Starting phenix.real_space_refine on Fri Jun 6 19:23:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8hmv_34903/06_2025/8hmv_34903.cif Found real_map, /net/cci-nas-00/data/ceres_data/8hmv_34903/06_2025/8hmv_34903.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.91 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8hmv_34903/06_2025/8hmv_34903.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8hmv_34903/06_2025/8hmv_34903.map" model { file = "/net/cci-nas-00/data/ceres_data/8hmv_34903/06_2025/8hmv_34903.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8hmv_34903/06_2025/8hmv_34903.cif" } resolution = 2.91 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= 0.035 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: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 5168 2.51 5 N 1410 2.21 5 O 1497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8127 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2237 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 10, 'TRANS': 263} Chain breaks: 1 Chain: "C" Number of atoms: 1892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1892 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 3 Chain: "B" Number of atoms: 2601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2601 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Time building chain proxies: 5.71, per 1000 atoms: 0.70 Number of scatterers: 8127 At special positions: 0 Unit cell: (79.9, 103.7, 128.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1497 8.00 N 1410 7.00 C 5168 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.01 Conformation dependent library (CDL) restraints added in 1.1 seconds 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1932 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 42.9% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 30 through 55 Processing helix chain 'A' and resid 63 through 82 removed outlier: 4.155A pdb=" N PHE A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 90 Processing helix chain 'A' and resid 97 through 133 removed outlier: 3.579A pdb=" N PHE A 107 " --> pdb=" O GLN A 103 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 141 Processing helix chain 'A' and resid 142 through 161 removed outlier: 3.952A pdb=" N PHE A 161 " --> pdb=" O SER A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 165 Processing helix chain 'A' and resid 173 through 177 removed outlier: 3.627A pdb=" N ASP A 176 " --> pdb=" O TYR A 173 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N VAL A 177 " --> pdb=" O HIS A 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 173 through 177' Processing helix chain 'A' and resid 188 through 233 removed outlier: 5.055A pdb=" N ALA A 201 " --> pdb=" O MET A 197 " (cutoff:3.500A) Proline residue: A 202 - end of helix removed outlier: 3.866A pdb=" N VAL A 207 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG A 231 " --> pdb=" O GLU A 227 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE A 232 " --> pdb=" O ARG A 228 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N SER A 233 " --> pdb=" O GLN A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 278 removed outlier: 3.535A pdb=" N ARG A 256 " --> pdb=" O MET A 252 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N VAL A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE A 261 " --> pdb=" O ILE A 257 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N TYR A 262 " --> pdb=" O THR A 258 " (cutoff:3.500A) Proline residue: A 267 - end of helix Processing helix chain 'A' and resid 282 through 306 removed outlier: 4.038A pdb=" N PHE A 287 " --> pdb=" O ARG A 283 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU A 288 " --> pdb=" O PHE A 284 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N SER A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N PHE A 298 " --> pdb=" O ILE A 294 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N CYS A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 317 Processing helix chain 'C' and resid 12 through 39 removed outlier: 3.956A pdb=" N ALA C 39 " --> pdb=" O GLN C 35 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 51 No H-bonds generated for 'chain 'C' and resid 49 through 51' Processing helix chain 'C' and resid 52 through 60 removed outlier: 3.569A pdb=" N ILE C 56 " --> pdb=" O GLY C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 239 removed outlier: 3.617A pdb=" N GLN C 236 " --> pdb=" O LYS C 233 