 through 75 Processing helix chain 'E' and resid 77 through 91 Processing helix chain 'E' and resid 112 through 116 Processing helix chain 'E' and resid 118 through 123 Processing helix chain 'E' and resid 123 through 128 Processing helix chain 'E' and resid 128 through 133 Processing helix chain 'E' and resid 134 through 157 removed outlier: 3.504A pdb=" N HIS E 157 " --> pdb=" O ILE E 153 " (cutoff:3.500A) Processing helix chain 'E' and resid 162 through 218 Processing helix chain 'E' and resid 223 through 245 removed outlier: 3.706A pdb=" N GLU E 227 " --> pdb=" O GLY E 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 79 Processing helix chain 'F' and resid 107 through 127 removed outlier: 3.717A pdb=" N VAL F 118 " --> pdb=" O LEU F 114 " (cutoff:3.500A) Proline residue: F 119 - end of helix Processing helix chain 'F' and resid 127 through 133 Processing helix chain 'F' and resid 148 through 169 Processing helix chain 'F' and resid 172 through 178 removed outlier: 3.884A pdb=" N LYS F 176 " --> pdb=" O SER F 172 " (cutoff:3.500A) Processing helix chain 'F' and resid 179 through 189 Processing helix chain 'F' and resid 203 through 208 removed outlier: 3.505A pdb=" N ARG F 208 " --> pdb=" O LYS F 204 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 47 removed outlier: 3.920A pdb=" N ILE G 22 " --> pdb=" O LYS G 18 " (cutoff:3.500A) Processing helix chain 'G' and resid 47 through 79 Processing helix chain 'G' and resid 107 through 127 removed outlier: 3.636A pdb=" N GLN G 111 " --> pdb=" O ASN G 107 " (cutoff:3.500A) Proline residue: G 119 - end of helix Processing helix chain 'G' and resid 127 through 133 Processing helix chain 'G' and resid 148 through 168 removed outlier: 3.527A pdb=" N ASN G 152 " --> pdb=" O SER G 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 177 removed outlier: 3.587A pdb=" N LYS G 176 " --> pdb=" O SER G 172 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ASN G 177 " --> pdb=" O PRO G 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 172 through 177' Processing helix chain 'G' and resid 179 through 189 Processing helix chain 'G' and resid 224 through 228 Processing sheet with id=AA1, first strand: chain 'A' and resid 92 through 98 removed outlier: 3.630A pdb=" N ARG A 106 " --> pdb=" O GLN A 94 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLU A 96 " --> pdb=" O ILE A 104 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N ILE A 104 " --> pdb=" O GLU A 96 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLU A 98 " --> pdb=" O GLU A 102 " (cutoff:3.500A) removed outlier: 5.036A pdb=" N GLU A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 91 through 98 removed outlier: 3.656A pdb=" N ARG B 106 " --> pdb=" O GLN B 94 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N GLU B 96 " --> pdb=" O ILE B 104 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N ILE B 104 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N GLU B 98 " --> pdb=" O GLU B 102 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N GLU B 102 " --> pdb=" O GLU B 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 91 through 97 removed outlier: 3.647A pdb=" N ARG C 106 " --> pdb=" O GLN C 94 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N GLU C 96 " --> pdb=" O ILE C 104 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N ILE C 104 " --> pdb=" O GLU C 96 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 91 through 98 removed outlier: 3.554A pdb=" N ARG D 106 " --> pdb=" O GLN D 94 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N GLU D 96 " --> pdb=" O ILE D 104 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N ILE D 104 " --> pdb=" O GLU D 96 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU D 98 " --> pdb=" O GLU D 102 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLU D 102 " --> pdb=" O GLU D 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 92 through 98 removed outlier: 3.771A pdb=" N ARG E 106 " --> pdb=" O GLN E 94 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLU E 96 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N ILE E 104 " --> pdb=" O GLU E 96 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLU E 98 " --> pdb=" O GLU E 102 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N GLU E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 82 through 85 removed outlier: 4.923A pdb=" N PHE F 93 " --> pdb=" O VAL F 210 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N VAL F 210 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N GLU F 211 " --> pdb=" O ILE F 139 " (cutoff:3.500A) removed outlier: 5.486A pdb=" N ILE F 139 " --> pdb=" O GLU F 211 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ARG F 213 " --> pdb=" O ILE F 137 " (cutoff:3.500A) removed outlier: 4.912A pdb=" N ILE F 137 " --> pdb=" O ARG F 213 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLN F 215 " --> pdb=" O LYS F 135 " (cutoff:3.500A) removed outlier: 11.823A pdb=" N LYS F 135 " --> pdb=" O PHE F 190 " (cutoff:3.500A) removed outlier: 11.281A pdb=" N ALA F 192 " --> pdb=" O LYS F 135 " (cutoff:3.500A) removed outlier: 9.054A pdb=" N ILE F 137 " --> pdb=" O ALA F 192 " (cutoff:3.500A) removed outlier: 9.382A pdb=" N GLY F 194 " --> pdb=" O ILE F 137 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE F 139 " --> pdb=" O GLY F 194 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N SER F 196 " --> pdb=" O ILE F 139 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLY F 141 " --> pdb=" O SER F 196 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 83 through 85 removed outlier: 3.783A pdb=" N GLU G 211 " --> pdb=" O GLU G 140 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLN G 215 " --> pdb=" O GLN G 136 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N GLN G 136 " --> pdb=" O GLN G 215 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N LEU G 191 " --> pdb=" O LYS G 135 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ILE G 137 " --> pdb=" O LEU G 191 " (cutoff:3.500A) 1023 hydrogen bonds defined for protein. 