Starting phenix.real_space_refine on Wed Mar 12 06:54:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f6h_31480/03_2025/7f6h_31480.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f6h_31480/03_2025/7f6h_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_31480/03_2025/7f6h_31480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f6h_31480/03_2025/7f6h_31480.map" model { file = "/net/cci-nas-00/data/ceres_data/7f6h_31480/03_2025/7f6h_31480.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f6h_31480/03_2025/7f6h_31480.cif" } resolution = 2.9 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= 0.004 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.77, per 1000 atoms: 0.65 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: 1.77 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.83 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: 2.10 Time building geometry restraints manager: 2.12 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: 4329 23.95 - 47.90: 215 47.90 - 71.86: 14 71.86 - 95.81: 13 95.81 - 119.76: 2 Dihedral angle restraints: 4573 sinusoidal: 1898 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 4570 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: 0.930 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: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.520 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 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: 0.010 Load rotamer database and sin/cos tables:13.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 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 7496 Z= 0.719 Angle : 0.990 9.952 10171 Z= 0.608 Chirality : 0.069 0.483 1170 Planarity : 0.004 0.042 1273 Dihedral : 14.048 119.760 2829 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 6.26 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 (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: 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 TRP 0.028 0.003 TRP C 82 HIS 0.014 0.003 HIS C 225 PHE 0.022 0.003 PHE A 319 TYR 0.033 0.003 TYR C 105 ARG 0.014 0.001 ARG C 251 *********************** 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 : 0.726 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: 1.1255 time to fit residues: 149.0183 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 : 0.730 ------------------------------------------------------------------------------- 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 75 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 69 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 42 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 80 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 HIS A 246 GLN B 246 ASN C 88 ASN C 220 GLN C 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.157211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.122467 restraints weight = 7782.166| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 2.50 r_work: 0.3244 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7496 Z= 0.186 Angle : 0.546 9.861 10171 Z= 0.289 Chirality : 0.042 0.132 1170 Planarity : 0.004 0.039 1273 Dihedral : 4.944 28.185 1126 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.23 % Allowed : 9.68 % Favored : 88.09 % 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: 0.56 (0.27), residues: 905 helix: 2.05 (0.25), residues: 390 sheet: -0.25 (0.37), residues: 187 loop : -1.33 (0.31), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.004 0.001 HIS A 206 PHE 0.014 0.001 PHE C 199 TYR 0.016 0.001 TYR A 215 ARG 0.003 0.000 ARG A 196 *********************** 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: 18 poor density : 103 time to evaluate : 0.743 Fit side-chains REVERT: B 35 ASP cc_start: 0.6660 (m-30) cc_final: 0.6001 (m-30) REVERT: B 303 GLN cc_start: 0.7457 (tm-30) cc_final: 0.7126 (tm-30) REVERT: C 96 ARG cc_start: 0.8260 (ttm170) cc_final: 0.8057 (ttm110) REVERT: C 322 ASP cc_start: 0.8150 (m-30) cc_final: 0.7848 (m-30) REVERT: D 42 GLU cc_start: 0.7970 (mt-10) cc_final: 0.7590 (mt-10) outliers start: 18 outliers final: 6 residues processed: 116 average time/residue: 1.1338 time to fit residues: 139.5470 Evaluate side-chains 101 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.794 ------------------------------------------------------------------------------- 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 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 31 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 75 optimal weight: 0.0370 chunk 76 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 0.0870 chunk 15 optimal weight: 4.9990 chunk 44 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 overall best weight: 0.6036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN ** A 315 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 266 HIS C 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.157362 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.122349 restraints weight = 