Starting phenix.real_space_refine on Thu Jul 2 07:04:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7f6h_31480/07_2026/7f6h_31480.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f6h_31480/07_2026/7f6h_31480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f6h_31480/07_2026/7f6h_31480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f6h_31480/07_2026/7f6h_31480.map" model { file = "/net/cci-nas-00/data/ceres_data/7f6h_31480/07_2026/7f6h_31480.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f6h_31480/07_2026/7f6h_31480.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/7f6h_31480/07_2026/7f6h_31480.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7f6h_31480/07_2026/7f6h_31480.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 57 5.16 5 C 4701 2.51 5 N 1243 2.21 5 O 1341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7342 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 305, 2448 Classifications: {'peptide': 305} Link IDs: {'PTRANS': 9, 'TRANS': 295} Chain: "L" Number of atoms: 75 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 75 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 3, 'TRANS': 5} Chain: "B" Number of atoms: 1873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1873 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 220} Chain breaks: 1 Chain: "C" Number of atoms: 2530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2530 Classifications: {'peptide': 330} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 324} Chain: "D" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 360 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 4, 'TRANS': 42} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.44, per 1000 atoms: 0.20 Number of scatterers: 7342 At special positions: 0 Unit cell: (101.4, 93.288, 123.708, 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 57 16.00 O 1341 8.00 N 1243 7.00 C 4701 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 47 " - pdb=" SG CYS A 304 " distance=2.03 Simple disulfide: pdb=" SG CYS A 130 " - pdb=" SG CYS A 211 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.48 Conformation dependent library (CDL) restraints added in 476.4 milliseconds 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1738 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 9 sheets defined 44.6% alpha, 18.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 51 through 85 removed outlier: 3.649A pdb=" N TRP A 55 " --> pdb=" O GLU A 51 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N THR A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) Proline residue: A 61 - end of helix removed outlier: 3.553A pdb=" N HIS A 85 " --> pdb=" O VAL A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 119 Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 126 through 160 Processing helix chain 'A' and resid 170 through 196 Proline residue: A 191 - end of helix Processing helix chain 'A' and resid 217 through 230 removed outlier: 3.770A pdb=" N GLU A 221 " --> pdb=" O SER A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 254 Processing helix chain 'A' and resid 265 through 298 removed outlier: 3.536A pdb=" N THR A 269 " --> pdb=" O GLU A 265 " (cutoff:3.500A) Proline residue: A 285 - end of helix Processing helix chain 'A' and resid 303 through 318 Processing helix chain 'A' and resid 319 through 333 removed outlier: 3.792A pdb=" N SER A 325 " --> pdb=" O ALA A 321 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N CYS A 326 " --> pdb=" O TYR A 322 " (cutoff:3.500A) Proline residue: A 329 - end of helix Processing helix chain 'A' and resid 336 through 351 Processing helix chain 'B' and resid 15 through 37 Processing helix chain 'B' and resid 51 through 63 Processing helix chain 'B' and resid 212 through 217 removed outlier: 4.112A pdb=" N TRP B 216 " --> pdb=" O GLU B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 221 Processing helix chain 'B' and resid 233 through 237 removed outlier: 3.879A pdb=" N ASP B 236 " --> pdb=" O SER B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 246 through 261 removed outlier: 3.511A pdb=" N GLU B 250 " --> pdb=" O ASN B 246 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR B 261 " --> pdb=" O THR B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 262 through 265 removed outlier: 3.737A pdb=" N GLN B 265 " --> pdb=" O PRO B 262 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 262 through 265' Processing helix chain 'B' and resid 275 through 283 Processing helix chain 'B' and resid 303 through 315 removed outlier: 3.816A pdb=" N GLU B 307 " --> pdb=" O GLN B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 356 Processing helix chain 'C' and resid 12 through 25 Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 16 through 24 