3018 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: 2.04 Time building geometry restraints manager: 1.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2261 1.31 - 1.44: 3902 1.44 - 1.56: 8420 1.56 - 1.69: 136 1.69 - 1.82: 85 Bond restraints: 14804 Sorted by residual: bond pdb=" C38 PEE B 503 " pdb=" C39 PEE B 503 " ideal model delta sigma weight residual 1.523 1.352 0.171 2.00e-02 2.50e+03 7.28e+01 bond pdb=" C38 PEE C 502 " pdb=" C39 PEE C 502 " ideal model delta sigma weight residual 1.523 1.353 0.170 2.00e-02 2.50e+03 7.19e+01 bond pdb=" C38 PEE D 502 " pdb=" C39 PEE D 502 " ideal model delta sigma weight residual 1.523 1.354 0.169 2.00e-02 2.50e+03 7.16e+01 bond pdb=" C38 PEE E 502 " pdb=" C39 PEE E 502 " ideal model delta sigma weight residual 1.523 1.354 0.169 2.00e-02 2.50e+03 7.15e+01 bond pdb=" C38 PEE B 501 " pdb=" C39 PEE B 501 " ideal model delta sigma weight residual 1.523 1.355 0.168 2.00e-02 2.50e+03 7.07e+01 ... (remaining 14799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.43: 19818 10.43 - 20.85: 19 20.85 - 31.28: 0 31.28 - 41.70: 0 41.70 - 52.13: 10 Bond angle restraints: 19847 Sorted by residual: angle pdb=" C38 PEE B 501 " pdb=" C39 PEE B 501 " pdb=" C40 PEE B 501 " ideal model delta sigma weight residual 112.47 164.60 -52.13 3.00e+00 1.11e-01 3.02e+02 angle pdb=" C38 PEE D 502 " pdb=" C39 PEE D 502 " pdb=" C40 PEE D 502 " ideal model delta sigma weight residual 112.47 164.54 -52.07 3.00e+00 1.11e-01 3.01e+02 angle pdb=" C38 PEE E 502 " pdb=" C39 PEE E 502 " pdb=" C40 PEE E 502 " ideal model delta sigma weight residual 112.47 164.03 -51.56 3.00e+00 1.11e-01 2.95e+02 angle pdb=" C38 PEE C 502 " pdb=" C39 PEE C 502 " pdb=" C40 PEE C 502 " ideal model delta sigma weight residual 112.47 163.86 -51.39 3.00e+00 1.11e-01 2.93e+02 angle pdb=" C38 PEE B 503 " pdb=" C39 PEE B 503 " pdb=" C40 PEE B 503 " ideal model delta sigma weight residual 112.47 163.83 -51.36 3.00e+00 1.11e-01 2.93e+02 ... (remaining 19842 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.69: 8712 33.69 - 67.37: 432 67.37 - 101.06: 30 101.06 - 134.74: 19 134.74 - 168.43: 9 Dihedral angle restraints: 9202 sinusoidal: 4151 harmonic: 5051 Sorted by residual: dihedral pdb=" C4 PEE B 503 " pdb=" O4P PEE B 503 " pdb=" P PEE B 503 " pdb=" O3P PEE B 503 " ideal model delta sinusoidal sigma weight residual 171.78 -19.79 -168.43 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" C3 PEE D 502 " pdb=" C1 PEE D 502 " pdb=" C2 PEE D 502 " pdb=" O3P PEE D 502 " ideal model delta sinusoidal sigma weight residual 62.73 -100.90 163.63 1 3.00e+01 1.11e-03 2.09e+01 dihedral pdb=" O2 PEE D 502 " pdb=" C1 PEE D 502 " pdb=" C2 PEE D 502 " pdb=" O3P PEE D 502 " ideal model delta sinusoidal sigma weight residual 300.04 140.39 159.65 1 3.00e+01 1.11e-03 2.07e+01 ... (remaining 9199 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.115: 2139 0.115 - 0.230: 22 0.230 - 0.346: 0 0.346 - 0.461: 0 0.461 - 0.576: 5 Chirality restraints: 2166 Sorted by residual: chirality pdb=" C2 PEE B 503 " pdb=" C1 PEE B 503 " pdb=" C3 PEE B 503 " pdb=" O2 PEE B 503 " both_signs ideal model delta sigma weight residual False -2.33 -2.90 0.58 2.00e-01 2.50e+01 8.29e+00 chirality pdb=" C2 PEE E 502 " pdb=" C1 PEE E 502 " pdb=" C3 PEE E 502 " pdb=" O2 PEE E 502 " both_signs ideal model delta sigma weight residual False -2.33 -2.87 0.54 2.00e-01 2.50e+01 7.36e+00 chirality pdb=" C2 PEE C 502 " pdb=" C1 PEE C 502 " pdb=" C3 PEE C 502 " pdb=" O2 PEE C 502 " both_signs ideal model delta sigma weight residual False -2.33 -2.87 0.54 2.00e-01 2.50e+01 7.35e+00 ... (remaining 2163 not shown) Planarity restraints: 2431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 54 " -0.264 9.50e-02 1.11e+02 1.19e-01 8.84e+00 pdb=" NE ARG B 54 " 0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 54 " -0.006 2.00e-02 2.50e+03 pdb=" NH1 ARG B 54 " 0.005 2.00e-02 2.50e+03 pdb=" NH2 ARG B 54 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR C 162 " -0.037 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO C 163 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO C 163 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 163 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN E 120 " 0.010 2.00e-02 2.50e+03 1.95e-02 3.79e+00 pdb=" C GLN E 120 " -0.034 2.00e-02 2.50e+03 pdb=" O GLN E 120 " 0.013 2.00e-02 2.50e+03 pdb=" N GLN E 121 " 0.011 2.00e-02 2.50e+03 ... (remaining 2428 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 436 2.70 - 3.25: 14553 3.25 - 3.80: 25142 3.80 - 4.35: 