Starting phenix.real_space_refine on Fri Jun 13 05:22:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qyy_18766/06_2025/8qyy_18766.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qyy_18766/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qyy_18766/06_2025/8qyy_18766.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qyy_18766/06_2025/8qyy_18766.map" model { file = "/net/cci-nas-00/data/ceres_data/8qyy_18766/06_2025/8qyy_18766.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qyy_18766/06_2025/8qyy_18766.cif" } resolution = 2.56 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.16, per 1000 atoms: 0.89 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: 3.92 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.33 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: 4.29 Time building geometry restraints manager: 4.55 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: 8.600 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: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 39.070 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.070 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:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.680 ------------------------------------------------------------------------------- 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 : 8.37 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.027 0.002 TRP A 196 HIS 0.003 0.001 HIS D 82 PHE 0.016 0.002 PHE G 217 TYR 0.017 0.002 TYR D 208 ARG 0.009 0.001 ARG B 54 Details of bonding type rmsd hydrogen bonds : bond 0.11895 ( 1023) hydrogen bonds : angle 4.81168 ( 3018) SS BOND : bond 0.00127 ( 4) SS BOND : angle 0.60682 ( 8) covalent geometry : bond 0.00859 (14804) covalent geometry : angle 1.39923 (19847) *********************** 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 : 1.573 Fit side-chains 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: 0.6356 (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: 0.4155 (mptt) outliers start: 0 outliers final: 0 residues processed: 251 average time/residue: 1.7332 time to fit residues: 468.1618 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 : 1.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 8.9990 chunk 127 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 85 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 chunk 131 optimal weight: 0.0870 chunk 50 optimal weight: 0.7980 chunk 80 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 152 optimal weight: 0.9980 overall best weight: 0.6158 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.193047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.125869 restraints weight = 23903.298| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.07 r_work: 0.3417 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.3275 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3275 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3258 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3258 r_free = 0.3258 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 = 0.3258 r_free = 0.3258 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3258 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1804 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= 0.148 Angle : 0.546 7.676 19855 Z= 0.280 Chirality : 0.039 0.165 2166 Planarity : 0.004 0.057 2431 Dihedral : 18.843 177.201 2550 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 1.38 % Allowed : 8.15 % Favored : 90.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.11 (0.20), residues: 1707 helix: 3.14 (0.14), residues: 1162 sheet: -0.28 (0.78), residues: 50 loop : -0.45 (0.29), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 196 HIS 0.005 0.001 HIS A 92 PHE 0.016 0.001 PHE F 217 TYR 0.019 0.001 TYR A 149 ARG 0.006 0.001 ARG G 60 Details of bonding type rmsd hydrogen bonds : bond 0.04822 ( 1023) hydrogen bonds : angle 3.94460 ( 3018) SS BOND : bond 0.00476 ( 4) SS BOND : angle 1.28703 ( 8) covalent geometry : bond 0.00328 (14804) covalent geometry : angle 0.54536 (19847) *********************** 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 163 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 142 time to evaluate : 1.