Starting phenix.real_space_refine on Thu Sep 18 06:31:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qyy_18766/09_2025/8qyy_18766.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qyy_18766/09_2025/8qyy_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_18766/09_2025/8qyy_18766.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qyy_18766/09_2025/8qyy_18766.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qyy_18766/09_2025/8qyy_18766.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qyy_18766/09_2025/8qyy_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-2.0-5805/lib/python3.9/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: 4.28, per 1000 atoms: 0.29 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: 1.18 Conformation dependent library (CDL) restraints added in 795.0 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.45 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: 2.73 Time building geometry restraints manager: 1.56 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: 8752 33.69 - 67.37: 310 67.37 - 101.06: 32 101.06 - 134.74: 19 134.74 - 168.43: 9 Dihedral angle restraints: 9122 sinusoidal: 4071 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 9119 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: 10.180 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: 0.240 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.840 Find NCS groups from input model: 0.340 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:6.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 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= 0.425 Angle : 1.399 52.126 19855 Z= 0.530 Chirality : 0.049 0.576 2166 Planarity : 0.005 0.119 2431 Dihedral : 18.644 168.427 5834 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 aren 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 covalent geometry : bond 0.00859 (14804) covalent geometry : angle 1.39923 (19847) SS BOND : bond 0.00127 ( 4) SS BOND : angle 0.60682 ( 8) hydrogen bonds : bond 0.11895 ( 1023) hydrogen bonds : angle 4.81168 ( 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 : 0.589 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: 0.8827 time to fit residues: 237.4687 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 : 0.597 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 G 48 GLN G 51 GLN ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 199 ASN G 215 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.192194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.123189 restraints weight = 31850.298| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.38 r_work: 0.3372 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3359 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3359 r_free = 0.3359 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 = 0.3359 r_free = 0.3359 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3359 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8080 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 14808 Z= 0.157 Angle : 0.569 7.986 19855 Z= 0.288 Chirality : 0.041 0.182 2166 Planarity : 0.004 0.058 2431 Dihedral : 18.824 176.130 2550 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.45 % Allowed : 8.54 % Favored : 90.01 % 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 aren not related in a simple way. whole: 3.02 (0.20), residues: 1707 helix: 3.05 (0.14), residues: 1165 sheet: -0.28 (0.80), residues: 50 loop : -0.43 (0.29), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 60 TYR 0.018 0.002 TYR A 149 PHE 0.018 0.002 PHE F 217 TRP 0.023 0.002 TRP A 196 HIS 0.006 0.001 HIS A 92 Details of bonding type rmsd covalent geometry : bond 0.00358 (14804) covalent geometry : angle 0.56818 (19847) SS BOND : bond 0.00407 ( 4) SS BOND : angle 1.16001 ( 8) hydrogen bonds : bond 0.04890 ( 1023) hydrogen bonds : angle 3.96028 ( 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 165 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 143 time to evaluate : 0.597 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7042 (OUTLIER) cc_final: 0.6624 (pt0) REVERT: B 72 LYS cc_start: 0.8357 (tttp) cc_final: 0.7831 (ttmt) REVERT: B 130 GLU cc_start: 