Starting phenix.real_space_refine on Thu Jul 2 07:19:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8gbj_29917/07_2026/8gbj_29917.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gbj_29917/07_2026/8gbj_29917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8gbj_29917/07_2026/8gbj_29917.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8gbj_29917/07_2026/8gbj_29917.cif" model { file = "/net/cci-nas-00/data/ceres_data/8gbj_29917/07_2026/8gbj_29917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gbj_29917/07_2026/8gbj_29917.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8gbj_29917/07_2026/8gbj_29917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gbj_29917/07_2026/8gbj_29917.map" } resolution = 3.11 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 50 5.16 5 C 4685 2.51 5 N 1296 2.21 5 O 1421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7467 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 570 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "C" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2494 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 11, 'TRANS': 305} Chain breaks: 2 Chain: "D" Number of atoms: 2318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2318 Classifications: {'peptide': 308} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 299} Chain breaks: 2 Chain: "X" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1878 Classifications: {'peptide': 232} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 225} Chain breaks: 3 Chain: "G" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 114 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.28, per 1000 atoms: 0.17 Number of scatterers: 7467 At special positions: 0 Unit cell: (84.39, 81.78, 112.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 P 15 15.00 O 1421 8.00 N 1296 7.00 C 4685 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS B 60 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 382.2 milliseconds 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1732 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 5 sheets defined 53.7% alpha, 18.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'B' and resid 12 through 22 removed outlier: 3.573A pdb=" N HIS B 22 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 32 Processing helix chain 'B' and resid 34 through 43 Processing helix chain 'B' and resid 45 through 60 removed outlier: 3.512A pdb=" N GLU B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 75 Processing helix chain 'C' and resid 20 through 31 Processing helix chain 'C' and resid 34 through 39 removed outlier: 3.740A pdb=" N LEU C 39 " --> pdb=" O GLU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 51 Processing helix chain 'C' and resid 53 through 67 removed outlier: 3.841A pdb=" N GLU C 67 " --> pdb=" O ILE C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 97 Processing helix chain 'C' and resid 104 through 111 Processing helix chain 'C' and resid 130 through 143 removed outlier: 4.323A pdb=" N GLN C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 149 removed outlier: 6.143A pdb=" N CYS C 147 " --> pdb=" O ILE C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 188 Processing helix chain 'C' and resid 189 through 198 removed outlier: 4.092A pdb=" N ASP C 198 " --> pdb=" O LYS C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 207 Processing helix chain 'C' and resid 215 through 233 Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 245 through 250 Processing helix chain 'C' and resid 254 through 276 Processing helix chain 'C' and resid 303 through 308 Processing helix chain 'D' and resid 13 through 23 Processing helix chain 'D' and resid 27 through 34 Processing helix chain 'D' and resid 35 through 44 Processing helix chain 'D' and resid 46 through 62 Processing helix chain 'D' and resid 68 through 79 removed outlier: 3.915A pdb=" N THR D 77 " --> pdb=" O GLU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 93 Processing helix chain 'D' and resid 112 through 127 Processing helix chain 'D' and resid 142 through 154 Processing helix chain 'D' and resid 156 through 166 Processing helix chain 'D' and resid 174 through 193 Processing helix chain 'D' and resid 207 through 213 removed outlier: 3.866A pdb=" N VAL D 211 " --> pdb=" O SER D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 221 through 239 Processing helix chain 'D' and resid 264 through 270 removed outlier: 3.765A pdb=" N TRP D 268 " --> pdb=" O LEU D 264 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N PHE D 270 " --> pdb=" O ARG D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 312 through 314 No H-bonds generated for 'chain 'D' and resid 312 through 314' Processing helix chain 'X' and resid 23 through 28 removed outlier: 3.614A pdb=" N ILE X 27 " --> pdb=" O