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.517A pdb=" N ASN D 59 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 200 through 201 Processing sheet with id=AA2, first strand: chain 'B' and resid 190 through 195 removed outlier: 3.631A pdb=" N ILE B 190 " --> pdb=" O ASP B 205 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N LEU B 40 " --> pdb=" O ARG B 202 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL B 204 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU B 42 " --> pdb=" O VAL B 204 " (cutoff:3.500A) removed outlier: 9.959A pdb=" N SER B 225 " --> pdb=" O GLU B 39 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LYS B 41 " --> pdb=" O SER B 225 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N MET B 227 " --> pdb=" O LYS B 41 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU B 43 " --> pdb=" O MET B 227 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU B 229 " --> pdb=" O LEU B 43 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N LEU B 45 " --> pdb=" O LEU B 229 " (cutoff:3.500A) removed outlier: 8.760A pdb=" N ALA B 231 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N VAL B 269 " --> pdb=" O TYR B 325 " (cutoff:3.500A) removed outlier: 8.174A pdb=" N HIS B 327 " --> pdb=" O VAL B 269 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N LEU B 271 " --> pdb=" O HIS B 327 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 52 removed outlier: 6.012A pdb=" N THR C 47 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N ASN C 340 " --> pdb=" O THR C 47 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N PHE C 335 " --> pdb=" O SER C 331 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER C 331 " --> pdb=" O PHE C 335 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.649A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ASP C 83 " --> pdb=" O LYS C 89 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N LYS C 89 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.863A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.752A pdb=" N CYS C 166 " --> pdb=" O THR C 179 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N THR C 179 " --> pdb=" O CYS C 166 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N LEU C 168 " --> pdb=" O THR C 177 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 187 through 192 removed outlier: 4.039A pdb=" N SER C 207 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA C 208 " --> pdb=" O THR C 221 " (cutoff:3.500A) removed outlier: 4.633A pdb=" N THR C 221 " --> pdb=" O ALA C 208 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU C 210 " --> pdb=" O ARG C 219 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.172A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 5.929A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 273 through 278 removed outlier: 6.663A pdb=" N GLY C 288 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N VAL C 276 " --> pdb=" O LEU C 286 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU C 286 " --> pdb=" O VAL C 276 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N PHE C 278 " --> pdb=" O LEU C 284 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N LEU C 284 " --> pdb=" O PHE C 278 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N CYS C 294 " --> pdb=" O VAL C 307 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N VAL C 307 " --> pdb=" O CYS C 294 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N VAL C 296 " --> pdb=" O ALA C 305 " (cutoff:3.500A) 367 hydrogen bonds defined for protein. 1080 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: 0.87 Time building geometry restraints manager: 0.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 2304 1.34 - 1.46: 1658 1.46 - 1.58: 3450 1.58 - 1.71: 0 1.71 - 1.83: 84 Bond restraints: 7496 Sorted by residual: bond pdb=" C10 CLR A 501 " pdb=" C5 CLR A 501 " ideal model delta sigma weight residual 1.519 1.383 0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" C10 CLR A 502 " pdb=" C5 CLR A 502 " ideal model delta sigma weight residual 1.519 1.387 0.132 2.00e-02 2.50e+03 4.37e+01 bond pdb=" C4 CLR A 501 " pdb=" C5 CLR A 501 " ideal model delta sigma weight residual 1.506 1.381 0.125 2.00e-02 2.50e+03 3.93e+01 bond pdb=" C4 CLR A 502 " pdb=" C5 CLR A 502 " ideal model delta sigma weight residual 1.506 1.383 0.123 2.00e-02 2.50e+03 3.76e+01 bond pdb=" C6 CLR A 501 " pdb=" C7 CLR A 501 " ideal model delta sigma weight residual 1.492 1.390 0.102 2.00e-02 2.50e+03 2.62e+01 ... (remaining 7491 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 9527 1.99 - 3.98: 576 3.98 - 5.97: 51 5.97 - 7.96: 16 7.96 - 9.95: 1 Bond angle restraints: 10171 Sorted by residual: angle pdb=" N PRO A 61 " pdb=" CA PRO A 61 " pdb=" C PRO A 61 " ideal model delta sigma weight residual 110.70 118.46 -7.76 1.22e+00 6.72e-01 4.04e+01 