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7091 (OUTLIER) cc_final: 0.6820 (pt0) REVERT: B 72 LYS cc_start: 0.8394 (tttp) cc_final: 0.7861 (ttmt) REVERT: B 130 GLU cc_start: 0.8799 (mm-30) cc_final: 0.8005 (mp0) REVERT: C 61 LYS cc_start: 0.8489 (mmtm) cc_final: 0.7902 (mptt) REVERT: C 175 ARG cc_start: 0.7565 (mmm160) cc_final: 0.6790 (ttm-80) REVERT: D 162 THR cc_start: 0.7966 (OUTLIER) cc_final: 0.7345 (t) REVERT: F 9 LYS cc_start: 0.3531 (mptt) cc_final: 0.2537 (tmtt) REVERT: F 32 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8482 (pp-130) REVERT: F 62 GLN cc_start: 0.6708 (mm-40) cc_final: 0.6321 (tt0) REVERT: F 175 GLN cc_start: 0.2813 (mm-40) cc_final: 0.1987 (tt0) REVERT: F 187 ARG cc_start: 0.1508 (mtt-85) cc_final: 0.1146 (mtt180) REVERT: F 238 GLU cc_start: 0.1385 (mp0) cc_final: -0.2436 (mt-10) REVERT: G 9 LYS cc_start: 0.6529 (tptt) cc_final: 0.6204 (mtpt) REVERT: G 13 SER cc_start: 0.3797 (p) cc_final: 0.3370 (t) REVERT: G 28 MET cc_start: 0.8744 (mmp) cc_final: 0.8384 (mmm) REVERT: G 51 GLN cc_start: 0.6532 (mt0) cc_final: 0.6201 (mt0) REVERT: G 220 LYS cc_start: 0.4982 (mmtt) cc_final: 0.4102 (mptt) outliers start: 21 outliers final: 7 residues processed: 155 average time/residue: 1.7264 time to fit residues: 290.3021 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 : 2.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 GLU Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain D residue 14 VAL Chi-restraints excluded: chain D residue 43 ILE Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain D residue 204 LYS Chi-restraints excluded: chain F residue 32 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 86 optimal weight: 3.9990 chunk 22 optimal weight: 0.9990 chunk 160 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 87 optimal weight: 0.8980 chunk 125 optimal weight: 0.9980 chunk 157 optimal weight: 9.9990 chunk 132 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 76 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 HIS C 157 HIS D 120 GLN F 87 HIS G 79 ASN ** G 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 215 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.190514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.119817 restraints weight = 37341.961| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.60 r_work: 0.3310 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3323 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3323 r_free = 0.3323 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3323 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 14808 Z= 0.166 Angle : 0.529 8.482 19855 Z= 0.273 Chirality : 0.040 0.179 2166 Planarity : 0.004 0.058 2431 Dihedral : 17.983 178.942 2550 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.77 % Allowed : 9.92 % Favored : 88.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.20), residues: 1707 helix: 3.07 (0.14), residues: 1168 sheet: -0.30 (0.80), residues: 50 loop : -0.44 (0.29), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 196 HIS 0.006 0.001 HIS D 82 PHE 0.017 0.002 PHE E 189 TYR 0.016 0.001 TYR A 208 ARG 0.006 0.000 ARG F 159 Details of bonding type rmsd hydrogen bonds : bond 0.04853 ( 1023) hydrogen bonds : angle 3.87659 ( 3018) SS BOND : bond 0.00171 ( 4) SS BOND : angle 0.47296 ( 8) covalent geometry : bond 0.00386 (14804) covalent geometry : angle 0.52940 (19847) *********************** 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 156 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 129 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6780 (pt0) REVERT: A 120 GLN cc_start: 0.8717 (OUTLIER) cc_final: 0.8397 (tm-30) REVERT: B 61 LYS cc_start: 0.8160 (mmtt) cc_final: 0.7892 (mmpt) REVERT: B 72 LYS cc_start: 0.8389 (tttp) cc_final: 0.7806 (ttmp) REVERT: B 130 GLU cc_start: 0.8660 (mm-30) cc_final: 0.7970 (mp0) REVERT: C 61 LYS cc_start: 0.8441 (mmtm) cc_final: 0.8001 (mppt) REVERT: C 175 ARG cc_start: 0.7539 (mmm160) cc_final: 0.6749 (ttm-80) REVERT: E 61 LYS cc_start: 0.8199 (mmtm) cc_final: 0.7709 (mppt) REVERT: F 9 LYS cc_start: 0.3367 (mptt) cc_final: 0.2567 (ttpt) REVERT: F 62 GLN cc_start: 0.6675 (mm-40) cc_final: 0.6271 (tt0) REVERT: F 175 GLN cc_start: 0.2736 (mm-40) cc_final: 0.1871 (tt0) REVERT: F 187 ARG cc_start: 0.1633 (mtt-85) cc_final: 0.1290 (mtt180) REVERT: F 238 GLU cc_start: 0.1287 (mp0) cc_final: -0.2725 (mt-10) REVERT: G 9 LYS cc_start: 0.6640 (tptt) cc_final: 0.6306 (mtpt) REVERT: G 13 SER cc_start: 0.4557 (p) cc_final: 0.4078 (t) REVERT: G 220 LYS cc_start: 0.4995 (mmtt) cc_final: 0.4162 (mptt) outliers start: 27 outliers final: 9 residues processed: 146 average time/residue: 1.5817 time to fit residues: 250.2709 Evaluate side-chains 127 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 116 time to evaluate : 1.773 ------------------------------------------------------------------------------- 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 F residue 49 ARG 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 52 optimal weight: 0.6980 chunk 159 optimal weight: 10.0000 chunk 45 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 132 optimal weight: 20.0000 chunk 150 optimal weight: 6.9990 chunk 119 optimal weight: 0.5980 chunk 147 optimal weight: 0.5980 chunk 114 optimal weight: 0.5980 chunk 87 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.4301 r_free = 0.4301 target = 0.191262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.123126 restraints weight = 25773.535| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.19 r_work: 0.3362 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- 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: 0.8099 moved from start: 0.2705 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= 0.133 Angle : 0.478 8.601 19855 Z= 0.248 Chirality : 0.038 0.170 2166 Planarity : 0.004 0.057 2431 Dihedral : 17.213 178.382 2550 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.71 % Allowed : 10.97 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.20), residues: 1707 helix: 3.22 (0.14), residues: 1166 sheet: -0.13 (0.72), residues: 60 loop : -0.48 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 196 HIS 0.003 0.001 HIS D 82 PHE 0.018 0.001 PHE E 189 TYR 0.014 0.001 TYR E 208 ARG 0.003 0.000 ARG G 213 Details of bonding type rmsd hydrogen bonds : bond 0.04409 ( 1023) hydrogen bonds : angle 3.74977 ( 3018) SS BOND : bond 0.00188 ( 4) SS BOND : angle 0.41823 ( 8) covalent geometry : bond 0.00299 (14804) covalent geometry : angle 0.47784 (19847) *********************** 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 162 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7019 (OUTLIER) cc_final: 0.6732 (pt0) REVERT: A 120 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.8435 (tm-30) REVERT: B 61 LYS cc_start: 0.8156 (mmtt) cc_final: 0.7916 (mmpt) REVERT: B 72 LYS cc_start: 0.8424 (tttp) cc_final: 0.7848 (ttmp) REVERT: B 130 GLU cc_start: 0.8599 (mm-30) cc_final: 0.7939 (mp0) REVERT: C 61 LYS cc_start: 0.8409 (mmtm) cc_final: 0.7963 (mppt) REVERT: C 175 ARG cc_start: 0.7471 (mmm160) cc_final: 0.6744 (ttm-80) REVERT: E 61 LYS cc_start: 0.8230 (mmtm) cc_final: 0.7746 (mppt) REVERT: F 1 MET cc_start: 0.5265 (ttp) cc_final: 0.4950 (ttt) REVERT: F 9 LYS cc_start: 0.3306 (mptt) cc_final: 0.2526 (ttpt) REVERT: F 33 VAL cc_start: 0.8564 (OUTLIER) cc_final: 0.8198 (t) REVERT: F 62 GLN cc_start: 0.6758 (mm-40) cc_final: 0.6350 (tt0) REVERT: F 175 GLN cc_start: 0.2731 (mm-40) cc_final: 0.1924 (tt0) REVERT: F 238 GLU cc_start: 0.1090 (mp0) cc_final: -0.2311 (mt-10) REVERT: G 9 LYS cc_start: 0.6683 (tptt) cc_final: 0.6320 (mtpt) REVERT: G 13 SER cc_start: 0.4706 (p) cc_final: 0.4235 (t) REVERT: G 28 MET cc_start: 0.8725 (mmp) cc_final: 0.8454 (mmm) REVERT: G 220 LYS cc_start: 0.5127 (mmtt) cc_final: 0.4224 (mptt) outliers start: 26 outliers final: 7 residues processed: 151 average time/residue: 1.5518 time to fit residues: 254.4196 Evaluate side-chains 134 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 124 time to evaluate : 1.550 ------------------------------------------------------------------------------- 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 162 THR Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 49 ARG Chi-restraints excluded: chain F residue 214 MET 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 68 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 101 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 146 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 104 optimal weight: 0.5980 chunk 102 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 84 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4294 r_free = 0.4294 target = 0.190518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.121358 restraints weight = 30319.925| |-----------------------------------------------------------------------------| r_work (start): 0.3487 rms_B_bonded: 2.36 r_work: 0.3335 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 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 = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2942 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= 0.137 Angle : 0.493 10.958 19855 Z= 0.253 Chirality : 0.038 0.263 2166 Planarity : 0.004 0.057 2431 Dihedral : 16.816 179.487 2550 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 