7965.599| |-----------------------------------------------------------------------------| r_work (start): 0.3386 rms_B_bonded: 2.54 r_work: 0.3240 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7496 Z= 0.182 Angle : 0.514 9.660 10171 Z= 0.272 Chirality : 0.041 0.133 1170 Planarity : 0.003 0.039 1273 Dihedral : 4.457 29.498 1125 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.73 % Allowed : 13.03 % Favored : 84.24 % 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 (0.28), residues: 905 helix: 2.32 (0.25), residues: 391 sheet: -0.24 (0.37), residues: 188 loop : -1.25 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 82 HIS 0.003 0.001 HIS C 54 PHE 0.013 0.001 PHE C 234 TYR 0.006 0.001 TYR A 215 ARG 0.005 0.000 ARG A 252 *********************** 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 124 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 102 time to evaluate : 0.810 Fit side-chains REVERT: A 203 ASP cc_start: 0.7914 (m-30) cc_final: 0.7602 (m-30) REVERT: A 330 LEU cc_start: 0.8246 (tp) cc_final: 0.7982 (mt) REVERT: B 32 ASP cc_start: 0.6685 (m-30) cc_final: 0.6340 (m-30) REVERT: B 35 ASP cc_start: 0.6525 (m-30) cc_final: 0.5849 (m-30) REVERT: B 303 GLN cc_start: 0.7374 (tm-30) cc_final: 0.6947 (tm-30) REVERT: C 254 ASP cc_start: 0.7910 (t0) cc_final: 0.7677 (t0) REVERT: C 311 HIS cc_start: 0.7885 (OUTLIER) cc_final: 0.5642 (m90) REVERT: C 322 ASP cc_start: 0.8024 (m-30) cc_final: 0.7720 (m-30) REVERT: D 42 GLU cc_start: 0.7912 (mt-10) cc_final: 0.7487 (mt-10) outliers start: 22 outliers final: 8 residues processed: 116 average time/residue: 1.0927 time to fit residues: 134.9920 Evaluate side-chains 103 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ASN 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 270 ILE 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 6 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 87 optimal weight: 0.0060 chunk 40 optimal weight: 4.9990 chunk 43 optimal weight: 0.6980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN A 134 ASN A 263 GLN A 315 GLN A 324 ASN C 340 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.156689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.121421 restraints weight = 7928.391| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 2.52 r_work: 0.3232 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3232 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.1797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7496 Z= 0.198 Angle : 0.521 10.323 10171 Z= 0.273 Chirality : 0.041 0.136 1170 Planarity : 0.003 0.039 1273 Dihedral : 4.428 30.087 1125 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.60 % Allowed : 14.02 % Favored : 82.38 % 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: 0.87 (0.28), residues: 905 helix: 2.40 (0.25), residues: 391 sheet: -0.29 (0.37), residues: 190 loop : -1.18 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.004 0.001 HIS C 54 PHE 0.014 0.001 PHE B 255 TYR 0.014 0.001 TYR A 215 ARG 0.006 0.000 ARG C 96 *********************** 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 130 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 101 time to evaluate : 0.880 Fit side-chains REVERT: A 192 MET cc_start: 0.7408 (mmm) cc_final: 0.7058 (mmp) REVERT: A 207 ASN cc_start: 0.7539 (OUTLIER) cc_final: 0.7244 (m-40) REVERT: A 330 LEU cc_start: 0.8299 (tp) cc_final: 0.7982 (mt) REVERT: B 35 ASP cc_start: 0.6554 (m-30) cc_final: 0.5887 (m-30) REVERT: B 303 GLN cc_start: 0.7447 (tm-30) cc_final: 0.6978 (tm-30) REVERT: C 254 ASP cc_start: 0.7974 (t0) cc_final: 0.7737 (t0) REVERT: C 322 ASP cc_start: 0.8032 (m-30) cc_final: 0.7726 (m-30) REVERT: D 42 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7537 (mt-10) outliers start: 29 outliers final: 10 residues processed: 121 average time/residue: 1.0721 time to fit residues: 138.1634 Evaluate side-chains 107 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 207 ASN Chi-restraints excluded: chain A residue 229 ASN 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 C residue 47 THR Chi-restraints excluded: chain C residue 270 ILE Chi-restraints excluded: chain C residue 331 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 87 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 chunk 52 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 43 optimal weight: 0.0050 chunk 2 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 chunk 56 optimal weight: 0.6980 chunk 73 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 120 ASN A 134 ASN A 263 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.158226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.123107 restraints weight = 7866.253| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 2.52 r_work: 0.3256 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7461 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7496 Z= 0.166 Angle : 0.506 10.080 10171 Z= 0.264 Chirality : 0.041 0.133 1170 Planarity : 0.003 0.039 1273 