0.8637 (mm-30) cc_final: 0.7943 (mp0) REVERT: C 61 LYS cc_start: 0.8415 (mmtm) cc_final: 0.7885 (mptt) REVERT: C 175 ARG cc_start: 0.7458 (mmm160) cc_final: 0.6769 (ttm-80) REVERT: D 162 THR cc_start: 0.8007 (OUTLIER) cc_final: 0.7398 (t) REVERT: F 9 LYS cc_start: 0.3455 (mptt) cc_final: 0.2513 (tmtt) REVERT: F 32 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8434 (pp-130) REVERT: F 62 GLN cc_start: 0.6820 (mm-40) cc_final: 0.6540 (tt0) REVERT: F 175 GLN cc_start: 0.2810 (mm-40) cc_final: 0.1949 (tt0) REVERT: F 187 ARG cc_start: 0.1495 (mtt-85) cc_final: 0.1119 (mtt180) REVERT: F 238 GLU cc_start: 0.1380 (mp0) cc_final: -0.2503 (mt-10) REVERT: G 9 LYS cc_start: 0.6525 (tptt) cc_final: 0.6141 (mmmt) REVERT: G 13 SER cc_start: 0.3959 (p) cc_final: 0.3589 (t) REVERT: G 28 MET cc_start: 0.8726 (mmp) cc_final: 0.8388 (mmm) REVERT: G 51 GLN cc_start: 0.6572 (mt0) cc_final: 0.6236 (mt0) REVERT: G 220 LYS cc_start: 0.4880 (mmtt) cc_final: 0.4047 (mptt) outliers start: 22 outliers final: 7 residues processed: 157 average time/residue: 0.7968 time to fit residues: 135.3785 Evaluate side-chains 131 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 121 time to evaluate : 0.584 ------------------------------------------------------------------------------- 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 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: 7.9990 chunk 44 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 132 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 138 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 112 optimal weight: 2.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4292 r_free = 0.4292 target = 0.190209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.123682 restraints weight = 20568.465| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.92 r_work: 0.3400 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14808 Z= 0.156 Angle : 0.516 7.793 19855 Z= 0.266 Chirality : 0.039 0.173 2166 Planarity : 0.004 0.058 2431 Dihedral : 17.901 178.982 2550 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.64 % Allowed : 10.32 % Favored : 88.04 % 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 aren not related in a simple way. whole: 3.09 (0.20), residues: 1707 helix: 3.12 (0.14), residues: 1167 sheet: -0.37 (0.80), residues: 50 loop : -0.45 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 159 TYR 0.013 0.001 TYR A 208 PHE 0.017 0.002 PHE E 189 TRP 0.019 0.002 TRP A 196 HIS 0.005 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00363 (14804) covalent geometry : angle 0.51601 (19847) SS BOND : bond 0.00181 ( 4) SS BOND : angle 0.52930 ( 8) hydrogen bonds : bond 0.04760 ( 1023) hydrogen bonds : angle 3.83276 ( 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 158 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 133 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6867 (pt0) REVERT: A 120 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8485 (tm-30) REVERT: B 61 LYS cc_start: 0.8182 (mmtt) cc_final: 0.7896 (mmpt) REVERT: B 72 LYS cc_start: 0.8438 (tttp) cc_final: 0.7867 (ttmp) REVERT: B 130 GLU cc_start: 0.8749 (mm-30) cc_final: 0.8034 (mp0) REVERT: C 61 LYS cc_start: 0.8469 (mmtm) cc_final: 0.8015 (mppt) REVERT: C 175 ARG cc_start: 0.7661 (mmm160) cc_final: 0.6872 (ttm-80) REVERT: D 102 GLU cc_start: 0.6355 (tp30) cc_final: 0.6122 (tp30) REVERT: E 61 LYS cc_start: 0.8202 (mmtm) cc_final: 0.7713 (mppt) REVERT: F 9 LYS cc_start: 0.3457 (mptt) cc_final: 0.2616 (ttpt) REVERT: F 62 GLN cc_start: 0.6896 (mm-40) cc_final: 0.6593 (tt0) REVERT: F 132 LYS cc_start: 0.5225 (mtpt) cc_final: 0.4544 (ptmt) REVERT: F 175 GLN cc_start: 0.2761 (mm-40) cc_final: 0.1930 (tt0) REVERT: F 187 ARG cc_start: 0.1660 (mtt-85) cc_final: 0.1394 (mtt180) REVERT: F 238 GLU cc_start: 0.1287 (mp0) cc_final: -0.2280 (mt-10) REVERT: G 9 LYS cc_start: 0.6640 (tptt) cc_final: 0.6300 (mtpt) REVERT: G 13 SER cc_start: 0.4154 (p) cc_final: 0.3661 (t) REVERT: G 220 LYS cc_start: 0.5049 (mmtt) cc_final: 0.4162 (mptt) outliers start: 25 outliers final: 8 residues processed: 148 average time/residue: 0.8276 time to fit residues: 132.2828 Evaluate side-chains 132 