angle pdb=" N LEU B 358 " pdb=" CA LEU B 358 " pdb=" C LEU B 358 " ideal model delta sigma weight residual 113.41 106.93 6.48 1.22e+00 6.72e-01 2.83e+01 angle pdb=" CA PRO A 61 " pdb=" C PRO A 61 " pdb=" N PRO A 62 " ideal model delta sigma weight residual 117.93 124.19 -6.26 1.20e+00 6.94e-01 2.72e+01 angle pdb=" C ILE C 81 " pdb=" N TRP C 82 " pdb=" CA TRP C 82 " ideal model delta sigma weight residual 122.64 129.12 -6.48 1.70e+00 3.46e-01 1.45e+01 angle pdb=" CA ASN C 36 " pdb=" C ASN C 36 " pdb=" O ASN C 36 " ideal model delta sigma weight residual 122.63 117.75 4.88 1.29e+00 6.01e-01 1.43e+01 ... (remaining 10166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.95: 4235 23.95 - 47.90: 207 47.90 - 71.86: 14 71.86 - 95.81: 3 95.81 - 119.76: 2 Dihedral angle restraints: 4461 sinusoidal: 1786 harmonic: 2675 Sorted by residual: dihedral pdb=" CB CYS A 47 " pdb=" SG CYS A 47 " pdb=" SG CYS A 304 " pdb=" CB CYS A 304 " ideal model delta sinusoidal sigma weight residual 93.00 137.05 -44.05 1 1.00e+01 1.00e-02 2.70e+01 dihedral pdb=" CA THR A 209 " pdb=" C THR A 209 " pdb=" N ALA A 210 " pdb=" CA ALA A 210 " ideal model delta harmonic sigma weight residual -180.00 -156.62 -23.38 0 5.00e+00 4.00e-02 2.19e+01 dihedral pdb=" C10 CLR A 502 " pdb=" C1 CLR A 502 " pdb=" C2 CLR A 502 " pdb=" C3 CLR A 502 " ideal model delta sinusoidal sigma weight residual -56.83 62.93 -119.76 1 3.00e+01 1.11e-03 1.60e+01 ... (remaining 4458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 1035 0.097 - 0.193: 114 0.193 - 0.290: 12 0.290 - 0.386: 7 0.386 - 0.483: 2 Chirality restraints: 1170 Sorted by residual: chirality pdb=" C14 CLR A 502 " pdb=" C13 CLR A 502 " pdb=" C15 CLR A 502 " pdb=" C8 CLR A 502 " both_signs ideal model delta sigma weight residual False -2.32 -2.80 0.48 2.00e-01 2.50e+01 5.83e+00 chirality pdb=" C14 CLR A 501 " pdb=" C13 CLR A 501 " pdb=" C15 CLR A 501 " pdb=" C8 CLR A 501 " both_signs ideal model delta sigma weight residual False -2.32 -2.75 0.44 2.00e-01 2.50e+01 4.75e+00 chirality pdb=" C10 CLR A 502 " pdb=" C1 CLR A 502 " pdb=" C5 CLR A 502 " pdb=" C9 CLR A 502 " both_signs ideal model delta sigma weight residual False -2.85 -2.46 -0.38 2.00e-01 2.50e+01 3.70e+00 ... (remaining 1167 not shown) Planarity restraints: 1273 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS C 218 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.68e+00 pdb=" C CYS C 218 " -0.048 2.00e-02 2.50e+03 pdb=" O CYS C 218 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG C 219 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 105 " 0.012 2.00e-02 2.50e+03 1.44e-02 4.16e+00 pdb=" CG TYR C 105 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR C 105 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR C 105 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR C 105 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TYR C 105 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR C 105 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 105 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA C 140 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.18e+00 pdb=" C ALA C 140 " -0.031 2.00e-02 2.50e+03 pdb=" O ALA C 140 " 0.011 2.00e-02 2.50e+03 pdb=" N GLY C 141 " 0.011 2.00e-02 2.50e+03 ... (remaining 1270 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1516 2.78 - 3.31: 6876 3.31 - 3.84: 11724 3.84 - 4.37: 14566 4.37 - 4.90: 25223 Nonbonded interactions: 59905 Sorted by model distance: nonbonded pdb=" O ARG C 68 " pdb=" OG SER C 84 " model vdw 2.246 3.040 nonbonded pdb=" O MET A 320 " pdb=" OG SER A 323 " model vdw 2.314 3.040 nonbonded pdb=" NH2 ARG A 196 " pdb=" O GLY L 4 " model vdw 2.332 3.120 nonbonded pdb=" NZ LYS A 260 " pdb=" OD2 ASP B 346 " model vdw 2.345 3.120 nonbonded pdb=" OE2 GLU B 17 " pdb=" NH2 ARG B 20 " model vdw 2.363 3.120 ... (remaining 59900 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: 1.170 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.200 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 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 : 0.011 0.136 7498 Z= 0.555 Angle : 0.991 9.952 10175 Z= 0.608 Chirality : 0.069 0.483 1170 Planarity : 0.004 0.042 1273 Dihedral : 13.234 119.760 2717 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.87 % Allowed : 1.74 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.26), residues: 905 helix: 1.16 (0.25), residues: 390 sheet: 0.06 (0.38), residues: 175 loop : -1.67 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 251 TYR 0.033 0.003 TYR C 105 PHE 0.022 0.003 PHE A 319 TRP 0.028 0.003 TRP C 82 HIS 0.014 0.003 HIS C 225 Details of bonding type rmsd/Z covalent geometry : bond 0.01101 / 0.55 ( 7496) covalent geometry : angle 0.98986 / 0.61 (10171) SS BOND : bond 0.00682 / 0.33 ( 2) SS BOND : angle 2.87664 / 1.17 ( 4) hydrogen bonds : bond 0.12866 / 8.37 ( 367) hydrogen bonds : angle 5.37487 / 4.02 ( 1080) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 118 time to evaluate : 0.172 Fit side-chains REVERT: A 184 CYS cc_start: 0.7103 (m) cc_final: 0.6494 (m) REVERT: B 32 ASP cc_start: 0.7491 (m-30) cc_final: 0.7289 (m-30) REVERT: C 217 MET cc_start: 0.7725 (ptm) cc_final: 0.7471 (ptm) REVERT: C 322 ASP cc_start: 0.7862 (m-30) cc_final: 0.7586 (m-30) outliers start: 7 outliers final: 2 residues processed: 125 average time/residue: 0.5136 time to fit residues: 67.8953 Evaluate side-chains 95 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 93 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 199 VAL Chi-restraints excluded: chain B residue 230 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 206 HIS A 246 GLN A 324 ASN B 246 ASN C 88 ASN C 220 GLN C 340 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.155577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.120667 restraints weight = 7955.015| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.51 r_work: 0.3223 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3065 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7498 Z= 0.152 Angle : 0.572 10.396 10175 Z= 0.302 Chirality : 0.043 0.134 1170 Planarity : 0.004 0.039 1273 Dihedral : 6.741 110.866 1014 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.48 % Allowed : 9.93 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.27), residues: 905 helix: 1.97 (0.25), residues: 389 sheet: -0.28 (0.37), residues: 188 loop : -1.31 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 196 TYR 0.017 0.001 TYR A 215 PHE 0.014 0.001 PHE C 199 TRP 0.016 0.001 TRP C 82 HIS 0.004 0.001 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 7496) covalent geometry : angle 0.57034 / 0.30 (10171) SS BOND : bond 0.00348 / 0.17 ( 2) SS BOND : angle 2.21737 / 0.87 ( 4) hydrogen bonds : bond 0.05424 / 3.45 ( 367) hydrogen bonds : angle 4.36497 / 3.18 ( 1080) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 101 time to evaluate : 0.206 Fit side-chains REVERT: B 35 ASP cc_start: 0.6726 (m-30) cc_final: 0.6059 (m-30) REVERT: B 303 GLN cc_start: 0.7528 (tm-30) cc_final: 0.7211 (tm-30) REVERT: C 96 ARG cc_start: 0.8262 (ttm170) cc_final: 0.8055 (ttm110) REVERT: C 322 ASP cc_start: 0.8187 (m-30) cc_final: 0.7885 (m-30) REVERT: D 42 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7604 (mt-10) outliers start: 20 outliers final: 7 residues processed: 115 average time/residue: 0.4938 time to fit residues: 60.1990 Evaluate side-chains 101 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 312 VAL Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain C residue 274 THR Chi-restraints excluded: chain C residue 331 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 87 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 41 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 57 optimal weight: 0.0770 chunk 61 optimal weight: 0.6980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN A 263 GLN ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 HIS C 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.157173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.122226 restraints weight = 7867.699| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 2.52 r_work: 0.3240 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7797 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7498 Z= 0.125 Angle : 0.520 10.002 10175 Z= 0.274 Chirality : 0.041 0.133 1170 Planarity : 0.003 0.039 1273 Dihedral : 6.655 113.349 1013 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.61 % Allowed : 13.28 % Favored : 84.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.27), residues: 905 helix: 2.28 (0.25), residues: 390 sheet: -0.27 (0.37), residues: 188 loop : -1.27 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 252 TYR 0.007 0.001 TYR C 59 PHE 0.013 0.001 PHE C 234 TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 7496) covalent geometry : angle 0.51886 / 0.27 (10171) SS BOND : bond 0.00296 / 0.14 ( 2) SS BOND : angle 2.00886 / 0.77 ( 4) hydrogen bonds : bond 0.04712 / 3.00 ( 367) hydrogen bonds : angle 4.11461 / 2.99 ( 1080) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 0.278 Fit side-chains REVERT: A 192 MET cc_start: 0.7387 (mmm) cc_final: 0.7120 (mmp) REVERT: A 203 ASP cc_start: 0.7932 (m-30) cc_final: 0.7632 (m-30) REVERT: A 330 LEU cc_start: 0.8287 (tp) cc_final: 0.7975 (mt) REVERT: B 32 ASP cc_start: 0.6711 (m-30) cc_final: 0.6378 (m-30) REVERT: B 35 ASP cc_start: 0.6541 (m-30) cc_final: 0.5869 (m-30) REVERT: B 303 GLN cc_start: 0.7383 (tm-30) cc_final: 0.6972 (tm-30) REVERT: C 217 MET cc_start: 0.7918 (ptp) cc_final: 0.7241 (ptm) REVERT: C 254 ASP cc_start: 0.7908 (t0) cc_final: 