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N CYS C 237 " --> pdb=" O TRP C 234 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE C 238 " --> pdb=" O ILE C 235 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASN C 239 " --> pdb=" O GLN C 236 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 233 through 239' Processing helix chain 'C' and resid 264 through 279 removed outlier: 3.934A pdb=" N GLU C 268 " --> pdb=" O ASN C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 283 removed outlier: 4.188A pdb=" N ARG C 283 " --> pdb=" O ARG C 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 280 through 283' Processing helix chain 'C' and resid 295 through 303 removed outlier: 3.540A pdb=" N LEU C 302 " --> pdb=" O ALA C 298 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 311 Processing helix chain 'C' and resid 314 through 318 Processing helix chain 'C' and resid 331 through 350 removed outlier: 3.735A pdb=" N THR C 335 " --> pdb=" O ASP C 331 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA C 337 " --> pdb=" O ARG C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 24 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 8 through 24 removed outlier: 3.838A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 removed outlier: 3.696A pdb=" N ASP G 48 " --> pdb=" O ALA G 45 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 45 through 48' Processing helix chain 'N' and resid 28 through 32 removed outlier: 3.863A pdb=" N TYR N 32 " --> pdb=" O PHE N 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 Processing sheet with id=AA1, first strand: chain 'C' and resid 210 through 214 removed outlier: 6.362A pdb=" N HIS C 41 " --> pdb=" O HIS C 220 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N PHE C 222 " --> pdb=" O HIS C 41 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU C 43 " --> pdb=" O PHE C 222 " (cutoff:3.500A) removed outlier: 9.659A pdb=" N ALA C 243 " --> pdb=" O THR C 40 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ARG C 42 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N ILE C 245 " --> pdb=" O ARG C 42 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LEU C 44 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N VAL C 247 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU C 46 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE C 244 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N PHE C 290 " --> pdb=" O ILE C 244 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE C 246 " --> pdb=" O PHE C 290 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL C 287 " --> pdb=" O TYR C 360 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N HIS C 362 " --> pdb=" O VAL C 287 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU C 289 " --> pdb=" O HIS C 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.632A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 4.028A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.253A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.680A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.643A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.400A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.625A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.606A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.591A pdb=" N SER N 71 " --> pdb=" O TYR N 80 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 6.889A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 387 hydrogen bonds defined for protein. 1104 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: 2.23 Time building geometry restraints manager: 2.40 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: 2638 1.34 - 1.46: 1404 1.46 - 1.57: 4192 1.57 - 1.69: 0 1.69 - 1.81: 71 Bond restraints: 8305 Sorted by residual: bond pdb=" CG1 ILE B 58 " pdb=" CD1 ILE B 58 " ideal model delta sigma weight residual 1.513 1.463 0.050 3.90e-02 6.57e+02 1.64e+00 bond pdb=" CG1 ILE B 123 " pdb=" CD1 ILE B 123 " ideal model delta sigma weight residual 1.513 1.470 0.043 3.90e-02 6.57e+02 1.23e+00 bond pdb=" C HIS A 61 " pdb=" O HIS A 61 " ideal model delta sigma weight residual 1.235 1.246 -0.011 1.10e-02 8.26e+03 1.07e+00 bond pdb=" CB ASN C 239 " pdb=" CG ASN C 239 " ideal model delta sigma weight residual 1.516 1.492 0.024 2.50e-02 1.60e+03 9.50e-01 bond pdb=" CB THR B 274 " pdb=" CG2 THR B 274 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.48e-01 ... (remaining 8300 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 