SER X 23 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLU X 28 " --> pdb=" O LEU X 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 23 through 28' Processing helix chain 'X' and resid 53 through 67 Processing helix chain 'X' and resid 88 through 100 Processing helix chain 'X' and resid 104 through 114 removed outlier: 3.798A pdb=" N ARG X 114 " --> pdb=" O TYR X 110 " (cutoff:3.500A) Processing helix chain 'X' and resid 122 through 138 removed outlier: 4.310A pdb=" N SER X 135 " --> pdb=" O TYR X 131 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET X 136 " --> pdb=" O SER X 132 " (cutoff:3.500A) Processing helix chain 'X' and resid 150 through 153 Processing helix chain 'X' and resid 154 through 162 Processing helix chain 'X' and resid 165 through 170 Processing helix chain 'X' and resid 170 through 187 Processing helix chain 'X' and resid 228 through 233 Processing sheet with id=AA1, first strand: chain 'B' and resid 65 through 66 removed outlier: 6.785A pdb=" N ALA C 155 " --> pdb=" O TYR C 209 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N PHE C 211 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE C 157 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLU C 154 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ILE C 240 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL C 156 " --> pdb=" O ILE C 240 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ASP C 242 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE C 158 " --> pdb=" O ASP C 242 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 65 through 66 removed outlier: 6.785A pdb=" N ALA C 155 " --> pdb=" O TYR C 209 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N PHE C 211 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE C 157 " --> pdb=" O PHE C 211 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLU C 154 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 8.513A pdb=" N ILE C 240 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N VAL C 156 " --> pdb=" O ILE C 240 " (cutoff:3.500A) removed outlier: 7.358A pdb=" N ASP C 242 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ILE C 158 " --> pdb=" O ASP C 242 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N LYS C 119 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N LEU C 282 " --> pdb=" O LYS C 119 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N THR C 121 " --> pdb=" O LEU C 282 " (cutoff:3.500A) removed outlier: 7.671A pdb=" N ASN C 284 " --> pdb=" O THR C 121 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE C 123 " --> pdb=" O ASN C 284 " (cutoff:3.500A) removed outlier: 7.577A pdb=" N MET C 286 " --> pdb=" O ILE C 123 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N GLY C 125 " --> pdb=" O MET C 286 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N THR C 120 " --> pdb=" O ILE C 311 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N LEU C 313 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLU C 122 " --> pdb=" O LEU C 313 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N PHE C 315 " --> pdb=" O GLU C 122 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N CYS C 124 " --> pdb=" O PHE C 315 " (cutoff:3.500A) removed outlier: 8.822A pdb=" N TRP C 317 " --> pdb=" O CYS C 124 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS C 328 " --> pdb=" O ARG C 312 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE C 314 " --> pdb=" O LEU C 326 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU C 326 " --> pdb=" O ILE C 314 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N HIS C 316 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ALA C 324 " --> pdb=" O HIS C 316 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N ARG C 322 " --> pdb=" O PHE C 339 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 66 through 67 removed outlier: 6.050A pdb=" N LEU X 79 " --> pdb=" O ILE X 147 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ASP X 149 " --> pdb=" O LEU X 79 " (cutoff:3.500A) removed outlier: 5.521A pdb=" N ILE X 81 " --> pdb=" O ASP X 149 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY X 48 " --> pdb=" O THR X 195 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE X 43 " --> pdb=" O HIS X 237 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N MET X 239 " --> pdb=" O ILE X 43 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLU X 45 " --> pdb=" O MET X 239 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N PHE X 241 " --> pdb=" O GLU X 45 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N HIS X 47 " --> pdb=" O PHE X 241 " (cutoff:3.500A) removed outlier: 9.112A pdb=" N LYS X 243 " --> pdb=" O HIS X 47 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLN X 252 " --> pdb=" O GLN X 244 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 167 through 