Starting phenix.real_space_refine on Thu Jun 12 20:50:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5k12_8194/06_2025/5k12_8194.cif Found real_map, /net/cci-nas-00/data/ceres_data/5k12_8194/06_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_8194/06_2025/5k12_8194.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5k12_8194/06_2025/5k12_8194.map" model { file = "/net/cci-nas-00/data/ceres_data/5k12_8194/06_2025/5k12_8194.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5k12_8194/06_2025/5k12_8194.cif" } resolution = 1.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D, F Time building chain proxies: 6.07, per 1000 atoms: 0.41 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: 3.33 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.30 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: 4.41 Time building geometry restraints manager: 3.92 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: 0.11 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' 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: 1.080 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: 0.740 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 29.850 Find NCS groups from input model: 0.320 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: 0.010 Load rotamer database and sin/cos tables:13.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.070 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.027 0.005 TRP D 178 HIS 0.011 0.004 HIS E 82 PHE 0.049 0.006 PHE D 436 TYR 0.043 0.005 TYR D 95 ARG 0.009 0.001 ARG D 478 Details of bonding type rmsd hydrogen bonds : bond 0.21108 ( 846) hydrogen bonds : angle 7.60959 ( 2412) covalent geometry : bond 0.00849 (14070) covalent geometry : angle 0.97483 (18996) *********************** 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 : 1.554 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: 1.4925 time to fit residues: 607.8899 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 : 1.722 ------------------------------------------------------------------------------- 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 146 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 88 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 136 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 82 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 158 optimal weight: 6.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- 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 388 ASN B 463 GLN B 484 ASN 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 82 HIS ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 388 ASN ** E 450 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 388 ASN ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 463 GLN F 484 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.113497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.100694 restraints weight = 23738.330| |-----------------------------------------------------------------------------| r_work (start): 0.3765 rms_B_bonded: 1.43 r_work: 0.3690 rms_B_bonded: 1.78 restraints_weight: 0.5000 r_work: 0.3590 rms_B_bonded: 3.03 restraints_weight: 0.2500 r_work (final): 0.3590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.3394 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= 0.147 Angle : 0.613 6.689 18996 Z= 0.325 Chirality : 0.045 0.147 2052 Planarity : 0.006 0.056 2454 Dihedral : 4.949 21.301 1952 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 0.89 % Allowed : 10.45 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.19), residues: 1740 helix: 0.55 (0.16), residues: 924 sheet: -0.64 (0.27), residues: 282 loop : -0.20 (0.27), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 385 HIS 0.004 0.001 HIS B 57 PHE 0.018 0.002 PHE A 436 TYR 0.010 0.001 TYR E 382 ARG 0.010 0.001 ARG C 466 Details of bonding type rmsd hydrogen bonds : bond 0.04179 ( 846) hydrogen bonds : angle 4.51287 ( 2412) covalent geometry : bond 0.00331 (14070) covalent geometry : angle 0.61306 (18996) *********************** 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 246 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 233 time to evaluate : 1.532 Fit side-chains REVERT: A 176 MET cc_start: 0.9087 (mmp) cc_final: 