0.7678 (t0) REVERT: C 311 HIS cc_start: 0.7871 (OUTLIER) cc_final: 0.5637 (m90) REVERT: C 322 ASP cc_start: 0.8033 (m-30) cc_final: 0.7725 (m-30) REVERT: D 42 GLU cc_start: 0.7916 (mt-10) cc_final: 0.7478 (mt-10) outliers start: 21 outliers final: 8 residues processed: 115 average time/residue: 0.4709 time to fit residues: 57.6737 Evaluate side-chains 100 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 356 TYR Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 331 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 51 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 87 optimal weight: 0.1980 chunk 6 optimal weight: 1.9990 chunk 52 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 ASN A 134 ASN A 263 GLN A 315 GLN C 340 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.154238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.118828 restraints weight = 8022.269| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.53 r_work: 0.3202 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 7498 Z= 0.154 Angle : 0.554 11.149 10175 Z= 0.289 Chirality : 0.043 0.139 1170 Planarity : 0.004 0.040 1273 Dihedral : 6.621 111.466 1013 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.72 % Allowed : 14.14 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.28), residues: 905 helix: 2.28 (0.25), residues: 391 sheet: -0.34 (0.37), residues: 190 loop : -1.27 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 96 TYR 0.014 0.001 TYR A 215 PHE 0.014 0.002 PHE A 319 TRP 0.014 0.001 TRP C 82 HIS 0.005 0.001 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 ( 7496) covalent geometry : angle 0.55295 / 0.29 (10171) SS BOND : bond 0.00371 / 0.18 ( 2) SS BOND : angle 1.96590 / 0.77 ( 4) hydrogen bonds : bond 0.05178 / 3.29 ( 367) hydrogen bonds : angle 4.16278 / 3.02 ( 1080) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 101 time to evaluate : 0.254 Fit side-chains REVERT: A 192 MET cc_start: 0.7563 (mmm) cc_final: 0.7295 (mmp) REVERT: B 35 ASP cc_start: 0.6681 (m-30) cc_final: 0.6009 (m-30) REVERT: B 57 LYS cc_start: 0.6433 (OUTLIER) cc_final: 0.5946 (ttmt) REVERT: B 225 SER cc_start: 0.8909 (t) cc_final: 0.8655 (m) REVERT: B 303 GLN cc_start: 0.7562 (tm-30) cc_final: 0.7066 (tm-30) REVERT: C 217 MET cc_start: 0.7997 (ptp) cc_final: 0.7540 (ptm) REVERT: C 254 ASP cc_start: 0.8253 (t0) cc_final: 0.8018 (t0) REVERT: C 322 ASP cc_start: 0.8206 (m-30) cc_final: 0.7889 (m-30) REVERT: D 42 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7607 (mt-10) outliers start: 30 outliers final: 13 residues processed: 125 average time/residue: 0.4366 time to fit residues: 58.2754 Evaluate side-chains 107 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 93 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain B residue 57 LYS Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 38 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 68 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 51 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 ASN A 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.154616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.119307 restraints weight = 7918.577| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.53 r_work: 0.3204 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7498 Z= 0.143 Angle : 0.544 11.423 10175 Z= 0.282 Chirality : 0.042 0.137 1170 Planarity : 0.004 0.040 1273 Dihedral : 6.607 111.405 1013 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 3.72 % Allowed : 14.27 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.28), residues: 905 helix: 2.35 (0.26), residues: 390 sheet: -0.38 (0.37), residues: 192 loop : -1.20 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 96 TYR 0.014 0.001 TYR A 215 PHE 0.013 0.001 PHE C 199 TRP 0.016 0.001 TRP C 82 HIS 0.004 0.001 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 ( 7496) covalent geometry : angle 0.54275 / 0.28 (10171) SS BOND : bond 0.00358 / 0.17 ( 2) SS BOND : angle 1.95392 / 0.75 ( 4) hydrogen bonds : bond 0.04940 / 3.13 ( 367) hydrogen bonds : angle 4.09040 / 2.97 ( 1080) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.281 Fit side-chains REVERT: A 207 ASN cc_start: 0.7499 (OUTLIER) cc_final: 0.7198 (m-40) REVERT: A 330 LEU cc_start: 0.8300 (tp) cc_final: 0.8008 (mt) REVERT: B 32 ASP cc_start: 0.6710 (m-30) cc_final: 0.6438 (m-30) REVERT: B 35 ASP cc_start: 0.6654 (m-30) cc_final: 0.5972 (m-30) REVERT: B 225 SER cc_start: 0.8899 (t) cc_final: 0.8624 (m) REVERT: B 259 ILE cc_start: 0.7779 (OUTLIER) cc_final: 0.7063 (pt) REVERT: B 303 GLN cc_start: 0.7600 (tm-30) cc_final: 0.7119 (tm-30) REVERT: C 217 MET cc_start: 0.8062 (ptp) cc_final: 0.7540 (ptm) REVERT: C 254 ASP cc_start: 0.8261 (t0) cc_final: 0.7989 (t0) REVERT: C 311 HIS cc_start: 0.7810 (OUTLIER) cc_final: 0.5744 (m90) REVERT: C 322 ASP cc_start: 0.8243 (m-30) cc_final: 0.7931 (m-30) REVERT: D 42 GLU cc_start: 0.7957 (mt-10) cc_final: 0.7597 (mt-10) outliers start: 30 outliers final: 17 residues processed: 115 average time/residue: 0.4616 time to fit residues: 56.4332 Evaluate side-chains 114 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 207 ASN Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 260 LYS Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 38 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 27 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 28 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 52 optimal weight: 4.9990 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 ASN A 134 ASN C 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.154911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.119574 restraints weight = 7936.588| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 2.53 r_work: 0.3207 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7498 Z= 0.137 Angle : 0.538 11.673 10175 Z= 0.278 Chirality : 0.042 0.136 1170 Planarity : 0.004 0.040 1273 Dihedral : 6.536 110.942 1013 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 4.34 % Allowed : 15.01 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.84 (0.28), residues: 905 helix: 2.41 (0.26), residues: 390 sheet: -0.39 (0.37), residues: 192 loop : -1.17 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 96 TYR 0.013 0.001 TYR A 215 PHE 0.013 0.001 PHE B 255 TRP 0.018 0.001 TRP C 82 HIS 0.004 0.001 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.14 ( 7496) covalent geometry : angle 0.53640 / 0.28 (10171) SS BOND : bond 0.00312 / 0.15 ( 2) SS BOND : angle 1.91003 / 0.73 ( 4) hydrogen bonds : bond 0.04832 / 3.06 ( 367) hydrogen bonds : angle 4.06474 / 2.95 ( 1080) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 96 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 322 TYR cc_start: 0.8598 (OUTLIER) cc_final: 0.8357 (m-80) REVERT: A 330 LEU cc_start: 0.8295 (tp) cc_final: 0.7977 (mt) REVERT: B 32 ASP cc_start: 0.6690 (m-30) cc_final: 0.6381 (m-30) REVERT: B 35 ASP cc_start: 0.6568 (m-30) cc_final: 0.5837 (m-30) REVERT: B 225 SER cc_start: 0.8828 (t) cc_final: 0.8551 (m) REVERT: B 303 GLN cc_start: 0.7498 (tm-30) cc_final: 0.7053 (tm-30) REVERT: B 349 LEU cc_start: 0.7757 (OUTLIER) cc_final: 0.7527 (tp) REVERT: C 234 PHE cc_start: 0.8846 (OUTLIER) cc_final: 0.8313 (m-80) REVERT: C 254 ASP cc_start: 0.7937 (t0) cc_final: 0.7673 (t0) REVERT: C 311 HIS cc_start: 0.7699 (OUTLIER) cc_final: 0.5658 (m90) REVERT: C 322 ASP cc_start: 0.8080 (m-30) cc_final: 0.7765 (m-30) REVERT: D 42 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7523 (mt-10) outliers start: 35 outliers final: 18 residues processed: 121 average time/residue: 0.4335 time to fit residues: 55.9992 Evaluate side-chains 116 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 322 TYR Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain D residue 38 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 0.0770 chunk 75 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 61 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.3344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 ASN A 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.152082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.116178 restraints weight = 8034.401| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 2.55 r_work: 0.3165 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7966 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 0.054 7498 Z= 0.192 Angle : 0.597 13.508 10175 Z= 0.307 Chirality : 0.044 0.141 1170 Planarity : 0.004 0.041 1273 Dihedral : 6.675 110.521 1013 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 4.34 % Allowed : 15.38 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.28), residues: 905 helix: 2.22 (0.26), residues: 390 sheet: -0.43 (0.37), residues: 192 loop : -1.20 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 96 TYR 0.013 0.001 TYR C 59 PHE 0.015 0.002 PHE B 255 TRP 0.019 0.002 TRP C 82 HIS 0.005 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.19 ( 7496) covalent geometry : angle 0.59602 / 0.31 (10171) SS BOND : bond 0.00410 / 0.20 ( 2) SS BOND : angle 2.02153 / 0.79 ( 4) hydrogen bonds : bond 0.05668 / 3.58 ( 367) hydrogen bonds : angle 4.23232 / 3.09 ( 1080) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 95 time to evaluate : 0.185 Fit side-chains REVERT: A 330 LEU cc_start: 0.8339 (tp) cc_final: 0.8045 (mp) REVERT: B 32 ASP cc_start: 0.6781 (m-30) cc_final: 0.6492 (m-30) REVERT: B 35 ASP cc_start: 0.6724 (m-30) cc_final: 0.5986 (m-30) REVERT: B 225 SER cc_start: 0.8929 (t) cc_final: 0.8699 (m) REVERT: B 303 GLN cc_start: 0.7598 (tm-30) cc_final: 0.7085 (tm-30) REVERT: B 349 LEU cc_start: 0.7930 (OUTLIER) cc_final: 0.7691 (tp) REVERT: C 156 GLN cc_start: 0.7996 (mt0) cc_final: 0.7715 (mt0) REVERT: C 234 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8113 (m-80) REVERT: C 254 ASP cc_start: 0.8232 (t0) cc_final: 0.7918 (t0) REVERT: C 311 HIS cc_start: 0.8035 (OUTLIER) cc_final: 0.6114 (m90) REVERT: C 322 ASP cc_start: 0.8301 (m-30) cc_final: 0.7963 (m-30) REVERT: D 42 GLU cc_start: 0.7972 (mt-10) cc_final: 0.7600 (mt-10) outliers start: 35 outliers final: 17 residues processed: 118 average time/residue: 0.3866 time to fit residues: 48.7919 Evaluate side-chains 113 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 93 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 331 SER Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 38 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.9980 chunk 21 optimal weight: 0.0870 chunk 80 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 51 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 ASN A 134 ASN C 266 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.155320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.119722 restraints weight = 7982.642| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.55 r_work: 0.3212 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3212 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7498 Z= 0.132 Angle : 0.540 12.875 10175 Z= 0.278 Chirality : 0.042 0.134 1170 Planarity : 0.004 0.041 1273 Dihedral : 6.618 110.777 1013 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.60 % Allowed : 16.63 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.28), residues: 905 helix: 2.39 (0.26), residues: 390 sheet: -0.39 (0.37), residues: 192 loop : -1.18 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 96 TYR 0.015 0.001 TYR A 215 PHE 0.013 0.001 PHE B 255 TRP 0.019 0.001 TRP C 82 HIS 0.003 0.001 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.13 ( 7496) covalent geometry : angle 0.53830 / 0.28 (10171) SS BOND : bond 0.00309 / 0.15 ( 2) SS BOND : angle 1.96318 / 0.75 ( 4) hydrogen bonds : bond 0.04784 / 3.03 ( 367) hydrogen bonds : angle 4.02603 / 2.94 ( 1080) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 99 time to evaluate : 0.277 Fit side-chains REVERT: A 330 LEU cc_start: 0.8300 (tp) cc_final: 0.7975 (mt) REVERT: B 32 ASP cc_start: 0.6684 (m-30) cc_final: 0.6439 (m-30) REVERT: B 35 ASP cc_start: 0.6569 (m-30) cc_final: 0.5828 (m-30) REVERT: B 225 SER cc_start: 0.8837 (t) cc_final: 0.8578 (m) REVERT: B 303 GLN cc_start: 0.7498 (tm-30) cc_final: 0.7086 (tm-30) REVERT: B 349 LEU cc_start: 0.7708 (OUTLIER) cc_final: 0.7479 (tp) REVERT: C 234 PHE cc_start: 0.8897 (OUTLIER) cc_final: 0.8199 (m-80) REVERT: C 254 ASP cc_start: 0.7941 (t0) cc_final: 0.7673 (t0) REVERT: C 311 HIS cc_start: 0.7710 (OUTLIER) cc_final: 0.5753 (m90) REVERT: C 322 ASP cc_start: 0.8108 (m-30) cc_final: 0.7780 (m-30) REVERT: D 42 GLU cc_start: 0.7881 (mt-10) cc_final: 0.7466 (mt-10) outliers start: 29 outliers final: 14 residues processed: 120 average time/residue: 0.4272 time to fit residues: 54.6444 Evaluate side-chains 112 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 331 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 0.0770 chunk 24 optimal weight: 0.8980 chunk 67 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 ASN A 134 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.156006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.120477 restraints weight = 7853.175| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.54 r_work: 0.3218 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7498 Z= 0.129 Angle : 0.540 12.616 10175 Z= 0.279 Chirality : 0.042 0.210 1170 Planarity : 0.004 0.041 1273 Dihedral : 6.546 110.310 1013 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.85 % Allowed : 17.37 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.28), residues: 905 helix: 2.46 (0.26), residues: 390 sheet: -0.33 (0.38), residues: 192 loop : -1.19 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 96 TYR 0.013 0.001 TYR C 59 PHE 0.014 0.001 PHE B 255 TRP 0.019 0.001 TRP C 82 HIS 0.003 0.001 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.13 ( 7496) covalent geometry : angle 0.53869 / 0.28 (10171) SS BOND : bond 0.00299 / 0.14 ( 2) SS BOND : angle 1.92932 / 0.74 ( 4) hydrogen bonds : bond 0.04632 / 2.93 ( 367) hydrogen bonds : angle 3.96831 / 2.89 ( 1080) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.285 Fit side-chains REVERT: A 330 LEU cc_start: 0.8283 (tp) cc_final: 0.7958 (mt) REVERT: B 35 ASP cc_start: 0.6541 (m-30) cc_final: 0.5817 (m-30) REVERT: B 225 SER cc_start: 0.8826 (t) cc_final: 0.8558 (m) REVERT: B 303 GLN cc_start: 0.7501 (tm-30) cc_final: 0.7101 (tm-30) REVERT: B 349 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7454 (tp) REVERT: C 234 PHE cc_start: 