171 removed outlier: 6.349A pdb=" N VAL D 132 " --> pdb=" O GLN D 168 " (cutoff:3.500A) removed outlier: 7.465A pdb=" N VAL D 170 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N TYR D 134 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N ASN D 131 " --> pdb=" O VAL D 200 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL D 202 " --> pdb=" O ASN D 131 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LYS D 201 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL D 246 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N VAL D 203 " --> pdb=" O VAL D 246 " (cutoff:3.500A) removed outlier: 7.476A pdb=" N THR D 248 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL D 205 " --> pdb=" O THR D 248 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N VAL D 102 " --> pdb=" O THR D 274 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ILE D 276 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU D 104 " --> pdb=" O ILE D 276 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LEU D 278 " --> pdb=" O GLU D 104 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL D 106 " --> pdb=" O LEU D 278 " (cutoff:3.500A) removed outlier: 8.789A pdb=" N THR D 280 " --> pdb=" O VAL D 106 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N LEU D 277 " --> pdb=" O LEU D 295 " (cutoff:3.500A) removed outlier: 5.555A pdb=" N LEU D 295 " --> pdb=" O LEU D 277 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ASP D 279 " --> pdb=" O ALA D 293 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ALA D 293 " --> pdb=" O ASP D 279 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'D' and resid 251 through 253 382 hydrogen bonds defined for protein. 1095 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.05 Time building geometry restraints manager: 0.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2444 1.34 - 1.46: 1285 1.46 - 1.57: 3765 1.57 - 1.69: 25 1.69 - 1.81: 72 Bond restraints: 7591 Sorted by residual: bond pdb=" O3A ANP X 301 " pdb=" PB ANP X 301 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" O3A ANP D 401 " pdb=" PB ANP D 401 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.34e+01 bond pdb=" O3A ANP C 401 " pdb=" PB ANP C 401 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.25e+01 bond pdb=" N3B ANP X 301 " pdb=" PG ANP X 301 " ideal model delta sigma weight residual 1.795 1.688 0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 1.795 1.689 0.106 2.00e-02 2.50e+03 2.82e+01 ... (remaining 7586 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.49: 10189 3.49 - 6.98: 71 6.98 - 10.48: 12 10.48 - 13.97: 2 13.97 - 17.46: 3 Bond angle restraints: 10277 Sorted by residual: angle pdb=" PB ANP X 301 " pdb=" N3B ANP X 301 " pdb=" PG ANP X 301 " ideal model delta sigma weight residual 126.95 109.49 17.46 3.00e+00 1.11e-01 3.39e+01 angle pdb=" PB ANP C 401 " pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 126.95 110.36 16.59 3.00e+00 1.11e-01 3.06e+01 angle pdb=" PB ANP D 401 " pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 126.95 110.60 16.35 3.00e+00 1.11e-01 2.97e+01 angle pdb=" C GLN D 220 " pdb=" N ARG D 221 " pdb=" CA ARG D 221 " ideal model delta sigma weight residual 122.49 116.55 5.94 1.55e+00 4.16e-01 1.47e+01 angle pdb=" O1B ANP D 401 " pdb=" PB ANP D 401 " pdb=" O2B ANP D 401 " ideal model delta sigma weight residual 120.08 108.86 11.22 3.00e+00 1.11e-01 1.40e+01 ... (remaining 10272 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.76: 4205 19.76 - 39.52: 268 39.52 - 59.28: 56 59.28 - 79.04: 14 79.04 - 98.80: 7 Dihedral angle restraints: 4550 sinusoidal: 1879 harmonic: 2671 Sorted by residual: dihedral pdb=" CA LEU C 278 " pdb=" C LEU C 278 " pdb=" N ALA C 279 " pdb=" CA ALA C 279 " ideal model delta harmonic sigma weight residual 180.00 162.27 17.73 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA THR B 42 " pdb=" C THR B 42 " pdb=" N GLY B 43 " pdb=" CA GLY B 43 " ideal model delta harmonic sigma weight residual 180.00 -162.44 -17.56 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" O1B ANP C 401 " pdb=" N3B ANP C 401 " pdb=" PB ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sinusoidal sigma weight residual 35.15 -63.65 98.80 1 3.00e+01 1.11e-03 1.23e+01 ... (remaining 4547 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 995 0.057 - 0.113: 189 0.113 - 0.170: 17 0.170 - 0.227: 1 0.227 - 0.283: 3 Chirality restraints: 1205 Sorted by residual: chirality pdb=" C3' ANP D 401 " pdb=" C2' ANP D 401 " pdb=" C4' ANP D 401 " pdb=" O3' ANP D 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C3' ANP X 301 " pdb=" C2' ANP X 301 " pdb=" C4' ANP X 301 " pdb=" O3' ANP X 301 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C3' ANP C 401 " pdb=" C2' ANP C 401 " pdb=" C4' ANP C 401 " pdb=" O3' ANP C 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1202 