Starting phenix.real_space_refine on Thu Aug 6 02:00:24 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vqo_65271/08_2026/9vqo_65271_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vqo_65271/08_2026/9vqo_65271.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 { model { file = "/net/cci-nas-00/data/ceres_data/9vqo_65271/08_2026/9vqo_65271_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vqo_65271/08_2026/9vqo_65271_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9vqo_65271/08_2026/9vqo_65271.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vqo_65271/08_2026/9vqo_65271.map" } 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= 0.003 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 118 5.16 5 C 8363 2.51 5 N 2030 2.21 5 O 2200 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 12711 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3081 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3081 Classifications: {'peptide': 386} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 375} Chain: "B" Number of atoms: 3210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3210 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 394} Chain breaks: 1 Chain: "C" Number of atoms: 3210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3210 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 394} Chain breaks: 1 Chain: "D" Number of atoms: 3210 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3210 Classifications: {'peptide': 402} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 394} Chain breaks: 1 Time building chain proxies: 2.89, per 1000 atoms: 0.23 Number of scatterers: 12711 At special positions: 0 Unit cell: (116.25, 115.32, 111.6, 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 118 16.00 O 2200 8.00 N 2030 7.00 C 8363 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.10 Conformation dependent library (CDL) restraints added in 586.1 milliseconds 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3036 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 3 sheets defined 81.3% alpha, 1.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 8 through 26 removed outlier: 4.392A pdb=" N PHE A 26 " --> pdb=" O PHE A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 39 through 66 Processing helix chain 'A' and resid 70 through 96 removed outlier: 4.131A pdb=" N LEU A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER A 82 " --> pdb=" O ALA A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 116 removed outlier: 4.578A pdb=" N SER A 116 " --> pdb=" O ARG A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 161 Proline residue: A 154 - end of helix Processing helix chain 'A' and resid 179 through 236 removed outlier: 4.270A pdb=" N TYR A 207 " --> pdb=" O GLY A 203 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N LEU A 208 " --> pdb=" O GLY A 204 " (cutoff:3.500A) Proline residue: A 216 - end of helix removed outlier: 4.073A pdb=" N LYS A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 292 removed outlier: 5.195A pdb=" N ILE A 269 " --> pdb=" O LYS A 265 " (cutoff:3.500A) removed outlier: 5.008A pdb=" N VAL A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 332 removed outlier: 3.893A pdb=" N TYR A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N TYR A 330 " --> pdb=" O LEU A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 334 through 338 Processing helix chain 'A' and resid 339 through 355 removed outlier: 4.077A pdb=" N LEU A 345 " --> pdb=" O LYS A 341 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ILE A 346 " --> pdb=" O GLU A 342 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N MET A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 391 Processing helix chain 'B' and resid 12 through 17 Processing helix chain 'B' and resid 17 through 27 Processing helix chain 'B' and resid 38 through 67 Processing helix chain 'B' and resid 70 through 97 removed outlier: 3.873A pdb=" N CYS B 87 " --> pdb=" O PHE B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 106 Processing helix chain 'B' and resid 117 through 153 Processing helix chain 'B' and resid 154 through 156 No H-bonds generated for 'chain 'B' and resid 154 through 156' Processing helix chain 'B' and resid 192 through 246 removed outlier: 4.364A pdb=" N LYS B 239 " --> pdb=" O LYS B 235 " (cutoff:3.500A) Proline residue: B 240 - end of helix removed outlier: 3.959A pdb=" N SER B 245 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 382 removed outlier: 5.505A pdb=" N ALA B 361 " --> pdb=" O ASP B 357 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N ALA B 362 " --> pdb=" O THR B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 388 through 429 removed outlier: 3.905A pdb=" N PHE B 408 " --> pdb=" O GLN B 404 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N PHE B 411 " --> pdb=" O HIS B 407 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N MET B 423 " --> pdb=" O SER B 419 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 434 Processing helix chain 'B' and resid 435 through 449 Processing helix chain 'B' and resid 464 through 486 Processing helix chain 'C' and resid 12 through 17 Processing helix chain 'C' and resid 17 through 27 Processing helix chain 'C' and resid 38 through 67 Processing helix chain 'C' and resid 71 through 97 removed outlier: 3.737A pdb=" N CYS C 87 " --> pdb=" O PHE C 83 