Starting phenix.real_space_refine on Thu Sep 26 22:53:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k12_8194/09_2024/5k12_8194.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k12_8194/09_2024/5k12_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k12_8194/09_2024/5k12_8194.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k12_8194/09_2024/5k12_8194.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k12_8194/09_2024/5k12_8194.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5k12_8194/09_2024/5k12_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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 6.32, per 1000 atoms: 0.43 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: 3.69 Conformation dependent library (CDL) restraints added in 1.6 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: 4.51 Time building geometry restraints manager: 4.27 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: 0.00 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: 0.560 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: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 31.960 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.040 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:12.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.240 ------------------------------------------------------------------------------- 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= 0.557 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 *********************** 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 fitting. rotamer outliers: 12 poor density : 373 time to evaluate : 1.682 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: 1.4423 time to fit residues: 587.9364 Evaluate side-chains 189 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 185 time to evaluate : 1.790 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 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= 0.218 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 *********************** 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 fitting. rotamer outliers: 13 poor density : 233 time to evaluate : 1.876 Fit side-chains REVERT: A 176 MET cc_start: 0.7777 (mmp) cc_final: 0.7440 (mmt) REVERT: A 374 ASN cc_start: 0.7749 (m110) cc_final: 0.7495 (t0) REVERT: C 176 MET cc_start: 0.7766 (mmp) cc_final: 0.7457 (mmt) REVERT: E 374 ASN cc_start: 0.7727 (m110) cc_final: 0.7507 (t0) REVERT: F 374 ASN cc_start: 0.7711 (m110) cc_final: 0.7467 (t0) outliers start: 13 outliers final: 0 residues processed: 243 average time/residue: 1.2500 time to fit residues: 335.0091 Evaluate side-chains 156 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 87 optimal weight: 20.0000 chunk 49 optimal weight: 9.9990 chunk 131 optimal weight: 1.9990 chunk 107 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 158 optimal weight: 9.9990 chunk 171 optimal weight: 3.9990 chunk 140 optimal weight: 4.9990 chunk 156 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 126 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 A 193 ASN A 205 GLN A 209 HIS B 82 HIS B 84 GLN B 135 ASN B 209 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 C 193 ASN C 205 GLN C 209 HIS D 82 HIS ** D 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 193 ASN D 205 GLN D 209 HIS D 414 GLN E 82 HIS E 84 GLN E 139 ASN E 209 HIS E 414 GLN ** E 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 82 HIS F 84 GLN F 205 GLN F 209 HIS ** F 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7093 moved from start: 0.3753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14070 Z= 0.359 Angle : 0.608 5.394 18996 Z= 0.321 Chirality : 0.046 0.138 2052 Planarity : 0.006 0.066 2454 Dihedral : 4.737 18.396 1944 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 1.23 % Allowed : 11.95 % Favored : 86.82 % 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: 1.03 (0.20), residues: 1740 helix: 1.48 (0.16), residues: 936 sheet: -0.75 (0.27), residues: 288 loop : 0.29 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP F 385 HIS 0.004 0.002 HIS C 391 PHE 0.022 0.002 PHE A 436 TYR 0.017 0.002 TYR D 95 ARG 0.006 0.001 ARG F 466 *********************** 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 185 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 167 time to evaluate : 1.675 Fit side-chains REVERT: B 140 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6586 (mt-10) REVERT: C 465 MET cc_start: 0.7670 (OUTLIER) cc_final: 0.7356 (mtp) outliers start: 18 outliers final: 6 residues processed: 181 average time/residue: 1.4706 time to fit residues: 290.0864 Evaluate side-chains 146 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 138 time to evaluate : 1.648 ------------------------------------------------------------------------------- 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 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 156 optimal weight: 20.0000 chunk 119 optimal weight: 10.0000 chunk 82 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 106 optimal weight: 4.9990 chunk 158 optimal weight: 10.0000 chunk 168 optimal weight: 4.9990 chunk 150 optimal weight: 7.9990 chunk 45 optimal weight: 10.0000 chunk 140 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 205 GLN B 193 ASN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN C 205 GLN D 84 GLN E 193 ASN F 193 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 14070 Z= 0.372 Angle : 0.585 5.434 18996 Z= 0.311 Chirality : 0.046 0.136 2052 Planarity : 0.006 0.065 2454 Dihedral : 4.620 18.543 1944 