Starting phenix.real_space_refine on Thu Sep 18 05:19:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5k12_8194/09_2025/5k12_8194.cif Found real_map, /net/cci-nas-00/data/ceres_data/5k12_8194/09_2025/5k12_8194.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5k12_8194/09_2025/5k12_8194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5k12_8194/09_2025/5k12_8194.map" model { file = "/net/cci-nas-00/data/ceres_data/5k12_8194/09_2025/5k12_8194.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5k12_8194/09_2025/5k12_8194.cif" } resolution = 1.8 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 72 5.16 5 C 8670 2.51 5 N 2454 2.21 5 O 3660 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14856 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 2295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 294, 2295 Classifications: {'peptide': 294} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 282} Chain breaks: 1 Chain: "A" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 181 Classifications: {'water': 181} Link IDs: {None: 180} Chain: "B" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 182 Classifications: {'water': 182} Link IDs: {None: 181} Chain: "C" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 180 Classifications: {'water': 180} Link IDs: {None: 179} Chain: "D" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 181 Classifications: {'water': 181} Link IDs: {None: 180} Chain: "E" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 181 Classifications: {'water': 181} Link IDs: {None: 180} Chain: "F" Number of atoms: 181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 181 Classifications: {'water': 181} Link IDs: {None: 180} Restraints were copied for chains: B, C, D, E, F Time building chain proxies: 2.37, per 1000 atoms: 0.16 Number of scatterers: 14856 At special positions: 0 Unit cell: (91.091, 96.187, 159.887, 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 72 16.00 O 3660 8.00 N 2454 7.00 C 8670 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: 1.49 Conformation dependent library (CDL) restraints added in 542.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3192 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 3 sheets defined 57.8% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 100 through 118 removed outlier: 3.609A pdb=" N VAL A 118 " --> pdb=" O LYS A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 136 Processing helix chain 'A' and resid 137 through 155 removed outlier: 3.571A pdb=" N LYS A 155 " --> pdb=" O GLU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 186 Processing helix chain 'A' and resid 193 through 197 Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 213 through 225 Processing helix chain 'A' and resid 372 through 374 No H-bonds generated for 'chain 'A' and resid 372 through 374' Processing helix chain 'A' and resid 375 through 391 Processing helix chain 'A' and resid 398 through 418 removed outlier: 3.535A pdb=" N GLU A 415 " --> pdb=" O MET A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 441 Processing helix chain 'A' and resid 444 through 469 removed outlier: 3.791A pdb=" N ILE A 448 " --> pdb=" O SER A 444 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 489 Processing helix chain 'B' and resid 100 through 118 removed outlier: 3.608A pdb=" N VAL B 118 " --> pdb=" O LYS B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 132 through 136 Processing helix chain 'B' and resid 137 through 155 removed outlier: 3.571A pdb=" N LYS B 155 " --> pdb=" O GLU B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 186 Processing helix chain 'B' and resid 193 through 197 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 213 through 225 Processing helix chain 'B' and resid 372 through 374 No H-bonds generated for 'chain 'B' and resid 372 through 374' Processing helix chain 'B' and resid 375 through 391 Processing helix chain 'B' and resid 398 through 418 removed outlier: 3.535A pdb=" N GLU B 415 " --> pdb=" O MET B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 433 through 441 Processing helix chain 'B' and resid 444 through 469 removed outlier: 3.792A pdb=" N ILE B 448 " --> pdb=" O SER B 444 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 489 Processing helix chain 'C' and resid 100 through 118 removed outlier: 3.609A pdb=" N VAL C 118 " --> pdb=" O LYS C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 136 Processing helix chain 'C' and resid 137 through 155 removed outlier: 3.570A pdb=" N LYS C 155 " --> pdb=" O GLU C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 186 Processing helix chain 'C' and resid 193 through 197 Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 213 through 225 Processing helix chain 'C' and resid 372 through 374 No H-bonds generated for 'chain 'C' and resid 372 through 374' Processing helix chain 'C' and resid 375 through 391 Processing helix chain 'C' and resid 398 through 418 removed outlier: 3.535A pdb=" N GLU C 415 " --> pdb=" O MET C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 433 through 441 Processing helix chain 'C' and resid 444 through 469 removed outlier: 3.791A pdb=" N ILE C 448 " --> pdb=" O SER C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 489 Processing helix chain 'D' and resid 100 through 118 removed outlier: 3.609A pdb=" N VAL D 118 " --> pdb=" O LYS D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 132 through 136 Processing helix chain 'D' and resid 137 through 155 removed outlier: 3.571A pdb=" N LYS D 155 " --> pdb=" O GLU D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 172 through 186 Processing helix chain 'D' and resid 193 through 197 Processing helix chain 'D' and resid 202 through 206 Processing helix chain 'D' and resid 213 through 225 Processing helix chain 'D' and resid 372 through 374 No H-bonds generated for 'chain 'D' and resid 372 through 374' Processing helix chain 'D' and resid 375 through 391 Processing helix chain 'D' and resid 398 through 418 removed outlier: 3.534A pdb=" N GLU D 415 " --> pdb=" O MET D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 