Starting phenix.real_space_refine on Wed Feb 12 07:38:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gbj_29917/02_2025/8gbj_29917.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gbj_29917/02_2025/8gbj_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8gbj_29917/02_2025/8gbj_29917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gbj_29917/02_2025/8gbj_29917.map" model { file = "/net/cci-nas-00/data/ceres_data/8gbj_29917/02_2025/8gbj_29917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gbj_29917/02_2025/8gbj_29917.cif" } resolution = 3.11 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= 0.000 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 5.06, per 1000 atoms: 0.68 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: 2.01 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.81 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: 2.06 Time building geometry restraints manager: 2.25 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: 4232 19.76 - 39.52: 288 39.52 - 59.28: 70 59.28 - 79.04: 31 79.04 - 98.80: 13 Dihedral angle restraints: 4634 sinusoidal: 1963 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 4631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 998 0.057 - 0.113: 187 0.113 - 0.170: 16 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: 1.070 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.380 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 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 7591 Z= 0.417 Angle : 0.818 17.461 10277 Z= 0.372 Chirality : 0.045 0.283 1205 Planarity : 0.004 0.057 1267 Dihedral : 16.138 98.797 2899 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.62 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 (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: 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 TRP 0.014 0.002 TRP C 317 HIS 0.006 0.001 HIS B 50 PHE 0.014 0.001 PHE X 80 TYR 0.023 0.002 TYR B 46 ARG 0.007 0.001 ARG X 224 *********************** 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 : 0.788 Fit side-chains REVERT: B 28 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8147 (tt0) REVERT: B 29 ASP cc_start: 0.8695 (m-30) cc_final: 0.8413 (m-30) outliers start: 3 outliers final: 0 residues processed: 117 average time/residue: 0.2292 time to fit residues: 35.4064 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 : 0.821 ------------------------------------------------------------------------------- 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 76 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 46 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 250 HIS ** X 86 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.188197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.156402 restraints weight = 8109.239| |-----------------------------------------------------------------------------| r_work (start): 0.3697 rms_B_bonded: 1.85 r_work: 0.3567 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 7591 Z= 0.317 Angle : 0.619 9.424 10277 Z= 0.307 Chirality : 0.044 0.153 1205 Planarity : 0.005 0.046 1267 Dihedral : 12.423 76.196 1149 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.50 % Allowed : 6.70 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.03 (0.28), residues: 908 helix: 0.91 (0.25), residues: 448 sheet: -0.76 (0.41), residues: 155 loop : -0.74 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 317 HIS 0.003 0.001 HIS X 86 PHE 0.012 0.001 PHE X 270 TYR 0.016 0.002 TYR B 46 ARG 0.005 0.001 ARG X 64 *********************** 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 115 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 111 time to evaluate : 0.960 Fit side-chains REVERT: B 29 ASP cc_start: 0.8744 (m-30) cc_final: 0.8417 (m-30) REVERT: C 129 VAL cc_start: 0.8366 (p) cc_final: 0.8159 (p) outliers start: 4 outliers final: 3 residues processed: 113 average time/residue: 0.2209 time to fit residues: 33.2892 Evaluate side-chains 104 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 101 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 204 ILE 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 72 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 89 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 4 optimal weight: 0.7980 chunk 87 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 181 GLN C 250 HIS ** X 86 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 = 0.4088 r_free = 0.4088 target = 0.186096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.154496 restraints weight = 8331.781| |-----------------------------------------------------------------------------| r_work (start): 0.3705 rms_B_bonded: 2.08 r_work: 0.3576 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3431 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3431 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7591 Z= 0.283 Angle : 0.573 8.932 10277 Z= 0.289 Chirality : 0.042 0.165 1205 Planarity : 0.004 0.036 1267 Dihedral : 11.217 78.855 1146 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.61 % Allowed : 9.80 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.05 (0.28), residues: 908 helix: 0.89 (0.25), residues: 448 sheet: -0.93 (0.42), residues: 154 loop : -0.77 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 