0.8872 (OUTLIER) cc_final: 0.8261 (m-80) REVERT: C 254 ASP cc_start: 0.7934 (t0) cc_final: 0.7655 (t0) REVERT: C 311 HIS cc_start: 0.7703 (OUTLIER) cc_final: 0.5772 (m90) REVERT: C 322 ASP cc_start: 0.8082 (m-30) cc_final: 0.7757 (m-30) REVERT: D 42 GLU cc_start: 0.7882 (mt-10) cc_final: 0.7504 (mt-10) outliers start: 23 outliers final: 14 residues processed: 114 average time/residue: 0.4944 time to fit residues: 60.1155 Evaluate side-chains 112 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 95 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 VAL Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 331 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 42 optimal weight: 0.2980 chunk 35 optimal weight: 0.3980 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN A 263 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.156554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.121018 restraints weight = 7878.962| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.54 r_work: 0.3230 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3230 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7498 Z= 0.125 Angle : 0.536 12.577 10175 Z= 0.276 Chirality : 0.042 0.193 1170 Planarity : 0.004 0.041 1273 Dihedral : 6.543 110.491 1013 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.48 % Allowed : 17.74 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.28), residues: 905 helix: 2.50 (0.26), residues: 390 sheet: -0.26 (0.38), residues: 192 loop : -1.21 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 96 TYR 0.014 0.001 TYR A 215 PHE 0.015 0.001 PHE B 255 TRP 0.019 0.001 TRP C 82 HIS 0.003 0.001 HIS C 54 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 7496) covalent geometry : angle 0.53460 / 0.28 (10171) SS BOND : bond 0.00304 / 0.15 ( 2) SS BOND : angle 1.89255 / 0.72 ( 4) hydrogen bonds : bond 0.04523 / 2.86 ( 367) hydrogen bonds : angle 3.92304 / 2.86 ( 1080) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1810 Ramachandran restraints generated. 905 Oldfield, 0 Emsley, 905 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 97 time to evaluate : 0.291 Fit side-chains REVERT: A 330 LEU cc_start: 0.8279 (tp) cc_final: 0.7958 (mt) REVERT: B 35 ASP cc_start: 0.6566 (m-30) cc_final: 0.5835 (m-30) REVERT: B 225 SER cc_start: 0.8854 (t) cc_final: 0.8596 (m) REVERT: B 303 GLN cc_start: 0.7503 (tm-30) cc_final: 0.7109 (tm-30) REVERT: B 349 LEU cc_start: 0.7692 (OUTLIER) cc_final: 0.7456 (tp) REVERT: C 234 PHE cc_start: 0.8857 (OUTLIER) cc_final: 0.8332 (m-80) REVERT: C 254 ASP cc_start: 0.7924 (t0) cc_final: 0.7642 (t0) REVERT: C 311 HIS cc_start: 0.7709 (OUTLIER) cc_final: 0.5791 (m90) REVERT: C 322 ASP cc_start: 0.8072 (m-30) cc_final: 0.7749 (m-30) REVERT: D 42 GLU cc_start: 0.7864 (mt-10) cc_final: 0.7433 (mt-10) outliers start: 20 outliers final: 15 residues processed: 110 average time/residue: 0.4662 time to fit residues: 54.7916 Evaluate side-chains 111 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 141 LEU Chi-restraints excluded: chain A residue 148 LEU Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 229 ASN Chi-restraints excluded: chain A residue 343 SER Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 230 VAL Chi-restraints excluded: chain B residue 296 ASP Chi-restraints excluded: chain B residue 349 LEU Chi-restraints excluded: chain C residue 33 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 262 MET Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 321 THR Chi-restraints excluded: chain C residue 331 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 23 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.153475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.117587 restraints weight = 7832.697| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 2.53 r_work: 0.3193 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 7498 Z= 0.168 Angle : 0.583 14.072 10175 Z= 0.299 Chirality : 0.043 0.181 1170 Planarity : 0.004 0.041 1273 Dihedral : 6.636 109.705 1013 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.85 % Allowed : 17.99 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.28), residues: 905 helix: 2.38 (0.26), residues: 389 sheet: -0.23 (0.38), residues: 190 loop : -1.26 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 96 TYR 0.016 0.001 TYR A 215 PHE 0.015 0.002 PHE B 255 TRP 0.020 0.001 TRP C 82 HIS 0.004 0.001 HIS B 327 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.17 ( 7496) covalent geometry : angle 0.58153 / 0.30 (10171) SS BOND : bond 0.00373 / 0.18 ( 2) SS BOND : angle 1.94060 / 0.75 ( 4) hydrogen bonds : bond 0.05242 / 3.32 ( 367) hydrogen bonds : angle 4.09141 / 2.98 ( 1080) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2436.97 seconds wall clock time: 42 minutes 17.69 seconds (2537.69 seconds total)