0.8622 (mmt) REVERT: A 374 ASN cc_start: 0.8618 (m110) cc_final: 0.8062 (t0) REVERT: A 402 GLU cc_start: 0.8133 (mt-10) cc_final: 0.7910 (mt-10) REVERT: B 374 ASN cc_start: 0.8625 (m-40) cc_final: 0.8097 (t0) REVERT: B 402 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7831 (mt-10) REVERT: C 176 MET cc_start: 0.9095 (mmp) cc_final: 0.8666 (mmt) REVERT: D 374 ASN cc_start: 0.8586 (m-40) cc_final: 0.8075 (t0) REVERT: D 402 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7794 (mt-10) REVERT: D 415 GLU cc_start: 0.7799 (tm-30) cc_final: 0.7473 (pp20) REVERT: E 374 ASN cc_start: 0.8614 (m110) cc_final: 0.8102 (t0) REVERT: E 415 GLU cc_start: 0.7973 (tm-30) cc_final: 0.7520 (pp20) REVERT: F 374 ASN cc_start: 0.8621 (m110) cc_final: 0.8081 (t0) outliers start: 13 outliers final: 0 residues processed: 243 average time/residue: 1.2710 time to fit residues: 340.4764 Evaluate side-chains 161 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 161 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 104 optimal weight: 10.0000 chunk 67 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 163 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 145 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 173 optimal weight: 10.0000 chunk 169 optimal weight: 2.9990 chunk 170 optimal weight: 9.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 HIS ** 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 82 HIS ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN B 189 HIS ** B 414 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** D 82 HIS ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 205 GLN D 414 GLN E 82 HIS ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 139 ASN ** E 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 414 GLN ** E 450 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 205 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.109147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.097825 restraints weight = 24174.616| |-----------------------------------------------------------------------------| r_work (start): 0.3735 rms_B_bonded: 1.32 r_work: 0.3641 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3546 rms_B_bonded: 2.91 restraints_weight: 0.2500 r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.3736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14070 Z= 0.192 Angle : 0.570 5.349 18996 Z= 0.301 Chirality : 0.045 0.131 2052 Planarity : 0.006 0.066 2454 Dihedral : 4.582 18.496 1944 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.02 % Allowed : 12.36 % Favored : 86.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.20), residues: 1740 helix: 1.61 (0.16), residues: 936 sheet: -0.68 (0.27), residues: 288 loop : 0.27 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 385 HIS 0.003 0.001 HIS F 57 PHE 0.019 0.002 PHE A 436 TYR 0.015 0.002 TYR E 382 ARG 0.006 0.001 ARG F 466 Details of bonding type rmsd hydrogen bonds : bond 0.03924 ( 846) hydrogen bonds : angle 4.20320 ( 2412) covalent geometry : bond 0.00446 (14070) covalent geometry : angle 0.57029 (18996) *********************** 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 186 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 1.736 Fit side-chains REVERT: B 140 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8228 (mt-10) REVERT: B 374 ASN cc_start: 0.8683 (m-40) cc_final: 0.8151 (t0) REVERT: B 402 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7921 (mt-10) REVERT: C 465 MET cc_start: 0.8581 (OUTLIER) cc_final: 0.8343 (mtp) REVERT: D 374 ASN cc_start: 0.8659 (m-40) cc_final: 0.8124 (t0) REVERT: D 402 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7888 (mt-10) REVERT: D 415 GLU cc_start: 0.7867 (tm-30) cc_final: 0.7515 (pp20) REVERT: F 374 ASN cc_start: 0.8650 (m110) cc_final: 0.8129 (t0) outliers start: 15 outliers final: 5 residues processed: 181 average time/residue: 1.4926 time to fit residues: 294.2485 Evaluate side-chains 151 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 144 time to evaluate : 1.569 ------------------------------------------------------------------------------- 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 C residue 475 LEU Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain E residue 431 VAL 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 166 optimal weight: 10.0000 chunk 124 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 111 optimal weight: 8.9990 chunk 165 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 109 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 94 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 138 optimal weight: 8.