not shown) Planarity restraints: 1267 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 300 " -0.127 9.50e-02 1.11e+02 5.70e-02 2.04e+00 pdb=" NE ARG D 300 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG D 300 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG D 300 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG D 300 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 254 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.89e+00 pdb=" C ASP D 254 " 0.024 2.00e-02 2.50e+03 pdb=" O ASP D 254 " -0.009 2.00e-02 2.50e+03 pdb=" N ARG D 255 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 46 " -0.013 2.00e-02 2.50e+03 9.55e-03 1.82e+00 pdb=" CG TYR B 46 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR B 46 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 46 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 46 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 46 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 46 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 46 " 0.000 2.00e-02 2.50e+03 ... (remaining 1264 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 116 2.64 - 3.20: 7025 3.20 - 3.77: 12480 3.77 - 4.33: 17604 4.33 - 4.90: 28440 Nonbonded interactions: 65665 Sorted by model distance: nonbonded pdb=" OG1 THR X 83 " pdb=" O SER X 150 " model vdw 2.073 3.040 nonbonded pdb=" O1B ANP D 401 " pdb=" O2G ANP D 401 " model vdw 2.094 3.040 nonbonded pdb=" OG1 THR C 200 " pdb=" OD1 ASP C 202 " model vdw 2.156 3.040 nonbonded pdb=" O LEU D 58 " pdb=" OG SER D 62 " model vdw 2.179 3.040 nonbonded pdb=" OG SER B 45 " pdb=" O PRO C 18 " model vdw 2.192 3.040 ... (remaining 65660 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.010 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: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.360 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.147 7592 Z= 0.309 Angle : 0.821 17.461 10279 Z= 0.380 Chirality : 0.046 0.283 1205 Planarity : 0.004 0.057 1267 Dihedral : 14.171 98.797 2815 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.37 % Allowed : 0.37 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.15 (0.28), residues: 908 helix: 0.91 (0.25), residues: 444 sheet: -0.48 (0.41), residues: 152 loop : -0.63 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG X 224 TYR 0.023 0.002 TYR B 46 PHE 0.014 0.001 PHE X 80 TRP 0.014 0.002 TRP C 317 HIS 0.006 0.001 HIS B 50 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.31 ( 7591) covalent geometry : angle 0.82082 / 0.38 (10277) SS BOND : bond 0.00432 / 0.23 ( 1) SS BOND : angle 1.44387 / 0.78 ( 2) hydrogen bonds : bond 0.14382 / 9.40 ( 375) hydrogen bonds : angle 6.41466 / 4.64 ( 1095) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 115 time to evaluate : 0.337 Fit side-chains REVERT: B 28 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8147 (tt0) REVERT: B 29 ASP cc_start: 0.8694 (m-30) cc_final: 0.8413 (m-30) outliers start: 3 outliers final: 0 residues processed: 117 average time/residue: 0.0850 time to fit residues: 13.3522 Evaluate side-chains 105 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 0.269 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 178 GLN C 250 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4110 r_free = 0.4110 target = 0.188669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.157797 restraints weight = 8182.230| |-----------------------------------------------------------------------------| r_work (start): 0.3702 rms_B_bonded: 1.75 r_work: 0.3584 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 7592 Z= 0.169 Angle : 0.583 9.663 10279 Z= 0.295 Chirality : 0.043 0.158 1205 Planarity : 0.004 0.037 1267 Dihedral : 10.529 78.465 1065 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.74 % Allowed : 6.70 % Favored : 92.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.28), residues: 908 helix: 0.97 (0.25), residues: 446 sheet: -0.64 (0.42), residues: 151 loop : -0.67 (0.36), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG X 64 TYR 0.018 0.001 TYR B 46 PHE 0.011 0.001 PHE X 80 TRP 0.011 0.001 TRP C 317 HIS 0.005 0.001 HIS X 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.17 ( 7591) covalent geometry : angle 0.58271 / 0.30 (10277) SS BOND : bond 0.00156 / 0.08 ( 1) SS BOND : angle 0.96854 / 0.53 ( 2) hydrogen bonds : bond 0.03893 / 2.63 ( 375) hydrogen bonds : angle 4.97533 / 3.52 ( 1095) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 108 time to evaluate : 0.213 Fit side-chains REVERT: B 29 ASP cc_start: 0.8671 (m-30) cc_final: 0.8342 (m-30) REVERT: C 129 VAL cc_start: 0.8213 (p) cc_final: 0.7988 (p) REVERT: C 204 ILE cc_start: 0.7815 (OUTLIER) cc_final: 0.7423 (mm) REVERT: X 64 ARG cc_start: 0.7907 (mtp85) cc_final: 0.7482 (mmm160) REVERT: X 233 GLN cc_start: 0.8378 (pt0) cc_final: 0.8159 (pt0) outliers start: 6 outliers final: 3 residues processed: 111 average time/residue: 0.0868 time to fit residues: 12.9457 Evaluate side-chains 100 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 96 time to evaluate : 0.