11002 1.76 - 3.53: 223 3.53 - 5.29: 22 5.29 - 7.06: 6 7.06 - 8.82: 3 Bond angle restraints: 11256 Sorted by residual: angle pdb=" N ASN A 60 " pdb=" CA ASN A 60 " pdb=" C ASN A 60 " ideal model delta sigma weight residual 111.71 107.92 3.79 1.34e+00 5.57e-01 8.01e+00 angle pdb=" N PHE B 234 " pdb=" CA PHE B 234 " pdb=" C PHE B 234 " ideal model delta sigma weight residual 110.50 114.31 -3.81 1.41e+00 5.03e-01 7.32e+00 angle pdb=" C SER B 74 " pdb=" N GLN B 75 " pdb=" CA GLN B 75 " ideal model delta sigma weight residual 120.31 124.27 -3.96 1.52e+00 4.33e-01 6.79e+00 angle pdb=" C GLY A 169 " pdb=" N LYS A 170 " pdb=" CA LYS A 170 " ideal model delta sigma weight residual 121.59 130.41 -8.82 3.54e+00 7.98e-02 6.21e+00 angle pdb=" CA GLN A 103 " pdb=" CB GLN A 103 " pdb=" CG GLN A 103 " ideal model delta sigma weight residual 114.10 118.76 -4.66 2.00e+00 2.50e-01 5.43e+00 ... (remaining 11251 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.26: 4470 17.26 - 34.51: 373 34.51 - 51.77: 59 51.77 - 69.02: 12 69.02 - 86.28: 8 Dihedral angle restraints: 4922 sinusoidal: 1940 harmonic: 2982 Sorted by residual: dihedral pdb=" CA PRO A 57 " pdb=" C PRO A 57 " pdb=" N LEU A 58 " pdb=" CA LEU A 58 " ideal model delta harmonic sigma weight residual 180.00 -143.08 -36.92 0 5.00e+00 4.00e-02 5.45e+01 dihedral pdb=" CA LEU C 291 " pdb=" C LEU C 291 " pdb=" N ASN C 292 " pdb=" CA ASN C 292 " ideal model delta harmonic sigma weight residual 180.00 -152.38 -27.62 0 5.00e+00 4.00e-02 3.05e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 -153.96 -26.04 0 5.00e+00 4.00e-02 2.71e+01 ... (remaining 4919 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 639 0.028 - 0.056: 372 0.056 - 0.084: 162 0.084 - 0.112: 68 0.112 - 0.140: 24 Chirality restraints: 1265 Sorted by residual: chirality pdb=" CA ILE B 43 " pdb=" N ILE B 43 " pdb=" C ILE B 43 " pdb=" CB ILE B 43 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.92e-01 chirality pdb=" CA TRP A 291 " pdb=" N TRP A 291 " pdb=" C TRP A 291 " pdb=" CB TRP A 291 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.51e-01 chirality pdb=" CA PRO N 100 " pdb=" N PRO N 100 " pdb=" C PRO N 100 " pdb=" CB PRO N 100 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.47e-01 ... (remaining 1262 not shown) Planarity restraints: 1431 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 56 " -0.045 5.00e-02 4.00e+02 6.93e-02 7.68e+00 pdb=" N PRO A 57 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 57 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO A 57 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 266 " 0.031 5.00e-02 4.00e+02 4.60e-02 3.38e+00 pdb=" N PRO A 267 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 267 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 267 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 162 " -0.025 5.00e-02 4.00e+02 3.80e-02 2.30e+00 pdb=" N PRO A 163 " 0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 163 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 163 " -0.021 5.00e-02 4.00e+02 ... (remaining 1428 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 203 2.70 - 3.25: 7636 3.25 - 3.80: 12121 3.80 - 4.35: 16263 4.35 - 4.90: 28420 Nonbonded interactions: 64643 Sorted by model distance: nonbonded pdb=" OG SER B 245 " pdb=" OD1 ASP B 247 " model vdw 2.150 3.040 nonbonded pdb=" OH TYR C 318 " pdb=" OD2 ASP C 343 " model vdw 2.155 3.040 nonbonded pdb=" OD1 ASP B 228 " pdb=" OH TYR N 117 " model vdw 2.213 3.040 nonbonded pdb=" OD1 ASN C 239 " pdb=" NZ LYS B 57 " model vdw 2.232 3.120 nonbonded pdb=" O GLY B 310 " pdb=" NZ LYS B 337 " model vdw 2.240 3.120 ... (remaining 64638 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: 3.170 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.760 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:13.