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 193 ASN A 205 GLN ** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 193 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 ASN C 205 GLN ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 HIS ** 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 = 0.3865 r_free = 0.3865 target = 0.106469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.094980 restraints weight = 24383.409| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.36 r_work: 0.3604 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.3507 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14070 Z= 0.262 Angle : 0.599 5.441 18996 Z= 0.318 Chirality : 0.047 0.140 2052 Planarity : 0.006 0.065 2454 Dihedral : 4.650 18.114 1944 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.30 % Allowed : 12.30 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.20), residues: 1740 helix: 1.79 (0.17), residues: 930 sheet: -0.75 (0.28), residues: 288 loop : 0.45 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 385 HIS 0.006 0.002 HIS A 82 PHE 0.020 0.002 PHE A 436 TYR 0.016 0.002 TYR D 382 ARG 0.004 0.001 ARG C 466 Details of bonding type rmsd hydrogen bonds : bond 0.04132 ( 846) hydrogen bonds : angle 4.27961 ( 2412) covalent geometry : bond 0.00604 (14070) covalent geometry : angle 0.59873 (18996) *********************** 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 182 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 163 time to evaluate : 2.508 Fit side-chains REVERT: A 138 ASP cc_start: 0.8367 (m-30) cc_final: 0.8148 (m-30) REVERT: B 140 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8311 (mt-10) REVERT: B 374 ASN cc_start: 0.8778 (m110) cc_final: 0.8223 (t0) REVERT: D 134 LYS cc_start: 0.8869 (OUTLIER) cc_final: 0.8601 (mmtm) REVERT: D 374 ASN cc_start: 0.8780 (m-40) cc_final: 0.8214 (t0) REVERT: E 415 GLU cc_start: 0.8274 (pp20) cc_final: 0.7639 (pp20) REVERT: E 419 ARG cc_start: 0.7710 (mtm-85) cc_final: 0.7397 (mpp80) REVERT: E 471 TYR cc_start: 0.8219 (m-80) cc_final: 0.7952 (m-80) REVERT: F 471 TYR cc_start: 0.8205 (m-80) cc_final: 0.7954 (m-80) outliers start: 19 outliers final: 5 residues processed: 179 average time/residue: 1.5715 time to fit residues: 308.5029 Evaluate side-chains 152 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 145 time to evaluate : 1.555 ------------------------------------------------------------------------------- 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 100 SER Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 475 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 3 optimal weight: 10.0000 chunk 100 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 129 optimal weight: 7.9990 chunk 90 optimal weight: 10.0000 chunk 130 optimal weight: 4.9990 chunk 111 optimal weight: 5.9990 chunk 154 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 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 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 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN C 437 GLN C 484 ASN D 84 GLN D 205 GLN ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 189 HIS E 437 GLN ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 193 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.106119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.093368 restraints weight = 24723.728| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 1.45 r_work: 0.3594 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.3495 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14070 Z= 0.263 Angle : 0.585 5.788 18996 Z= 0.311 Chirality : 0.046 0.146 2052 Planarity : 0.005 0.065 2454 Dihedral : 4.562 17.427 1944 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.30 % Allowed : 13.46 % Favored : 85.