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.84 % Allowed : 11.89 % Favored : 86.27 % 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: 1.33 (0.20), residues: 1740 helix: 1.78 (0.17), residues: 936 sheet: -0.74 (0.28), residues: 288 loop : 0.41 (0.28), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 385 HIS 0.005 0.002 HIS A 82 PHE 0.018 0.002 PHE A 436 TYR 0.015 0.002 TYR A 382 ARG 0.009 0.001 ARG A 419 *********************** 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 188 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 161 time to evaluate : 1.572 Fit side-chains REVERT: B 140 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6564 (mt-10) REVERT: D 134 LYS cc_start: 0.8358 (OUTLIER) cc_final: 0.8125 (mmtm) outliers start: 27 outliers final: 6 residues processed: 184 average time/residue: 1.4551 time to fit residues: 292.1859 Evaluate side-chains 149 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 141 time to evaluate : 1.745 ------------------------------------------------------------------------------- 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 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 475 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 95 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 125 optimal weight: 2.9990 chunk 69 optimal weight: 9.9990 chunk 143 optimal weight: 20.0000 chunk 116 optimal weight: 8.9990 chunk 0 optimal weight: 2.9990 chunk 85 optimal weight: 20.0000 chunk 150 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 56 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 205 GLN ** B 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN D 205 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.4122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14070 Z= 0.267 Angle : 0.528 5.955 18996 Z= 0.280 Chirality : 0.043 0.130 2052 Planarity : 0.005 0.067 2454 Dihedral : 4.419 20.176 1944 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.16 % Allowed : 13.32 % Favored : 85.52 % 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: 1.69 (0.20), residues: 1740 helix: 2.12 (0.17), residues: 936 sheet: -0.70 (0.29), residues: 288 loop : 0.52 (0.28), residues: 516 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 0.013 0.001 PHE C 436 TYR 0.011 0.001 TYR B 382 ARG 0.005 0.000 ARG A 174 *********************** 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 185 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 168 time to evaluate : 1.812 Fit side-chains REVERT: B 134 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.8048 (mmmm) REVERT: B 140 GLU cc_start: 0.6937 (OUTLIER) cc_final: 0.6550 (mt-10) REVERT: D 134 LYS cc_start: 0.8330 (OUTLIER) cc_final: 0.8096 (mmtm) outliers start: 17 outliers final: 4 residues processed: 184 average time/residue: 1.5042 time to fit residues: 301.4095 Evaluate side-chains 147 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 140 time to evaluate : 1.720 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 151 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 98 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 168 optimal weight: 7.9990 chunk 139 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 13 optimal weight: 9.9990 chunk 55 optimal weight: 5.9990 chunk 88 optimal weight: 10.0000 chunk 162 optimal weight: 10.0000 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN A 437 GLN C 205 GLN C 437 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.4234 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= 0.254 Angle : 0.513 5.829 18996 Z= 0.274 Chirality : 0.043 0.127 2052 Planarity : 0.005 0.063 2454 Dihedral : 4.338 20.012 1944 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 2.05 % Allowed : 13.52 % Favored : 84.43 % 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: 1.82 (0.21), residues: 1740 helix: 2.23 (0.17), residues: 936 sheet: -0.75 (0.29), residues: 288 loop : 0.65 (0.29), residues: 516 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 0.024 0.002 PHE A 220 TYR 0.013 0.001 TYR C 113 ARG 0.007 0.000 ARG C 174 *********************** 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 194 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 164 time to evaluate : 1.790 Fit side-chains REVERT: B 134 LYS cc_start: 0.8294 (OUTLIER) cc_final: 0.8051 (mmmm) REVERT: B 140 GLU cc_start: 0.6932 (OUTLIER) cc_final: 0.6539 (mt-10) REVERT: D 134 LYS cc_start: 0.8321 (OUTLIER) cc_final: 0.8087 (mmtm) outliers start: 30 outliers final: 6 residues processed: 189 average time/residue: 1.4118 time to fit residues: 291.7999 Evaluate side-chains 150 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 141 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP 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 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 18 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 167 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 102 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 66 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN A 437 GLN C 205 GLN C 437 GLN D 205 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.4360 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= 0.237 Angle : 0.502 5.808 18996 Z= 0.269 Chirality : 0.043 0.130 2052 Planarity : 0.005 0.060 2454 Dihedral : 4.283 20.630 1944 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.23 % Allowed : 14.21 % 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: 1.92 (0.21), residues: 1740 helix: 2.31 (0.17), residues: 936 sheet: -0.73 (0.29), residues: 288 loop : 0.70 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 