433 through 441 Processing helix chain 'D' and resid 444 through 469 removed outlier: 3.792A pdb=" N ILE D 448 " --> pdb=" O SER D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 489 Processing helix chain 'E' and resid 100 through 118 removed outlier: 3.608A pdb=" N VAL E 118 " --> pdb=" O LYS E 114 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 136 Processing helix chain 'E' and resid 137 through 155 removed outlier: 3.571A pdb=" N LYS E 155 " --> pdb=" O GLU E 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 172 through 186 Processing helix chain 'E' and resid 193 through 197 Processing helix chain 'E' and resid 202 through 206 Processing helix chain 'E' and resid 213 through 225 Processing helix chain 'E' and resid 372 through 374 No H-bonds generated for 'chain 'E' and resid 372 through 374' Processing helix chain 'E' and resid 375 through 391 Processing helix chain 'E' and resid 398 through 418 removed outlier: 3.535A pdb=" N GLU E 415 " --> pdb=" O MET E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 433 through 441 Processing helix chain 'E' and resid 444 through 469 removed outlier: 3.791A pdb=" N ILE E 448 " --> pdb=" O SER E 444 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 489 Processing helix chain 'F' and resid 100 through 118 removed outlier: 3.608A pdb=" N VAL F 118 " --> pdb=" O LYS F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 132 through 136 Processing helix chain 'F' and resid 137 through 155 removed outlier: 3.571A pdb=" N LYS F 155 " --> pdb=" O GLU F 151 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 186 Processing helix chain 'F' and resid 193 through 197 Processing helix chain 'F' and resid 202 through 206 Processing helix chain 'F' and resid 213 through 225 Processing helix chain 'F' and resid 372 through 374 No H-bonds generated for 'chain 'F' and resid 372 through 374' Processing helix chain 'F' and resid 375 through 391 Processing helix chain 'F' and resid 398 through 418 removed outlier: 3.534A pdb=" N GLU F 415 " --> pdb=" O MET F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 433 through 441 Processing helix chain 'F' and resid 444 through 469 removed outlier: 3.791A pdb=" N ILE F 448 " --> pdb=" O SER F 444 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 489 Processing sheet with id=AA1, first strand: chain 'A' and resid 163 through 166 removed outlier: 6.597A pdb=" N CYS A 89 " --> pdb=" O VAL A 164 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ALA A 166 " --> pdb=" O CYS A 89 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY A 91 " --> pdb=" O ALA A 166 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY A 92 " --> pdb=" O ALA A 125 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLU A 76 " --> pdb=" O LYS A 130 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLU E 76 " --> pdb=" O LYS E 130 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY E 92 " --> pdb=" O ALA E 125 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N CYS E 89 " --> pdb=" O VAL E 164 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ALA E 166 " --> pdb=" O CYS E 89 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY E 91 " --> pdb=" O ALA E 166 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 163 through 166 removed outlier: 6.597A pdb=" N CYS B 89 " --> pdb=" O VAL B 164 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ALA B 166 " --> pdb=" O CYS B 89 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N GLY B 91 " --> pdb=" O ALA B 166 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY B 92 " --> pdb=" O ALA B 125 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLU B 76 " --> pdb=" O LYS B 130 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLU D 76 " --> pdb=" O LYS D 130 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY D 92 " --> pdb=" O ALA D 125 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N CYS D 89 " --> pdb=" O VAL D 164 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ALA D 166 " --> pdb=" O CYS D 89 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY D 91 " --> pdb=" O ALA D 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 163 through 166 removed outlier: 6.597A pdb=" N CYS C 89 " --> pdb=" O VAL C 164 " (cutoff:3.500A) removed outlier: 7.802A pdb=" N ALA C 166 " --> pdb=" O CYS C 89 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY C 91 " --> pdb=" O ALA C 166 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLY C 92 " --> pdb=" O ALA C 125 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N GLU C 76 " --> pdb=" O LYS C 130 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N GLU F 76 " --> pdb=" O LYS F 130 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N GLY F 92 " --> pdb=" O ALA F 125 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N CYS F 89 " --> pdb=" O VAL F 164 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N ALA F 166 " --> pdb=" O CYS F 89 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N GLY F 91 " --> pdb=" O ALA F 166 " (cutoff:3.500A) 846 hydrogen bonds defined for protein. 2412 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: 2.62 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4323 1.33 - 1.45: 2468 1.45 - 1.57: 7159 1.57 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 14070 Sorted by residual: bond pdb=" C LYS E 201 " pdb=" N PRO E 202 " ideal model delta sigma weight residual 1.329 1.389 -0.060 1.25e-02 6.40e+03 2.29e+01 bond pdb=" C LYS D 201 " pdb=" N PRO D 202 " ideal model delta sigma weight residual 1.329 1.389 -0.060 1.25e-02 6.40e+03 2.28e+01 bond pdb=" C LYS C 201 " pdb=" N PRO C 202 " ideal model delta sigma weight residual 1.329 1.389 -0.060 1.25e-02 6.40e+03 2.28e+01 bond pdb=" C LYS A 201 " pdb=" N PRO A 202 " ideal model delta sigma weight residual 1.329 1.389 -0.059 1.25e-02 6.40e+03 2.26e+01 bond pdb=" C LYS F 201 " pdb=" N PRO F 202 " ideal model delta sigma weight residual 1.329 1.389 -0.059 1.25e-02 6.40e+03 2.24e+01 ... (remaining 14065 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.79: 18660 2.79 - 5.58: 300 5.58 - 