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.20), residues: 1740 helix: 1.94 (0.17), residues: 930 sheet: -0.75 (0.29), residues: 288 loop : 0.46 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 385 HIS 0.005 0.002 HIS E 450 PHE 0.017 0.002 PHE C 436 TYR 0.015 0.002 TYR B 382 ARG 0.006 0.001 ARG D 419 Details of bonding type rmsd hydrogen bonds : bond 0.04011 ( 846) hydrogen bonds : angle 4.23420 ( 2412) covalent geometry : bond 0.00607 (14070) covalent geometry : angle 0.58516 (18996) *********************** 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 175 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 1.536 Fit side-chains REVERT: A 134 LYS cc_start: 0.8835 (OUTLIER) cc_final: 0.8620 (mmmm) REVERT: A 138 ASP cc_start: 0.8389 (m-30) cc_final: 0.8178 (m-30) REVERT: B 140 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8282 (mt-10) REVERT: B 374 ASN cc_start: 0.8773 (m110) cc_final: 0.8230 (t0) REVERT: B 402 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7939 (mt-10) REVERT: D 134 LYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8643 (mmtm) REVERT: D 374 ASN cc_start: 0.8763 (m-40) cc_final: 0.8212 (t0) REVERT: D 402 GLU cc_start: 0.8312 (mt-10) cc_final: 0.7902 (mt-10) REVERT: D 430 ILE cc_start: 0.6064 (OUTLIER) cc_final: 0.5777 (tt) REVERT: E 415 GLU cc_start: 0.8256 (pp20) cc_final: 0.7945 (pp20) REVERT: E 430 ILE cc_start: 0.6146 (OUTLIER) cc_final: 0.5860 (tt) REVERT: F 140 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.8246 (mt-10) outliers start: 19 outliers final: 7 residues processed: 175 average time/residue: 1.6588 time to fit residues: 315.5682 Evaluate side-chains 159 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 146 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LYS Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 138 ASP 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 C residue 475 LEU Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain F residue 140 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 54 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 13 optimal weight: 9.9990 chunk 101 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 127 optimal weight: 10.0000 chunk 121 optimal weight: 5.9990 chunk 146 optimal weight: 7.9990 chunk 118 optimal weight: 5.9990 chunk 133 optimal weight: 8.9990 chunk 147 optimal weight: 4.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN A 437 GLN B 84 GLN C 84 GLN ** C 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN C 437 GLN ** E 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 GLN ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 189 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.106214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.094952 restraints weight = 24542.834| |-----------------------------------------------------------------------------| r_work (start): 0.3700 rms_B_bonded: 1.31 r_work: 0.3605 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.3509 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.4100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 14070 Z= 0.242 Angle : 0.568 6.249 18996 Z= 0.301 Chirality : 0.045 0.140 2052 Planarity : 0.005 0.061 2454 Dihedral : 4.481 17.218 1944 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.98 % Allowed : 13.18 % Favored : 84.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.20), residues: 1740 helix: 2.03 (0.17), residues: 930 sheet: -0.84 (0.29), residues: 288 loop : 0.55 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 385 HIS 0.005 0.002 HIS E 450 PHE 0.015 0.002 PHE C 436 TYR 0.014 0.002 TYR B 382 ARG 0.004 0.001 ARG F 419 Details of bonding type rmsd hydrogen bonds : bond 0.03891 ( 846) hydrogen bonds : angle 4.19013 ( 2412) covalent geometry : bond 0.00560 (14070) covalent geometry : angle 0.56764 (18996) *********************** 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 188 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 1.759 Fit side-chains REVERT: A 134 LYS cc_start: 0.8838 (OUTLIER) cc_final: 0.8625 (mmmm) REVERT: A 138 ASP cc_start: 0.8383 (m-30) cc_final: 0.8161 (m-30) REVERT: A 430 ILE cc_start: 0.6155 (OUTLIER) cc_final: 0.5821 (tt) REVERT: B 134 LYS cc_start: 0.8865 (OUTLIER) cc_final: 0.8576 (mmmm) REVERT: B 140 