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 122 time to evaluate : 0.579 ------------------------------------------------------------------------------- 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 43 ILE 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 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: 0.5980 chunk 66 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 118 optimal weight: 0.6980 chunk 167 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 0.1980 chunk 112 optimal weight: 4.9990 chunk 47 optimal weight: 0.6980 chunk 83 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4302 r_free = 0.4302 target = 0.191453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.124989 restraints weight = 23606.444| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.03 r_work: 0.3401 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3259 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3259 r_free = 0.3259 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 = 0.3259 r_free = 0.3259 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3259 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8182 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 14808 Z= 0.117 Angle : 0.462 8.869 19855 Z= 0.240 Chirality : 0.037 0.171 2166 Planarity : 0.004 0.057 2431 Dihedral : 17.119 178.488 2550 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 1.64 % Allowed : 11.04 % Favored : 87.32 % 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 aren not related in a simple way. whole: 3.30 (0.20), residues: 1707 helix: 3.30 (0.14), residues: 1166 sheet: -0.04 (0.72), residues: 60 loop : -0.47 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 49 TYR 0.013 0.001 TYR E 208 PHE 0.018 0.001 PHE E 189 TRP 0.014 0.001 TRP A 196 HIS 0.003 0.000 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00259 (14804) covalent geometry : angle 0.46237 (19847) SS BOND : bond 0.00134 ( 4) SS BOND : angle 0.32740 ( 8) hydrogen bonds : bond 0.04256 ( 1023) hydrogen bonds : angle 3.68920 ( 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 171 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7106 (OUTLIER) cc_final: 0.6865 (pt0) REVERT: A 120 GLN cc_start: 0.8796 (OUTLIER) cc_final: 0.8489 (tm-30) REVERT: B 61 LYS cc_start: 0.8222 (mmtt) cc_final: 0.7924 (mmpt) REVERT: B 72 LYS cc_start: 0.8437 (tttp) cc_final: 0.7865 (ttmp) REVERT: B 130 GLU cc_start: 0.8746 (mm-30) cc_final: 0.7979 (mp0) REVERT: C 61 LYS cc_start: 0.8446 (mmtm) cc_final: 0.7937 (mppt) REVERT: C 175 ARG cc_start: 0.7667 (mmm160) cc_final: 0.6875 (ttm-80) REVERT: D 102 GLU cc_start: 0.6278 (tp30) cc_final: 0.6020 (tp30) REVERT: E 61 LYS cc_start: 0.8227 (mmtm) cc_final: 0.7714 (mppt) REVERT: F 9 LYS cc_start: 0.3440 (mptt) cc_final: 0.2588 (ttpt) REVERT: F 33 VAL cc_start: 0.8589 (OUTLIER) cc_final: 0.8248 (t) REVERT: F 62 GLN cc_start: 0.6903 (mm-40) cc_final: 0.6637 (tt0) REVERT: F 66 ARG cc_start: 0.6193 (ptm-80) cc_final: 0.5990 (ptm160) REVERT: F 132 LYS cc_start: 0.4742 (mtpt) cc_final: 0.4309 (ptmt) REVERT: F 175 GLN cc_start: 0.2812 (mm-40) cc_final: 0.1987 (tt0) REVERT: F 238 GLU cc_start: 0.1103 (mp0) cc_final: -0.2374 (mt-10) REVERT: G 9 LYS cc_start: 0.6682 (tptt) cc_final: 0.6310 (mtpt) REVERT: G 13 SER cc_start: 0.4493 (p) cc_final: 0.3990 (t) REVERT: G 220 LYS cc_start: 0.5116 (mmtt) cc_final: 0.4185 (mptt) outliers start: 25 outliers final: 7 residues processed: 160 average time/residue: 0.7765 time to fit residues: 134.7399 Evaluate side-chains 142 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 132 time to evaluate : 0.652 ------------------------------------------------------------------------------- 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 33 VAL 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: 9.9990 chunk 122 optimal weight: 1.9990 chunk 143 optimal weight: 0.5980 chunk 30 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 164 optimal weight: 0.0980 chunk 4 optimal weight: 2.9990 chunk 95 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.190978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.121668 restraints weight = 31747.185| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.42 