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 106 Processing helix chain 'C' and resid 107 through 109 No H-bonds generated for 'chain 'C' and resid 107 through 109' Processing helix chain 'C' and resid 117 through 155 removed outlier: 3.582A pdb=" N ASP C 121 " --> pdb=" O PHE C 117 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE C 155 " --> pdb=" O THR C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 192 through 246 removed outlier: 4.316A pdb=" N LYS C 239 " --> pdb=" O LYS C 235 " (cutoff:3.500A) Proline residue: C 240 - end of helix removed outlier: 3.774A pdb=" N SER C 245 " --> pdb=" O LEU C 241 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 382 removed outlier: 5.819A pdb=" N ALA C 361 " --> pdb=" O ASP C 357 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N ALA C 362 " --> pdb=" O THR C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 388 through 428 removed outlier: 3.899A pdb=" N PHE C 408 " --> pdb=" O GLN C 404 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N PHE C 411 " --> pdb=" O HIS C 407 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N MET C 423 " --> pdb=" O SER C 419 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLU C 424 " --> pdb=" O SER C 420 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 434 Processing helix chain 'C' and resid 435 through 450 Processing helix chain 'C' and resid 464 through 486 Processing helix chain 'D' and resid 12 through 17 Processing helix chain 'D' and resid 17 through 27 Processing helix chain 'D' and resid 38 through 67 Processing helix chain 'D' and resid 70 through 97 removed outlier: 3.761A pdb=" N CYS D 87 " --> pdb=" O PHE D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 106 Processing helix chain 'D' and resid 117 through 155 removed outlier: 3.634A pdb=" N THR D 154 " --> pdb=" O TRP D 150 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N PHE D 155 " --> pdb=" O THR D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 244 removed outlier: 4.319A pdb=" N LYS D 239 " --> pdb=" O LYS D 235 " (cutoff:3.500A) Proline residue: D 240 - end of helix Processing helix chain 'D' and resid 328 through 382 removed outlier: 5.583A pdb=" N ALA D 361 " --> pdb=" O ASP D 357 " (cutoff:3.500A) removed outlier: 5.223A pdb=" N ALA D 362 " --> pdb=" O THR D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 388 through 429 removed outlier: 3.963A pdb=" N PHE D 408 " --> pdb=" O GLN D 404 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N PHE D 411 " --> pdb=" O HIS D 407 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N MET D 423 " --> pdb=" O SER D 419 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N GLU D 424 " --> pdb=" O SER D 420 " (cutoff:3.500A) Processing helix chain 'D' and resid 430 through 434 Processing helix chain 'D' and resid 435 through 450 Processing helix chain 'D' and resid 464 through 486 Processing sheet with id=AA1, first strand: chain 'B' and resid 160 through 165 Processing sheet with id=AA2, first strand: chain 'C' and resid 160 through 165 Processing sheet with id=AA3, first strand: chain 'D' and resid 160 through 165 1063 hydrogen bonds defined for protein. 3156 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: 2.11 Time building geometry restraints manager: 1.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3823 1.34 - 1.46: 3389 1.46 - 1.58: 5617 1.58 - 1.70: 0 1.70 - 1.82: 200 Bond restraints: 13029 Sorted by residual: bond pdb=" CA VAL C 481 " pdb=" CB VAL C 481 " ideal model delta sigma weight residual 1.540 1.566 -0.026 1.25e-02 6.40e+03 4.17e+00 bond pdb=" N VAL C 481 " pdb=" CA VAL C 481 " ideal model delta sigma weight residual 1.461 1.476 -0.015 1.19e-02 7.06e+03 1.61e+00 bond pdb=" CA VAL A 215 " pdb=" CB VAL A 215 " ideal model delta sigma weight residual 1.534 1.543 -0.008 6.80e-03 2.16e+04 1.40e+00 bond pdb=" CA VAL A 215 " pdb=" C VAL A 215 " ideal model delta sigma weight residual 1.520 1.529 -0.010 8.80e-03 1.29e+04 1.24e+00 bond pdb=" CG GLN A 104 " pdb=" CD GLN A 104 " ideal model delta sigma weight residual 1.516 1.542 -0.026 2.50e-02 1.60e+03 1.06e+00 ... (remaining 13024 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 17268 1.39 - 2.78: 306 2.78 - 4.17: 73 4.17 - 5.57: 11 5.57 - 6.96: 3 Bond angle restraints: 17661 Sorted by residual: angle pdb=" N VAL C 481 " pdb=" CA VAL C 481 " pdb=" CB VAL C 481 " ideal model delta sigma weight residual 110.54 114.54 -4.00 1.36e+00 5.41e-01 8.66e+00 angle pdb=" C VAL C 51 " pdb=" CA VAL C 51 " pdb=" CB VAL C 51 " ideal model delta sigma weight residual 111.97 108.80 3.17 1.28e+00 6.10e-01 6.12e+00 angle pdb=" N ASN A 370 " pdb=" CA ASN A 370 " pdb=" C ASN A 370 " ideal model delta sigma weight residual 111.14 108.63 2.51 1.08e+00 8.57e-01 5.39e+00 angle pdb=" CB MET C 162 " pdb=" CG MET C 162 " pdb=" SD MET C 162 " ideal model delta sigma weight residual 112.70 119.66 -6.96 3.00e+00 1.11e-01 5.38e+00 angle pdb=" C VAL B 44 " pdb=" CA VAL B 44 " pdb=" CB VAL B 44 " ideal model delta sigma weight residual 111.88 109.14 2.74 1.28e+00 6.10e-01 4.57e+00 ... (remaining 17656 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 6649 17.96 - 35.92: 724 35.92 - 53.88: 198 53.88 - 71.84: 21 71.84 - 89.79: 14 Dihedral angle restraints: 7606 sinusoidal: 2907 harmonic: 4699 Sorted by residual: dihedral pdb=" CA PHE A 290 " pdb=" C PHE A 290 " pdb=" N MET A 291 " pdb=" CA MET