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8292 (mt-10) REVERT: B 374 ASN cc_start: 0.8779 (m110) cc_final: 0.8227 (t0) REVERT: B 402 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7966 (mt-10) REVERT: B 430 ILE cc_start: 0.6271 (OUTLIER) cc_final: 0.5925 (tt) REVERT: C 430 ILE cc_start: 0.6099 (OUTLIER) cc_final: 0.5846 (tt) REVERT: D 134 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8658 (mmtm) REVERT: D 374 ASN cc_start: 0.8767 (m-40) cc_final: 0.8206 (t0) REVERT: D 402 GLU cc_start: 0.8324 (mt-10) cc_final: 0.7956 (mt-10) REVERT: D 430 ILE cc_start: 0.6140 (OUTLIER) cc_final: 0.5870 (tt) REVERT: E 415 GLU cc_start: 0.8198 (pp20) cc_final: 0.7899 (pp20) REVERT: E 430 ILE cc_start: 0.6098 (OUTLIER) cc_final: 0.5811 (tt) REVERT: F 430 ILE cc_start: 0.6170 (OUTLIER) cc_final: 0.5946 (tt) outliers start: 29 outliers final: 6 residues processed: 186 average time/residue: 1.5022 time to fit residues: 304.5714 Evaluate side-chains 162 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LYS 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 162 VAL Chi-restraints excluded: chain C residue 430 ILE Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 475 LEU Chi-restraints excluded: chain E residue 430 ILE Chi-restraints excluded: chain F residue 430 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 27 optimal weight: 20.0000 chunk 144 optimal weight: 10.0000 chunk 169 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 80 optimal weight: 9.9990 chunk 168 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 147 optimal weight: 8.9990 chunk 166 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 GLN A 437 GLN A 484 ASN B 484 ASN C 189 HIS C 205 GLN C 437 GLN D 205 GLN D 484 ASN E 84 GLN E 193 ASN E 437 GLN E 484 ASN ** F 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 484 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.105799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.093027 restraints weight = 25039.838| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 1.47 r_work: 0.3585 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3491 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.4144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 14070 Z= 0.270 Angle : 0.589 7.759 18996 Z= 0.313 Chirality : 0.046 0.144 2052 Planarity : 0.005 0.058 2454 Dihedral : 4.532 17.562 1944 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.64 % Allowed : 13.80 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.20), residues: 1740 helix: 1.99 (0.17), residues: 930 sheet: -0.87 (0.29), residues: 288 loop : 0.54 (0.28), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 385 HIS 0.005 0.002 HIS E 450 PHE 0.015 0.002 PHE C 436 TYR 0.017 0.002 TYR A 113 ARG 0.004 0.001 ARG D 419 Details of bonding type rmsd hydrogen bonds : bond 0.04035 ( 846) hydrogen bonds : angle 4.23331 ( 2412) covalent geometry : bond 0.00623 (14070) covalent geometry : angle 0.58898 (18996) *********************** 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 190 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 1.795 Fit side-chains REVERT: A 134 LYS cc_start: 0.8845 (OUTLIER) cc_final: 0.8631 (mmmm) REVERT: A 430 ILE cc_start: 0.6138 (OUTLIER) cc_final: 0.5928 (tt) REVERT: B 134 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8592 (mmmm) REVERT: B 140 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8144 (mt-10) REVERT: B 374 ASN cc_start: 0.8794 (m110) cc_final: 0.8262 (t0) REVERT: B 430 ILE cc_start: 0.6300 (OUTLIER) cc_final: 0.5989 (tt) REVERT: C 138 ASP cc_start: 0.8385 (m-30) cc_final: 0.8155 (m-30) REVERT: C 430 ILE cc_start: 0.6018 (OUTLIER) cc_final: 0.5798 (tt) REVERT: D 134 LYS cc_start: 0.8911 (OUTLIER) cc_final: 0.8673 (mmtm) REVERT: D 374 ASN cc_start: 0.8790 (m-40) cc_final: 0.8253 (t0) REVERT: D 430 ILE cc_start: 0.6165 (OUTLIER) cc_final: 0.5885 (tt) REVERT: E 430 ILE cc_start: 0.6104 (OUTLIER) cc_final: 0.5814 (tt) REVERT: F 140 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8233 (mt-10) REVERT: F 430 ILE cc_start: 0.6153 (OUTLIER) cc_final: 0.5912 (tt) outliers start: 24 outliers final: 7 residues processed: 190 average time/residue: 1.4227 time to fit residues: 295.4913 Evaluate side-chains 164 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LYS 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 138 ASP 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 C residue 430 ILE Chi-restraints excluded: chain C residue 475 LEU Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 475 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 154 optimal weight: 0.8980 chunk 162 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 156 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 66 optimal weight: 0.0670 chunk 70 optimal weight: 0.9990 chunk 76 optimal weight: 2.9990 chunk 144 optimal weight: 8.