r_work: 0.3338 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3355 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3355 r_free = 0.3355 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 = 0.3355 r_free = 0.3355 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3355 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2875 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= 0.136 Angle : 0.488 10.105 19855 Z= 0.250 Chirality : 0.039 0.274 2166 Planarity : 0.004 0.056 2431 Dihedral : 16.742 177.653 2550 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.45 % Allowed : 12.29 % Favored : 86.27 % 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 aren not related in a simple way. whole: 3.25 (0.20), residues: 1707 helix: 3.26 (0.14), residues: 1165 sheet: -0.16 (0.73), residues: 60 loop : -0.47 (0.29), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 49 TYR 0.012 0.001 TYR A 208 PHE 0.019 0.001 PHE E 189 TRP 0.014 0.001 TRP A 196 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00314 (14804) covalent geometry : angle 0.48842 (19847) SS BOND : bond 0.00097 ( 4) SS BOND : angle 0.30167 ( 8) hydrogen bonds : bond 0.04396 ( 1023) hydrogen bonds : angle 3.73117 ( 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 160 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.633 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7054 (OUTLIER) cc_final: 0.6798 (pt0) REVERT: A 120 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8407 (tm-30) REVERT: B 61 LYS cc_start: 0.8232 (mmtt) cc_final: 0.7953 (mmpt) REVERT: B 72 LYS cc_start: 0.8402 (tttp) cc_final: 0.7820 (ttmp) REVERT: B 130 GLU cc_start: 0.8631 (mm-30) cc_final: 0.7933 (mp0) REVERT: C 61 LYS cc_start: 0.8400 (mmtm) cc_final: 0.7935 (mppt) REVERT: C 175 ARG cc_start: 0.7507 (mmm160) cc_final: 0.6737 (ttm-80) REVERT: E 61 LYS cc_start: 0.8242 (mmtm) cc_final: 0.7713 (mppt) REVERT: F 9 LYS cc_start: 0.3290 (mptt) cc_final: 0.2476 (tttm) REVERT: F 33 VAL cc_start: 0.8552 (OUTLIER) cc_final: 0.8177 (t) REVERT: F 62 GLN cc_start: 0.6884 (mm-40) cc_final: 0.6612 (tt0) REVERT: F 66 ARG cc_start: 0.6147 (ptm-80) cc_final: 0.5589 (ptm160) REVERT: F 175 GLN cc_start: 0.2820 (mm-40) cc_final: 0.1945 (tt0) REVERT: F 238 GLU cc_start: 0.1187 (mp0) cc_final: -0.2255 (mt-10) REVERT: G 9 LYS cc_start: 0.6643 (tptt) cc_final: 0.6294 (mtpt) REVERT: G 13 SER cc_start: 0.4585 (p) cc_final: 0.4092 (t) REVERT: G 220 LYS cc_start: 0.4815 (mmtt) cc_final: 0.4018 (mptt) outliers start: 22 outliers final: 9 residues processed: 150 average time/residue: 0.7827 time to fit residues: 127.2839 Evaluate side-chains 136 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 124 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 120 GLN 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 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: 5.9990 chunk 41 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 137 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 147 optimal weight: 0.6980 chunk 150 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 164 optimal weight: 9.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 51 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.190011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.121367 restraints weight = 27427.817| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 2.23 r_work: 0.3351 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 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 = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3339 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14808 Z= 0.146 Angle : 0.501 9.754 19855 Z= 0.257 Chirality : 0.039 0.186 2166 Planarity : 0.004 0.056 2431 Dihedral : 16.410 171.553 2550 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.64 % Allowed : 12.55 % Favored : 85.81 % 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 aren not related in a simple way. whole: 3.25 (0.20), residues: 1707 helix: 3.24 (0.14), residues: 1159 sheet: -0.59 (0.73), residues: 57 loop : -0.30 (0.29), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 49 TYR 0.013 0.001 TYR A 208 PHE 0.019 0.001 PHE E 189 TRP 0.018 0.002 TRP A 196 