32382 4.35 - 4.90: 54724 Nonbonded interactions: 127237 Sorted by model distance: nonbonded pdb=" OE1 GLU F 95 " pdb=" NE ARG F 98 " model vdw 2.153 3.120 nonbonded pdb=" OE1 GLU A 210 " pdb=" O HOH A 601 " model vdw 2.162 3.040 nonbonded pdb="CA CA E 503 " pdb=" O HOH A 606 " model vdw 2.167 2.510 nonbonded pdb=" N LEU A 80 " pdb=" O HOH A 602 " model vdw 2.167 3.120 nonbonded pdb=" OH TYR E 208 " pdb=" OA4 CDL E 501 " model vdw 2.171 3.040 ... (remaining 127232 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 1 through 174 or resid 176 through 233 or resid 235 throug \ h 245)) selection = (chain 'B' and (resid 1 through 174 or resid 176 through 233 or resid 235 throug \ h 245)) selection = (chain 'C' and (resid 1 through 174 or resid 176 through 233 or resid 235 throug \ h 245)) selection = (chain 'D' and (resid 1 through 174 or resid 176 through 233 or resid 235 throug \ h 245)) selection = (chain 'E' and (resid 1 through 174 or resid 176 through 233 or resid 235 throug \ h 245)) } ncs_group { reference = chain 'F' selection = chain 'G' } 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=0.00 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: 12.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.220 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 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 : 0.009 0.171 14808 Z= 0.460 Angle : 1.435 52.126 19855 Z= 0.541 Chirality : 0.049 0.576 2166 Planarity : 0.005 0.119 2431 Dihedral : 19.818 168.427 5914 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.90 (0.20), residues: 1707 helix: 2.93 (0.14), residues: 1151 sheet: -0.45 (0.78), residues: 50 loop : -0.28 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 54 TYR 0.017 0.002 TYR D 208 PHE 0.016 0.002 PHE G 217 TRP 0.027 0.002 TRP A 196 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00929 / 0.46 (14804) covalent geometry : angle 1.43486 / 0.54 (19847) SS BOND : bond 0.00127 / 0.06 ( 4) SS BOND : angle 0.60682 / 0.28 ( 8) hydrogen bonds : bond 0.11895 / 7.64 ( 1023) hydrogen bonds : angle 4.81168 / 3.57 ( 3018) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 251 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LYS cc_start: 0.8139 (tttm) cc_final: 0.7412 (ttpt) REVERT: B 72 LYS cc_start: 0.8328 (tttp) cc_final: 0.7917 (ttmm) REVERT: B 103 LYS cc_start: 0.7968 (tttm) cc_final: 0.7735 (tttm) REVERT: B 130 GLU cc_start: 0.8501 (mm-30) cc_final: 0.7909 (mp0) REVERT: E 130 GLU cc_start: 0.8273 (mm-30) cc_final: 0.7632 (mp0) REVERT: F 9 LYS cc_start: 0.3275 (mptt) cc_final: 0.2679 (ttpt) REVERT: F 49 ARG cc_start: 0.7655 (mpt-90) cc_final: 0.7083 (tpp-160) REVERT: F 62 GLN cc_start: 0.6865 (mm-40) cc_final: 0.6594 (tt0) REVERT: F 187 ARG cc_start: 0.1674 (mtt-85) cc_final: 0.1295 (mtt180) REVERT: F 238 GLU cc_start: 0.1107 (mp0) cc_final: -0.2045 (mt-10) REVERT: G 13 SER cc_start: 0.4291 (p) cc_final: 0.3895 (t) REVERT: G 220 LYS cc_start: 0.4862 (mmtt) cc_final: 0.4154 (mptt) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 0.6664 time to fit residues: 180.2420 Evaluate side-chains 129 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 129 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.5980 chunk 130 optimal weight: 10.0000 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 GLN A 82 HIS A 156 ASN ** B 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 165 GLN C 85 ASN C 121 GLN D 57 ASN D 171 ASN E 70 HIS E 157 HIS F 158 GLN F 215 GLN G 48 GLN G 51 GLN ** G 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 ASN G 215 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.192967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.123452 restraints weight = 31678.446| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.42 r_work: 0.3368 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3368 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3357 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3357 r_free = 0.3357 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3357 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 14808 Z= 0.158 Angle : 0.560 9.188 19855 Z= 0.285 Chirality : 0.040 0.195 2166 Planarity : 0.004 0.057 2431 Dihedral : 20.212 177.484 2630 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.45 % Allowed : 8.21 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.07 (0.20), residues: 1707 helix: 3.11 (0.14), residues: 1162 sheet: -0.28 (0.78), residues: 50 loop : -0.45 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 90 TYR 0.018 0.002 TYR A 149 PHE 0.017 0.002 PHE F 217 TRP 0.022 0.002 TRP A 196 HIS 0.005 0.001 HIS A 92 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 (14804) covalent geometry : angle 0.55967 / 0.28 (19847) SS BOND : bond 0.00461 / 0.23 ( 4) SS BOND : angle 1.31661 / 0.76 ( 8) hydrogen bonds : bond 0.04966 / 3.24 ( 1023) hydrogen bonds : angle 3.98088 / 2.96 ( 3018) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.6772 (pt0) REVERT: B 72 LYS cc_start: 0.8377 (tttp) cc_final: 0.7858 (ttmt) REVERT: B 130 GLU cc_start: 0.8648 (mm-30) cc_final: 0.7965 (mp0) REVERT: C 61 LYS cc_start: 0.8410 (mmtm) cc_final: 0.7913 (mptt) REVERT: C 175 ARG cc_start: 0.7472 (mmm160) cc_final: 0.6781 (ttm-80) REVERT: D 162 THR cc_start: 0.8017 (OUTLIER) cc_final: 0.7400 (t) REVERT: F 9 LYS