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.7924 ------------------------------------------------------------------------------- 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 205 GLN A 437 GLN A 484 ASN B 484 ASN C 205 GLN C 484 ASN D 484 ASN E 437 GLN E 484 ASN F 84 GLN F 484 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.108822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.096560 restraints weight = 24444.921| |-----------------------------------------------------------------------------| r_work (start): 0.3723 rms_B_bonded: 1.44 r_work: 0.3647 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 2.95 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.4448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14070 Z= 0.117 Angle : 0.502 8.853 18996 Z= 0.268 Chirality : 0.041 0.128 2052 Planarity : 0.005 0.062 2454 Dihedral : 4.197 18.263 1944 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 1.16 % Allowed : 15.71 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.21), residues: 1740 helix: 2.33 (0.17), residues: 930 sheet: -0.80 (0.29), residues: 282 loop : 0.61 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 385 HIS 0.005 0.001 HIS E 450 PHE 0.009 0.001 PHE E 436 TYR 0.012 0.001 TYR A 113 ARG 0.004 0.000 ARG F 419 Details of bonding type rmsd hydrogen bonds : bond 0.03198 ( 846) hydrogen bonds : angle 4.01470 ( 2412) covalent geometry : bond 0.00270 (14070) covalent geometry : angle 0.50243 (18996) *********************** 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 201 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 1.670 Fit side-chains REVERT: A 134 LYS cc_start: 0.8806 (OUTLIER) cc_final: 0.8584 (mmmm) REVERT: A 374 ASN cc_start: 0.8622 (m110) cc_final: 0.8154 (t0) REVERT: B 140 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8189 (mt-10) REVERT: B 374 ASN cc_start: 0.8675 (m110) cc_final: 0.8169 (t0) REVERT: B 402 GLU cc_start: 0.8308 (mt-10) cc_final: 0.7884 (mt-10) REVERT: B 430 ILE cc_start: 0.6089 (OUTLIER) cc_final: 0.5805 (tt) REVERT: C 374 ASN cc_start: 0.8623 (m110) cc_final: 0.8135 (t0) REVERT: D 134 LYS cc_start: 0.8821 (OUTLIER) cc_final: 0.8555 (mmtm) REVERT: D 374 ASN cc_start: 0.8679 (m-40) cc_final: 0.8150 (t0) REVERT: D 402 GLU cc_start: 0.8304 (mt-10) cc_final: 0.7890 (mt-10) REVERT: D 430 ILE cc_start: 0.5909 (OUTLIER) cc_final: 0.5633 (tt) REVERT: E 140 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.8240 (mt-10) REVERT: E 374 ASN cc_start: 0.8601 (m110) cc_final: 0.8122 (t0) REVERT: E 430 ILE cc_start: 0.5861 (OUTLIER) cc_final: 0.5576 (tt) REVERT: F 140 GLU cc_start: 0.8632 (OUTLIER) cc_final: 0.8103 (mt-10) REVERT: F 374 ASN cc_start: 0.8643 (m110) cc_final: 0.8175 (t0) outliers start: 17 outliers final: 4 residues processed: 200 average time/residue: 1.4598 time to fit residues: 318.6567 Evaluate side-chains 166 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 154 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 475 LEU Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 430 ILE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 73 optimal weight: 3.9990 chunk 143 optimal weight: 7.9990 chunk 24 optimal weight: 6.9990 chunk 40 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 27 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 0.0030 chunk 170 optimal weight: 7.9990 overall best weight: 4.1998 ------------------------------------------------------------------------------- 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 205 GLN A 437 GLN B 484 ASN C 205 GLN C 484 ASN D 205 GLN E 437 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 = 0.107034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.095622 