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain X residue 118 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 48 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 88 optimal weight: 0.6980 chunk 38 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.191168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.160202 restraints weight = 8096.146| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 1.82 r_work: 0.3473 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7592 Z= 0.182 Angle : 0.567 9.388 10279 Z= 0.288 Chirality : 0.042 0.163 1205 Planarity : 0.004 0.037 1267 Dihedral : 10.303 74.482 1062 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.87 % Allowed : 9.31 % Favored : 89.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.28), residues: 908 helix: 0.94 (0.24), residues: 447 sheet: -0.81 (0.41), residues: 155 loop : -0.62 (0.36), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 291 TYR 0.013 0.001 TYR B 46 PHE 0.012 0.001 PHE X 80 TRP 0.007 0.001 TRP C 317 HIS 0.004 0.001 HIS X 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 ( 7591) covalent geometry : angle 0.56736 / 0.29 (10277) SS BOND : bond 0.00211 / 0.11 ( 1) SS BOND : angle 0.70666 / 0.40 ( 2) hydrogen bonds : bond 0.03717 / 2.58 ( 375) hydrogen bonds : angle 4.80926 / 3.41 ( 1095) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 103 time to evaluate : 0.272 Fit side-chains REVERT: B 29 ASP cc_start: 0.8650 (m-30) cc_final: 0.8300 (m-30) REVERT: C 301 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8778 (mp) REVERT: D 201 LYS cc_start: 0.7811 (mmmt) cc_final: 0.7587 (tptm) REVERT: X 64 ARG cc_start: 0.7840 (mtp85) cc_final: 0.7395 (mmm160) outliers start: 7 outliers final: 5 residues processed: 106 average time/residue: 0.0829 time to fit residues: 12.2364 Evaluate side-chains 105 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 99 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 204 ILE Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain X residue 118 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 44 optimal weight: 0.0010 chunk 68 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 71 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 72 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 8 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 250 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.195016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.164245 restraints weight = 8191.307| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 1.79 r_work: 0.3597 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3457 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.3457 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7592 Z= 0.131 Angle : 0.521 8.052 10279 Z= 0.265 Chirality : 0.041 0.182 1205 Planarity : 0.004 0.036 1267 Dihedral : 10.099 69.672 1062 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 11.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.24 % Allowed : 10.30 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.28), residues: 908 helix: 1.08 (0.25), residues: 448 sheet: -0.89 (0.41), residues: 155 loop : -0.66 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 291 TYR 0.011 0.001 TYR C 210 PHE 0.012 0.001 PHE D 173 TRP 0.008 0.001 TRP C 317 HIS 0.004 0.001 HIS X 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 ( 7591) covalent geometry : angle 0.52084 / 0.27 (10277) SS BOND : bond 0.00156 / 0.08 ( 1) SS BOND : angle 0.46604 / 0.26 ( 2) hydrogen bonds : bond 0.03289 / 2.24 ( 375) hydrogen bonds : angle 4.62096 / 3.28 ( 1095) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 105 time to evaluate : 0.277 Fit side-chains REVERT: B 28 GLN cc_start: 0.8283 (tt0) cc_final: 0.7964 (tt0) REVERT: B 29 ASP cc_start: 0.8591 (m-30) cc_final: 0.8249 (m-30) REVERT: X 22 SER cc_start: 0.8925 (t) cc_final: 0.8709 (m) REVERT: X 64 ARG cc_start: 0.7818 (mtp85) cc_final: 0.7356 (mmm160) outliers start: 10 outliers final: 6 residues processed: 110 average time/residue: 0.0721 time to fit residues: 11.1465 Evaluate side-chains 108 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 102 time to evaluate : 0.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain X residue 83 THR Chi-restraints excluded: chain X residue 118 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 89 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 90 optimal weight: 0.8980 chunk 70 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 250 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.189302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.157365 restraints weight = 8180.088| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 1.87 r_work: 0.3512 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7592 Z= 0.141 Angle : 0.516 7.874 10279 Z= 0.263 Chirality : 0.041 0.175 1205 Planarity : 0.004 0.038 1267 Dihedral : 10.003 67.959 1062 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 11.