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00341 (14804) covalent geometry : angle 0.50076 (19847) SS BOND : bond 0.00164 ( 4) SS BOND : angle 0.42456 ( 8) hydrogen bonds : bond 0.04473 ( 1023) hydrogen bonds : angle 3.76960 ( 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 156 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 131 time to evaluate : 0.530 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7221 (OUTLIER) cc_final: 0.6965 (pm20) REVERT: A 120 GLN cc_start: 0.8767 (OUTLIER) cc_final: 0.8433 (tm-30) REVERT: B 61 LYS cc_start: 0.8282 (mmtt) cc_final: 0.8000 (mmpt) REVERT: B 72 LYS cc_start: 0.8450 (tttp) cc_final: 0.7856 (ttmp) REVERT: B 130 GLU cc_start: 0.8607 (mm-30) cc_final: 0.7917 (mp0) REVERT: B 210 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7541 (tm-30) REVERT: C 61 LYS cc_start: 0.8430 (mmtm) cc_final: 0.8016 (mtmt) REVERT: C 175 ARG cc_start: 0.7527 (mmm160) cc_final: 0.6788 (ttm-80) REVERT: E 61 LYS cc_start: 0.8258 (mmtm) cc_final: 0.7732 (mppt) REVERT: F 9 LYS cc_start: 0.3368 (mptt) cc_final: 0.2525 (ttpt) REVERT: F 33 VAL cc_start: 0.8581 (OUTLIER) cc_final: 0.8236 (t) REVERT: F 62 GLN cc_start: 0.6958 (mm-40) cc_final: 0.6709 (tt0) REVERT: F 175 GLN cc_start: 0.2910 (mm-40) cc_final: 0.2517 (tt0) REVERT: G 9 LYS cc_start: 0.6630 (tptt) cc_final: 0.6270 (mtpt) REVERT: G 28 MET cc_start: 0.8747 (mmp) cc_final: 0.8490 (mmm) REVERT: G 220 LYS cc_start: 0.4878 (mmtt) cc_final: 0.4073 (mptt) outliers start: 25 outliers final: 10 residues processed: 144 average time/residue: 0.7929 time to fit residues: 123.2901 Evaluate side-chains 138 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 124 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 210 GLU 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 214 MET 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: 2.9990 chunk 83 optimal weight: 0.7980 chunk 123 optimal weight: 0.8980 chunk 38 optimal weight: 0.7980 chunk 131 optimal weight: 0.4980 chunk 126 optimal weight: 0.6980 chunk 154 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 159 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 117 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4281 r_free = 0.4281 target = 0.189453 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.122961 restraints weight = 22888.972| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.99 r_work: 0.3384 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3229 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3229 r_free = 0.3229 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 = 0.3229 r_free = 0.3229 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3229 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3246 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= 0.138 Angle : 0.486 9.092 19855 Z= 0.251 Chirality : 0.038 0.184 2166 Planarity : 0.004 0.056 2431 Dihedral : 16.029 168.906 2550 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.31 % Allowed : 13.07 % 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 aren not related in a simple way. whole: 3.25 (0.20), residues: 1707 helix: 3.24 (0.14), residues: 1160 sheet: -0.59 (0.75), residues: 57 loop : -0.30 (0.29), residues: 490 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 0.018 0.001 PHE E 189 TRP 0.019 0.002 TRP A 196 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00322 (14804) covalent geometry : angle 0.48561 (19847) SS BOND : bond 0.00140 ( 4) SS BOND : angle 0.32209 ( 8) hydrogen bonds : bond 0.04358 ( 1023) hydrogen bonds : angle 3.73758 ( 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 144 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 124 time to evaluate : 0.645 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7237 (OUTLIER) cc_final: 0.6910 (pm20) REVERT: A 105 VAL cc_start: 0.8850 (p) cc_final: 0.8644 (m) REVERT: A 120 GLN cc_start: 0.8825 (OUTLIER) cc_final: 0.8488 (tt0) REVERT: B 51 LYS cc_start: 0.8209 (OUTLIER) cc_final: 0.7963 (tttm) REVERT: B 61 LYS cc_start: 0.8343 (mmtt) cc_final: 0.7995 (mmpt) REVERT: B 72 LYS cc_start: 0.8457 (tttp) cc_final: 0.7808 (ttmm) REVERT: B 130 GLU cc_start: 0.8767 (mm-30) cc_final: 0.7983 (mp0) REVERT: B 210 