cc_start: 0.3477 (mptt) cc_final: 0.2534 (tmtt) REVERT: F 32 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8427 (pp-130) REVERT: F 62 GLN cc_start: 0.6805 (mm-40) cc_final: 0.6518 (tt0) REVERT: F 175 GLN cc_start: 0.2831 (mm-40) cc_final: 0.2010 (tt0) REVERT: F 187 ARG cc_start: 0.1496 (mtt-85) cc_final: 0.0988 (mtt180) REVERT: F 238 GLU cc_start: 0.1369 (mp0) cc_final: -0.2481 (mt-10) REVERT: G 9 LYS cc_start: 0.6537 (tptt) cc_final: 0.6149 (mmmt) REVERT: G 13 SER cc_start: 0.4027 (p) cc_final: 0.3659 (t) REVERT: G 28 MET cc_start: 0.8747 (mmp) cc_final: 0.8402 (mmm) REVERT: G 51 GLN cc_start: 0.6545 (mt0) cc_final: 0.6212 (mt0) REVERT: G 220 LYS cc_start: 0.4896 (mmtt) cc_final: 0.4069 (mptt) outliers start: 22 outliers final: 8 residues processed: 159 average time/residue: 0.6319 time to fit residues: 109.0656 Evaluate side-chains 134 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain F residue 32 MET Chi-restraints excluded: chain F residue 244 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 162 optimal weight: 4.9990 chunk 44 optimal weight: 0.8980 chunk 21 optimal weight: 0.3980 chunk 51 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 126 optimal weight: 6.9990 chunk 138 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 112 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 70 HIS D 120 GLN F 87 HIS G 79 ASN ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.188652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.121911 restraints weight = 20620.559| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 1.91 r_work: 0.3368 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3225 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3225 r_free = 0.3225 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3225 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 14808 Z= 0.196 Angle : 0.554 7.991 19855 Z= 0.285 Chirality : 0.041 0.180 2166 Planarity : 0.004 0.058 2431 Dihedral : 18.687 178.322 2630 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.91 % Allowed : 9.99 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.92 (0.20), residues: 1707 helix: 2.97 (0.14), residues: 1166 sheet: -0.32 (0.80), residues: 50 loop : -0.48 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 159 TYR 0.017 0.002 TYR A 208 PHE 0.018 0.002 PHE A 181 TRP 0.021 0.002 TRP A 196 HIS 0.006 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00465 / 0.20 (14804) covalent geometry : angle 0.55358 / 0.29 (19847) SS BOND : bond 0.00197 / 0.10 ( 4) SS BOND : angle 0.52480 / 0.28 ( 8) hydrogen bonds : bond 0.05131 / 3.37 ( 1023) hydrogen bonds : angle 3.96675 / 2.95 ( 3018) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 133 time to evaluate : 0.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7186 (OUTLIER) cc_final: 0.6909 (pt0) REVERT: A 120 GLN cc_start: 0.8776 (OUTLIER) cc_final: 0.8479 (tm-30) REVERT: B 61 LYS cc_start: 0.8234 (mmtt) cc_final: 0.7905 (mmpt) REVERT: B 72 LYS cc_start: 0.8460 (tttp) cc_final: 0.7870 (ttmp) REVERT: B 130 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8021 (mp0) REVERT: C 61 LYS cc_start: 0.8542 (mmtm) cc_final: 0.8074 (mppt) REVERT: C 175 ARG cc_start: 0.7689 (mmm160) cc_final: 0.6879 (ttm-80) REVERT: D 102 GLU cc_start: 0.6300 (tp30) cc_final: 0.6061 (tp30) REVERT: E 61 LYS cc_start: 0.8242 (mmtm) cc_final: 0.7724 (mppt) REVERT: F 9 LYS cc_start: 0.3442 (mptt) cc_final: 0.2603 (ttpt) REVERT: F 62 GLN cc_start: 0.6800 (mm-40) cc_final: 0.6467 (tt0) REVERT: F 132 LYS cc_start: 0.5191 (mtpt) cc_final: 0.4420 (ptmt) REVERT: F 175 GLN cc_start: 0.2818 (mm-40) cc_final: 0.1921 (tt0) REVERT: F 187 ARG cc_start: 0.1556 (mtt-85) cc_final: 0.1039 (mtt180) REVERT: F 238 GLU cc_start: 0.1309 (mp0) cc_final: -0.2620 (mt-10) REVERT: G 9 LYS cc_start: 0.6709 (tptt) cc_final: 0.6347 (mtpt) REVERT: G 13 SER cc_start: 0.4488 (p) cc_final: 0.3995 (t) REVERT: G 220 LYS cc_start: 0.5218 (mmtt) cc_final: 0.4335 (mptt) outliers start: 29 outliers final: 9 residues processed: 151 average time/residue: 0.6013 time to fit residues: 98.4798 Evaluate side-chains 134 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain F residue 49 ARG Chi-restraints excluded: chain G residue 39 MET Chi-restraints excluded: chain G residue 54 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 51 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 66 optimal weight: 0.6980 chunk 15 optimal weight: 0.9980 chunk 118 optimal weight: 0.5980 chunk 167 optimal weight: 0.9990 chunk 41 optimal weight: 0.7980 chunk 59 optimal weight: 0.0980 chunk 112 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 83 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 51 GLN ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.191408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.123961 restraints weight = 23561.990| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.10 r_work: 0.3374 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work: 0.3239 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 14808 Z= 0.120 Angle : 0.470 8.892 19855 Z= 0.244 Chirality : 0.037 0.168 2166 Planarity : 0.004 0.058 2431 Dihedral : 17.478 179.169 2630 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.58 % Allowed : 11.24 % Favored : 87.