8.36: 24 8.36 - 11.15: 6 11.15 - 13.94: 6 Bond angle restraints: 18996 Sorted by residual: angle pdb=" C LYS B 201 " pdb=" N PRO B 202 " pdb=" CA PRO B 202 " ideal model delta sigma weight residual 120.14 114.09 6.05 1.06e+00 8.90e-01 3.25e+01 angle pdb=" C LYS A 201 " pdb=" N PRO A 202 " pdb=" CA PRO A 202 " ideal model delta sigma weight residual 120.14 114.11 6.03 1.06e+00 8.90e-01 3.23e+01 angle pdb=" C LYS E 201 " pdb=" N PRO E 202 " pdb=" CA PRO E 202 " ideal model delta sigma weight residual 120.14 114.11 6.03 1.06e+00 8.90e-01 3.23e+01 angle pdb=" C LYS D 201 " pdb=" N PRO D 202 " pdb=" CA PRO D 202 " ideal model delta sigma weight residual 120.14 114.13 6.01 1.06e+00 8.90e-01 3.21e+01 angle pdb=" C LYS F 201 " pdb=" N PRO F 202 " pdb=" CA PRO F 202 " ideal model delta sigma weight residual 120.14 114.14 6.00 1.06e+00 8.90e-01 3.21e+01 ... (remaining 18991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.69: 7476 11.69 - 23.38: 678 23.38 - 35.06: 138 35.06 - 46.75: 60 46.75 - 58.44: 12 Dihedral angle restraints: 8364 sinusoidal: 3336 harmonic: 5028 Sorted by residual: dihedral pdb=" CA LYS B 423 " pdb=" C LYS B 423 " pdb=" N HIS B 424 " pdb=" CA HIS B 424 " ideal model delta harmonic sigma weight residual 180.00 159.46 20.54 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA LYS C 423 " pdb=" C LYS C 423 " pdb=" N HIS C 424 " pdb=" CA HIS C 424 " ideal model delta harmonic sigma weight residual 180.00 159.49 20.51 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA LYS E 423 " pdb=" C LYS E 423 " pdb=" N HIS E 424 " pdb=" CA HIS E 424 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 8361 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1460 0.058 - 0.116: 442 0.116 - 0.174: 128 0.174 - 0.233: 10 0.233 - 0.291: 12 Chirality restraints: 2052 Sorted by residual: chirality pdb=" CG LEU B 397 " pdb=" CB LEU B 397 " pdb=" CD1 LEU B 397 " pdb=" CD2 LEU B 397 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.11e+00 chirality pdb=" CG LEU F 397 " pdb=" CB LEU F 397 " pdb=" CD1 LEU F 397 " pdb=" CD2 LEU F 397 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" CG LEU E 397 " pdb=" CB LEU E 397 " pdb=" CD1 LEU E 397 " pdb=" CD2 LEU E 397 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.09e+00 ... (remaining 2049 not shown) Planarity restraints: 2454 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE D 436 " 0.023 2.00e-02 2.50e+03 2.14e-02 7.99e+00 pdb=" CG PHE D 436 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE D 436 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE D 436 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE D 436 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE D 436 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE D 436 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 436 " -0.023 2.00e-02 2.50e+03 2.13e-02 7.92e+00 pdb=" CG PHE C 436 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 PHE C 436 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE C 436 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE C 436 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE C 436 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE C 436 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE F 436 " 0.023 2.00e-02 2.50e+03 2.13e-02 7.90e+00 pdb=" CG PHE F 436 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE F 436 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE F 436 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE F 436 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE F 436 " 0.003 2.00e-02 2.50e+03 pdb=" CZ PHE F 436 " 0.008 2.00e-02 2.50e+03 ... (remaining 2451 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 672 2.62 - 3.19: 14245 3.19 - 3.76: 25473 3.76 - 4.33: 38298 4.33 - 4.90: 57865 Nonbonded interactions: 136553 Sorted by model distance: nonbonded pdb=" O ARG F 211 " pdb=" O HOH F 601 " model vdw 2.051 3.040 nonbonded pdb=" O ARG B 211 " pdb=" O HOH B 601 " model vdw 2.051 3.040 nonbonded pdb=" O ARG A 211 " pdb=" O HOH A 601 " model vdw 2.051 3.040 nonbonded pdb=" O ARG D 211 " pdb=" O HOH D 601 " model vdw 2.051 3.040 nonbonded pdb=" O ARG E 211 " pdb=" O HOH E 601 " model vdw 2.051 3.040 ... (remaining 136548 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.840 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: 0.300 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 13.830 Find NCS groups from input model: 0.140 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: 0.000 Load rotamer database and sin/cos tables:9.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 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 : 0.008 0.060 14070 Z= 0.390 Angle : 0.975 13.941 18996 Z= 0.546 Chirality : 0.061 0.291 2052 Planarity : 0.007 0.046 2454 Dihedral : 10.269 58.440 5172 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 19.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 0.82 % Allowed : 0.82 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 aren not related in a simple way. whole: -2.53 (0.18), residues: 1740 helix: -2.23 (0.13), residues: 924 sheet: -0.80 (0.25), residues: 288 loop : -0.57 (0.27), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 478 TYR 0.043 0.005 TYR D 95 PHE 0.049 0.006 PHE D 436 TRP 0.027 0.005 TRP D 178 HIS 0.011 0.004 HIS E 82 Details of bonding type rmsd covalent geometry : bond 0.00849 (14070) covalent geometry : angle 0.97483 (18996) hydrogen bonds : bond 0.21108 ( 846) hydrogen bonds : angle 7.60959 ( 2412) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 373 time to evaluate : 0.569 Fit side-chains revert: symmetry clash REVERT: B 101 VAL cc_start: 0.8395 (t) cc_final: 0.8158 (p) REVERT: B 486 ILE cc_start: 0.6662 (OUTLIER) cc_final: 0.6388 (mt) REVERT: C 101 VAL cc_start: 0.8253 (t) cc_final: 0.8034 (p) REVERT: D 486 ILE cc_start: 0.6696 (OUTLIER) cc_final: 0.6469 (mt) REVERT: E 486 ILE cc_start: 0.6702 (OUTLIER) cc_final: 0.6495 (mt) REVERT: F 486 ILE cc_start: 0.6676 (OUTLIER) cc_final: 0.6427 (mt) outliers start: 12 outliers final: 0 residues processed: 375 average time/residue: 0.7240 time to fit residues: 293.9258 Evaluate side-chains 189 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 185 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 486 ILE Chi-restraints excluded: chain D residue 486 ILE Chi-restraints excluded: chain E residue 486 ILE Chi-restraints excluded: chain F residue 486 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.3980 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 0.0020 chunk 91 optimal weight: 5.9990 chunk 149 optimal weight: 6.9990 overall best weight: 1.