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.7709 (tm-30) REVERT: C 61 LYS cc_start: 0.8500 (mmtm) cc_final: 0.8001 (mppt) REVERT: C 121 GLN cc_start: 0.9054 (OUTLIER) cc_final: 0.7957 (mt0) REVERT: C 175 ARG cc_start: 0.7674 (mmm160) cc_final: 0.6835 (ttm-80) REVERT: E 61 LYS cc_start: 0.8262 (mmtm) cc_final: 0.7676 (mppt) REVERT: F 9 LYS cc_start: 0.3450 (mptt) cc_final: 0.2637 (ttpt) REVERT: F 33 VAL cc_start: 0.8620 (OUTLIER) cc_final: 0.8246 (t) REVERT: F 62 GLN cc_start: 0.6929 (mm-40) cc_final: 0.6646 (tt0) REVERT: F 175 GLN cc_start: 0.2701 (mm-40) cc_final: 0.2427 (tt0) REVERT: G 220 LYS cc_start: 0.4844 (mmtt) cc_final: 0.4075 (mptt) outliers start: 20 outliers final: 9 residues processed: 135 average time/residue: 0.7500 time to fit residues: 110.5964 Evaluate side-chains 132 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 120 GLN Chi-restraints excluded: chain B residue 51 LYS Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C 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 214 MET 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: 0.3980 chunk 75 optimal weight: 0.5980 chunk 45 optimal weight: 0.9990 chunk 154 optimal weight: 0.9980 chunk 158 optimal weight: 8.9990 chunk 29 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 139 optimal weight: 6.9990 chunk 137 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 157 HIS 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 = 0.4290 r_free = 0.4290 target = 0.190325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.122895 restraints weight = 23054.715| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 2.06 r_work: 0.3378 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3223 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3223 r_free = 0.3223 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 = 0.3223 r_free = 0.3223 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3223 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.3381 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= 0.131 Angle : 0.478 9.349 19855 Z= 0.246 Chirality : 0.038 0.188 2166 Planarity : 0.004 0.055 2431 Dihedral : 15.776 166.228 2550 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.45 % Allowed : 13.27 % Favored : 85.28 % 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 aren not related in a simple way. whole: 3.31 (0.20), residues: 1707 helix: 3.29 (0.14), residues: 1163 sheet: -0.41 (0.75), residues: 57 loop : -0.33 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG G 213 TYR 0.012 0.001 TYR E 208 PHE 0.019 0.001 PHE E 189 TRP 0.020 0.002 TRP A 196 HIS 0.004 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00301 (14804) covalent geometry : angle 0.47796 (19847) SS BOND : bond 0.00114 ( 4) SS BOND : angle 0.40135 ( 8) hydrogen bonds : bond 0.04269 ( 1023) hydrogen bonds : angle 3.70533 ( 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 150 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6975 (pm20) REVERT: A 120 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8529 (tm-30) REVERT: B 61 LYS cc_start: 0.8364 (mmtt) cc_final: 0.8024 (mmpt) REVERT: B 72 LYS cc_start: 0.8492 (tttp) cc_final: 0.7856 (ttmm) REVERT: B 130 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8022 (mp0) REVERT: B 210 GLU cc_start: 0.8370 (OUTLIER) cc_final: 0.7789 (tm-30) REVERT: C 61 LYS cc_start: 0.8462 (mmtm) cc_final: 0.7982 (mppt) REVERT: C 175 ARG cc_start: 0.7706 (mmm160) cc_final: 0.6900 (ttm-80) REVERT: E 61 LYS cc_start: 0.8279 (mmtm) cc_final: 0.7694 (mppt) REVERT: F 33 VAL cc_start: 0.8643 (OUTLIER) cc_final: 0.8279 (t) REVERT: F 62 GLN cc_start: 0.6902 (mm-40) cc_final: 0.6624 (tt0) REVERT: F 136 GLN cc_start: 0.3976 (OUTLIER) cc_final: 0.3652 (mt0) REVERT: F 175 GLN cc_start: 0.2672 (mm-40) cc_final: 0.2408 (tt0) REVERT: G 220 LYS cc_start: 0.4732 (mmtt) cc_final: 0.3985 (mptt) outliers start: 22 outliers final: 12 residues processed: 141 average time/residue: 0.7478 time to fit residues: 114.7198 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 : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 202 ILE Chi-restraints excluded: chain B residue 210 GLU 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 