A 291 " ideal model delta harmonic sigma weight residual 180.00 161.40 18.60 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CB GLU A 342 " pdb=" CG GLU A 342 " pdb=" CD GLU A 342 " pdb=" OE1 GLU A 342 " ideal model delta sinusoidal sigma weight residual 0.00 84.74 -84.74 1 3.00e+01 1.11e-03 9.69e+00 dihedral pdb=" CA ASN A 370 " pdb=" CB ASN A 370 " pdb=" CG ASN A 370 " pdb=" OD1 ASN A 370 " ideal model delta sinusoidal sigma weight residual -90.00 -153.47 63.47 2 2.00e+01 2.50e-03 9.61e+00 ... (remaining 7603 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1597 0.037 - 0.073: 326 0.073 - 0.110: 109 0.110 - 0.146: 15 0.146 - 0.183: 1 Chirality restraints: 2048 Sorted by residual: chirality pdb=" CB THR B 89 " pdb=" CA THR B 89 " pdb=" OG1 THR B 89 " pdb=" CG2 THR B 89 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" CA ILE A 172 " pdb=" N ILE A 172 " pdb=" C ILE A 172 " pdb=" CB ILE A 172 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CB ILE A 110 " pdb=" CA ILE A 110 " pdb=" CG1 ILE A 110 " pdb=" CG2 ILE A 110 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.51e-01 ... (remaining 2045 not shown) Planarity restraints: 2140 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE B 136 " 0.009 2.00e-02 2.50e+03 1.83e-02 3.35e+00 pdb=" C PHE B 136 " -0.032 2.00e-02 2.50e+03 pdb=" O PHE B 136 " 0.012 2.00e-02 2.50e+03 pdb=" N PHE B 137 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 134 " -0.009 2.00e-02 2.50e+03 1.82e-02 3.33e+00 pdb=" C LYS B 134 " 0.032 2.00e-02 2.50e+03 pdb=" O LYS B 134 " -0.012 2.00e-02 2.50e+03 pdb=" N LEU B 135 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 136 " -0.009 2.00e-02 2.50e+03 1.74e-02 3.03e+00 pdb=" C PHE C 136 " 0.030 2.00e-02 2.50e+03 pdb=" O PHE C 136 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE C 137 " -0.010 2.00e-02 2.50e+03 ... (remaining 2137 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1300 2.74 - 3.28: 13663 3.28 - 3.82: 23257 3.82 - 4.36: 25536 4.36 - 4.90: 45443 Nonbonded interactions: 109199 Sorted by model distance: nonbonded pdb=" NZ LYS A 89 " pdb=" OD1 ASN A 201 " model vdw 2.199 3.120 nonbonded pdb=" O GLY A 28 " pdb=" OG1 THR A 42 " model vdw 2.208 3.040 nonbonded pdb=" O TYR D 205 " pdb=" OG SER D 209 " model vdw 2.215 3.040 nonbonded pdb=" O VAL C 481 " pdb=" CG GLN C 484 " model vdw 2.217 3.440 nonbonded pdb=" O ASP B 16 " pdb=" NH1 ARG B 133 " model vdw 2.267 3.120 ... (remaining 109194 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 0.850 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 12.280 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 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 : 0.003 0.028 13029 Z= 0.145 Angle : 0.504 6.957 17661 Z= 0.288 Chirality : 0.035 0.183 2048 Planarity : 0.003 0.031 2140 Dihedral : 16.294 89.794 4570 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 0.00 % Allowed : 24.03 % Favored : 75.97 % 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: 2.98 (0.21), residues: 1578 helix: 2.52 (0.14), residues: 1238 sheet: -0.07 (0.76), residues: 42 loop : -0.07 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 133 TYR 0.008 0.001 TYR A 380 PHE 0.013 0.001 PHE A 139 TRP 0.009 0.001 TRP A 294 HIS 0.005 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 (13029) covalent geometry : angle 0.50403 / 0.29 (17661) hydrogen bonds : bond 0.09408 / 6.29 ( 1063) hydrogen bonds : angle 4.73982 / 3.48 ( 3156) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.477 Fit side-chains REVERT: A 22 PHE cc_start: 0.6744 (t80) cc_final: 0.6408 (t80) REVERT: A 26 PHE cc_start: 0.7389 (m-10) cc_final: 0.7128 (m-10) REVERT: B 193 MET cc_start: 0.6749 (pmm) cc_final: 0.6355 (tmm) REVERT: C 332 MET cc_start: 0.7890 (mmp) cc_final: 0.7209 (mtm) REVERT: C 424 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7319 (tp30) REVERT: D 173 PRO cc_start: 0.9137 (Cg_endo) cc_final: 0.8862 (Cg_exo) REVERT: D 194 PHE cc_start: 0.7844 (m-80) cc_final: 0.7516 (m-80) outliers start: 0 outliers final: 2 residues processed: 202 average time/residue: 0.5688 time to fit residues: 125.6169 Evaluate side-chains 190 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 188 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain D residue 203 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 149 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 370 ASN B 33 ASN C 232 GLN ** D 443 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.110406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.087576 restraints weight = 17028.723| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.86 r_work: 0.2897 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.2770 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2770 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.0947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13029 Z= 0.132 Angle : 0.460 6.339 17661 Z= 0.248 Chirality : 0.037 0.163 2048 Planarity : 0.003 0.031 2140 Dihedral : 3.653 42.885 1709 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 3.38 % Allowed : 20.07 % Favored : 76.55 % 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: 3.74 (0.20), residues: 1578 helix: 3.07 (0.13), residues: 1240 sheet: -0.15 (0.75), residues: 42 loop : 0.13 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 178 TYR 0.010 0.001 TYR D 124 PHE 0.016 0.001 PHE A 139 TRP 0.006 0.001 TRP A 