317 HIS 0.005 0.001 HIS X 86 PHE 0.010 0.001 PHE C 211 TYR 0.011 0.001 TYR C 210 ARG 0.004 0.000 ARG D 300 *********************** 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 115 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.749 Fit side-chains REVERT: B 29 ASP cc_start: 0.8654 (m-30) cc_final: 0.8341 (m-30) REVERT: X 64 ARG cc_start: 0.7908 (mtp85) cc_final: 0.7493 (mmm160) outliers start: 13 outliers final: 7 residues processed: 108 average time/residue: 0.1984 time to fit residues: 29.1433 Evaluate side-chains 102 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 95 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 3 VAL Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain X residue 83 THR 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 70 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 66 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 64 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 178 GLN C 250 HIS C 276 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.190864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.159689 restraints weight = 8173.771| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.19 r_work: 0.3536 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 7591 Z= 0.246 Angle : 0.549 8.399 10277 Z= 0.276 Chirality : 0.042 0.195 1205 Planarity : 0.004 0.037 1267 Dihedral : 10.807 79.207 1146 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.49 % Allowed : 11.04 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.01 (0.28), residues: 908 helix: 0.99 (0.25), residues: 448 sheet: -1.06 (0.41), residues: 154 loop : -0.75 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 317 HIS 0.004 0.001 HIS X 86 PHE 0.011 0.001 PHE C 99 TYR 0.011 0.001 TYR C 210 ARG 0.004 0.000 ARG D 291 *********************** 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: 12 poor density : 103 time to evaluate : 0.831 Fit side-chains REVERT: B 28 GLN cc_start: 0.8339 (tt0) cc_final: 0.8045 (tt0) REVERT: B 29 ASP cc_start: 0.8541 (m-30) cc_final: 0.8231 (m-30) REVERT: X 28 GLU cc_start: 0.6826 (tt0) cc_final: 0.6416 (tt0) REVERT: X 64 ARG cc_start: 0.7897 (mtp85) cc_final: 0.7484 (mmm160) outliers start: 12 outliers final: 8 residues processed: 108 average time/residue: 0.2125 time to fit residues: 31.5787 Evaluate side-chains 105 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 3 VAL Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain X residue 83 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 89 optimal weight: 2.9990 chunk 84 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 80 optimal weight: 0.8980 chunk 50 optimal weight: 0.0020 chunk 2 optimal weight: 0.9980 chunk 43 optimal weight: 4.9990 chunk 16 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 250 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.189744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.157982 restraints weight = 8171.962| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 2.27 r_work: 0.3630 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7591 Z= 0.205 Angle : 0.513 7.599 10277 Z= 0.261 Chirality : 0.040 0.171 1205 Planarity : 0.004 0.037 1267 Dihedral : 10.503 81.543 1146 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.11 % Allowed : 12.16 % Favored : 85.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.19 (0.28), residues: 908 helix: 1.18 (0.25), residues: 448 sheet: -1.11 (0.41), residues: 158 loop : -0.64 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 317 HIS 0.003 0.001 HIS X 86 PHE 0.014 0.001 PHE C 99 TYR 0.010 0.001 TYR C 210 ARG 0.003 0.000 ARG D 291 *********************** 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 123 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.795 Fit side-chains REVERT: B 28 GLN cc_start: 0.8350 (tt0) cc_final: 0.8045 (tt0) REVERT: B 29 ASP cc_start: 0.8420 (m-30) cc_final: 0.8101 (m-30) REVERT: C 11 GLN cc_start: 0.7253 (mm-40) cc_final: 0.6941 (mm110) REVERT: X 64 ARG cc_start: 0.7816 (mtp85) cc_final: 0.7409 (mmm160) REVERT: X 89 MET cc_start: 0.7883 (tpt) cc_final: 0.7486 (tpt) REVERT: X 148 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8385 (tt) outliers start: 17 outliers final: 9 residues processed: 118 average time/residue: 0.1981 time to fit residues: 31.9732 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 : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 3 VAL Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain X residue 83 THR Chi-restraints excluded: chain X residue 144 CYS Chi-restraints excluded: chain X residue 148 LEU Chi-restraints excluded: chain X residue 173 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 74 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 2 optimal weight: 0.7980 chunk 59 optimal weight: 0.8980 chunk 73 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 250 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.191142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.159926 restraints weight = 8174.561| |-----------------------------------------------------------------------------| r_work (start): 0.3659 rms_B_bonded: 2.26 r_work: 0.3535 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 7591 Z= 0.221 Angle : 0.524 7.702 10277 Z= 0.264 Chirality : 0.041 0.190 1205 Planarity : 0.004 0.037 1267 Dihedral : 10.360 82.221 1146 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 10.