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 82 HIS ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN A 388 ASN A 463 GLN A 484 ASN ** B 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 HIS ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 209 HIS B 388 ASN B 463 GLN B 484 ASN ** C 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN C 374 ASN C 388 ASN C 484 ASN ** D 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 374 ASN D 388 ASN D 463 GLN D 484 ASN ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 HIS ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 ASN E 463 GLN E 484 ASN ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 388 ASN F 463 GLN F 484 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.113471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.101911 restraints weight = 24047.660| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.36 r_work: 0.3691 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14070 Z= 0.151 Angle : 0.614 6.678 18996 Z= 0.326 Chirality : 0.045 0.147 2052 Planarity : 0.006 0.057 2454 Dihedral : 4.937 21.425 1952 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.16 % Allowed : 10.25 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 aren not related in a simple way. whole: 0.04 (0.19), residues: 1740 helix: 0.52 (0.16), residues: 924 sheet: -0.63 (0.27), residues: 282 loop : -0.18 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 466 TYR 0.010 0.001 TYR E 382 PHE 0.018 0.002 PHE A 436 TRP 0.016 0.002 TRP D 385 HIS 0.004 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00341 (14070) covalent geometry : angle 0.61410 (18996) hydrogen bonds : bond 0.04224 ( 846) hydrogen bonds : angle 4.50734 ( 2412) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 232 time to evaluate : 0.577 Fit side-chains REVERT: A 176 MET cc_start: 0.9110 (mmp) cc_final: 0.8638 (mmt) REVERT: A 374 ASN cc_start: 0.8621 (m110) cc_final: 0.8062 (t0) REVERT: A 402 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7897 (mt-10) REVERT: B 374 ASN cc_start: 0.8638 (m-40) cc_final: 0.8108 (t0) REVERT: B 402 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7824 (mt-10) REVERT: C 176 MET cc_start: 0.9116 (mmp) cc_final: 0.8678 (mmt) REVERT: D 374 ASN cc_start: 0.8594 (m-40) cc_final: 0.8078 (t0) REVERT: D 402 GLU cc_start: 0.8104 (mt-10) cc_final: 0.7773 (mt-10) REVERT: D 415 GLU cc_start: 0.7802 (tm-30) cc_final: 0.7462 (pp20) REVERT: E 374 ASN cc_start: 0.8619 (m110) cc_final: 0.8104 (t0) REVERT: F 374 ASN cc_start: 0.8618 (m110) cc_final: 0.8076 (t0) outliers start: 17 outliers final: 1 residues processed: 245 average time/residue: 0.6298 time to fit residues: 169.6390 Evaluate side-chains 160 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 159 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 0.9980 chunk 99 optimal weight: 2.9990 chunk 2 optimal weight: 20.0000 chunk 135 optimal weight: 8.9990 chunk 125 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 168 optimal weight: 0.6980 chunk 101 optimal weight: 1.9990 chunk 23 optimal weight: 20.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN B 189 HIS B 414 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN ** D 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 414 GLN ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 ASN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.113391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.100768 restraints weight = 24430.355| |-----------------------------------------------------------------------------| r_work (start): 0.3777 rms_B_bonded: 1.43 r_work: 0.3702 rms_B_bonded: 1.77 restraints_weight: 0.5000 r_work: 0.3605 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 14070 Z= 0.114 Angle : 0.514 5.887 18996 Z= 0.270 Chirality : 0.042 0.131 2052 Planarity : 0.005 0.069 2454 Dihedral : 4.313 19.635 1944 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 0.96 % Allowed : 11.82 % Favored : 87.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 aren not related in a simple way. whole: 1.28 (0.20), residues: 1740 helix: 1.76 (0.17), residues: 936 sheet: -0.57 (0.29), residues: 282 loop : 0.18 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 419 TYR 0.015 0.001 TYR F 471 PHE 0.015 0.001 PHE A 436 TRP 0.013 0.002 TRP F 385 HIS 0.003 0.001 HIS A 450 Details of bonding type rmsd covalent geometry : bond 0.00256 (14070) covalent geometry : angle 0.51435 (18996) hydrogen bonds : bond 0.03319 ( 846) hydrogen bonds : angle 4.05087 ( 2412) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 205 time to evaluate : 0.492 Fit side-chains REVERT: A 374 ASN cc_start: 0.8581 (m110) cc_final: 0.8077 (t0) REVERT: B 140 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8312 (mt-10) REVERT: B 374 ASN cc_start: 0.8559 (m-40) cc_final: 0.8053 (t0) REVERT: B 402 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7783 (mt-10) REVERT: C 374 ASN cc_start: 0.8611 (m110) cc_final: 0.8098 (t0) REVERT: C 465 MET cc_start: 0.8538 (OUTLIER) cc_final: 0.8275 (mtp) REVERT: D 374 ASN cc_start: 0.8534 (m-40) cc_final: 0.8023 (t0) REVERT: D 402 GLU cc_start: 0.8076 (mt-10) cc_final: 0.7717 (mt-10) REVERT: E 168 ASP cc_start: 0.6961 (OUTLIER) cc_final: 0.6755 (m-30) REVERT: E 374 ASN cc_start: 0.8556 (m110) cc_final: 0.8051 (t0) REVERT: F 168 ASP cc_start: 0.6941 (OUTLIER) cc_final: 0.6728 (m-30) REVERT: F 374 ASN cc_start: 0.8523 (m110) cc_final: 0.7994 (t0) outliers start: 14 outliers final: 2 residues processed: 214 average time/residue: 0.6967 time to fit residues: 162.0009 Evaluate side-chains 164 