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.22 (0.20), residues: 1707 helix: 3.24 (0.14), residues: 1165 sheet: -0.04 (0.73), residues: 60 loop : -0.48 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 159 TYR 0.013 0.001 TYR E 208 PHE 0.017 0.001 PHE E 189 TRP 0.014 0.001 TRP D 84 HIS 0.003 0.000 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.12 (14804) covalent geometry : angle 0.47042 / 0.24 (19847) SS BOND : bond 0.00142 / 0.07 ( 4) SS BOND : angle 0.35424 / 0.19 ( 8) hydrogen bonds : bond 0.04331 / 2.85 ( 1023) hydrogen bonds : angle 3.72366 / 2.78 ( 3018) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6904 (pt0) REVERT: A 120 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8532 (tm-30) REVERT: B 61 LYS cc_start: 0.8238 (mmtt) cc_final: 0.7934 (mmpt) REVERT: B 72 LYS cc_start: 0.8463 (tttp) cc_final: 0.7898 (ttmp) REVERT: B 130 GLU cc_start: 0.8778 (mm-30) cc_final: 0.8017 (mp0) REVERT: C 61 LYS cc_start: 0.8486 (mmtm) cc_final: 0.7996 (mppt) REVERT: C 175 ARG cc_start: 0.7678 (mmm160) cc_final: 0.6897 (ttm-80) REVERT: D 102 GLU cc_start: 0.6323 (tp30) cc_final: 0.6079 (tp30) REVERT: E 61 LYS cc_start: 0.8250 (mmtm) cc_final: 0.7732 (mppt) REVERT: F 9 LYS cc_start: 0.3444 (mptt) cc_final: 0.2580 (ttpt) REVERT: F 33 VAL cc_start: 0.8614 (OUTLIER) cc_final: 0.8220 (t) REVERT: F 62 GLN cc_start: 0.6903 (mm-40) cc_final: 0.6596 (tt0) REVERT: F 175 GLN cc_start: 0.2850 (mm-40) cc_final: 0.1964 (tt0) REVERT: F 187 ARG cc_start: 0.1750 (mtt-85) cc_final: 0.1499 (mtt180) REVERT: F 238 GLU cc_start: 0.1176 (mp0) cc_final: -0.2313 (mt-10) REVERT: G 9 LYS cc_start: 0.6647 (tptt) cc_final: 0.6311 (mtpt) REVERT: G 13 SER cc_start: 0.4506 (p) cc_final: 0.3990 (t) REVERT: G 220 LYS cc_start: 0.4949 (mmtt) cc_final: 0.4043 (mptt) outliers start: 24 outliers final: 8 residues processed: 156 average time/residue: 0.5983 time to fit residues: 101.6650 Evaluate side-chains 137 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 126 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 49 ARG Chi-restraints excluded: chain G residue 54 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 143 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 86 optimal weight: 0.6980 chunk 164 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 51 GLN ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.190872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.121323 restraints weight = 31864.309| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.40 r_work: 0.3345 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3345 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 14808 Z= 0.135 Angle : 0.489 9.322 19855 Z= 0.251 Chirality : 0.038 0.241 2166 Planarity : 0.004 0.057 2431 Dihedral : 16.972 177.287 2630 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.84 % Allowed : 11.83 % Favored : 86.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.21 (0.20), residues: 1707 helix: 3.22 (0.14), residues: 1165 sheet: -0.08 (0.74), residues: 60 loop : -0.47 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 159 TYR 0.014 0.001 TYR E 208 PHE 0.017 0.001 PHE E 189 TRP 0.013 0.002 TRP D 84 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (14804) covalent geometry : angle 0.48860 / 0.25 (19847) SS BOND : bond 0.00098 / 0.05 ( 4) SS BOND : angle 0.31651 / 0.15 ( 8) hydrogen bonds : bond 0.04408 / 2.90 ( 1023) hydrogen bonds : angle 3.74305 / 2.79 ( 3018) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 134 time to evaluate : 0.568 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7075 (OUTLIER) cc_final: 0.6830 (pt0) REVERT: A 120 GLN cc_start: 0.8791 (OUTLIER) cc_final: 0.8460 (tm-30) REVERT: B 51 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7900 (tttm) REVERT: B 61 LYS cc_start: 0.8218 (mmtt) cc_final: 0.7930 (mmpt) REVERT: B 72 LYS cc_start: 0.8426 (tttp) cc_final: 0.7828 (ttmp) REVERT: B 130 GLU cc_start: 0.8625 (mm-30) cc_final: 0.7941 (mp0) REVERT: C 61 LYS cc_start: 0.8431 (mmtm) cc_final: 0.8011 (mtmt) REVERT: C 175 ARG cc_start: 0.7499 (mmm160) cc_final: 0.6752 (ttm-80) REVERT: E 61 LYS cc_start: 0.8252 (mmtm) cc_final: 0.7718 (mppt) REVERT: F 9 LYS cc_start: 0.3273 (mptt) cc_final: 0.2461 (tttm) REVERT: F 33 VAL cc_start: 0.8547 (OUTLIER) cc_final: 0.8174 (t) REVERT: F 62 GLN cc_start: 0.6906 (mm-40) cc_final: 0.6617 (tt0) REVERT: F 175 GLN cc_start: 0.2820 (mm-40) cc_final: 0.2516 (tt0) REVERT: G 9 LYS cc_start: 0.6661 (tptt) cc_final: 0.6314 (mtpt) REVERT: G 13 SER cc_start: 0.4592 (p) cc_final: 0.4111 (t) REVERT: G 220 LYS cc_start: 0.4869 (mmtt) cc_final: 0.4058 (mptt) outliers start: 28 outliers final: 12 residues processed: 148 average time/residue: 0.6071 time to fit residues: 97.8002 Evaluate side-chains 140 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 49 ARG Chi-restraints excluded: chain G residue 54 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 60 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 136 optimal weight: 9.9990 chunk 41 optimal weight: 0.6980 chunk 62 optimal weight: 0.5980 chunk 137 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 147 optimal weight: 0.7980 chunk 150 optimal weight: 5.9990 chunk 79 optimal weight: 0.9980 chunk 164 optimal weight: 7.