294 HIS 0.005 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.13 (13029) covalent geometry : angle 0.45964 / 0.25 (17661) hydrogen bonds : bond 0.04658 / 3.07 ( 1063) hydrogen bonds : angle 3.45340 / 2.53 ( 3156) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 214 time to evaluate : 0.491 Fit side-chains REVERT: A 22 PHE cc_start: 0.6925 (t80) cc_final: 0.6604 (t80) REVERT: A 26 PHE cc_start: 0.7277 (m-10) cc_final: 0.7007 (m-10) REVERT: A 161 LEU cc_start: 0.6569 (OUTLIER) cc_final: 0.6291 (mp) REVERT: A 367 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8327 (tp) REVERT: B 193 MET cc_start: 0.6708 (pmm) cc_final: 0.6158 (tmm) REVERT: C 232 GLN cc_start: 0.8975 (mm110) cc_final: 0.8729 (tp40) REVERT: C 424 GLU cc_start: 0.7905 (tm-30) cc_final: 0.7464 (tp30) REVERT: D 141 LEU cc_start: 0.8244 (OUTLIER) cc_final: 0.8019 (mm) REVERT: D 173 PRO cc_start: 0.9074 (Cg_endo) cc_final: 0.8843 (Cg_exo) REVERT: D 194 PHE cc_start: 0.8035 (m-80) cc_final: 0.7804 (m-80) REVERT: D 480 MET cc_start: 0.7457 (OUTLIER) cc_final: 0.7211 (mmm) outliers start: 47 outliers final: 16 residues processed: 240 average time/residue: 0.5564 time to fit residues: 146.2082 Evaluate side-chains 218 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 317 LEU Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 466 ASP Chi-restraints excluded: chain D residue 480 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 109 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 68 optimal weight: 6.9990 chunk 101 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 110 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 ASN ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN B 169 ASN D 49 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.110849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.087972 restraints weight = 17273.666| |-----------------------------------------------------------------------------| r_work (start): 0.3034 rms_B_bonded: 1.88 r_work: 0.2904 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 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 : 0.003 0.032 13029 Z= 0.126 Angle : 0.442 8.028 17661 Z= 0.238 Chirality : 0.036 0.172 2048 Planarity : 0.003 0.034 2140 Dihedral : 3.576 42.198 1709 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 3.31 % Allowed : 20.36 % Favored : 76.33 % 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: 3.86 (0.20), residues: 1578 helix: 3.18 (0.13), residues: 1240 sheet: -0.17 (0.77), residues: 42 loop : 0.09 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 178 TYR 0.010 0.001 TYR D 124 PHE 0.016 0.001 PHE A 139 TRP 0.007 0.001 TRP A 40 HIS 0.004 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.13 (13029) covalent geometry : angle 0.44215 / 0.24 (17661) hydrogen bonds : bond 0.04494 / 2.96 ( 1063) hydrogen bonds : angle 3.36818 / 2.47 ( 3156) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 205 time to evaluate : 0.480 Fit side-chains REVERT: A 22 PHE cc_start: 0.7072 (t80) cc_final: 0.6717 (t80) REVERT: A 26 PHE cc_start: 0.7269 (m-10) cc_final: 0.7006 (m-10) REVERT: A 161 LEU cc_start: 0.6466 (OUTLIER) cc_final: 0.5949 (mp) REVERT: A 163 GLN cc_start: 0.6289 (OUTLIER) cc_final: 0.5849 (pm20) REVERT: A 289 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.7930 (mp) REVERT: B 193 MET cc_start: 0.6654 (pmm) cc_final: 0.6142 (OUTLIER) REVERT: C 424 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7539 (tp30) REVERT: D 173 PRO cc_start: 0.9077 (Cg_endo) cc_final: 0.8832 (Cg_exo) REVERT: D 194 PHE cc_start: 0.8039 (m-80) cc_final: 0.7803 (m-80) REVERT: D 480 MET cc_start: 0.7447 (OUTLIER) cc_final: 0.7214 (mmm) outliers start: 46 outliers final: 18 residues processed: 229 average time/residue: 0.5489 time to fit residues: 137.4264 Evaluate side-chains 210 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 189 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 466 ASP Chi-restraints excluded: chain D residue 480 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 92 optimal weight: 0.9990 chunk 139 optimal weight: 0.7980 chunk 107 optimal weight: 0.0870 chunk 132 optimal weight: 6.9990 chunk 133 optimal weight: 8.9990 chunk 93 optimal weight: 6.9990 chunk 141 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 overall best weight: 0.7358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN B 169 ASN D 109 ASN D 413 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.111489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.088794 restraints weight = 17179.691| |-----------------------------------------------------------------------------| r_work (start): 0.3046 rms_B_bonded: 1.89 r_work: 0.2918 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 13029 Z= 0.116 Angle : 0.437 8.516 17661 Z= 0.233 Chirality : 0.036 0.177 2048 Planarity : 0.003 0.035 2140 Dihedral : 3.542 43.504 1709 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 2.81 % Allowed : 21.65 % Favored : 75.54 % 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: 3.94 (0.20), residues: 1578 helix: 3.24 (0.13), residues: 1238 sheet: 0.02 (0.79), residues: 42 loop : 0.07 (0.37), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 335 TYR 0.018 0.001 TYR B 379 PHE 0.016 0.001 PHE A 139 TRP 0.007 0.001 TRP A 40 HIS 0.004 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00244 / 0.12 (13029) covalent geometry : angle 