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 158 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain C residue 465 MET Chi-restraints excluded: chain E residue 168 ASP Chi-restraints excluded: chain F residue 168 ASP Chi-restraints excluded: chain F residue 431 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 34 optimal weight: 10.0000 chunk 3 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 151 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 74 optimal weight: 7.9990 chunk 143 optimal weight: 30.0000 chunk 91 optimal weight: 9.9990 chunk 108 optimal weight: 8.9990 chunk 131 optimal weight: 6.9990 chunk 92 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 ASN B 82 HIS ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 82 HIS ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 484 ASN D 82 HIS ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 225 ASN D 484 ASN E 82 HIS ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 463 GLN E 484 ASN F 82 HIS ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 GLN F 484 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.106311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.095158 restraints weight = 24503.924| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.31 r_work: 0.3608 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3513 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.3884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 14070 Z= 0.270 Angle : 0.609 6.326 18996 Z= 0.322 Chirality : 0.047 0.138 2052 Planarity : 0.006 0.061 2454 Dihedral : 4.604 18.048 1944 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.98 % Allowed : 12.57 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 aren not related in a simple way. whole: 1.45 (0.20), residues: 1740 helix: 1.85 (0.17), residues: 930 sheet: -0.74 (0.28), residues: 288 loop : 0.54 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 419 TYR 0.017 0.002 TYR B 382 PHE 0.021 0.002 PHE C 436 TRP 0.013 0.002 TRP F 385 HIS 0.004 0.001 HIS D 85 Details of bonding type rmsd covalent geometry : bond 0.00624 (14070) covalent geometry : angle 0.60943 (18996) hydrogen bonds : bond 0.04204 ( 846) hydrogen bonds : angle 4.26508 ( 2412) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: A 134 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8571 (mmmm) REVERT: B 140 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8291 (mt-10) REVERT: B 374 ASN cc_start: 0.8721 (m110) cc_final: 0.8201 (t0) REVERT: D 134 LYS cc_start: 0.8795 (OUTLIER) cc_final: 0.8521 (mmmm) REVERT: D 374 ASN cc_start: 0.8698 (m-40) cc_final: 0.8163 (t0) REVERT: E 471 TYR cc_start: 0.8118 (m-80) cc_final: 0.7842 (m-80) REVERT: F 471 TYR cc_start: 0.8113 (m-80) cc_final: 0.7871 (m-80) outliers start: 29 outliers final: 8 residues processed: 194 average time/residue: 0.7315 time to fit residues: 153.7226 Evaluate side-chains 160 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 149 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 147 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 154 optimal weight: 7.9990 chunk 161 optimal weight: 2.9990 chunk 148 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 143 optimal weight: 20.0000 chunk 65 optimal weight: 0.9990 chunk 163 optimal weight: 0.9980 chunk 106 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN B 57 HIS B 84 GLN B 484 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS C 205 GLN D 57 HIS D 84 GLN D 205 GLN ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 HIS E 484 ASN ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 HIS F 484 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.111131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.098114 restraints weight = 24599.476| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.50 r_work: 0.3674 rms_B_bonded: 1.80 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 3.06 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.4382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14070 Z= 0.101 Angle : 0.478 5.957 18996 Z= 0.253 Chirality : 0.041 0.130 2052 Planarity : 0.005 0.071 2454 Dihedral : 4.126 20.104 1944 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 1.16 % Allowed : 13.93 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 aren not related in a simple way. whole: 1.93 (0.21), residues: 1740 helix: 2.31 (0.17), residues: 936 sheet: -0.61 (0.30), residues: 282 loop : 0.63 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 419 TYR 0.012 0.001 TYR A 471 PHE 0.010 0.001 PHE A 436 TRP 0.011 0.001 TRP F 385 HIS 0.005 0.001 HIS C 450 Details of bonding type rmsd covalent geometry : bond 0.00223 (14070) covalent geometry : angle 0.47822 (18996) hydrogen bonds : bond 0.02999 ( 846) hydrogen bonds : angle 3.94780 ( 2412) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 179 time to evaluate : 0.560 Fit side-chains revert: symmetry clash REVERT: A 374 ASN cc_start: 0.8673 (m110) cc_final: 0.8186 (t0) REVERT: B 134 LYS cc_start: 0.8801 (OUTLIER) cc_final: 0.8501 (mmmm) REVERT: B 140 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8292 (mt-10) REVERT: B 374 ASN cc_start: 0.8656 (m110) cc_final: 0.8138 (t0) REVERT: B 402 GLU cc_start: 0.8313 (mt-10) cc_final: 0.7865 (mt-10) REVERT: C 374 ASN cc_start: 0.8673 (m110) cc_final: 0.8163 (t0) REVERT: D 134 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8548 (mmmm) REVERT: D 374 ASN cc_start: 0.8636 (m-40) cc_final: 0.8111 (t0) REVERT: D 402 GLU cc_start: 0.8242 (mt-10) cc_final: 0.7795 (mt-10) REVERT: D 430 ILE cc_start: 0.6015 (OUTLIER) cc_final: 0.5678 (tt) REVERT: E 374 ASN cc_start: 0.8621 (m110) cc_final: 0.8150 (t0) REVERT: F 374 ASN cc_start: 0.8641 (m110) cc_final: 0.8163 (t0) REVERT: F 415 GLU cc_start: 0.8059 (tm-30) cc_final: 0.7643 (pp20) outliers start: 17 outliers final: 4 residues processed: 194 average time/residue: 0.7332 time to fit residues: 153.6827 Evaluate side-chains 157 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 149 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain E residue 100 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 