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 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 : 0.005 0.050 8307 Z= 0.218 Angle : 0.635 8.822 11260 Z= 0.361 Chirality : 0.045 0.140 1265 Planarity : 0.004 0.069 1431 Dihedral : 13.376 86.277 2984 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.72 (0.26), residues: 1004 helix: 0.72 (0.26), residues: 400 sheet: -1.04 (0.32), residues: 229 loop : -1.30 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 291 HIS 0.010 0.001 HIS C 357 PHE 0.018 0.002 PHE A 272 TYR 0.016 0.002 TYR C 358 ARG 0.005 0.000 ARG C 265 Details of bonding type rmsd hydrogen bonds : bond 0.17782 ( 387) hydrogen bonds : angle 6.05805 ( 1104) SS BOND : bond 0.00205 ( 2) SS BOND : angle 0.86308 ( 4) covalent geometry : bond 0.00521 ( 8305) covalent geometry : angle 0.63483 (11256) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.854 Fit side-chains REVERT: C 274 LYS cc_start: 0.8181 (ttmt) cc_final: 0.7930 (ttmt) REVERT: B 36 ASN cc_start: 0.7654 (m-40) cc_final: 0.7354 (m-40) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 1.7051 time to fit residues: 174.5693 Evaluate side-chains 83 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.883 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 83 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 47 optimal weight: 3.9990 chunk 57 optimal weight: 0.8980 chunk 89 optimal weight: 0.8980 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 31 GLN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.140782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.108340 restraints weight = 9722.773| |-----------------------------------------------------------------------------| r_work (start): 0.3168 rms_B_bonded: 1.94 r_work: 0.3056 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8307 Z= 0.173 Angle : 0.565 8.781 11260 Z= 0.302 Chirality : 0.044 0.137 1265 Planarity : 0.004 0.064 1431 Dihedral : 4.748 38.322 1116 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.13 % Allowed : 7.77 % Favored : 91.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.21 (0.26), residues: 1004 helix: 1.25 (0.27), residues: 400 sheet: -0.46 (0.33), residues: 216 loop : -1.39 (0.30), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 291 HIS 0.009 0.001 HIS C 357 PHE 0.015 0.002 PHE B 151 TYR 0.015 0.001 TYR C 339 ARG 0.004 0.000 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.05887 ( 387) hydrogen bonds : angle 4.44002 ( 1104) SS BOND : bond 0.00299 ( 2) SS BOND : angle 0.73237 ( 4) covalent geometry : bond 0.00413 ( 8305) covalent geometry : angle 0.56514 (11256) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.889 Fit side-chains REVERT: A 263 ILE cc_start: 0.7684 (tp) cc_final: 0.7470 (tt) REVERT: B 25 CYS cc_start: 0.7897 (t) cc_final: 0.7464 (t) REVERT: B 36 ASN cc_start: 0.7978 (m-40) cc_final: 0.7623 (m-40) REVERT: B 44 GLN cc_start: 0.7632 (pt0) cc_final: 0.7365 (pm20) REVERT: B 52 ARG cc_start: 0.8277 (mtm-85) cc_final: 0.7975 (mtp-110) REVERT: B 197 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8155 (mmt180) REVERT: B 217 MET cc_start: 0.8852 (OUTLIER) cc_final: 0.8226 (ptt) outliers start: 10 outliers final: 4 residues processed: 95 average time/residue: 1.7549 time to fit residues: 174.3873 Evaluate side-chains 91 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 314 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 95 optimal weight: 0.4980 chunk 82 optimal weight: 6.9990 chunk 72 optimal weight: 0.6980 chunk 45 optimal weight: 4.9990 chunk 98 optimal weight: 0.0980 chunk 36 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 chunk 85 optimal weight: 0.1980 chunk 46 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 GLN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN N 31 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.142110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.109542 restraints weight = 9918.577| |-----------------------------------------------------------------------------| r_work (start): 0.3199 rms_B_bonded: 1.98 r_work: 0.3087 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8307 Z= 0.113 Angle : 0.480 7.545 11260 Z= 0.258 Chirality : 0.041 0.129 1265 Planarity : 0.004 0.061 1431 Dihedral : 4.362 36.607 1116 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.13 % Allowed : 10.47 % Favored : 88.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.25 (0.26), residues: 1004 helix: 1.71 (0.27), residues: 400 sheet: -0.11 (0.34), residues: 214 loop : -1.31 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 291 HIS 0.006 0.001 HIS C 357 PHE 0.013 0.001 PHE B 151 TYR 0.012 0.001 TYR C 339 ARG 0.002 0.000 ARG N 72 Details of bonding type rmsd hydrogen bonds : bond 0.04845 ( 387) hydrogen bonds : angle 4.08553 ( 1104) SS BOND : bond 0.00268 ( 2) SS BOND : angle 0.72649 ( 4) covalent geometry : bond 0.00250 ( 8305) covalent geometry : angle 0.47980 (11256) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 1.140 Fit side-chains REVERT: C 268 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7342 (tp30) REVERT: C 294 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.6342 (mp10) REVERT: B 25 CYS cc_start: 0.7913 (t) cc_final: 0.7581 (t) REVERT: B 36 ASN cc_start: 0.8008 (m-40) cc_final: 0.7662 (m-40) REVERT: B 44 GLN cc_start: 0.7600 (pt0) cc_final: 0.7369 (tt0) REVERT: B 52 ARG cc_start: 0.8254 (mtm-85) cc_final: 0.7921 (mtp-110) REVERT: B 217 MET cc_start: 0.8814 (OUTLIER) cc_final: 0.8170 (ptt) outliers start: 10 outliers final: 4 residues processed: 100 average time/residue: 1.5011 time to fit residues: 158.2595 Evaluate side-chains 98 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 185 TRP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 314 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 1 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 10 optimal weight: 0.6980 chunk 75 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 69 optimal weight: 4.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 GLN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.138294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.105799 restraints weight = 9876.473| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.95 r_work: 0.3029 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 8307 Z= 0.224 Angle : 0.590 8.507 11260 Z= 0.312 Chirality : 0.045 0.143 1265 Planarity : 0.004 0.060 1431 Dihedral : 4.639 35.905 1116 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.35 % Allowed : 12.61 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.14 (0.26), residues: 1004 helix: 1.53 (0.26), residues: 406 sheet: -0.14 (0.34), residues: 216 loop : -1.34 (0.30), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 291 HIS 0.010 0.001 HIS C 357 PHE 0.019 0.002 PHE B 234 TYR 0.022 0.002 TYR B 105 ARG 0.004 0.000 ARG N 118 Details of bonding type rmsd hydrogen bonds : bond 0.06157 ( 387) hydrogen bonds : angle 4.28340 ( 1104) SS BOND : bond 0.00386 ( 2) SS BOND : angle 1.14892 ( 4) covalent geometry : bond 0.00554 ( 8305) covalent geometry : angle 0.58942 (11256) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.974 Fit side-chains REVERT: C 268 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7530 (tp30) REVERT: B 25 CYS cc_start: 0.7949 (t) cc_final: 0.7565 (t) REVERT: B 36 ASN cc_start: 0.8022 (m-40) cc_final: 0.7678 (m-40) REVERT: B 52 ARG cc_start: 0.8319 (mtm-85) cc_final: 0.8020 (mtp-110) REVERT: B 217 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8191 (ptt) outliers start: 12 outliers final: 7 residues processed: 90 average time/residue: 1.6540 time to fit residues: 156.2049 Evaluate side-chains 94 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 ILE Chi-restraints excluded: chain A residue 185 TRP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 72 optimal weight: 0.6980 chunk 96 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 49 optimal weight: 8.9990 chunk 27 optimal weight: 0.9980 chunk 94 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 46 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 GLN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 16 ASN ** B 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.141950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.109279 restraints weight = 9769.232| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 1.97 r_work: 0.3075 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.1419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 8307 Z= 0.113 Angle : 0.478 7.284 11260 Z= 0.257 Chirality : 0.041 0.132 1265 Planarity : 0.004 0.059 1431 Dihedral : 4.282 35.238 1116 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.58 % Allowed : 12.84 % Favored : 85.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.46 (0.27), residues: 1004 helix: 1.90 (0.27), residues: 400 sheet: 0.08 (0.35), residues: 214 loop : -1.27 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 291 HIS 0.006 0.001 HIS C 357 PHE 0.012 0.001 PHE B 151 TYR 0.012 0.001 TYR C 339 ARG 0.002 0.000 ARG A 317 Details of bonding type rmsd hydrogen bonds : bond 0.04730 ( 387) hydrogen bonds : angle 3.96483 ( 1104) SS BOND : bond 0.00290 ( 2) SS BOND : angle 0.71204 ( 4) covalent geometry : bond 0.00252 ( 8305) covalent geometry : angle 0.47767 (11256) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.847 Fit side-chains REVERT: C 268 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7487 (tp30) REVERT: C 294 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.6455 (mp10) REVERT: B 19 ARG cc_start: 0.7638 (ttm110) cc_final: 0.7340 (ttp-110) REVERT: B 25 CYS cc_start: 0.7938 (t) cc_final: 0.7630 (t) REVERT: B 36 ASN cc_start: 0.8038 (m-40) cc_final: 0.7721 (m-40) REVERT: B 52 ARG cc_start: 0.8253 (mtm-85) cc_final: 0.8016 (mtp-110) REVERT: B 217 MET cc_start: 0.8834 (OUTLIER) cc_final: 0.8227 (ptt) outliers start: 14 outliers final: 7 residues processed: 99 average time/residue: 1.5414 time to fit residues: 160.3309 Evaluate side-chains 100 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 185 TRP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 6 optimal weight: 0.0670 chunk 84 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 68 optimal weight: 0.0970 chunk 67 optimal weight: 0.9990 chunk 90 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 98 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 GLN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.142843 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.110435 restraints weight = 9781.533| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.94 r_work: 0.3112 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 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 : 0.002 0.034 8307 Z= 0.108 Angle : 0.470 6.982 11260 Z= 0.252 Chirality : 0.041 0.127 1265 Planarity : 0.004 0.058 1431 Dihedral : 4.109 32.935 1116 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.35 % Allowed : 13.40 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.61 (0.27), residues: 1004 helix: 2.05 (0.27), residues: 401 sheet: 0.19 (0.35), residues: 210 loop : -1.25 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 291 HIS 0.006 0.001 HIS C 357 PHE 0.012 0.001 PHE B 292 TYR 0.011 0.001 TYR C 339 ARG 0.002 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.04416 ( 387) hydrogen bonds : angle 3.82612 ( 1104) SS BOND : bond 0.00289 ( 2) SS BOND : angle 0.71835 ( 4) covalent geometry : bond 0.00242 ( 8305) covalent geometry : angle 0.46956 (11256) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.871 Fit side-chains REVERT: C 268 GLU cc_start: 0.7824 (OUTLIER) cc_final: 0.7423 (tp30) REVERT: C 294 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.6260 (mp10) REVERT: B 25 CYS cc_start: 0.7925 (t) cc_final: 0.7686 (t) REVERT: B 36 ASN cc_start: 0.8030 (m-40) cc_final: 0.7723 (m-40) REVERT: B 52 ARG cc_start: 0.8273 (mtm-85) cc_final: 0.7981 (mtp-110) REVERT: B 217 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8549 (pmm) outliers start: 12 outliers final: 3 residues processed: 99 average time/residue: 1.5426 time to fit residues: 160.3462 Evaluate side-chains 93 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 87 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 TRP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 314 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 90 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 GLN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.140410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.107552 restraints weight = 9869.961| |-----------------------------------------------------------------------------| r_work (start): 0.3189 rms_B_bonded: 1.98 r_work: 0.3076 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2951 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 8307 Z= 0.164 Angle : 0.528 7.659 11260 Z= 0.281 Chirality : 0.043 0.143 1265 Planarity : 0.004 0.057 1431 Dihedral : 4.306 32.249 1116 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.80 % Allowed : 14.19 % Favored : 84.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.45 (0.27), residues: 1004 helix: 1.92 (0.26), residues: 400 sheet: -0.05 (0.34), residues: 218 loop : -1.23 (0.30), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 185 HIS 0.007 0.001 HIS C 357 PHE 0.015 0.002 PHE B 151 TYR 0.014 0.002 TYR C 339 ARG 0.003 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.05267 ( 387) hydrogen bonds : angle 3.99364 ( 1104) SS BOND : bond 0.00354 ( 2) SS BOND : angle 0.93100 ( 4) covalent geometry : bond 0.00397 ( 8305) covalent geometry : angle 0.52748 (11256) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.938 Fit side-chains REVERT: C 268 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.7497 (tp30) REVERT: C 294 GLN cc_start: 0.8271 (OUTLIER) cc_final: 0.6291 (mp10) REVERT: B 19 ARG cc_start: 0.7615 (ttm110) cc_final: 0.7362 (ttp-110) REVERT: B 25 CYS cc_start: 0.7892 (t) cc_final: 0.7681 (t) REVERT: B 36 ASN cc_start: 0.8058 (m-40) cc_final: 0.7735 (m-40) REVERT: B 52 ARG cc_start: 0.8262 (mtm-85) cc_final: 0.7974 (mtp-110) REVERT: B 217 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8183 (ptt) outliers start: 16 outliers final: 10 residues processed: 98 average time/residue: 1.5639 time to fit residues: 161.0491 Evaluate side-chains 103 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 185 TRP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 303 ILE Chi-restraints excluded: chain C residue 60 MET Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain C residue 357 HIS Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 314 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 94 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 41 optimal weight: 0.9980 chunk 58 optimal weight: 1.9990 chunk 19 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 31 GLN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.142459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.109799 restraints weight = 9824.484| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.95 r_work: 0.3104 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8307 Z= 0.117 Angle : 0.479 6.976 11260 Z= 0.257 Chirality : 0.042 0.144 1265 Planarity : 0.004 0.057 1431 Dihedral : 4.121 31.501 1116 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.35 % Allowed : 14.53 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.61 (0.27), residues: 1004 helix: 2.05 (0.27), residues: 401 sheet: 0.12 (0.35), residues: 214 loop : -1.19 (0.30), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 291 HIS 0.006 0.001 HIS C 357 PHE 0.013 0.001 PHE B 151 TYR 0.012 0.001 TYR B 59 ARG 0.005 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.04601 ( 387) hydrogen bonds : angle 3.85515 ( 1104) SS BOND : bond 0.00297 ( 2) SS BOND : angle 0.74747 ( 4) covalent geometry : bond 0.00270 ( 8305) covalent geometry : angle 0.47869 (11256) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 1.076 Fit side-chains REVERT: C 268 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7448 (tp30) REVERT: C 294 GLN cc_start: 0.8248 (OUTLIER) cc_final: 0.6257 (mp10) REVERT: B 52 ARG cc_start: 0.8260 (mtm-85) cc_final: 0.7972 (mtp-110) REVERT: B 217 MET cc_start: 0.8828 (OUTLIER) cc_final: 0.8547 (pmm) outliers start: 12 outliers final: 7 residues processed: 98 average time/residue: 1.6282 time to fit residues: 167.7418 Evaluate side-chains 98 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 185 TRP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain C residue 239 ASN Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 85 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 66 optimal weight: 0.0270 chunk 60 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.0442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 GLN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 268 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.141338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.108371 restraints weight = 9939.342| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 1.99 r_work: 0.3084 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2959 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8307 Z= 0.140 Angle : 0.507 7.332 11260 Z= 0.271 Chirality : 0.042 0.153 1265 Planarity : 0.004 0.056 1431 Dihedral : 4.185 30.624 1116 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.80 % Allowed : 14.53 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: 0.56 (0.27), residues: 1004 helix: 2.03 (0.26), residues: 401 sheet: -0.01 (0.34), residues: 218 loop : -1.20 (0.30), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 291 HIS 0.007 0.001 HIS C 357 PHE 0.015 0.001 PHE B 292 TYR 0.013 0.001 TYR C 339 ARG 0.006 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.04932 ( 387) hydrogen bonds : angle 3.90604 ( 1104) SS BOND : bond 0.00331 ( 2) SS BOND : angle 0.83960 ( 4) covalent geometry : bond 0.00334 ( 8305) covalent geometry : angle 0.50715 (11256) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.886 Fit side-chains REVERT: C 268 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7511 (tp30) REVERT: C 294 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.6336 (mp10) REVERT: B 19 ARG cc_start: 0.7655 (ttm110) cc_final: 0.7450 (ttp-110) REVERT: B 52 ARG cc_start: 0.8271 (mtm-85) cc_final: 0.8028 (mtp-110) REVERT: B 217 MET cc_start: 0.8832 (OUTLIER) cc_final: 0.8217 (ptt) outliers start: 16 outliers final: 9 residues processed: 94 average time/residue: 1.6907 time to fit residues: 166.9815 Evaluate side-chains 96 