0.43735 / 0.23 (17661) hydrogen bonds : bond 0.04335 / 2.86 ( 1063) hydrogen bonds : angle 3.30576 / 2.43 ( 3156) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 203 time to evaluate : 0.492 Fit side-chains REVERT: A 22 PHE cc_start: 0.7058 (t80) cc_final: 0.6643 (t80) REVERT: A 26 PHE cc_start: 0.7160 (m-10) cc_final: 0.6897 (m-10) REVERT: A 33 ASP cc_start: 0.6890 (t0) cc_final: 0.6681 (m-30) REVERT: A 70 LEU cc_start: 0.8164 (mm) cc_final: 0.7946 (OUTLIER) REVERT: A 289 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.7871 (mp) REVERT: B 193 MET cc_start: 0.6630 (pmm) cc_final: 0.6110 (OUTLIER) REVERT: C 41 MET cc_start: 0.7819 (tpp) cc_final: 0.7504 (tpt) REVERT: C 140 MET cc_start: 0.8390 (mmp) cc_final: 0.8150 (mmm) REVERT: C 385 ASN cc_start: 0.8214 (p0) cc_final: 0.7219 (m110) REVERT: C 424 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7476 (tp30) REVERT: C 451 LYS cc_start: 0.8421 (mmtm) cc_final: 0.8206 (mmtm) REVERT: D 169 ASN cc_start: 0.7290 (t0) cc_final: 0.7072 (t0) REVERT: D 173 PRO cc_start: 0.9020 (Cg_endo) cc_final: 0.8766 (Cg_exo) REVERT: D 480 MET cc_start: 0.7406 (mmt) cc_final: 0.7181 (mmm) outliers start: 39 outliers final: 17 residues processed: 228 average time/residue: 0.5329 time to fit residues: 133.6486 Evaluate side-chains 205 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 466 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 39 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 1 optimal weight: 8.9990 chunk 146 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 157 optimal weight: 0.6980 chunk 102 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 ASN ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN B 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.109998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.087248 restraints weight = 17292.939| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 1.89 r_work: 0.2892 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.1500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13029 Z= 0.142 Angle : 0.475 9.221 17661 Z= 0.249 Chirality : 0.037 0.184 2048 Planarity : 0.003 0.036 2140 Dihedral : 3.386 22.773 1707 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 3.17 % Allowed : 21.65 % Favored : 75.18 % 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: 3.85 (0.20), residues: 1578 helix: 3.16 (0.13), residues: 1240 sheet: 0.03 (0.77), residues: 42 loop : 0.06 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 335 TYR 0.010 0.001 TYR D 124 PHE 0.020 0.001 PHE A 139 TRP 0.010 0.001 TRP A 40 HIS 0.003 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (13029) covalent geometry : angle 0.47518 / 0.25 (17661) hydrogen bonds : bond 0.04489 / 2.97 ( 1063) hydrogen bonds : angle 3.33173 / 2.45 ( 3156) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 193 time to evaluate : 0.483 Fit side-chains REVERT: A 26 PHE cc_start: 0.7313 (m-10) cc_final: 0.7096 (m-10) REVERT: A 33 ASP cc_start: 0.6964 (t0) cc_final: 0.6708 (m-30) REVERT: A 163 GLN cc_start: 0.6274 (OUTLIER) cc_final: 0.5808 (pm20) REVERT: A 289 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7891 (mp) REVERT: A 300 TYR cc_start: 0.6400 (OUTLIER) cc_final: 0.6029 (m-10) REVERT: B 193 MET cc_start: 0.6607 (pmm) cc_final: 0.6128 (OUTLIER) REVERT: C 140 MET cc_start: 0.8392 (mmp) cc_final: 0.8129 (mmm) REVERT: C 152 THR cc_start: 0.8427 (m) cc_final: 0.8073 (p) REVERT: C 332 MET cc_start: 0.8034 (mmp) cc_final: 0.7298 (mtm) REVERT: C 385 ASN cc_start: 0.8315 (p0) cc_final: 0.7356 (m110) REVERT: C 424 GLU cc_start: 0.7941 (tm-30) cc_final: 0.7492 (tp30) REVERT: D 173 PRO cc_start: 0.9010 (Cg_endo) cc_final: 0.8750 (Cg_exo) outliers start: 44 outliers final: 21 residues processed: 221 average time/residue: 0.5731 time to fit residues: 138.4280 Evaluate side-chains 208 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 219 MET Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 466 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 101 optimal weight: 0.5980 chunk 7 optimal weight: 0.8980 chunk 80 optimal weight: 6.9990 chunk 35 optimal weight: 0.0170 chunk 77 optimal weight: 0.9980 chunk 97 optimal weight: 4.9990 chunk 107 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 130 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN B 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.112334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.089644 restraints weight = 17178.320| |-----------------------------------------------------------------------------| r_work (start): 0.3058 rms_B_bonded: 1.89 r_work: 0.2932 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 13029 Z= 0.111 Angle : 0.448 9.564 17661 Z= 0.235 Chirality : 0.036 0.190 2048 Planarity : 0.003 0.036 2140 Dihedral : 3.337 20.710 1707 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 2.88 % Allowed : 22.16 % Favored : 74.96 % 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: 3.92 (0.20), residues: 1578 helix: 3.22 (0.13), residues: 1244 sheet: 0.17 (0.78), residues: 42 loop : -0.03 (0.37), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 335 TYR 0.022 0.001 TYR B 379 PHE 0.017 0.001 PHE A 139 TRP 0.010 0.001 TRP A 133 HIS 0.004 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.11 (13029) covalent geometry : angle 0.44836 / 0.23 (17661) hydrogen bonds : bond 0.04233 / 2.79 ( 1063) hydrogen bonds : angle 3.26846 / 2.40 ( 3156) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 202 time to evaluate : 0.521 Fit side-chains REVERT: A 26 PHE cc_start: 0.7316 (m-10) cc_final: 0.7028 (m-10) REVERT: A 33 ASP cc_start: 0.6891 (t0) cc_final: 0.6640 (m-30) REVERT: A 119 ASP cc_start: 0.8082 (t70) cc_final: 0.7701 (t0) REVERT: A 163 GLN cc_start: 0.6177 (OUTLIER) cc_final: 0.5705 (pm20) REVERT: A 248 ASP cc_start: 0.8589 (t0) cc_final: 0.8246 (t0) REVERT: A 260 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8417 (tt) REVERT: A 289 ILE cc_start: 0.8372 (OUTLIER) cc_final: 0.7976 (mp) REVERT: A 300 TYR cc_start: 0.6405 (OUTLIER) cc_final: 0.6167 (m-10) REVERT: A 324 ASP cc_start: 0.8822 (t70) cc_final: 0.8544 (t70) REVERT: A 367 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8333 (tp) REVERT: B 193 MET cc_start: 0.6484 (pmm) cc_final: 0.6104 (pp-130) REVERT: B 379 TYR cc_start: 0.7729 (t80) cc_final: 0.7476 (t80) REVERT: C 41 MET cc_start: 0.7737 (tpp) cc_final: 0.7439 (tpt) REVERT: C 152 THR cc_start: 0.8464 (m) cc_final: 0.8130 (p) REVERT: C 385 ASN cc_start: 0.8278 (p0) cc_final: 0.7347 (m110) REVERT: C 424 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7465 (tp30) REVERT: D 173 PRO cc_start: 0.9038 (Cg_endo) cc_final: 0.8807 (Cg_exo) outliers start: 40 outliers final: 16 residues processed: 229 average time/residue: 0.5498 time to fit residues: 138.0561 Evaluate side-chains 204 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain B residue 41 MET Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 466 ASP Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 24 optimal weight: 4.9990 chunk 16 optimal weight: 9.9990 chunk 53 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 103 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 133 optimal weight: 5.9990 chunk 96 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 115 optimal weight: 0.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN B 169 ASN D 20 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.107575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.084697 restraints weight = 17463.710| |-----------------------------------------------------------------------------| r_work (start): 0.2981 rms_B_bonded: 1.89 r_work: 0.2850 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 13029 Z= 0.201 Angle : 0.523 9.729 17661 Z= 0.274 Chirality : 0.039 0.202 2048 Planarity : 0.003 0.036 2140 Dihedral : 3.504 26.802 1705 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 3.24 % Allowed : 22.45 % Favored : 74.32 % 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: 3.59 (0.20), residues: 1578 helix: 2.97 (0.13), residues: 1240 sheet: 0.09 (0.75), residues: 42 loop : -0.01 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 335 TYR 0.012 0.001 TYR A 380 PHE 0.019 0.002 PHE D 194 TRP 0.015 0.001 TRP A 40 HIS 0.003 0.001 HIS C 114 Details of bonding type rmsd/Z covalent geometry : bond 0.00480 / 0.20 (13029) covalent geometry : angle 0.52314 / 0.27 (17661) hydrogen bonds : bond 0.04857 / 3.22 ( 1063) hydrogen bonds : angle 3.44308 / 2.54 ( 3156) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 200 time to evaluate : 0.612 Fit side-chains REVERT: A 26 PHE cc_start: 0.7399 (m-10) cc_final: 0.7193 (m-10) REVERT: A 33 ASP cc_start: 0.7100 (t0) cc_final: 0.6840 (m-30) REVERT: A 95 ASN cc_start: 0.8182 (t0) cc_final: 0.7963 (t160) REVERT: A 130 ARG cc_start: 0.7467 (ttm170) cc_final: 0.7109 (mtm110) REVERT: A 163 GLN cc_start: 0.6141 (OUTLIER) cc_final: 0.5681 (pm20) REVERT: A 300 TYR cc_start: 0.6438 (OUTLIER) cc_final: 0.6207 (m-10) REVERT: B 193 MET cc_start: 0.6597 (pmm) cc_final: 0.6144 (tmm) REVERT: B 379 TYR cc_start: 0.7863 (t80) cc_final: 0.7540 (t80) REVERT: C 140 MET cc_start: 0.8420 (mmp) cc_final: 0.8194 (mmm) REVERT: C 332 MET cc_start: 0.8079 (mmp) cc_final: 0.7388 (mtm) REVERT: C 385 ASN cc_start: 0.8364 (p0) cc_final: 0.7547 (m110) REVERT: C 424 GLU cc_start: 0.7960 (tm-30) cc_final: 0.7516 (tp30) REVERT: D 173 PRO cc_start: 0.9039 (Cg_endo) cc_final: 0.8801 (Cg_exo) outliers start: 45 outliers final: 23 residues processed: 230 average time/residue: 0.5623 time to fit residues: 141.7830 Evaluate side-chains 214 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 306 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain B residue 69 GLU Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain B residue 389 VAL Chi-restraints excluded: chain B residue 483 VAL Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain C residue 476 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 466 ASP Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 15 optimal weight: 0.0870 chunk 128 optimal weight: 3.9990 chunk 69 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 88 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 54 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 chunk 114 optimal weight: 0.9990 overall best weight: 1.2762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 ASN ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN D 67 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.109648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.086884 restraints weight = 17098.627| |-----------------------------------------------------------------------------| r_work (start): 0.3018 rms_B_bonded: 1.89 r_work: 0.2889 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2761 