1.84 % Allowed : 11.70 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.20), residues: 1707 helix: 3.28 (0.14), residues: 1159 sheet: -0.03 (0.74), residues: 60 loop : -0.39 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 196 HIS 0.004 0.001 HIS D 82 PHE 0.018 0.001 PHE E 189 TYR 0.014 0.001 TYR E 208 ARG 0.002 0.000 ARG F 49 Details of bonding type rmsd hydrogen bonds : bond 0.04432 ( 1023) hydrogen bonds : angle 3.75318 ( 3018) SS BOND : bond 0.00111 ( 4) SS BOND : angle 0.29395 ( 8) covalent geometry : bond 0.00316 (14804) covalent geometry : angle 0.49333 (19847) *********************** 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 159 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 131 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6384 (tpp) cc_final: 0.6178 (ttm) REVERT: A 79 GLU cc_start: 0.7081 (OUTLIER) cc_final: 0.6802 (pt0) REVERT: A 120 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.8423 (tm-30) REVERT: B 61 LYS cc_start: 0.8192 (mmtt) cc_final: 0.7931 (mmpt) REVERT: B 72 LYS cc_start: 0.8432 (tttp) cc_final: 0.7842 (ttmp) REVERT: B 130 GLU cc_start: 0.8633 (mm-30) cc_final: 0.7950 (mp0) REVERT: C 61 LYS cc_start: 0.8434 (mmtm) cc_final: 0.8018 (mtmt) REVERT: C 121 GLN cc_start: 0.9027 (OUTLIER) cc_final: 0.8029 (mt0) REVERT: C 175 ARG cc_start: 0.7508 (mmm160) cc_final: 0.6752 (ttm-80) REVERT: E 61 LYS cc_start: 0.8256 (mmtm) cc_final: 0.7728 (mppt) REVERT: F 1 MET cc_start: 0.5266 (ttp) cc_final: 0.4938 (ttt) REVERT: F 9 LYS cc_start: 0.3316 (mptt) cc_final: 0.2513 (tttm) REVERT: F 33 VAL cc_start: 0.8588 (OUTLIER) cc_final: 0.8220 (t) REVERT: F 62 GLN cc_start: 0.6718 (mm-40) cc_final: 0.6326 (tt0) REVERT: F 175 GLN cc_start: 0.2826 (mm-40) cc_final: 0.2531 (tt0) REVERT: G 9 LYS cc_start: 0.6669 (tptt) cc_final: 0.6285 (mtpt) REVERT: G 13 SER cc_start: 0.4620 (p) cc_final: 0.4139 (t) REVERT: G 220 LYS cc_start: 0.4869 (mmtt) cc_final: 0.4071 (mptt) outliers start: 28 outliers final: 11 residues processed: 144 average time/residue: 1.6103 time to fit residues: 252.5706 Evaluate side-chains 136 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 121 time to evaluate : 1.671 ------------------------------------------------------------------------------- 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 C residue 121 GLN Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 49 ARG Chi-restraints excluded: chain G residue 54 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 75 optimal weight: 0.8980 chunk 165 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 148 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 chunk 108 optimal weight: 0.6980 chunk 111 optimal weight: 0.9990 chunk 163 optimal weight: 6.9990 chunk 59 optimal weight: 0.0020 chunk 138 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 157 HIS G 51 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.191147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.123095 restraints weight = 26706.332| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.22 r_work: 0.3362 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 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 = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3348 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3085 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= 0.123 Angle : 0.473 10.030 19855 Z= 0.242 Chirality : 0.038 0.179 2166 Planarity : 0.004 0.056 2431 Dihedral : 16.178 171.798 2550 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.58 % Allowed : 12.35 % Favored : 86.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.37 (0.20), residues: 1707 helix: 3.35 (0.14), residues: 1159 sheet: -0.54 (0.73), residues: 58 loop : -0.29 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 196 HIS 0.003 0.001 HIS D 82 PHE 0.018 0.001 PHE E 189 TYR 0.013 0.001 TYR E 208 ARG 0.002 0.000 ARG F 49 Details of bonding type rmsd hydrogen bonds : bond 0.04198 ( 1023) hydrogen bonds : angle 3.68572 ( 3018) SS BOND : bond 0.00124 ( 4) SS BOND : angle 0.32803 ( 8) covalent geometry : bond 0.00278 (14804) covalent geometry : angle 0.47277 (19847) *********************** 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: 24 poor density : 132 time to evaluate : 1.