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 185 TRP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain C residue 239 ASN Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain C residue 294 GLN Chi-restraints excluded: chain B residue 17 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain N residue 83 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 23 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 72 optimal weight: 0.0970 chunk 87 optimal weight: 0.7980 chunk 84 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 60 optimal weight: 1.9990 chunk 10 optimal weight: 0.2980 chunk 18 optimal weight: 0.8980 chunk 93 optimal weight: 0.0770 chunk 22 optimal weight: 0.9980 overall best weight: 0.4136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 ASN A 69 GLN C 31 GLN ** C 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 GLN B 268 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.144879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.112404 restraints weight = 9750.321| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 1.94 r_work: 0.3139 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3014 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8307 Z= 0.093 Angle : 0.447 6.219 11260 Z= 0.241 Chirality : 0.040 0.137 1265 Planarity : 0.003 0.056 1431 Dihedral : 3.892 29.374 1116 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.35 % Allowed : 15.20 % Favored : 83.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.80 (0.27), residues: 1004 helix: 2.28 (0.27), residues: 399 sheet: 0.19 (0.35), residues: 212 loop : -1.15 (0.30), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 291 HIS 0.005 0.001 HIS C 357 PHE 0.012 0.001 PHE A 209 TYR 0.010 0.001 TYR C 37 ARG 0.006 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.03955 ( 387) hydrogen bonds : angle 3.68913 ( 1104) SS BOND : bond 0.00260 ( 2) SS BOND : angle 0.61349 ( 4) covalent geometry : bond 0.00196 ( 8305) covalent geometry : angle 0.44703 (11256) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2008 Ramachandran restraints generated. 1004 Oldfield, 0 Emsley, 1004 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 94 time to evaluate : 0.960 Fit side-chains REVERT: A 126 ASP cc_start: 0.8628 (t70) cc_final: 0.8398 (t0) REVERT: C 268 GLU cc_start: 0.7821 (OUTLIER) cc_final: 0.7392 (tp30) REVERT: B 52 ARG cc_start: 0.8271 (mtm-85) cc_final: 0.7965 (mtp-110) REVERT: B 217 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8567 (pmm) outliers start: 12 outliers final: 3 residues processed: 100 average time/residue: 1.5609 time to fit residues: 164.0394 Evaluate side-chains 90 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 THR Chi-restraints excluded: chain A residue 185 TRP Chi-restraints excluded: chain A residue 226 SER Chi-restraints excluded: chain C residue 268 GLU Chi-restraints excluded: chain B residue 217 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 99 random chunks: chunk 35 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 31 optimal weight: 4.9990 chunk 41 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 96 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 31 GLN C 294 GLN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.142991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.110036 restraints weight = 9928.856| |-----------------------------------------------------------------------------| r_work (start): 0.3217 rms_B_bonded: 1.99 r_work: 0.3105 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2979 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8307 Z= 0.119 Angle : 0.480 6.893 11260 Z= 0.257 Chirality : 0.042 0.143 1265 Planarity : 0.004 0.055 1431 Dihedral : 3.965 27.889 1116 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.01 % Allowed : 15.77 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 0.78 (0.27), residues: 1004 helix: 2.22 (0.26), residues: 400 sheet: 0.16 (0.35), residues: 212 loop : -1.11 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 291 HIS 0.006 0.001 HIS C 357 PHE 0.018 0.001 PHE A 298 TYR 0.014 0.001 TYR B 59 ARG 0.005 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.04469 ( 387) hydrogen bonds : angle 3.76094 ( 1104) SS BOND : bond 0.00311 ( 2) SS BOND : angle 0.76654 ( 4) covalent geometry : bond 0.00281 ( 8305) covalent geometry : angle 0.48006 (11256) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6551.41 seconds wall clock time: 114 minutes 4.22 seconds (6844.22 seconds total)