9.9990 chunk 70 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 150 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 12 optimal weight: 0.9980 chunk 94 optimal weight: 0.9980 chunk 99 optimal weight: 0.8980 chunk 169 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN A 437 GLN B 82 HIS ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN C 437 GLN D 82 HIS ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 437 GLN ** E 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 82 HIS ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.111394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.100286 restraints weight = 24509.152| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 1.33 r_work: 0.3689 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8597 moved from start: 0.4609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 14070 Z= 0.098 Angle : 0.460 6.710 18996 Z= 0.244 Chirality : 0.040 0.131 2052 Planarity : 0.005 0.068 2454 Dihedral : 3.944 20.368 1944 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.16 % Allowed : 14.28 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 aren not related in a simple way. whole: 2.15 (0.21), residues: 1740 helix: 2.52 (0.17), residues: 930 sheet: -0.52 (0.30), residues: 282 loop : 0.71 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 419 TYR 0.013 0.001 TYR F 471 PHE 0.026 0.002 PHE A 220 TRP 0.010 0.001 TRP C 385 HIS 0.004 0.001 HIS F 450 Details of bonding type rmsd covalent geometry : bond 0.00218 (14070) covalent geometry : angle 0.46029 (18996) hydrogen bonds : bond 0.02896 ( 846) hydrogen bonds : angle 3.79131 ( 2412) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 199 time to evaluate : 0.530 Fit side-chains REVERT: A 374 ASN cc_start: 0.8581 (m110) cc_final: 0.8085 (t0) REVERT: B 140 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8246 (mt-10) REVERT: B 374 ASN cc_start: 0.8584 (m110) cc_final: 0.8081 (t0) REVERT: B 402 GLU cc_start: 0.8245 (mt-10) cc_final: 0.7841 (mt-10) REVERT: B 415 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7674 (tm-30) REVERT: C 374 ASN cc_start: 0.8606 (m110) cc_final: 0.8116 (t0) REVERT: D 374 ASN cc_start: 0.8599 (m-40) cc_final: 0.8089 (t0) REVERT: D 402 GLU cc_start: 0.8187 (mt-10) cc_final: 0.7790 (mt-10) REVERT: D 430 ILE cc_start: 0.5982 (OUTLIER) cc_final: 0.5699 (tt) REVERT: E 374 ASN cc_start: 0.8560 (m110) cc_final: 0.8099 (t0) REVERT: E 415 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7788 (pp20) REVERT: E 430 ILE cc_start: 0.5837 (OUTLIER) cc_final: 0.5609 (tt) REVERT: F 140 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.8277 (mt-10) REVERT: F 374 ASN cc_start: 0.8557 (m110) cc_final: 0.8074 (t0) REVERT: F 415 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7836 (pp20) outliers start: 17 outliers final: 6 residues processed: 212 average time/residue: 0.7297 time to fit residues: 167.9405 Evaluate side-chains 166 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 156 time to evaluate : 0.597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain F residue 140 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 11 optimal weight: 0.9980 chunk 29 optimal weight: 20.0000 chunk 46 optimal weight: 8.9990 chunk 25 optimal weight: 5.9990 chunk 91 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 45 optimal weight: 7.9990 chunk 56 optimal weight: 20.0000 chunk 98 optimal weight: 4.9990 chunk 97 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN A 437 GLN B 82 HIS B 193 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN C 205 GLN C 437 GLN D 82 HIS D 193 ASN D 205 GLN D 437 GLN E 82 HIS ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.107416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.094894 restraints weight = 24502.709| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.43 r_work: 0.3623 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 14070 Z= 0.182 Angle : 0.528 6.755 18996 Z= 0.279 Chirality : 0.043 0.128 2052 Planarity : 0.005 0.063 2454 Dihedral : 4.164 18.949 1944 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.43 % Allowed : 14.96 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 aren not related in a simple way. whole: 2.10 (0.21), residues: 1740 helix: 2.40 (0.17), residues: 930 sheet: -0.55 (0.29), residues: 288 loop : 0.87 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 419 TYR 0.013 0.001 TYR E 382 PHE 0.014 0.002 PHE C 436 TRP 0.011 0.001 TRP E 385 HIS 0.004 0.001 HIS F 450 Details of bonding type rmsd covalent geometry : bond 0.00421 (14070) covalent geometry : angle 0.52833 (18996) hydrogen bonds : bond 0.03547 ( 846) hydrogen bonds : angle 3.91608 ( 2412) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 0.619 Fit side-chains REVERT: A 374 ASN cc_start: 0.8691 (m110) cc_final: 0.8182 (t0) REVERT: A 419 ARG cc_start: 0.7770 (ttp-110) cc_final: 0.7317 (mpt-90) REVERT: B 140 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8280 (mt-10) REVERT: B 374 ASN cc_start: 0.8703 (m110) cc_final: 0.8183 (t0) REVERT: B 402 GLU cc_start: 0.8354 (mt-10) cc_final: 0.7961 (mt-10) REVERT: B 430 ILE cc_start: 0.6105 (OUTLIER) cc_final: 0.5804 (tt) REVERT: C 374 ASN cc_start: 0.8684 (m110) cc_final: 0.8166 (t0) REVERT: D 374 ASN cc_start: 0.8717 (m-40) cc_final: 0.8180 (t0) REVERT: D 402 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7879 (mt-10) REVERT: D 430 ILE cc_start: 0.6141 (OUTLIER) cc_final: 0.5835 (tt) REVERT: E 140 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8306 (mt-10) REVERT: E 374 ASN cc_start: 0.8613 (m110) cc_final: 0.8101 (t0) REVERT: E 430 ILE cc_start: 0.6016 (OUTLIER) cc_final: 0.5769 (tt) REVERT: F 87 THR cc_start: 0.8969 (OUTLIER) cc_final: 0.8752 (t) REVERT: F 140 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8248 (mt-10) REVERT: F 374 ASN cc_start: 0.8637 (m110) cc_final: 0.8115 (t0) outliers start: 21 outliers final: 9 residues processed: 179 average time/residue: 0.7360 time to fit residues: 143.1757 Evaluate side-chains 166 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 150 