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.24 % Allowed : 11.54 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.28), residues: 908 helix: 1.17 (0.25), residues: 448 sheet: -1.00 (0.41), residues: 154 loop : -0.64 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 291 TYR 0.012 0.001 TYR C 210 PHE 0.011 0.001 PHE C 99 TRP 0.006 0.001 TRP C 317 HIS 0.003 0.001 HIS X 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 ( 7591) covalent geometry : angle 0.51644 / 0.26 (10277) SS BOND : bond 0.00171 / 0.09 ( 1) SS BOND : angle 0.54443 / 0.31 ( 2) hydrogen bonds : bond 0.03237 / 2.22 ( 375) hydrogen bonds : angle 4.54696 / 3.22 ( 1095) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 0.170 Fit side-chains REVERT: B 28 GLN cc_start: 0.8295 (tt0) cc_final: 0.7968 (tt0) REVERT: B 29 ASP cc_start: 0.8557 (m-30) cc_final: 0.8215 (m-30) REVERT: C 129 VAL cc_start: 0.8251 (p) cc_final: 0.8039 (p) REVERT: X 22 SER cc_start: 0.9005 (t) cc_final: 0.8799 (m) REVERT: X 64 ARG cc_start: 0.7876 (mtp85) cc_final: 0.7439 (mmm160) outliers start: 10 outliers final: 8 residues processed: 107 average time/residue: 0.0755 time to fit residues: 11.2468 Evaluate side-chains 108 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain X residue 83 THR Chi-restraints excluded: chain X residue 118 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 59 optimal weight: 0.7980 chunk 18 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 80 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 74 optimal weight: 0.6980 chunk 75 optimal weight: 0.9980 chunk 85 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 250 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.193218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.163436 restraints weight = 8133.534| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 1.72 r_work: 0.3537 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7592 Z= 0.132 Angle : 0.512 7.720 10279 Z= 0.260 Chirality : 0.041 0.183 1205 Planarity : 0.004 0.038 1267 Dihedral : 9.883 68.538 1062 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 11.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.36 % Allowed : 12.03 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.28), residues: 908 helix: 1.23 (0.25), residues: 448 sheet: -1.05 (0.42), residues: 154 loop : -0.61 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 291 TYR 0.012 0.001 TYR C 210 PHE 0.013 0.001 PHE C 99 TRP 0.007 0.001 TRP C 317 HIS 0.003 0.001 HIS X 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.13 ( 7591) covalent geometry : angle 0.51164 / 0.26 (10277) SS BOND : bond 0.00179 / 0.09 ( 1) SS BOND : angle 0.48040 / 0.28 ( 2) hydrogen bonds : bond 0.03145 / 2.16 ( 375) hydrogen bonds : angle 4.49543 / 3.18 ( 1095) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.179 Fit side-chains REVERT: B 28 GLN cc_start: 0.8315 (tt0) cc_final: 0.7980 (tt0) REVERT: B 29 ASP cc_start: 0.8517 (m-30) cc_final: 0.8191 (m-30) REVERT: C 94 GLU cc_start: 0.7728 (mt-10) cc_final: 0.7524 (mt-10) REVERT: X 22 SER cc_start: 0.8997 (t) cc_final: 0.8776 (m) REVERT: X 64 ARG cc_start: 0.7857 (mtp85) cc_final: 0.7467 (mmm160) REVERT: X 148 LEU cc_start: 0.8623 (OUTLIER) cc_final: 0.8377 (tt) outliers start: 11 outliers final: 8 residues processed: 109 average time/residue: 0.0698 time to fit residues: 10.6888 Evaluate side-chains 106 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 97 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain X residue 83 THR Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 148 LEU Chi-restraints excluded: chain X residue 173 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 1 optimal weight: 3.9990 chunk 32 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 82 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 11 GLN C 250 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.190814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.158962 restraints weight = 8223.374| |-----------------------------------------------------------------------------| r_work (start): 0.3816 rms_B_bonded: 1.88 r_work: 0.3697 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7592 Z= 0.153 Angle : 0.532 8.181 10279 Z= 0.268 Chirality : 0.042 0.190 1205 Planarity : 0.004 0.038 1267 Dihedral : 9.788 68.910 1062 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.74 % Allowed : 13.03 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.28), residues: 