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 1 MET cc_start: 0.6358 (tpp) cc_final: 0.6145 (ttm) REVERT: A 79 GLU cc_start: 0.7180 (OUTLIER) cc_final: 0.6953 (pm20) REVERT: A 120 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8458 (tm-30) REVERT: B 61 LYS cc_start: 0.8237 (mmtt) cc_final: 0.7967 (mmpt) REVERT: B 72 LYS cc_start: 0.8386 (tttp) cc_final: 0.7810 (ttmp) REVERT: B 130 GLU cc_start: 0.8564 (mm-30) cc_final: 0.7916 (mp0) REVERT: C 61 LYS cc_start: 0.8359 (mmtm) cc_final: 0.7919 (mppt) REVERT: C 121 GLN cc_start: 0.9009 (OUTLIER) cc_final: 0.7982 (mt0) REVERT: C 175 ARG cc_start: 0.7465 (mmm160) cc_final: 0.6746 (ttm-80) REVERT: E 61 LYS cc_start: 0.8248 (mmtm) cc_final: 0.7724 (mppt) REVERT: F 1 MET cc_start: 0.5014 (ttp) cc_final: 0.4744 (ttt) REVERT: F 9 LYS cc_start: 0.3350 (mptt) cc_final: 0.2536 (ttpt) REVERT: F 33 VAL cc_start: 0.8584 (OUTLIER) cc_final: 0.8221 (t) REVERT: F 62 GLN cc_start: 0.6760 (mm-40) cc_final: 0.6374 (tt0) REVERT: F 175 GLN cc_start: 0.2672 (mm-40) cc_final: 0.2392 (tt0) REVERT: G 9 LYS cc_start: 0.6642 (tptt) cc_final: 0.6267 (mtpt) REVERT: G 220 LYS cc_start: 0.4816 (mmtt) cc_final: 0.4048 (mptt) outliers start: 24 outliers final: 13 residues processed: 144 average time/residue: 1.5695 time to fit residues: 246.2448 Evaluate side-chains 138 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.528 ------------------------------------------------------------------------------- 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 1 MET Chi-restraints excluded: chain B residue 202 ILE Chi-restraints excluded: chain C residue 14 VAL Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 121 GLN Chi-restraints excluded: chain D residue 61 LYS Chi-restraints excluded: chain D residue 121 GLN Chi-restraints excluded: chain D residue 161 SER Chi-restraints excluded: chain D residue 162 THR Chi-restraints excluded: chain D residue 167 SER Chi-restraints excluded: chain D residue 168 SER Chi-restraints excluded: chain D residue 184 SER Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 49 ARG Chi-restraints excluded: chain G residue 54 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 82 optimal weight: 1.9990 chunk 156 optimal weight: 10.0000 chunk 160 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 161 optimal weight: 4.9990 chunk 135 optimal weight: 8.9990 chunk 62 optimal weight: 0.6980 chunk 159 optimal weight: 5.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 157 HIS G 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.187789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.119544 restraints weight = 25029.474| |-----------------------------------------------------------------------------| r_work (start): 0.3464 rms_B_bonded: 2.14 r_work: 0.3314 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.3178 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3183 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3183 r_free = 0.3183 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3183 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 14808 Z= 0.197 Angle : 0.542 9.478 19855 Z= 0.278 Chirality : 0.041 0.199 2166 Planarity : 0.004 0.056 2431 Dihedral : 16.555 168.414 2550 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.51 % Allowed : 12.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.20), residues: 1707 helix: 3.04 (0.14), residues: 1165 sheet: -0.38 (0.76), residues: 57 loop : -0.37 (0.29), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 196 HIS 0.006 0.001 HIS D 82 PHE 0.020 0.002 PHE E 189 TYR 0.021 0.002 TYR E 208 ARG 0.006 0.000 ARG G 213 Details of bonding type rmsd hydrogen bonds : bond 0.04957 ( 1023) hydrogen bonds : angle 3.92830 ( 3018) SS BOND : bond 0.00120 ( 4) SS BOND : angle 0.37923 ( 8) covalent geometry : bond 0.00476 (14804) covalent geometry : angle 0.54252 (19847) *********************** 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 150 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 127 time to evaluate : 1.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6979 (pt0) REVERT: A 120 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8523 (tm-30) REVERT: B 61 LYS cc_start: 0.8418 (mmtt) cc_final: 0.8066 (mmpt) REVERT: B 72 LYS cc_start: 0.8564 (tttp) cc_final: 0.7900 (ttmm) REVERT: B 130 GLU cc_start: 0.8764 (mm-30) cc_final: 0.7999 (mp0) REVERT: C 61 LYS cc_start: 0.8580 (mmtm) cc_final: 0.8111 (mppt) REVERT: C 76 GLN cc_start: 0.7662 (OUTLIER) cc_final: 0.7461 (mm110) REVERT: C 121 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8064 (mt0) REVERT: C 175 ARG cc_start: 0.7749 (mmm160) cc_final: 0.6937 (ttm-80) REVERT: E 61 LYS cc_start: 0.8320 (mmtm) cc_final: 0.7726 (mppt) REVERT: F 9 LYS cc_start: 0.3530 (mptt) cc_final: 0.2569 (ttpt) REVERT: F 33 VAL cc_start: 0.8664 (OUTLIER) cc_final: 0.8323 (t) REVERT: F 62 GLN cc_start: 0.6807 (mm-40) cc_final: 0.6383 (tt0) REVERT: F 175 GLN cc_start: 0.2810 (mm-40) cc_final: 0.2488 (tt0) REVERT: G 9 LYS cc_start: 0.6667 (tptt) cc_final: 0.6309 (mtpt) REVERT: G 28 MET cc_start: 0.8823 (mmp) cc_final: 0.8489 (mmm) REVERT: G 220 LYS cc_start: 0.4943 (mmtt) cc_final: 0.4120 (mptt) outliers start: 23 outliers final: 11 residues processed: 139 average time/residue: 1.8923 time to fit residues: 285.9682 Evaluate side-chains 136 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 1.786 ------------------------------------------------------------------------------- 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 C residue 60 GLU Chi-restraints excluded: chain C residue 76 GLN Chi-restraints excluded: chain C residue 121 GLN 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 F residue 33 VAL Chi-restraints excluded: chain F residue 49 ARG Chi-restraints excluded: chain G residue 54 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 70 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 165 optimal weight: 0.0870 chunk 95 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 22 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 120 optimal weight: 0.0670 chunk 137 optimal weight: 7.9990 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 157 HIS G 51 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.190057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.121200 restraints weight = 33838.499| |-----------------------------------------------------------------------------| r_work (start): 0.3484 rms_B_bonded: 2.46 r_work: 0.3330 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3311 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3311 r_free = 0.3311 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3311 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.3339 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= 0.121 Angle : 0.482 9.614 19855 Z= 0.247 Chirality : 0.038 0.188 2166 Planarity : 0.004 0.055 2431 Dihedral : 16.089 167.311 2550 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.31 % Allowed : 13.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.30 (0.20), residues: 1707 helix: 3.28 (0.14), residues: 1160 sheet: -0.36 (0.75), residues: 57 loop : -0.31 (0.29), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 196 HIS 0.003 0.001 HIS C 157 PHE 0.018 0.001 PHE E 189 TYR 0.015 0.001 TYR E 208 ARG 0.002 0.000 ARG F 49 Details of bonding type rmsd hydrogen bonds : bond 0.04264 ( 1023) hydrogen bonds : angle 3.75179 ( 3018) SS BOND : bond 0.00113 ( 4) SS BOND : angle 0.34658 ( 8) covalent geometry : bond 0.00275 (14804) covalent geometry : angle 0.48204 (19847) *********************** 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 149 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 129 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7203 (OUTLIER) cc_final: 0.6908 (pm20) REVERT: A 120 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.8440 (tm-30) REVERT: B 61 LYS cc_start: 0.8340 (mmtt) cc_final: 0.8012 (mmpt) REVERT: B 72 LYS cc_start: 0.8406 (tttp) cc_final: 0.7751 (ttmm) REVERT: B 130 GLU cc_start: 0.8595 (mm-30) cc_final: 0.7874 (mp0) REVERT: C 61 LYS cc_start: 0.8439 (mmtm) cc_final: 0.7970 (mppt) REVERT: C 121 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.7964 (mt0) REVERT: C 175 ARG cc_start: 0.7503 (mmm160) cc_final: 0.6701 (ttm-80) REVERT: E 61 LYS cc_start: 0.8291 (mmtm) cc_final: 0.7692 (mppt) REVERT: F 1 MET cc_start: 0.5190 (ttp) cc_final: 0.4925 (ttt) REVERT: F 33 VAL cc_start: 0.8591 (OUTLIER) cc_final: 0.8226 (t) REVERT: F 62 GLN cc_start: 0.6821 (mm-40) cc_final: 0.6426 (tt0) REVERT: F 175 GLN cc_start: 0.2770 (mm-40) cc_final: 0.2506 (tt0) REVERT: G 9 LYS cc_start: 0.6664 (tptt) cc_final: 0.6306 (mtpt) REVERT: G 220 LYS cc_start: 0.4782 (mmtt) cc_final: 0.4075 (mptt) REVERT: G 237 LYS cc_start: 0.2509 (tptt) cc_final: 0.2205 (tmtm) outliers start: 20 outliers final: 9 residues processed: 141 average time/residue: 1.6899 time to fit residues: 259.7212 Evaluate side-chains 136 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 123 time to evaluate : 2.180 ------------------------------------------------------------------------------- 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 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 49 ARG 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 1 optimal weight: 0.9990 