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 147 ARG Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain F residue 87 THR Chi-restraints excluded: chain F residue 140 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 164 optimal weight: 1.9990 chunk 74 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 144 optimal weight: 9.9990 chunk 165 optimal weight: 5.9990 chunk 101 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 151 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 ASN A 205 GLN A 437 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN C 437 GLN D 437 GLN ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.106708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.095437 restraints weight = 24533.880| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.35 r_work: 0.3615 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3520 rms_B_bonded: 2.94 restraints_weight: 0.2500 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.4394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14070 Z= 0.193 Angle : 0.543 7.542 18996 Z= 0.286 Chirality : 0.044 0.137 2052 Planarity : 0.005 0.061 2454 Dihedral : 4.244 18.381 1944 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 1.64 % Allowed : 15.30 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 aren not related in a simple way. whole: 2.03 (0.21), residues: 1740 helix: 2.33 (0.17), residues: 930 sheet: -0.57 (0.29), residues: 288 loop : 0.85 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 419 TYR 0.013 0.001 TYR A 382 PHE 0.016 0.002 PHE D 436 TRP 0.010 0.001 TRP E 385 HIS 0.005 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00445 (14070) covalent geometry : angle 0.54314 (18996) hydrogen bonds : bond 0.03589 ( 846) hydrogen bonds : angle 3.98459 ( 2412) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.648 Fit side-chains REVERT: A 374 ASN cc_start: 0.8742 (m110) cc_final: 0.8221 (t0) REVERT: A 419 ARG cc_start: 0.7713 (ttp-110) cc_final: 0.7175 (mpt-90) REVERT: A 430 ILE cc_start: 0.6072 (OUTLIER) cc_final: 0.5868 (tt) REVERT: B 134 LYS cc_start: 0.8828 (OUTLIER) cc_final: 0.8564 (mmmm) REVERT: B 140 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8312 (mt-10) REVERT: B 374 ASN cc_start: 0.8745 (m110) cc_final: 0.8198 (t0) REVERT: B 402 GLU cc_start: 0.8373 (mt-10) cc_final: 0.7951 (mt-10) REVERT: B 430 ILE cc_start: 0.6168 (OUTLIER) cc_final: 0.5869 (tt) REVERT: C 374 ASN cc_start: 0.8691 (m110) cc_final: 0.8173 (t0) REVERT: C 415 GLU cc_start: 0.8148 (tm-30) cc_final: 0.7746 (pp20) REVERT: C 430 ILE cc_start: 0.5849 (OUTLIER) cc_final: 0.5641 (tt) REVERT: D 140 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8338 (mt-10) REVERT: D 374 ASN cc_start: 0.8755 (m-40) cc_final: 0.8204 (t0) REVERT: D 402 GLU cc_start: 0.8314 (mt-10) cc_final: 0.7915 (mt-10) REVERT: D 430 ILE cc_start: 0.6186 (OUTLIER) cc_final: 0.5899 (tt) REVERT: E 140 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8315 (mt-10) REVERT: E 430 ILE cc_start: 0.6012 (OUTLIER) cc_final: 0.5741 (tt) REVERT: F 140 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8267 (mt-10) REVERT: F 430 ILE cc_start: 0.6003 (OUTLIER) cc_final: 0.5781 (tt) outliers start: 24 outliers final: 9 residues processed: 182 average time/residue: 0.7332 time to fit residues: 145.2333 Evaluate side-chains 161 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain A residue 430 ILE Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 430 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 104 optimal weight: 8.9990 chunk 159 optimal weight: 4.9990 chunk 136 optimal weight: 8.9990 chunk 14 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 71 optimal weight: 9.9990 chunk 53 optimal weight: 9.9990 chunk 99 optimal weight: 0.9980 chunk 63 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN A 437 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN C 437 GLN D 205 GLN D 437 GLN ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.106930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.095831 restraints weight = 24693.553| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.29 r_work: 0.3629 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14070 Z= 0.174 Angle : 0.532 8.049 18996 Z= 0.280 Chirality : 0.043 0.132 2052 Planarity : 0.005 0.061 2454 Dihedral : 4.204 18.713 1944 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.23 % Allowed : 15.78 % Favored : 82.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 aren not related in a simple way. whole: 2.05 (0.21), residues: 1740 helix: 2.35 (0.17), residues: 930 sheet: -0.57 (0.29), residues: 288 loop : 0.86 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 419 TYR 0.012 0.001 TYR A 382 PHE 0.014 0.002 PHE C 436 TRP 0.010 0.001 TRP E 385 HIS 0.005 0.001 HIS F 450 Details of bonding type rmsd covalent geometry : bond 0.00404 (14070) covalent geometry : angle 0.53219 (18996) hydrogen bonds : bond 0.03488 ( 846) hydrogen bonds : angle 3.96674 ( 2412) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 157 time to evaluate : 0.680 Fit side-chains REVERT: A 374 ASN cc_start: 0.8683 (m110) cc_final: 0.8179 (t0) REVERT: A 415 GLU cc_start: 0.8183 (pp20) cc_final: 0.7936 (pp20) REVERT: B 134 LYS cc_start: 0.8755 (OUTLIER) cc_final: 0.8482 (mmmm) REVERT: B 140 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8265 (mt-10) REVERT: B 374 ASN cc_start: 0.8697 (m110) cc_final: 0.8156 (t0) REVERT: B 402 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7932 (mt-10) REVERT: B 430 ILE cc_start: 0.6177 (OUTLIER) cc_final: 0.5948 (tt) REVERT: C 374 ASN cc_start: 0.8615 (m110) cc_final: 0.8118 (t0) REVERT: C 415 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7752 (pp20) REVERT: D 140 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8295 (mt-10) REVERT: D 374 ASN cc_start: 0.8689 (m-40) cc_final: 0.8145 (t0) REVERT: D 402 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7892 (mt-10) REVERT: D 430 ILE cc_start: 0.6109 (OUTLIER) cc_final: 0.5831 (tt) REVERT: E 140 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8277 (mt-10) REVERT: E 430 ILE cc_start: 0.5948 (OUTLIER) cc_final: 