908 helix: 1.19 (0.25), residues: 448 sheet: -1.10 (0.41), residues: 158 loop : -0.59 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 290 TYR 0.013 0.001 TYR C 210 PHE 0.013 0.001 PHE C 99 TRP 0.007 0.001 TRP C 317 HIS 0.003 0.001 HIS X 86 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.15 ( 7591) covalent geometry : angle 0.53178 / 0.27 (10277) SS BOND : bond 0.00210 / 0.11 ( 1) SS BOND : angle 0.59098 / 0.34 ( 2) hydrogen bonds : bond 0.03219 / 2.21 ( 375) hydrogen bonds : angle 4.48856 / 3.17 ( 1095) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 99 time to evaluate : 0.279 Fit side-chains REVERT: B 28 GLN cc_start: 0.8371 (tt0) cc_final: 0.8033 (tt0) REVERT: B 29 ASP cc_start: 0.8563 (m-30) cc_final: 0.8239 (m-30) REVERT: X 64 ARG cc_start: 0.7867 (mtp85) cc_final: 0.7480 (mmm160) REVERT: X 148 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8409 (tt) outliers start: 14 outliers final: 11 residues processed: 106 average time/residue: 0.0651 time to fit residues: 9.6241 Evaluate side-chains 110 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 98 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain X residue 83 THR Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 148 LEU Chi-restraints excluded: chain X residue 173 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 89 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 0.3980 chunk 31 optimal weight: 0.7980 chunk 74 optimal weight: 0.5980 chunk 17 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 67 optimal weight: 0.0670 chunk 76 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.193019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.162000 restraints weight = 8243.177| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.81 r_work: 0.3564 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7592 Z= 0.125 Angle : 0.510 7.241 10279 Z= 0.259 Chirality : 0.041 0.214 1205 Planarity : 0.004 0.038 1267 Dihedral : 9.712 69.611 1062 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.49 % Allowed : 14.02 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.28), residues: 908 helix: 1.27 (0.25), residues: 448 sheet: -1.12 (0.40), residues: 158 loop : -0.56 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 291 TYR 0.012 0.001 TYR C 210 PHE 0.015 0.001 PHE C 99 TRP 0.009 0.001 TRP C 317 HIS 0.003 0.001 HIS D 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.13 ( 7591) covalent geometry : angle 0.50999 / 0.26 (10277) SS BOND : bond 0.00151 / 0.08 ( 1) SS BOND : angle 0.51523 / 0.30 ( 2) hydrogen bonds : bond 0.03088 / 2.12 ( 375) hydrogen bonds : angle 4.44462 / 3.14 ( 1095) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 101 time to evaluate : 0.177 Fit side-chains REVERT: B 28 GLN cc_start: 0.8278 (tt0) cc_final: 0.7920 (tt0) REVERT: B 29 ASP cc_start: 0.8451 (m-30) cc_final: 0.8128 (m-30) REVERT: X 64 ARG cc_start: 0.7869 (mtp85) cc_final: 0.7474 (mmm160) REVERT: X 148 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8386 (tt) outliers start: 12 outliers final: 9 residues processed: 109 average time/residue: 0.0732 time to fit residues: 11.1006 Evaluate side-chains 110 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain X residue 83 THR Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 148 LEU Chi-restraints excluded: chain X residue 173 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 0.9990 chunk 78 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 46 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 6.9990 chunk 31 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 250 HIS ** X 268 HIS ** 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 = 0.4147 r_free = 0.4147 target = 0.191628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.160050 restraints weight = 8166.986| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.86 r_work: 0.3672 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3529 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3529 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7592 Z= 0.150 Angle : 0.525 7.880 10279 Z= 0.265 Chirality : 0.041 0.191 1205 Planarity : 0.004 0.038 1267 Dihedral : 9.697 69.553 1062 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.61 % Allowed : 14.02 % Favored : 84.