chunk 102 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 165 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 73 optimal weight: 0.0770 chunk 152 optimal weight: 8.9990 overall best weight: 0.6340 ------------------------------------------------------------------------------- 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 = 0.4280 r_free = 0.4280 target = 0.189251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.122521 restraints weight = 24789.467| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 2.08 r_work: 0.3362 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3225 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3225 ------------------------------------------------------------------------------- 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: 0.8201 moved from start: 0.3437 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= 0.130 Angle : 0.483 10.154 19855 Z= 0.247 Chirality : 0.038 0.192 2166 Planarity : 0.004 0.058 2431 Dihedral : 15.735 168.032 2550 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.62 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.32 (0.20), residues: 1707 helix: 3.29 (0.14), residues: 1163 sheet: -0.34 (0.76), residues: 57 loop : -0.33 (0.29), residues: 487 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 196 HIS 0.004 0.001 HIS D 82 PHE 0.018 0.001 PHE E 189 TYR 0.015 0.001 TYR E 208 ARG 0.002 0.000 ARG F 49 Details of bonding type rmsd hydrogen bonds : bond 0.04267 ( 1023) hydrogen bonds : angle 3.73491 ( 3018) SS BOND : bond 0.00129 ( 4) SS BOND : angle 0.36366 ( 8) covalent geometry : bond 0.00302 (14804) covalent geometry : angle 0.48260 (19847) *********************** 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 144 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 1.776 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7260 (OUTLIER) cc_final: 0.6944 (pm20) REVERT: A 120 GLN cc_start: 0.8850 (OUTLIER) cc_final: 0.8531 (tm-30) REVERT: B 61 LYS cc_start: 0.8417 (mmtt) cc_final: 0.8055 (mmpt) REVERT: B 72 LYS cc_start: 0.8477 (tttp) cc_final: 0.7831 (ttmm) REVERT: B 130 GLU cc_start: 0.8756 (mm-30) cc_final: 0.7981 (mp0) REVERT: C 61 LYS cc_start: 0.8526 (mmtm) cc_final: 0.8009 (mppt) REVERT: C 121 GLN cc_start: 0.9056 (OUTLIER) cc_final: 0.8092 (mt0) REVERT: C 175 ARG cc_start: 0.7724 (mmm160) cc_final: 0.6887 (ttm-80) REVERT: D 156 ASN cc_start: 0.8142 (m110) cc_final: 0.7650 (m-40) REVERT: E 61 LYS cc_start: 0.8285 (mmtm) cc_final: 0.7667 (mppt) REVERT: F 33 VAL cc_start: 0.8627 (OUTLIER) cc_final: 0.8265 (t) REVERT: F 62 GLN cc_start: 0.6840 (mm-40) cc_final: 0.6447 (tt0) REVERT: F 175 GLN cc_start: 0.2738 (mm-40) cc_final: 0.2482 (tt0) REVERT: G 9 LYS cc_start: 0.6702 (tptt) cc_final: 0.6335 (mtpt) REVERT: G 220 LYS cc_start: 0.4707 (mmtt) cc_final: 0.3978 (mptt) outliers start: 18 outliers final: 10 residues processed: 138 average time/residue: 1.6740 time to fit residues: 251.7593 Evaluate side-chains 137 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 123 time to evaluate : 1.936 ------------------------------------------------------------------------------- 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 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 49 ARG 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 147 optimal weight: 0.6980 chunk 130 optimal weight: 0.0980 chunk 14 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 120 optimal weight: 0.0060 chunk 64 optimal weight: 3.9990 chunk 134 optimal weight: 10.0000 chunk 158 optimal weight: 9.9990 chunk 153 optimal weight: 7.9990 chunk 88 optimal weight: 0.5980 chunk 92 optimal weight: 1.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 = 0.4297 r_free = 0.4297 target = 0.191156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.124042 restraints weight = 25813.275| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.17 r_work: 0.3377 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.3247 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3247 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3236 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3236 r_free = 0.3236 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 = 0.3236 r_free = 0.3236 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3236 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 14808 Z= 0.110 Angle : 0.474 12.887 19855 Z= 0.241 Chirality : 0.037 0.185 2166 Planarity : 0.004 0.057 2431 Dihedral : 15.457 171.804 2550 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 