0.5680 (tt) REVERT: F 140 GLU cc_start: 0.8617 (OUTLIER) cc_final: 0.8210 (mt-10) REVERT: F 374 ASN cc_start: 0.8626 (m110) cc_final: 0.8146 (t0) REVERT: F 430 ILE cc_start: 0.5941 (OUTLIER) cc_final: 0.5713 (tt) outliers start: 18 outliers final: 9 residues processed: 175 average time/residue: 0.7554 time to fit residues: 143.6920 Evaluate side-chains 158 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain F residue 140 GLU Chi-restraints excluded: chain F residue 430 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 85 optimal weight: 10.0000 chunk 74 optimal weight: 20.0000 chunk 87 optimal weight: 20.0000 chunk 122 optimal weight: 0.0570 chunk 52 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 110 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 131 optimal weight: 0.9990 chunk 23 optimal weight: 5.9990 chunk 48 optimal weight: 0.9980 overall best weight: 2.0104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN A 437 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN C 437 GLN D 437 GLN ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.109028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.097463 restraints weight = 24416.770| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.39 r_work: 0.3657 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.3561 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.4618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14070 Z= 0.123 Angle : 0.517 8.953 18996 Z= 0.272 Chirality : 0.042 0.137 2052 Planarity : 0.005 0.064 2454 Dihedral : 4.069 19.618 1944 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.57 % Allowed : 15.71 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 aren not related in a simple way. whole: 2.11 (0.21), residues: 1740 helix: 2.39 (0.17), residues: 936 sheet: -0.51 (0.30), residues: 282 loop : 0.85 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 419 TYR 0.010 0.001 TYR E 471 PHE 0.027 0.002 PHE A 220 TRP 0.009 0.001 TRP C 385 HIS 0.005 0.001 HIS F 450 Details of bonding type rmsd covalent geometry : bond 0.00284 (14070) covalent geometry : angle 0.51708 (18996) hydrogen bonds : bond 0.03117 ( 846) hydrogen bonds : angle 3.88887 ( 2412) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3480 Ramachandran restraints generated. 1740 Oldfield, 0 Emsley, 1740 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.639 Fit side-chains REVERT: A 374 ASN cc_start: 0.8671 (m110) cc_final: 0.8143 (t0) REVERT: A 419 ARG cc_start: 0.7674 (ttp-110) cc_final: 0.7318 (mpt-90) REVERT: B 134 LYS cc_start: 0.8813 (OUTLIER) cc_final: 0.8520 (mmmm) REVERT: B 140 GLU cc_start: 0.8636 (OUTLIER) cc_final: 0.8293 (mt-10) REVERT: B 374 ASN cc_start: 0.8679 (m110) cc_final: 0.8141 (t0) REVERT: B 402 GLU cc_start: 0.8332 (mt-10) cc_final: 0.7918 (mt-10) REVERT: B 430 ILE cc_start: 0.6100 (OUTLIER) cc_final: 0.5841 (tt) REVERT: C 374 ASN cc_start: 0.8653 (m110) cc_final: 0.8124 (t0) REVERT: D 140 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8353 (mt-10) REVERT: D 374 ASN cc_start: 0.8702 (m-40) cc_final: 0.8153 (t0) REVERT: D 402 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7884 (mt-10) REVERT: D 411 MET cc_start: 0.8888 (tpp) cc_final: 0.8677 (tpt) REVERT: D 414 GLN cc_start: 0.9066 (tt0) cc_final: 0.8697 (tp-100) REVERT: E 140 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8312 (mt-10) REVERT: E 374 ASN cc_start: 0.8598 (m110) cc_final: 0.8133 (t0) REVERT: E 430 ILE cc_start: 0.5939 (OUTLIER) cc_final: 0.5685 (tt) REVERT: F 140 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8269 (mt-10) REVERT: F 374 ASN cc_start: 0.8617 (m110) cc_final: 0.8139 (t0) outliers start: 23 outliers final: 10 residues processed: 178 average time/residue: 0.7008 time to fit residues: 136.3306 Evaluate side-chains 163 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 SER Chi-restraints excluded: chain A residue 162 VAL Chi-restraints excluded: chain B residue 134 LYS Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 430 ILE Chi-restraints excluded: chain C residue 78 TYR Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain D residue 100 SER Chi-restraints excluded: chain D residue 140 GLU Chi-restraints excluded: chain E residue 100 SER Chi-restraints excluded: chain E residue 140 GLU Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain F residue 140 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 169 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 160 optimal weight: 1.9990 chunk 170 optimal weight: 9.9990 chunk 171 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 86 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 76 optimal weight: 7.9990 chunk 115 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 GLN ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 193 ASN ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 193 ASN F 205 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.106746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.094699 restraints weight = 24609.287| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 1.40 r_work: 0.3619 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.4529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14070 Z= 0.189 Angle : 0.551 8.847 18996 Z= 0.291 Chirality : 0.044 0.133 2052 Planarity : 0.005 0.059 2454 Dihedral : 4.221 20.941 1944 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.23 % Allowed : 15.98 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 aren not related in a simple way. whole: 2.03 (0.21), residues: 1740 helix: 2.32 (0.17), residues: 930 sheet: -0.54 (0.29), residues: 288 loop : 0.85 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 419 TYR 0.013 0.001 TYR C 382 PHE 0.013 0.002 PHE C 436 TRP 0.010 0.001 TRP E 385 HIS 0.005 0.001 HIS F 450 Details of bonding type rmsd covalent geometry : bond 0.00437 (14070) covalent geometry : angle 0.55061 (18996) hydrogen bonds : bond 0.03575 ( 846) hydrogen bonds : angle 3.96154 ( 2412) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9706.37 seconds wall clock time: 165 minutes 24.92 seconds (9924.92 seconds total)