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.24 % Allowed : 13.40 % Favored : 85.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.17 (0.28), residues: 908 helix: 1.19 (0.25), residues: 448 sheet: -1.18 (0.40), residues: 158 loop : -0.64 (0.35), residues: 302 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 317 HIS 0.003 0.001 HIS X 86 PHE 0.015 0.001 PHE C 99 TYR 0.011 0.001 TYR C 210 ARG 0.003 0.000 ARG D 300 *********************** 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 108 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.817 Fit side-chains REVERT: B 28 GLN cc_start: 0.8220 (tt0) cc_final: 0.7856 (tt0) REVERT: B 29 ASP cc_start: 0.8483 (m-30) cc_final: 0.8154 (m-30) REVERT: X 64 ARG cc_start: 0.7851 (mtp85) cc_final: 0.7420 (mmm160) REVERT: X 148 LEU cc_start: 0.8642 (OUTLIER) cc_final: 0.8400 (tt) outliers start: 10 outliers final: 7 residues processed: 103 average time/residue: 0.1988 time to fit residues: 27.8454 Evaluate side-chains 105 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 97 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 24 optimal weight: 5.9990 chunk 71 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 85 optimal weight: 2.9990 chunk 84 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 250 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.183688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.152196 restraints weight = 8272.073| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 1.92 r_work: 0.3536 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 7591 Z= 0.342 Angle : 0.603 9.537 10277 Z= 0.300 Chirality : 0.043 0.175 1205 Planarity : 0.004 0.037 1267 Dihedral : 10.461 81.073 1146 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.49 % Allowed : 14.27 % 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 (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: -0.12 (0.28), residues: 908 helix: 0.86 (0.24), residues: 454 sheet: -1.30 (0.40), residues: 157 loop : -0.65 (0.36), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 317 HIS 0.004 0.001 HIS X 86 PHE 0.017 0.002 PHE C 99 TYR 0.012 0.001 TYR C 210 ARG 0.005 0.000 ARG D 300 *********************** 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 106 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.795 Fit side-chains REVERT: B 28 GLN cc_start: 0.8325 (tt0) cc_final: 0.8019 (tt0) REVERT: B 29 ASP cc_start: 0.8602 (m-30) cc_final: 0.8278 (m-30) REVERT: X 64 ARG cc_start: 0.7804 (mtp85) cc_final: 0.7285 (mmm160) REVERT: X 148 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8464 (tt) outliers start: 12 outliers final: 8 residues processed: 101 average time/residue: 0.2110 time to fit residues: 28.5773 Evaluate side-chains 98 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 89 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 X residue 83 THR Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 144 CYS 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 49 optimal weight: 0.9980 chunk 3 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 18 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 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 = 0.4119 r_free = 0.4119 target = 0.189319 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.158033 restraints weight = 8289.496| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 2.30 r_work: 0.3505 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3358 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3358 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7591 Z= 0.207 Angle : 0.531 7.202 10277 Z= 0.269 Chirality : 0.041 0.229 1205 Planarity : 0.004 0.037 1267 Dihedral : 10.286 86.087 1146 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.36 % Allowed : 14.89 % Favored : 83.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.03 (0.28), residues: 908 helix: 1.08 (0.25), residues: 454 sheet: -1.30 (0.40), residues: 158 loop : -0.72 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 317 HIS 0.003 0.001 HIS X 98 PHE 0.015 0.001 PHE C 99 TYR 0.011 0.001 TYR C 210 ARG 0.003 0.000 ARG D 291 *********************** 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 110 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 99 time to evaluate : 0.872 Fit side-chains REVERT: B 28 GLN cc_start: 0.8237 (tt0) cc_final: 0.7894 (tt0) REVERT: B 29 ASP cc_start: 0.8457 (m-30) cc_final: 0.8138 (m-30) REVERT: D 300 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7591 (pmt170) REVERT: X 64 ARG cc_start: 0.7791 (mtp85) cc_final: 0.7337 (mmm160) REVERT: X 89 MET cc_start: 0.7824 (tpt) cc_final: 0.7596 (tpt) REVERT: X 148 LEU cc_start: 0.8689 (OUTLIER) cc_final: 0.8419 (tt) outliers start: 11 outliers final: 7 residues processed: 107 average time/residue: 0.2092 time to fit residues: 30.1454 Evaluate side-chains 105 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 96 time to evaluate : 0.