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 51 GLN ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.189787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.121154 restraints weight = 27578.140| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.26 r_work: 0.3340 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 14808 Z= 0.149 Angle : 0.501 9.206 19855 Z= 0.257 Chirality : 0.039 0.182 2166 Planarity : 0.004 0.056 2431 Dihedral : 16.471 173.111 2630 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.64 % Allowed : 12.29 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.23 (0.20), residues: 1707 helix: 3.21 (0.14), residues: 1160 sheet: -0.61 (0.75), residues: 57 loop : -0.28 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 49 TYR 0.015 0.001 TYR E 208 PHE 0.017 0.002 PHE E 189 TRP 0.015 0.002 TRP A 196 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.15 (14804) covalent geometry : angle 0.50070 / 0.26 (19847) SS BOND : bond 0.00174 / 0.09 ( 4) SS BOND : angle 0.42456 / 0.22 ( 8) hydrogen bonds : bond 0.04521 / 2.98 ( 1023) hydrogen bonds : angle 3.77846 / 2.82 ( 3018) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 123 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7216 (OUTLIER) cc_final: 0.6920 (pm20) REVERT: A 120 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.8472 (tm-30) REVERT: B 61 LYS cc_start: 0.8300 (mmtt) cc_final: 0.8015 (mmpt) REVERT: B 72 LYS cc_start: 0.8433 (tttp) cc_final: 0.7844 (ttmp) REVERT: B 130 GLU cc_start: 0.8610 (mm-30) cc_final: 0.7889 (mp0) REVERT: C 61 LYS cc_start: 0.8462 (mmtm) cc_final: 0.8051 (mtmt) REVERT: C 175 ARG cc_start: 0.7559 (mmm160) cc_final: 0.6800 (ttm-80) REVERT: E 61 LYS cc_start: 0.8269 (mmtm) cc_final: 0.7710 (mppt) REVERT: F 9 LYS cc_start: 0.3375 (mptt) cc_final: 0.2529 (ttpt) REVERT: F 33 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8201 (t) REVERT: F 62 GLN cc_start: 0.6902 (mm-40) cc_final: 0.6597 (tt0) REVERT: F 175 GLN cc_start: 0.2677 (mm-40) cc_final: 0.2375 (tt0) REVERT: G 9 LYS cc_start: 0.6660 (tptt) cc_final: 0.6292 (mtpt) REVERT: G 220 LYS cc_start: 0.4808 (mmtt) cc_final: 0.4072 (mptt) outliers start: 25 outliers final: 13 residues processed: 138 average time/residue: 0.5644 time to fit residues: 84.6736 Evaluate side-chains 138 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 49 ARG Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain G residue 54 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 30 optimal weight: 3.9990 chunk 83 optimal weight: 0.9990 chunk 123 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 131 optimal weight: 8.9990 chunk 126 optimal weight: 1.9990 chunk 154 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 159 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 156 ASN F 136 GLN ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 175 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.188555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.122217 restraints weight = 22975.239| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.99 r_work: 0.3365 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3214 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3214 r_free = 0.3214 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3214 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 14808 Z= 0.151 Angle : 0.502 9.323 19855 Z= 0.257 Chirality : 0.039 0.194 2166 Planarity : 0.004 0.056 2431 Dihedral : 16.151 168.179 2630 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.45 % Allowed : 12.94 % Favored : 85.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.19 (0.20), residues: 1707 helix: 3.19 (0.14), residues: 1159 sheet: -0.46 (0.75), residues: 57 loop : -0.33 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 49 TYR 0.016 0.001 TYR E 208 PHE 0.021 0.001 PHE E 189 TRP 0.017 0.002 TRP A 196 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (14804) covalent geometry : angle 0.50224 / 0.26 (19847) SS BOND : bond 0.00156 / 0.08 ( 4) SS BOND : angle 0.35615 / 0.17 ( 8) hydrogen bonds : bond 0.04501 / 2.97 ( 1023) hydrogen bonds : angle 3.79618 / 2.83 ( 3018) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7276 (OUTLIER) cc_final: 0.6974 (pm20) REVERT: A 120 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.8557 (tm-30) REVERT: B 51 LYS cc_start: 0.8246 (OUTLIER) cc_final: 0.7994 (tttm) REVERT: B 61 LYS cc_start: 0.8388 (mmtt) cc_final: 0.8029 (mmpt) REVERT: B 72 LYS cc_start: 0.8517 (tttp) cc_final: 0.7866 (ttmm) REVERT: B 130 GLU cc_start: 0.8743 (mm-30) cc_final: 0.7928 (mp0) REVERT: C 61 LYS cc_start: 0.8554 (mmtm) cc_final: 0.8083 (mtmt) REVERT: C 175 ARG cc_start: 0.7699 (mmm160) cc_final: 0.6913 (ttm-80) REVERT: E 61 LYS cc_start: 0.8301 (mmtm) cc_final: 0.7692 (mppt) REVERT: F 33 VAL cc_start: 0.8638 (OUTLIER) cc_final: 0.8289 (t) REVERT: F 62 GLN cc_start: 0.6974 (mm-40) cc_final: 0.6760 (tt0) REVERT: F 66 ARG cc_start: 0.6190 (ptm-80) cc_final: 0.5961 (ptm160) REVERT: F 175 GLN cc_start: 0.2768 (mm-40) cc_final: 0.2493 (tt0) REVERT: G 28 MET cc_start: 0.8777 (mmp) cc_final: 0.8505 (mmm) REVERT: G 220 LYS cc_start: 0.4924 (mmtt) cc_final: 0.4123 (mptt) outliers start: 22 outliers final: 13 residues processed: 141 average time/residue: 0.5846 time to fit residues: 89.7298 Evaluate side-chains 137 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 120 