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 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 0.041 13029 Z= 0.145 Angle : 0.497 9.406 17661 Z= 0.258 Chirality : 0.038 0.209 2048 Planarity : 0.003 0.036 2140 Dihedral : 3.465 25.474 1705 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 2.59 % Allowed : 23.53 % Favored : 73.88 % 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: 3.65 (0.20), residues: 1578 helix: 3.02 (0.13), residues: 1240 sheet: 0.09 (0.74), residues: 42 loop : -0.04 (0.36), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 335 TYR 0.014 0.001 TYR B 379 PHE 0.016 0.001 PHE D 137 TRP 0.011 0.001 TRP A 40 HIS 0.004 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.14 (13029) covalent geometry : angle 0.49748 / 0.26 (17661) hydrogen bonds : bond 0.04548 / 3.01 ( 1063) hydrogen bonds : angle 3.36889 / 2.48 ( 3156) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 194 time to evaluate : 0.498 Fit side-chains REVERT: A 26 PHE cc_start: 0.7432 (m-10) cc_final: 0.7206 (m-10) REVERT: A 33 ASP cc_start: 0.7094 (t0) cc_final: 0.6820 (m-30) REVERT: A 95 ASN cc_start: 0.8233 (t0) cc_final: 0.8022 (t160) REVERT: A 130 ARG cc_start: 0.7422 (ttm170) cc_final: 0.7080 (mtm110) REVERT: A 300 TYR cc_start: 0.6455 (OUTLIER) cc_final: 0.6168 (m-10) REVERT: B 193 MET cc_start: 0.6559 (pmm) cc_final: 0.6118 (tmm) REVERT: B 379 TYR cc_start: 0.7905 (t80) cc_final: 0.7544 (t80) REVERT: C 41 MET cc_start: 0.7822 (tpp) cc_final: 0.7536 (tpt) REVERT: C 140 MET cc_start: 0.8367 (mmp) cc_final: 0.8118 (mmm) REVERT: C 332 MET cc_start: 0.8081 (mmp) cc_final: 0.7357 (mtm) REVERT: C 385 ASN cc_start: 0.8283 (p0) cc_final: 0.7514 (m110) REVERT: C 424 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7503 (tp30) REVERT: D 18 MET cc_start: 0.8687 (tpp) cc_final: 0.8479 (tpp) REVERT: D 173 PRO cc_start: 0.9070 (Cg_endo) cc_final: 0.8847 (Cg_exo) outliers start: 36 outliers final: 22 residues processed: 221 average time/residue: 0.5629 time to fit residues: 136.1704 Evaluate side-chains 211 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 153 ILE Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 328 LYS Chi-restraints excluded: chain D residue 466 ASP Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 96 optimal weight: 0.1980 chunk 41 optimal weight: 2.9990 chunk 116 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 148 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 146 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN B 169 ASN D 67 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.109945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.087113 restraints weight = 17236.650| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 1.90 r_work: 0.2892 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13029 Z= 0.142 Angle : 0.504 9.974 17661 Z= 0.262 Chirality : 0.037 0.207 2048 Planarity : 0.003 0.037 2140 Dihedral : 3.458 24.792 1705 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.01 % Favored : 98.99 % Rotamer: Outliers : 1.94 % Allowed : 23.60 % Favored : 74.46 % 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: 3.67 (0.20), residues: 1578 helix: 3.05 (0.13), residues: 1238 sheet: 0.12 (0.74), residues: 42 loop : -0.07 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 335 TYR 0.013 0.001 TYR B 379 PHE 0.017 0.001 PHE A 139 TRP 0.014 0.001 TRP A 40 HIS 0.004 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 (13029) covalent geometry : angle 0.50425 / 0.26 (17661) hydrogen bonds : bond 0.04523 / 3.00 ( 1063) hydrogen bonds : angle 3.37474 / 2.48 ( 3156) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 0.483 Fit side-chains REVERT: A 26 PHE cc_start: 0.7438 (m-10) cc_final: 0.7176 (m-10) REVERT: A 33 ASP cc_start: 0.7090 (t0) cc_final: 0.6775 (m-30) REVERT: A 95 ASN cc_start: 0.8230 (t0) cc_final: 0.8014 (t160) REVERT: A 130 ARG cc_start: 0.7370 (ttm170) cc_final: 0.7031 (mtm110) REVERT: A 161 LEU cc_start: 0.6639 (mm) cc_final: 0.5552 (mp) REVERT: A 163 GLN cc_start: 0.6222 (OUTLIER) cc_final: 0.5737 (pm20) REVERT: A 300 TYR cc_start: 0.6494 (OUTLIER) cc_final: 0.6171 (m-10) REVERT: B 193 MET cc_start: 0.6556 (pmm) cc_final: 0.6126 (tmm) REVERT: B 379 TYR cc_start: 0.7928 (t80) cc_final: 0.7645 (t80) REVERT: C 41 MET cc_start: 0.7806 (tpp) cc_final: 0.7498 (tpt) REVERT: C 140 MET cc_start: 0.8383 (mmp) cc_final: 0.8140 (mmm) REVERT: C 332 MET cc_start: 0.8103 (mmp) cc_final: 0.7381 (mtm) REVERT: C 385 ASN cc_start: 0.8302 (p0) cc_final: 0.7521 (m110) REVERT: C 424 GLU cc_start: 0.7957 (tm-30) cc_final: 0.7522 (tp30) REVERT: D 18 MET cc_start: 0.8731 (tpp) cc_final: 0.8511 (tpp) REVERT: D 173 PRO cc_start: 0.9052 (Cg_endo) cc_final: 0.8824 (Cg_exo) outliers start: 27 outliers final: 22 residues processed: 210 average time/residue: 0.5328 time to fit residues: 122.2598 Evaluate side-chains 210 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 186 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 300 TYR Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain B residue 382 THR Chi-restraints excluded: chain C residue 55 MET Chi-restraints excluded: chain C residue 113 THR Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 450 GLN Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 203 ILE Chi-restraints excluded: chain D residue 466 ASP Chi-restraints excluded: chain D residue 483 VAL Chi-restraints