Dihedral : 4.263 29.650 1125 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 2.98 % Allowed : 14.76 % Favored : 82.26 % 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: 1.00 (0.28), residues: 905 helix: 2.53 (0.26), residues: 391 sheet: -0.21 (0.37), residues: 190 loop : -1.16 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 82 HIS 0.003 0.001 HIS C 54 PHE 0.014 0.001 PHE B 255 TYR 0.012 0.001 TYR A 215 ARG 0.008 0.000 ARG C 96 *********************** 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 121 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 97 time to evaluate : 1.064 Fit side-chains REVERT: A 192 MET cc_start: 0.7353 (mmm) cc_final: 0.7046 (mmp) REVERT: A 330 LEU cc_start: 0.8294 (tp) cc_final: 0.7987 (mt) REVERT: B 32 ASP cc_start: 0.6674 (m-30) cc_final: 0.6361 (m-30) REVERT: B 35 ASP cc_start: 0.6549 (m-30) cc_final: 0.5878 (m-30) REVERT: B 303 GLN cc_start: 0.7478 (tm-30) cc_final: 0.7041 (tm-30) REVERT: C 215 GLU cc_start: 0.7771 (tm-30) cc_final: 0.7564 (pp20) REVERT: C 254 ASP cc_start: 0.7933 (t0) cc_final: 0.7716 (t0) REVERT: C 311 HIS cc_start: 0.7680 (OUTLIER) cc_final: 0.5547 (m90) REVERT: C 322 ASP cc_start: 0.8017 (m-30) cc_final: 0.7721 (m-30) REVERT: D 42 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7499 (mt-10) outliers start: 24 outliers final: 12 residues processed: 115 average time/residue: 1.2139 time to fit residues: 149.3707 Evaluate side-chains 106 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 229 ASN Chi-restraints excluded: chain A residue 327 LEU 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 356 TYR Chi-restraints excluded: chain C residue 47 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 58 optimal weight: 0.5980 chunk 67 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 chunk 21 optimal weight: 0.0020 chunk 84 optimal weight: 0.5980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.158285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.123026 restraints weight = 7928.909| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.54 r_work: 0.3253 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7496 Z= 0.167 Angle : 0.504 10.519 10171 Z= 0.262 Chirality : 0.041 0.133 1170 Planarity : 0.003 0.038 1273 Dihedral : 4.156 29.359 1125 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.47 % Allowed : 15.14 % Favored : 81.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.05 (0.28), residues: 905 helix: 2.58 (0.26), residues: 391 sheet: -0.16 (0.37), residues: 190 loop : -1.16 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 82 HIS 0.003 0.001 HIS C 54 PHE 0.015 0.001 PHE B 255 TYR 0.009 0.001 TYR A 215 ARG 0.008 0.000 ARG C 96 *********************** 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 127 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 99 time to evaluate : 0.766 Fit side-chains REVERT: A 168 MET cc_start: 0.7377 (mmm) cc_final: 0.7140 (mmm) REVERT: A 330 LEU cc_start: 0.8294 (tp) cc_final: 0.7982 (mt) REVERT: B 35 ASP cc_start: 0.6562 (m-30) cc_final: 0.5864 (m-30) REVERT: B 303 GLN cc_start: 0.7426 (tm-30) cc_final: 0.6979 (tm-30) REVERT: C 254 ASP cc_start: 0.7856 (t0) cc_final: 0.7602 (t0) REVERT: C 311 HIS cc_start: 0.7705 (OUTLIER) cc_final: 0.5643 (m90) REVERT: C 322 ASP cc_start: 0.7983 (m-30) cc_final: 0.7688 (m-30) REVERT: D 42 GLU cc_start: 0.7919 (mt-10) cc_final: 0.7450 (mt-10) outliers start: 28 outliers final: 15 residues processed: 119 average time/residue: 1.0118 time to fit residues: 128.8141 Evaluate side-chains 111 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 95 time to evaluate : 0.850 ------------------------------------------------------------------------------- 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 327 LEU 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 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 270 ILE Chi-restraints excluded: chain C residue 311 HIS Chi-restraints excluded: chain C residue 331 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 31 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 4 optimal weight: 0.0060 chunk 2 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 61 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 42 optimal weight: 0.3980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.157195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.124053 restraints weight = 7773.188| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.39 r_work: 0.3267 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3112 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7496 Z= 0.169 Angle : 0.508 10.960 10171 Z= 0.264 Chirality : 0.041 0.181 1170 Planarity : 0.003 0.038 1273 Dihedral : 4.187 29.319 1125 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 3.10 % Allowed : 16.50 % Favored : 80.40 % 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: 1.09 (0.28), residues: 905 helix: 2.60 (0.26), residues: 391 sheet: -0.13 (0.37), residues: 190 loop : -1.15 