132 LYS Chi-restraints excluded: chain F residue 136 GLN Chi-restraints excluded: chain F residue 214 MET 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: 1.9990 chunk 67 optimal weight: 0.5980 chunk 108 optimal weight: 0.7980 chunk 161 optimal weight: 0.2980 chunk 139 optimal weight: 0.5980 chunk 64 optimal weight: 0.9980 chunk 136 optimal weight: 2.9990 chunk 82 optimal weight: 0.6980 chunk 118 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4293 r_free = 0.4293 target = 0.190583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.121929 restraints weight = 30541.520| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.35 r_work: 0.3357 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3340 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 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 = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3413 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= 0.123 Angle : 0.478 9.293 19855 Z= 0.246 Chirality : 0.038 0.189 2166 Planarity : 0.004 0.057 2431 Dihedral : 15.671 165.229 2550 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.51 % Allowed : 13.27 % Favored : 85.22 % 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 aren not related in a simple way. whole: 3.33 (0.20), residues: 1707 helix: 3.31 (0.14), residues: 1163 sheet: -0.36 (0.76), residues: 57 loop : -0.37 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 77 TYR 0.012 0.001 TYR E 208 PHE 0.020 0.001 PHE E 189 TRP 0.022 0.002 TRP A 196 HIS 0.003 0.001 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00281 (14804) covalent geometry : angle 0.47523 (19847) SS BOND : bond 0.00080 ( 4) SS BOND : angle 2.60921 ( 8) hydrogen bonds : bond 0.04193 ( 1023) hydrogen bonds : angle 3.70043 ( 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 152 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.588 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7191 (OUTLIER) cc_final: 0.6924 (pm20) REVERT: A 120 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.8417 (tm-30) REVERT: B 51 LYS cc_start: 0.8144 (OUTLIER) cc_final: 0.7888 (tttm) REVERT: B 61 LYS cc_start: 0.8331 (mmtt) cc_final: 0.8019 (mmpt) REVERT: B 72 LYS cc_start: 0.8412 (tttp) cc_final: 0.7765 (ttmm) REVERT: B 130 GLU cc_start: 0.8608 (mm-30) cc_final: 0.7928 (mp0) REVERT: B 210 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7564 (tm-30) REVERT: C 61 LYS cc_start: 0.8380 (mmtm) cc_final: 0.7929 (mppt) REVERT: C 121 GLN cc_start: 0.8942 (OUTLIER) cc_final: 0.7836 (mt0) REVERT: C 175 ARG cc_start: 0.7504 (mmm160) cc_final: 0.6730 (ttm-80) REVERT: E 61 LYS cc_start: 0.8263 (mmtm) cc_final: 0.7685 (mppt) REVERT: F 33 VAL cc_start: 0.8587 (OUTLIER) cc_final: 0.8236 (t) REVERT: F 62 GLN cc_start: 0.6909 (mm-40) cc_final: 0.6627 (tt0) REVERT: F 175 GLN cc_start: 0.2753 (mm-40) cc_final: 0.2434 (tt0) REVERT: G 220 LYS cc_start: 0.4669 (mmtt) cc_final: 0.3993 (mptt) outliers start: 23 outliers final: 12 residues processed: 141 average time/residue: 0.7703 time to fit residues: 117.7973 Evaluate side-chains 140 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 B residue 51 LYS Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain B residue 210 GLU 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 F residue 33 VAL Chi-restraints excluded: chain F residue 132 LYS Chi-restraints excluded: chain F residue 214 MET 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: 0.7980 chunk 11 optimal weight: 0.7980 chunk 44 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 9 optimal weight: 0.0030 chunk 54 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 145 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 53 optimal weight: 0.5980 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 157 HIS F 136 GLN ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.190917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.122768 restraints weight = 28017.892| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.26 r_work: 0.3358 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3358 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.3342 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.3474 