excluded: chain D residue 485 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 26 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 111 optimal weight: 1.9990 chunk 129 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 96 optimal weight: 0.3980 chunk 98 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 55 optimal weight: 0.0010 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 ASN B 169 ASN C 443 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.112765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.090152 restraints weight = 17193.733| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.86 r_work: 0.2942 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.1857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 13029 Z= 0.116 Angle : 0.500 12.237 17661 Z= 0.256 Chirality : 0.036 0.206 2048 Planarity : 0.003 0.037 2140 Dihedral : 3.382 20.964 1705 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % Rotamer: Outliers : 1.80 % Allowed : 24.10 % Favored : 74.10 % 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: 3.83 (0.20), residues: 1578 helix: 3.19 (0.13), residues: 1241 sheet: 0.28 (0.77), residues: 42 loop : -0.20 (0.36), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 335 TYR 0.018 0.001 TYR C 379 PHE 0.017 0.001 PHE A 139 TRP 0.014 0.001 TRP A 133 HIS 0.004 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (13029) covalent geometry : angle 0.49957 / 0.26 (17661) hydrogen bonds : bond 0.04251 / 2.81 ( 1063) hydrogen bonds : angle 3.30621 / 2.42 ( 3156) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3156 Ramachandran restraints generated. 1578 Oldfield, 0 Emsley, 1578 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.396 Fit side-chains REVERT: A 26 PHE cc_start: 0.7355 (m-10) cc_final: 0.7126 (m-10) REVERT: A 33 ASP cc_start: 0.6914 (t0) cc_final: 0.6616 (m-30) REVERT: A 130 ARG cc_start: 0.7337 (ttm170) cc_final: 0.6985 (mtm110) REVERT: A 163 GLN cc_start: 0.6294 (OUTLIER) cc_final: 0.5812 (pm20) REVERT: A 289 ILE cc_start: 0.8116 (OUTLIER) cc_final: 0.7777 (mp) REVERT: A 324 ASP cc_start: 0.8843 (t70) cc_final: 0.8607 (t70) REVERT: A 367 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8396 (tp) REVERT: B 193 MET cc_start: 0.6469 (pmm) cc_final: 0.6118 (pp-130) REVERT: B 379 TYR cc_start: 0.7789 (t80) cc_final: 0.7409 (t80) REVERT: C 41 MET cc_start: 0.7762 (tpp) cc_final: 0.7453 (tpt) REVERT: C 152 THR cc_start: 0.8440 (m) cc_final: 0.8114 (p) REVERT: C 332 MET cc_start: 0.8100 (mmp) cc_final: 0.7331 (mtm) REVERT: C 385 ASN cc_start: 0.8229 (p0) cc_final: 0.7399 (m110) REVERT: C 423 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.7703 (ttp) REVERT: C 424 GLU cc_start: 0.7943 (tm-30) cc_final: 0.7477 (tp30) REVERT: C 451 LYS cc_start: 0.8432 (mmtm) cc_final: 0.8185 (pptt) REVERT: D 173 PRO cc_start: 0.9081 (Cg_endo) cc_final: 0.8864 (Cg_exo) REVERT: D 219 MET cc_start: 0.8732 (ttm) cc_final: 0.8510 (ttm) outliers start: 25 outliers final: 12 residues processed: 206 average time/residue: 0.4999 time to fit residues: 112.9109 Evaluate side-chains 196 residues out of total 1390 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 180 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 THR Chi-restraints excluded: chain A residue 73 ILE Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 157 TYR Chi-restraints excluded: chain A residue 163 GLN Chi-restraints excluded: chain A residue 289 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 367 LEU Chi-restraints excluded: chain B residue 133 ARG Chi-restraints excluded: chain C residue 408 PHE Chi-restraints excluded: chain C residue 423 MET Chi-restraints excluded: chain C residue 475 VAL Chi-restraints excluded: chain D residue 141 LEU Chi-restraints excluded: chain D residue 164 VAL Chi-restraints excluded: chain D residue 466 ASP Chi-restraints excluded: chain D residue 483 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 60 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 55 optimal weight: 0.6980 chunk 35 optimal weight: 4.9990 chunk 122 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 120 optimal weight: 4.9990 chunk 149 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 261 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.112009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.089231 restraints weight = 17027.425| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.88 r_work: 0.2928 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13029 Z= 0.125 Angle : 0.505 12.275 17661 Z= 0.259 Chirality : 0.037 0.214 2048 Planarity : 0.003 0.038 2140 Dihedral : 3.352 20.800 1705 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 1.37 % Allowed : 24.46 % Favored : 74.17 % 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: 3.87 (0.20), residues: 1578 helix: 3.20 (0.13), residues: 1238 sheet: 0.27 (0.76), residues: 42 loop : -0.08 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 335 TYR 0.016 0.001 TYR C 379 PHE 0.019 0.001 PHE A 139 TRP 0.015 0.001 TRP A 133 HIS 0.004 0.001 HIS A 190 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.12 (13029) covalent geometry : angle 0.50544 / 0.26 (17661) hydrogen bonds : bond 0.04306 / 2.84 ( 1063) hydrogen bonds : angle 3.30877 / 2.43 ( 3156) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4302.53 seconds wall clock time: 74 minutes 28.74 seconds (4468.74 seconds total)