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 49 ARG Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain G residue 54 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 77 optimal weight: 0.0170 chunk 75 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 154 optimal weight: 7.9990 chunk 158 optimal weight: 6.9990 chunk 29 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 139 optimal weight: 10.0000 chunk 137 optimal weight: 6.9990 chunk 96 optimal weight: 0.6980 chunk 41 optimal weight: 0.5980 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 156 ASN ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4284 r_free = 0.4284 target = 0.189777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.123739 restraints weight = 23248.237| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 2.02 r_work: 0.3383 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 14808 Z= 0.125 Angle : 0.476 9.459 19855 Z= 0.244 Chirality : 0.038 0.186 2166 Planarity : 0.004 0.056 2431 Dihedral : 15.714 166.764 2630 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.51 % Allowed : 13.07 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.31 (0.20), residues: 1707 helix: 3.29 (0.14), residues: 1162 sheet: -0.41 (0.76), residues: 57 loop : -0.32 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 49 TYR 0.014 0.001 TYR E 208 PHE 0.018 0.001 PHE E 189 TRP 0.014 0.002 TRP A 196 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.13 (14804) covalent geometry : angle 0.47639 / 0.24 (19847) SS BOND : bond 0.00113 / 0.06 ( 4) SS BOND : angle 0.32984 / 0.16 ( 8) hydrogen bonds : bond 0.04218 / 2.78 ( 1023) hydrogen bonds : angle 3.70449 / 2.76 ( 3018) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7244 (OUTLIER) cc_final: 0.6943 (pm20) REVERT: A 120 GLN cc_start: 0.8863 (OUTLIER) cc_final: 0.8541 (tm-30) REVERT: B 61 LYS cc_start: 0.8373 (mmtt) cc_final: 0.8025 (mmpt) REVERT: B 72 LYS cc_start: 0.8468 (tttp) cc_final: 0.7825 (ttmm) REVERT: B 130 GLU cc_start: 0.8742 (mm-30) cc_final: 0.7975 (mp0) REVERT: C 61 LYS cc_start: 0.8493 (mmtm) cc_final: 0.8024 (mtmt) REVERT: C 175 ARG cc_start: 0.7709 (mmm160) cc_final: 0.6873 (ttm-80) REVERT: E 61 LYS cc_start: 0.8220 (mmtm) cc_final: 0.7633 (mppt) REVERT: F 33 VAL cc_start: 0.8623 (OUTLIER) cc_final: 0.8251 (t) REVERT: F 62 GLN cc_start: 0.6939 (mm-40) cc_final: 0.6681 (tt0) REVERT: F 175 GLN cc_start: 0.2731 (mm-40) cc_final: 0.2474 (tt0) REVERT: G 220 LYS cc_start: 0.4754 (mmtt) cc_final: 0.4013 (mptt) outliers start: 23 outliers final: 15 residues processed: 141 average time/residue: 0.5448 time to fit residues: 84.0193 Evaluate side-chains 139 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 49 ARG Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain G residue 54 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 57 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 67 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 161 optimal weight: 0.0770 chunk 139 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 118 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 111 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 = 0.4287 r_free = 0.4287 target = 0.190236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.122080 restraints weight = 30825.517| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.30 r_work: 0.3364 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3364 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3364 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14808 Z= 0.119 Angle : 0.481 12.852 19855 Z= 0.244 Chirality : 0.038 0.189 2166 Planarity : 0.004 0.056 2431 Dihedral : 15.424 172.324 2630 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.45 % Allowed : 13.67 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.30 (0.20), residues: 1707 helix: 3.28 (0.14), residues: 1168 sheet: -0.30 (0.75), residues: 57 loop : -0.38 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 77 TYR 0.013 0.001 TYR E 208 PHE 0.019 0.001 PHE E 189 TRP 0.015 0.002 TRP A 196 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.12 (14804) covalent geometry : angle 0.48060 / 0.24 (19847) SS BOND : bond 0.00095 / 0.05 ( 4) SS BOND : angle 0.33589 / 0.16 ( 8) hydrogen bonds : bond 0.04127 / 2.73 ( 1023) hydrogen bonds : angle 3.68980 / 2.75 ( 3018) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 131 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7176 (OUTLIER) cc_final: 0.6921 (pm20) REVERT: A 120 GLN cc_start: 0.8751 (OUTLIER) cc_final: 0.8480 (tm-30) REVERT: B 61 LYS cc_start: 0.8327 (mmtt) cc_final: 0.8013 (mmpt) REVERT: B 72 LYS cc_start: 0.8390 (tttp) cc_final: 0.7802 (ttmp) REVERT: B 130 GLU cc_start: 0.8585 (mm-30) cc_final: 0.7924 (mp0) REVERT: C 61 LYS cc_start: 0.8350 (mmtm) cc_final: 0.7950 (mtmt) REVERT: C 121 GLN cc_start: 0.8989 (OUTLIER) cc_final: 0.7876 (mt0) REVERT: C 175 ARG cc_start: 0.7512 (mmm160) cc_final: 0.6711 (ttm-80) REVERT: E 61 LYS cc_start: 0.8222 (mmtm) cc_final: 0.7640 (mppt) REVERT: F 33 VAL cc_start: 0.8537 (OUTLIER) cc_final: 0.8189 (t) REVERT: F 62 GLN cc_start: 0.6921 (mm-40) cc_final: 0.6669 (tt0) REVERT: F 175 GLN cc_start: 0.2881 (mm-40) cc_final: 0.2624 (tt0) REVERT: G 28 MET cc_start: 0.8696 (mmp) cc_final: 0.8385 (mmm) REVERT: G 220 LYS cc_start: 0.4646 (mmtt) cc_final: 0.4000 (mptt) outliers start: 22 outliers final: 16 residues processed: 144 average time/residue: 0.5945 time to fit residues: 93.7160 Evaluate side-chains 142 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 122 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 ILE Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 103 LYS Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 49 ARG Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain G residue 54 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 59 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 44 optimal weight: 0.5980 chunk 65 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 145 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 53 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 157 HIS ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.189760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.122537 restraints weight = 28249.521| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.21 r_work: 0.3371 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3371 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 14808 Z= 0.124 Angle : 0.487 11.682 19855 Z= 0.248 Chirality : 0.038 0.190 2166 Planarity : 0.004 0.056 2431 Dihedral : 15.333 171.514 2630 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.38 % Allowed : 14.06 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.29 (0.20), residues: 1707 helix: 3.27 (0.14), residues: 1168 sheet: -0.20 (0.76), residues: 57 loop : -0.40 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 106 TYR 0.013 0.001 TYR E 208 PHE 0.020 0.001 PHE E 189 TRP 0.017 0.002 TRP A 196 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (14804) covalent geometry : angle 0.48505 / 0.25 (19847) SS BOND : bond 0.00183 / 0.09 ( 4) SS BOND : angle 1.98900 / 0.77 ( 8) hydrogen bonds : bond 0.04150 / 2.74 ( 1023) hydrogen bonds : angle 3.70487 / 2.76 ( 3018) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3414 Ramachandran restraints generated. 1707 Oldfield, 0 Emsley, 1707 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.543 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7201 (OUTLIER) cc_final: 0.6944 (pm20) REVERT: A 120 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8473 (tm-30) REVERT: B 61 LYS cc_start: 0.8344 (mmtt) cc_final: 0.8041 (mmpt) REVERT: B 72 LYS cc_start: 0.8404 (tttp) cc_final: 0.7815 (ttmp) REVERT: B 130 GLU cc_start: 0.8591 (mm-30) cc_final: 0.7929 (mp0) REVERT: C 61 LYS cc_start: 0.8352 (mmtm) cc_final: 0.7912 (mppt) REVERT: C 121 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.7887 (mt0) REVERT: C 175 ARG cc_start: 0.7513 (mmm160) cc_final: 0.6706 (ttm-80) REVERT: E 61 LYS cc_start: 0.8228 (mmtm) cc_final: 0.7647 (mppt) REVERT: F 2 PHE cc_start: 0.5085 (m-80) cc_final: 0.3526 (t80) REVERT: F 33 VAL cc_start: 0.8567 (OUTLIER) cc_final: 0.8204 (t) REVERT: F 62 GLN cc_start: 0.6930 (mm-40) cc_final: 0.6667 (tt0) REVERT: F 175 GLN cc_start: 0.2764 (mm-40) cc_final: 0.2541 (tt0) REVERT: G 28 MET cc_start: 0.8704 (mmp) cc_final: 0.8401 (mmm) REVERT: G 220 LYS cc_start: 0.4660 (mmtt) cc_final: 0.4038 (mptt) outliers start: 21 outliers final: 14 residues processed: 136 average time/residue: 0.6180 time to fit residues: 91.9171 Evaluate side-chains 138 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain A residue 168 SER Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 200 LEU Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 49 ARG Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain G residue 54 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 132 optimal weight: 6.9990 chunk 113 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 88 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 55 optimal weight: 0.1980 chunk 108 optimal weight: 0.0980 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 157 HIS ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.190442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.122676 restraints weight = 32692.550| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.36 r_work: 0.3360 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3367 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3367 r_free = 0.3367 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3367 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 14808 Z= 0.113 Angle : 0.478 11.540 19855 Z= 0.244 Chirality : 0.037 0.186 2166 Planarity : 0.004 0.057 2431 Dihedral : 15.099 170.650 2630 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.31 % Allowed : 14.13 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.35 (0.20), residues: 1707 helix: 3.32 (0.14), residues: 1168 sheet: -0.16 (0.77), residues: 57 loop : -0.40 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 49 TYR 0.015 0.001 TYR D 149 PHE 0.021 0.001 PHE E 189 TRP 0.016 0.002 TRP A 196 HIS 0.003 0.000 HIS C 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 (14804) covalent geometry : angle 0.47731 / 0.24 (19847) SS BOND : bond 0.00078 / 0.04 ( 4) SS BOND : angle 1.53568 / 0.58 ( 8) hydrogen bonds : bond 0.03985 / 2.64 ( 1023) hydrogen bonds : angle 3.65567 / 2.72 ( 3018) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5453.07 seconds wall clock time: 93 minutes 22.26 seconds (5602.26 seconds total)