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= 0.119 Angle : 0.481 12.056 19855 Z= 0.246 Chirality : 0.038 0.189 2166 Planarity : 0.004 0.056 2431 Dihedral : 15.502 169.522 2550 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.18 % Allowed : 13.80 % Favored : 85.02 % 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 aren not related in a simple way. whole: 3.36 (0.20), residues: 1707 helix: 3.33 (0.14), residues: 1163 sheet: -0.25 (0.77), residues: 57 loop : -0.34 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG F 49 TYR 0.012 0.001 TYR E 208 PHE 0.020 0.001 PHE E 189 TRP 0.022 0.002 TRP A 196 HIS 0.003 0.001 HIS D 82 Details of bonding type rmsd covalent geometry : bond 0.00270 (14804) covalent geometry : angle 0.48042 (19847) SS BOND : bond 0.00073 ( 4) SS BOND : angle 1.43741 ( 8) hydrogen bonds : bond 0.04115 ( 1023) hydrogen bonds : angle 3.69424 ( 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: 18 poor density : 126 time to evaluate : 0.573 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6950 (pm20) REVERT: A 120 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8448 (tm-30) REVERT: B 51 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7918 (tttm) REVERT: B 61 LYS cc_start: 0.8324 (mmtt) cc_final: 0.8010 (mmpt) REVERT: B 72 LYS cc_start: 0.8407 (tttp) cc_final: 0.7830 (ttmp) REVERT: B 130 GLU cc_start: 0.8587 (mm-30) cc_final: 0.7915 (mp0) REVERT: C 61 LYS cc_start: 0.8353 (mmtm) cc_final: 0.7906 (mppt) REVERT: C 121 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.7897 (mt0) REVERT: C 175 ARG cc_start: 0.7489 (mmm160) cc_final: 0.6707 (ttm-80) REVERT: E 61 LYS cc_start: 0.8209 (mmtm) cc_final: 0.7648 (mppt) REVERT: F 2 PHE cc_start: 0.5081 (m-80) cc_final: 0.3332 (t80) REVERT: F 33 VAL cc_start: 0.8594 (OUTLIER) cc_final: 0.8265 (t) REVERT: F 62 GLN cc_start: 0.6863 (mm-40) cc_final: 0.6589 (tt0) REVERT: F 175 GLN cc_start: 0.2751 (mm-40) cc_final: 0.2520 (tt0) REVERT: G 220 LYS cc_start: 0.4649 (mmtt) cc_final: 0.4029 (mptt) outliers start: 18 outliers final: 10 residues processed: 135 average time/residue: 0.7561 time to fit residues: 110.8204 Evaluate side-chains 134 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 119 time to evaluate : 0.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain A residue 120 GLN 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 C 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 132 LYS Chi-restraints excluded: chain F residue 214 MET 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: 5.9990 chunk 113 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 88 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 108 optimal weight: 0.0980 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4289 r_free = 0.4289 target = 0.190313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.121476 restraints weight = 32360.060| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.42 r_work: 0.3344 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3341 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 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 = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3531 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= 0.126 Angle : 0.492 11.458 19855 Z= 0.251 Chirality : 0.038 0.187 2166 Planarity : 0.004 0.056 2431 Dihedral : 15.403 172.438 2550 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 1.05 % Allowed : 13.99 % Favored : 84.95 % 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 aren not related in a simple way. whole: 3.35 (0.20), residues: 1707 helix: 3.31 (0.14), residues: 1163 sheet: -0.18 (0.78), residues: 57 loop : -0.33 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 49 TYR 0.013 0.001 TYR D 149 PHE 0.022 0.001 PHE E 189 TRP 0.024 0.002 TRP A 196 HIS 0.004 0.001 HIS C 157 Details of bonding type rmsd covalent geometry : bond 0.00289 (14804) covalent geometry : angle 0.49110 (19847) SS BOND : bond 0.00083 ( 4) SS BOND : angle 1.13010 ( 8) hydrogen bonds : bond 0.04206 ( 1023) hydrogen bonds : angle 3.70384 ( 3018) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7392.29 seconds wall clock time: 126 minutes 36.45 seconds (7596.45 seconds total)