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 300 ARG Chi-restraints excluded: chain X residue 83 THR Chi-restraints excluded: chain X residue 144 CYS 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 10 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 68 optimal weight: 6.9990 chunk 6 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 chunk 40 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 250 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4080 r_free = 0.4080 target = 0.185490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.153735 restraints weight = 8367.167| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 2.29 r_work: 0.3522 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 7591 Z= 0.296 Angle : 0.582 8.854 10277 Z= 0.292 Chirality : 0.043 0.202 1205 Planarity : 0.004 0.037 1267 Dihedral : 10.369 84.095 1146 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.36 % Allowed : 15.14 % Favored : 83.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.10 (0.28), residues: 908 helix: 0.97 (0.24), residues: 455 sheet: -1.40 (0.40), residues: 158 loop : -0.74 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 317 HIS 0.003 0.001 HIS X 86 PHE 0.018 0.002 PHE C 99 TYR 0.012 0.001 TYR C 210 ARG 0.004 0.000 ARG D 300 *********************** 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 106 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.781 Fit side-chains REVERT: B 28 GLN cc_start: 0.8321 (tt0) cc_final: 0.7991 (tt0) REVERT: B 29 ASP cc_start: 0.8533 (m-30) cc_final: 0.8202 (m-30) REVERT: D 105 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8831 (mm) REVERT: D 300 ARG cc_start: 0.8055 (OUTLIER) cc_final: 0.7761 (pmt170) REVERT: X 64 ARG cc_start: 0.7759 (mtp85) cc_final: 0.7256 (mmm160) REVERT: X 148 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8381 (tt) outliers start: 11 outliers final: 7 residues processed: 102 average time/residue: 0.2167 time to fit residues: 29.6261 Evaluate side-chains 105 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 105 ILE Chi-restraints excluded: chain D residue 300 ARG Chi-restraints excluded: chain X residue 83 THR Chi-restraints excluded: chain X residue 144 CYS 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 52 optimal weight: 1.9990 chunk 10 optimal weight: 0.1980 chunk 51 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 7 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 76 optimal weight: 0.4980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 250 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.195845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.165620 restraints weight = 8252.473| |-----------------------------------------------------------------------------| r_work (start): 0.3844 rms_B_bonded: 1.95 r_work: 0.3683 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7591 Z= 0.196 Angle : 0.528 7.398 10277 Z= 0.267 Chirality : 0.041 0.184 1205 Planarity : 0.004 0.038 1267 Dihedral : 10.248 89.516 1146 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.12 % Allowed : 16.00 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.15 (0.28), residues: 908 helix: 1.21 (0.25), residues: 454 sheet: -1.26 (0.40), residues: 158 loop : -0.71 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 317 HIS 0.002 0.001 HIS X 237 PHE 0.017 0.001 PHE C 99 TYR 0.010 0.001 TYR C 210 ARG 0.003 0.000 ARG D 291 ********************** 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 110 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 101 time to evaluate : 0.666 Fit side-chains REVERT: B 28 GLN cc_start: 0.8275 (tt0) cc_final: 0.7926 (tp40) REVERT: B 29 ASP cc_start: 0.8462 (m-30) cc_final: 0.8171 (m-30) REVERT: C 129 VAL cc_start: 0.8228 (p) cc_final: 0.8026 (p) REVERT: X 64 ARG cc_start: 0.7831 (mtp85) cc_final: 0.7369 (mmm160) REVERT: X 148 LEU cc_start: 0.8451 (OUTLIER) cc_final: 0.8195 (tt) REVERT: X 239 MET cc_start: 0.7870 (mtt) cc_final: 0.7450 (mtt) outliers start: 9 outliers final: 7 residues processed: 106 average time/residue: 0.1986 time to fit residues: 28.9720 Evaluate side-chains 106 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 98 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 X residue 83 THR Chi-restraints excluded: chain X residue 144 CYS 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 44 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 83 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 58 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 35 optimal weight: 4.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 250 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.195543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.164884 restraints weight = 8202.730| |-----------------------------------------------------------------------------| r_work (start): 0.3838 rms_B_bonded: 2.17 r_work: 0.3673 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7591 Z= 0.210 Angle : 0.533 7.555 10277 Z= 0.270 Chirality : 0.041 0.196 1205 Planarity : 0.004 0.038 1267 Dihedral : 10.207 88.441 1146 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.36 % Allowed : 16.25 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.18 (0.28), residues: 908 helix: 1.25 (0.25), residues: 455 sheet: -1.26 (0.40), residues: 158 loop : -0.71 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 317 HIS 0.004 0.001 HIS C 307 PHE 0.018 0.001 PHE C 99 TYR 0.011 0.001 TYR C 210 ARG 0.003 0.000 ARG D 291 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3897.41 seconds wall clock time: 70 minutes 6.08 seconds (4206.08 seconds total)