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.28), residues: 908 helix: 1.24 (0.25), residues: 448 sheet: -1.17 (0.40), residues: 158 loop : -0.57 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 290 TYR 0.013 0.001 TYR C 210 PHE 0.015 0.001 PHE C 99 TRP 0.007 0.001 TRP C 317 HIS 0.008 0.001 HIS X 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.15 ( 7591) covalent geometry : angle 0.52526 / 0.27 (10277) SS BOND : bond 0.00235 / 0.12 ( 1) SS BOND : angle 0.57515 / 0.33 ( 2) hydrogen bonds : bond 0.03145 / 2.16 ( 375) hydrogen bonds : angle 4.46095 / 3.14 ( 1095) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.289 Fit side-chains REVERT: B 28 GLN cc_start: 0.8350 (tt0) cc_final: 0.8022 (tt0) REVERT: B 29 ASP cc_start: 0.8468 (m-30) cc_final: 0.8152 (m-30) REVERT: C 129 VAL cc_start: 0.8160 (p) cc_final: 0.7924 (p) REVERT: X 64 ARG cc_start: 0.7893 (mtp85) cc_final: 0.7510 (mmm160) REVERT: X 148 LEU cc_start: 0.8612 (OUTLIER) cc_final: 0.8393 (tt) outliers start: 13 outliers final: 10 residues processed: 106 average time/residue: 0.0705 time to fit residues: 10.3271 Evaluate side-chains 107 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain X residue 83 THR Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 148 LEU Chi-restraints excluded: chain X residue 173 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 70 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 60 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 67 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 chunk 66 optimal weight: 8.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 250 HIS ** X 268 HIS ** 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 = 0.4104 r_free = 0.4104 target = 0.187684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.157259 restraints weight = 8153.439| |-----------------------------------------------------------------------------| r_work (start): 0.3827 rms_B_bonded: 1.76 r_work: 0.3676 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3534 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7592 Z= 0.141 Angle : 0.524 7.541 10279 Z= 0.266 Chirality : 0.041 0.188 1205 Planarity : 0.004 0.038 1267 Dihedral : 9.681 71.172 1062 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 1.36 % Allowed : 14.39 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.26 (0.28), residues: 908 helix: 1.27 (0.25), residues: 448 sheet: -1.19 (0.40), residues: 158 loop : -0.58 (0.36), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 290 TYR 0.012 0.001 TYR C 210 PHE 0.017 0.001 PHE C 99 TRP 0.008 0.001 TRP C 317 HIS 0.007 0.001 HIS X 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 ( 7591) covalent geometry : angle 0.52441 / 0.27 (10277) SS BOND : bond 0.00218 / 0.11 ( 1) SS BOND : angle 0.58643 / 0.34 ( 2) hydrogen bonds : bond 0.03116 / 2.14 ( 375) hydrogen bonds : angle 4.43761 / 3.13 ( 1095) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 98 time to evaluate : 0.234 Fit side-chains REVERT: B 28 GLN cc_start: 0.8337 (tt0) cc_final: 0.8007 (tt0) REVERT: B 29 ASP cc_start: 0.8474 (m-30) cc_final: 0.8183 (m-30) REVERT: C 129 VAL cc_start: 0.8139 (p) cc_final: 0.7924 (p) REVERT: X 64 ARG cc_start: 0.7874 (mtp85) cc_final: 0.7501 (mmm160) REVERT: X 148 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8395 (tt) outliers start: 11 outliers final: 10 residues processed: 104 average time/residue: 0.0759 time to fit residues: 10.9439 Evaluate side-chains 107 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain C residue 301 LEU Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain X residue 83 THR Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 148 LEU Chi-restraints excluded: chain X residue 173 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 51 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 63 optimal weight: 0.5980 chunk 21 optimal weight: 0.1980 chunk 54 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 79 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 181 GLN C 250 HIS ** X 268 HIS ** 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 = 0.4124 r_free = 0.4124 target = 0.189710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.158734 restraints weight = 8185.069| |-----------------------------------------------------------------------------| r_work (start): 0.3713 rms_B_bonded: 1.80 r_work: 0.3592 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7592 Z= 0.131 Angle : 0.515 7.372 10279 Z= 0.261 Chirality : 0.040 0.184 1205 Planarity : 0.004 0.039 1267 Dihedral : 9.663 73.243 1062 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.86 % Allowed : 14.14 % Favored : 84.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.28), residues: 908 helix: 1.34 (0.25), residues: 448 sheet: -1.21 (0.40), residues: 158 loop : -0.61 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 290 TYR 0.012 0.001 TYR C 210 PHE 0.017 0.001 PHE C 99 TRP 0.007 0.001 TRP C 317 HIS 0.007 0.001 HIS X 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.13 ( 7591) covalent geometry : angle 0.51473 / 0.26 (10277) SS BOND : bond 0.00201 / 0.11 ( 1) SS BOND : angle 0.58961 / 0.34 ( 2) hydrogen bonds : bond 0.03072 / 2.11 ( 375) hydrogen bonds : angle 4.40370 / 3.11 ( 1095) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1745.65 seconds wall clock time: 30 minutes 42.11 seconds (1842.11 seconds total)