restraints weight = 24452.297| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.39 r_work: 0.3622 rms_B_bonded: 1.67 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: 0.8661 moved from start: 0.4412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14070 Z= 0.183 Angle : 0.546 7.243 18996 Z= 0.291 Chirality : 0.044 0.129 2052 Planarity : 0.005 0.060 2454 Dihedral : 4.279 19.449 1944 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.23 % Allowed : 16.39 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.21), residues: 1740 helix: 2.26 (0.17), residues: 930 sheet: -0.79 (0.29), residues: 288 loop : 0.70 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 385 HIS 0.005 0.001 HIS E 450 PHE 0.027 0.002 PHE C 220 TYR 0.012 0.001 TYR C 113 ARG 0.005 0.000 ARG F 419 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 846) hydrogen bonds : angle 4.06731 ( 2412) covalent geometry : bond 0.00427 (14070) covalent geometry : angle 0.54641 (18996) *********************** 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 174 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 1.641 Fit side-chains REVERT: A 134 LYS cc_start: 0.8778 (OUTLIER) cc_final: 0.8571 (mmmm) REVERT: A 374 ASN cc_start: 0.8647 (m110) cc_final: 0.8168 (t0) REVERT: B 134 LYS cc_start: 0.8760 (OUTLIER) cc_final: 0.8482 (mmmm) REVERT: B 140 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8147 (mt-10) REVERT: B 374 ASN cc_start: 0.8661 (m110) cc_final: 0.8159 (t0) REVERT: B 402 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7912 (mt-10) REVERT: B 430 ILE cc_start: 0.6107 (OUTLIER) cc_final: 0.5816 (tt) REVERT: C 374 ASN cc_start: 0.8588 (m110) cc_final: 0.8110 (t0) REVERT: C 402 GLU cc_start: 0.8069 (mt-10) cc_final: 0.7855 (mt-10) REVERT: D 134 LYS cc_start: 0.8772 (OUTLIER) cc_final: 0.8506 (mmtm) REVERT: D 374 ASN cc_start: 0.8664 (m-40) cc_final: 0.8139 (t0) REVERT: D 402 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7880 (mt-10) REVERT: D 430 ILE cc_start: 0.5956 (OUTLIER) cc_final: 0.5678 (tt) REVERT: E 140 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8195 (mt-10) REVERT: E 374 ASN cc_start: 0.8613 (m110) cc_final: 0.8121 (t0) REVERT: E 419 ARG cc_start: 0.7588 (ttp-110) cc_final: 0.7029 (mpt-90) REVERT: E 430 ILE cc_start: 0.5956 (OUTLIER) cc_final: 0.5663 (tt) REVERT: F 140 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.8126 (mt-10) REVERT: F 374 ASN cc_start: 0.8630 (m110) cc_final: 0.8144 (t0) outliers start: 18 outliers final: 5 residues processed: 172 average time/residue: 2.0650 time to fit residues: 386.7448 Evaluate side-chains 161 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 147 time to evaluate : 2.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LYS 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 475 LEU Chi-restraints excluded: chain D residue 134 LYS Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain D residue 475 LEU 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 97 optimal weight: 5.9990 chunk 27 optimal weight: 20.0000 chunk 107 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 124 optimal weight: 0.0050 chunk 123 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 172 optimal weight: 20.0000 chunk 10 optimal weight: 0.1980 chunk 102 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 overall best weight: 2.4400 ------------------------------------------------------------------------------- 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 205 GLN B 484 ASN C 205 GLN E 437 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.108375 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.097038 restraints weight = 24389.139| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 1.34 r_work: 0.3646 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.3559 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.4569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14070 Z= 0.133 Angle : 0.509 8.248 18996 Z= 0.271 Chirality : 0.042 0.127 2052 Planarity : 0.005 0.061 2454 Dihedral : 4.148 20.154 1944 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.02 % Allowed : 16.39 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.95 (0.21), residues: 1740 helix: 2.35 (0.17), residues: 930 sheet: -0.68 (0.29), residues: 282 loop : 0.67 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 385 HIS 0.005 0.001 HIS E 450 PHE 0.010 0.001 PHE E 436 TYR 0.011 0.001 TYR C 113 ARG 0.005 0.000 ARG F 419 Details of bonding type rmsd hydrogen bonds : bond 0.03260 ( 846) hydrogen bonds : angle 3.97244 ( 2412) covalent geometry : bond 0.00309 (14070) covalent geometry : angle 0.50910 (18996) ********************** 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 184 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 169 time to evaluate : 1.761 Fit side-chains REVERT: A 134 LYS cc_start: 0.8824 (OUTLIER) cc_final: 0.8610 (mmmm) REVERT: A 374 ASN cc_start: 0.8636 (m110) cc_final: 0.8125 (t0) REVERT: A 411 MET cc_start: 0.8482 (tpp) cc_final: 0.8266 (tpp) REVERT: B 134 LYS cc_start: 0.8792 (OUTLIER) cc_final: 0.8501 (mmmm) REVERT: B 140 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.8217 (mt-10) REVERT: B 374 ASN cc_start: 0.8659 (m110) cc_final: 0.8138 (t0) REVERT: B 402 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7913 (mt-10) REVERT: B 415 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7620 (pp20) REVERT: B 430 ILE cc_start: 0.6038 (OUTLIER) cc_final: 0.5800 (tt) REVERT: C 374 ASN cc_start: 0.8633 (m110) cc_final: 0.8097 (t0) REVERT: C 402 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7884 (mt-10) REVERT: D 134 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8519 (mmtm) REVERT: D 374 ASN cc_start: 0.8654 (m-40) cc_final: 0.8096 (t0) REVERT: D 402 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7858 (mt-10) REVERT: D 430 ILE cc_start: 0.5952 (OUTLIER) cc_final: 0.5675 (tt) REVERT: E 140 GLU cc_start: 0.8670 (OUTLIER) cc_final: 0.8282 (mt-10) REVERT: E 374 ASN cc_start: 0.8611 (m110) cc_final: 0.8108 (t0) REVERT: E 419 ARG cc_start: 0.7574 (ttp-110) cc_final: 0.7031 (mpt-90) REVERT: E 430 ILE cc_start: 0.5876 (OUTLIER) cc_final: 0.5632 (tt) REVERT: F 140 GLU cc_start: 0.8659 (OUTLIER) cc_final: 0.8257 (mt-10) REVERT: F 374 ASN cc_start: 0.8647 (m110) cc_final: 0.8147 (t0) REVERT: F 411 MET cc_start: 0.8619 (tpp) cc_final: 0.8260 (tpp) outliers start: 15 outliers final: 5 residues processed: 182 average time/residue: 1.6640 time to fit residues: 330.9017 Evaluate side-chains 168 residues out of total 1464 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 154 time to evaluate : 1.698 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 LYS 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 134 LYS Chi-restraints excluded: chain D residue 430 ILE 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 144 optimal weight: 8.9990 chunk 168 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 117 optimal weight: 20.0000 chunk 39 optimal weight: 0.0570 chunk 120 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 153 optimal weight: 0.0870 chunk 93 optimal weight: 0.9980 chunk 162 optimal weight: 9.9990 overall best weight: 2.2280 ------------------------------------------------------------------------------- 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 205 GLN C 205 GLN D 205 GLN E 437 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.108289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.097470 restraints weight = 24475.190| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.31 r_work: 0.3649 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 14070 Z= 0.127 Angle : 0.505 7.742 18996 Z= 0.269 Chirality : 0.042 0.128 2052 Planarity : 0.005 0.064 2454 Dihedral : 4.113 20.824 1944 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.09 % Allowed : 16.60 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.21), residues: 1740 helix: 2.39 (0.17), residues: 930 sheet: -0.58 (0.30), residues: 282 loop : 0.71 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 385 HIS 0.005 0.001 HIS E 450 PHE 0.027 0.002 PHE A 220 TYR 0.009 0.001 TYR C 113 ARG 0.004 0.000 ARG F 419 Details of bonding type rmsd hydrogen bonds : bond 0.03225 ( 846) hydrogen bonds : angle 3.93162 ( 2412) covalent geometry : bond 0.00294 (14070) covalent geometry : angle 0.50524 (18996) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 24021.93 seconds wall clock time: 421 minutes 8.78 seconds (25268.78 seconds total)