0.92 % Allowed : 14.13 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.43 (0.20), residues: 1707 helix: 3.40 (0.14), residues: 1162 sheet: -0.28 (0.76), residues: 57 loop : -0.36 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 196 HIS 0.003 0.000 HIS D 82 PHE 0.020 0.001 PHE E 189 TYR 0.012 0.001 TYR E 208 ARG 0.002 0.000 ARG F 49 Details of bonding type rmsd hydrogen bonds : bond 0.03992 ( 1023) hydrogen bonds : angle 3.66230 ( 3018) SS BOND : bond 0.00233 ( 4) SS BOND : angle 1.87146 ( 8) covalent geometry : bond 0.00243 (14804) covalent geometry : angle 0.47242 (19847) ********************** 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 148 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 1.610 Fit side-chains revert: symmetry clash REVERT: A 79 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6942 (pm20) REVERT: A 120 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8580 (tm-30) REVERT: B 1 MET cc_start: 0.6536 (ptp) cc_final: 0.6283 (ptm) REVERT: B 61 LYS cc_start: 0.8364 (mmtt) cc_final: 0.8005 (mmpt) REVERT: B 72 LYS cc_start: 0.8430 (tttp) cc_final: 0.7859 (ttmp) REVERT: B 130 GLU cc_start: 0.8705 (mm-30) cc_final: 0.7946 (mp0) REVERT: C 61 LYS cc_start: 0.8452 (mmtm) cc_final: 0.7925 (mppt) REVERT: C 121 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8162 (mt0) REVERT: C 175 ARG cc_start: 0.7699 (mmm160) cc_final: 0.6847 (ttm-80) REVERT: D 152 MET cc_start: 0.8538 (mmm) cc_final: 0.8048 (mmp) REVERT: D 156 ASN cc_start: 0.8120 (m110) cc_final: 0.7623 (m-40) REVERT: E 61 LYS cc_start: 0.8221 (mmtm) cc_final: 0.7617 (mppt) REVERT: F 1 MET cc_start: 0.5270 (ttp) cc_final: 0.4903 (ttt) REVERT: F 33 VAL cc_start: 0.8628 (OUTLIER) cc_final: 0.8259 (t) REVERT: F 62 GLN cc_start: 0.6767 (mm-40) cc_final: 0.6370 (tt0) REVERT: F 175 GLN cc_start: 0.2814 (mm-40) cc_final: 0.2597 (tt0) REVERT: G 28 MET cc_start: 0.8753 (mmp) cc_final: 0.8392 (mmm) REVERT: G 220 LYS cc_start: 0.4685 (mmtt) cc_final: 0.4020 (mptt) outliers start: 14 outliers final: 10 residues processed: 142 average time/residue: 1.8186 time to fit residues: 281.8300 Evaluate side-chains 139 residues out of total 1518 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 125 time to evaluate : 2.338 ------------------------------------------------------------------------------- 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 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 184 SER Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain F residue 49 ARG Chi-restraints excluded: chain G residue 54 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 27 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 50 optimal weight: 0.0970 chunk 131 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 167 optimal weight: 0.0370 chunk 135 optimal weight: 10.0000 chunk 57 optimal weight: 0.2980 chunk 90 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 overall best weight: 0.3256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 157 HIS E 85 ASN ** 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 = 0.4304 r_free = 0.4304 target = 0.191792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.124171 restraints weight = 30384.606| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.36 r_work: 0.3386 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3392 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3392 r_free = 0.3392 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3392 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 14808 Z= 0.106 Angle : 0.465 11.672 19855 Z= 0.236 Chirality : 0.037 0.181 2166 Planarity : 0.003 0.056 2431 Dihedral : 15.091 172.114 2550 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.92 % Allowed : 14.39 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.06 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.51 (0.20), residues: 1707 helix: 3.47 (0.14), residues: 1162 sheet: -0.21 (0.77), residues: 57 loop : -0.34 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 196 HIS 0.006 0.001 HIS C 157 PHE 0.020 0.001 PHE E 189 TYR 0.011 0.001 TYR E 208 ARG 0.002 0.000 ARG F 49 Details of bonding type rmsd hydrogen bonds : bond 0.03852 ( 1023) hydrogen bonds : angle 3.60404 ( 3018) SS BOND : bond 0.00085 ( 4) SS BOND : angle 1.60135 ( 8) covalent geometry : bond 0.00231 (14804) covalent geometry : angle 0.46351 (19847) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14706.88 seconds wall clock time: 258 minutes 17.44 seconds (15497.44 seconds total)