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 82 HIS 0.003 0.001 HIS C 54 PHE 0.015 0.001 PHE B 255 TYR 0.012 0.001 TYR A 215 ARG 0.009 0.000 ARG C 96 *********************** 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 119 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.808 Fit side-chains REVERT: A 163 MET cc_start: 0.7848 (OUTLIER) cc_final: 0.5732 (mpt) REVERT: A 330 LEU cc_start: 0.8336 (tp) cc_final: 0.8027 (mt) REVERT: B 35 ASP cc_start: 0.6694 (m-30) cc_final: 0.6014 (m-30) REVERT: B 303 GLN cc_start: 0.7553 (tm-30) cc_final: 0.7108 (tm-30) REVERT: C 217 MET cc_start: 0.8140 (ptp) cc_final: 0.7823 (pmm) REVERT: C 254 ASP cc_start: 0.8045 (t0) cc_final: 0.7800 (t0) REVERT: C 322 ASP cc_start: 0.8134 (m-30) cc_final: 0.7843 (m-30) REVERT: D 42 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7554 (mt-10) outliers start: 25 outliers final: 16 residues processed: 112 average time/residue: 1.0216 time to fit residues: 122.3165 Evaluate side-chains 110 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.800 ------------------------------------------------------------------------------- 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 163 MET Chi-restraints excluded: chain A residue 187 LEU Chi-restraints excluded: chain A residue 327 LEU 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 356 TYR 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 331 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 41 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 44 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 63 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.153840 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.118091 restraints weight = 7951.319| |-----------------------------------------------------------------------------| r_work (start): 0.3339 rms_B_bonded: 2.54 r_work: 0.3190 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 7496 Z= 0.275 Angle : 0.579 13.188 10171 Z= 0.299 Chirality : 0.043 0.143 1170 Planarity : 0.004 0.039 1273 Dihedral : 4.576 33.104 1125 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 3.47 % Allowed : 16.38 % Favored : 80.15 % 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: 0.90 (0.28), residues: 905 helix: 2.41 (0.26), residues: 390 sheet: -0.23 (0.37), residues: 190 loop : -1.17 (0.32), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 123 HIS 0.005 0.001 HIS C 54 PHE 0.015 0.002 PHE B 255 TYR 0.013 0.001 TYR A 215 ARG 0.010 0.000 ARG C 96 *********************** 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 123 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.777 Fit side-chains REVERT: A 322 TYR cc_start: 0.8658 (OUTLIER) cc_final: 0.8446 (m-80) REVERT: B 35 ASP cc_start: 0.6631 (m-30) cc_final: 0.5907 (m-30) REVERT: B 303 GLN cc_start: 0.7512 (tm-30) cc_final: 0.7045 (tm-30) REVERT: C 156 GLN cc_start: 0.7870 (mt0) cc_final: 0.7576 (mt0) REVERT: C 254 ASP cc_start: 0.7915 (t0) cc_final: 0.7639 (t0) REVERT: C 311 HIS cc_start: 0.7912 (OUTLIER) cc_final: 0.5812 (m90) REVERT: C 322 ASP cc_start: 0.8090 (m-30) cc_final: 0.7764 (m-30) REVERT: D 42 GLU cc_start: 0.7853 (mt-10) cc_final: 0.7427 (mt-10) outliers start: 28 outliers final: 16 residues processed: 114 average time/residue: 1.0037 time to fit residues: 122.4267 Evaluate side-chains 108 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.718 ------------------------------------------------------------------------------- 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 322 TYR 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 356 TYR 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 173 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 0 optimal weight: 7.9990 chunk 34 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 86 optimal weight: 0.8980 chunk 87 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 63 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.155914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.120217 restraints weight = 7888.768| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 2.54 r_work: 0.3217 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 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 : 0.003 0.038 7496 Z= 0.202 Angle : 0.541 13.035 10171 Z= 0.278 Chirality : 0.042 0.137 1170 Planarity : 0.004 0.039 1273 Dihedral : 4.416 32.279 1125 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 3.10 % Allowed : 17.25 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.96 (0.28), residues: 905 helix: 2.49 (0.26), residues: 391 sheet: -0.22 (0.38), residues: 190 loop : -1.17 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 82 HIS 0.003 0.001 HIS C 54 PHE 0.014 0.001 PHE B 255 TYR 0.011 0.001 TYR A 215 ARG 0.010 0.000 ARG C 96 *********************** 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 117 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.866 Fit side-chains REVERT: A 192 MET cc_start: 0.7097 (mmm) cc_final: 0.6634 (mmp) REVERT: A 330 LEU cc_start: 0.8235 (tp) cc_final: 0.7943 (mt) REVERT: B 35 ASP cc_start: 0.6596 (m-30) cc_final: 0.5885 (m-30) REVERT: B 303 GLN cc_start: 0.7493 (tm-30) cc_final: 0.7073 (tm-30) REVERT: C 234 PHE cc_start: 0.8848 (OUTLIER) cc_final: 0.8403 (m-80) REVERT: C 254 ASP cc_start: 0.7919 (t0) cc_final: 0.7644 (t0) REVERT: C 311 HIS cc_start: 0.7777 (OUTLIER) cc_final: 0.5575 (m90) REVERT: C 312 ASP cc_start: 0.7647 (p0) cc_final: 0.7446 (p0) REVERT: C 322 ASP cc_start: 0.8075 (m-30) cc_final: 0.7764 (m-30) REVERT: D 42 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7414 (mt-10) outliers start: 25 outliers final: 18 residues processed: 108 average time/residue: 0.9833 time to fit residues: 113.7446 Evaluate side-chains 112 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 92 time to evaluate : 0.789 ------------------------------------------------------------------------------- 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 59 MET 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 356 TYR 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 331 SER Chi-restraints excluded: chain D residue 38 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 83 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 chunk 41 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 74 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN C 266 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.155438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.119677 restraints weight = 7969.909| |-----------------------------------------------------------------------------| r_work (start): 0.3359 rms_B_bonded: 2.55 r_work: 0.3216 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7505 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7496 Z= 0.218 Angle : 0.551 13.253 10171 Z= 0.284 Chirality : 0.042 0.137 1170 Planarity : 0.004 0.040 1273 Dihedral : 4.449 32.434 1125 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.85 % Allowed : 17.62 % Favored : 79.53 % 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: 0.94 (0.28), residues: 905 helix: 2.46 (0.26), residues: 391 sheet: -0.23 (0.38), residues: 190 loop : -1.19 (0.32), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.004 0.001 HIS C 54 PHE 0.014 0.001 PHE B 255 TYR 0.014 0.001 TYR A 215 ARG 0.011 0.000 ARG C 96 ********************** 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 116 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.734 Fit side-chains REVERT: A 192 MET cc_start: 0.7101 (mmm) cc_final: 0.6720 (mmp) REVERT: A 330 LEU cc_start: 0.8267 (tp) cc_final: 0.7991 (mt) REVERT: B 35 ASP cc_start: 0.6616 (m-30) cc_final: 0.5902 (m-30) REVERT: B 303 GLN cc_start: 0.7498 (tm-30) cc_final: 0.7087 (tm-30) REVERT: C 234 PHE cc_start: 0.8868 (OUTLIER) cc_final: 0.8278 (m-80) REVERT: C 254 ASP cc_start: 0.7929 (t0) cc_final: 0.7659 (t0) REVERT: C 311 HIS cc_start: 0.7812 (OUTLIER) cc_final: 0.5633 (m90) REVERT: C 322 ASP cc_start: 0.8077 (m-30) cc_final: 0.7764 (m-30) REVERT: D 42 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7419 (mt-10) outliers start: 23 outliers final: 19 residues processed: 109 average time/residue: 1.0043 time to fit residues: 116.9333 Evaluate side-chains 113 residues out of total 806 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 92 time to evaluate : 0.851 ------------------------------------------------------------------------------- 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 59 MET 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 356 TYR 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 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 331 SER Chi-restraints excluded: chain D residue 38 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 69 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 48 optimal weight: 0.0870 chunk 54 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 75 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3756 r_free = 0.3756 target = 0.155874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.120166 restraints weight = 7872.161| |-----------------------------------------------------------------------------| r_work (start): 0.3366 rms_B_bonded: 2.53 r_work: 0.3223 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7496 Z= 0.210 Angle : 0.548 13.421 10171 Z= 0.281 Chirality : 0.042 0.136 1170 Planarity : 0.004 0.040 1273 Dihedral : 4.420 32.180 1125 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.98 % Allowed : 17.25 % 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 (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: 0.97 (0.28), residues: 905 helix: 2.48 (0.26), residues: 391 sheet: -0.15 (0.38), residues: 188 loop : -1.19 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP C 82 HIS 0.004 0.001 HIS C 54 PHE 0.014 0.001 PHE B 255 TYR 0.015 0.001 TYR A 215 ARG 0.011 0.000 ARG C 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4916.11 seconds wall clock time: 84 minutes 38.48 seconds (5078.48 seconds total)