385 HIS 0.005 0.001 HIS E 450 PHE 0.012 0.001 PHE A 436 TYR 0.012 0.001 TYR A 113 ARG 0.005 0.000 ARG C 174 *********************** 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 fitting. rotamer outliers: 18 poor density : 163 time to evaluate : 1.782 Fit side-chains REVERT: B 134 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.8031 (mmmm) REVERT: B 140 GLU cc_start: 0.6925 (OUTLIER) cc_final: 0.6511 (mt-10) REVERT: D 134 LYS cc_start: 0.8310 (OUTLIER) cc_final: 0.8079 (mmtm) outliers start: 18 outliers final: 6 residues processed: 181 average time/residue: 1.4384 time to fit residues: 284.2064 Evaluate side-chains 152 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 143 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 106 optimal weight: 0.6980 chunk 114 optimal weight: 20.0000 chunk 82 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 152 optimal weight: 3.9990 chunk 160 optimal weight: 0.9980 chunk 146 optimal weight: 20.0000 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 205 GLN A 437 GLN C 205 GLN C 437 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14070 Z= 0.167 Angle : 0.477 6.332 18996 Z= 0.256 Chirality : 0.041 0.127 2052 Planarity : 0.005 0.064 2454 Dihedral : 4.143 21.310 1944 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.75 % Allowed : 15.16 % Favored : 84.08 % 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: 2.41 (0.17), residues: 936 sheet: -0.63 (0.29), residues: 282 loop : 0.68 (0.29), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 385 HIS 0.005 0.001 HIS E 450 PHE 0.009 0.001 PHE C 436 TYR 0.009 0.001 TYR B 471 ARG 0.006 0.000 ARG F 419 *********************** 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 188 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 177 time to evaluate : 1.667 Fit side-chains REVERT: B 140 GLU cc_start: 0.6912 (OUTLIER) cc_final: 0.6474 (mt-10) REVERT: D 134 LYS cc_start: 0.8275 (OUTLIER) cc_final: 0.8052 (mmtm) REVERT: E 140 GLU cc_start: 0.6897 (OUTLIER) cc_final: 0.6517 (mt-10) outliers start: 11 outliers final: 5 residues processed: 186 average time/residue: 1.4691 time to fit residues: 300.2234 Evaluate side-chains 156 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 148 time to evaluate : 1.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 374 ASN 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 D residue 134 LYS Chi-restraints excluded: chain E residue 140 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 156 optimal weight: 6.9990 chunk 160 optimal weight: 0.9980 chunk 94 optimal weight: 10.0000 chunk 68 optimal weight: 20.0000 chunk 122 optimal weight: 0.0010 chunk 47 optimal weight: 0.9990 chunk 141 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 chunk 155 optimal weight: 0.8980 chunk 102 optimal weight: 0.9990 chunk 165 optimal weight: 4.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN A 437 GLN A 450 HIS C 205 GLN C 437 GLN D 189 HIS D 205 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.4808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 14070 Z= 0.145 Angle : 0.475 7.583 18996 Z= 0.256 Chirality : 0.041 0.137 2052 Planarity : 0.005 0.065 2454 Dihedral : 4.038 22.537 1944 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 0.89 % Allowed : 16.05 % 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 (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: 2.13 (0.21), residues: 1740 helix: 2.47 (0.17), residues: 936 sheet: -0.49 (0.30), residues: 282 loop : 0.72 (0.30), 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 0.029 0.001 PHE A 220 TYR 0.008 0.001 TYR D 471 ARG 0.006 0.000 ARG A 174 *********************** 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 202 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 189 time to evaluate : 1.656 Fit side-chains REVERT: B 140 GLU cc_start: 0.6917 (OUTLIER) cc_final: 0.6533 (mt-10) REVERT: E 140 GLU cc_start: 0.6883 (OUTLIER) cc_final: 0.6501 (mt-10) outliers start: 13 outliers final: 8 residues processed: 200 average time/residue: 1.4903 time to fit residues: 324.1057 Evaluate side-chains 159 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 149 time to evaluate : 1.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain A residue 374 ASN Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain D residue 374 ASN Chi-restraints excluded: chain E residue 140 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 100 optimal weight: 9.9990 chunk 78 optimal weight: 9.9990 chunk 114 optimal weight: 20.0000 chunk 173 optimal weight: 10.0000 chunk 159 optimal weight: 3.9990 chunk 138 optimal weight: 7.9990 chunk 14 optimal weight: 2.9990 chunk 106 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 109 optimal weight: 0.0000 chunk 147 optimal weight: 9.9990 overall best weight: 3.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 205 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7067 moved from start: 0.4663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14070 Z= 0.229 Angle : 0.525 8.613 18996 Z= 0.281 Chirality : 0.043 0.136 2052 Planarity : 0.005 0.060 2454 Dihedral : 4.176 20.974 1944 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.84 % Favored : 98.16 % Rotamer: Outliers : 0.89 % Allowed : 16.73 % 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: 2.03 (0.21), residues: 1740 helix: 2.33 (0.17), residues: 936 sheet: -0.48 (0.29), residues: 288 loop : 0.78 (0.30), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 385 HIS 0.009 0.001 HIS A 450 PHE 0.013 0.001 PHE B 63 TYR 0.018 0.001 TYR D 78 ARG 0.006 0.000 ARG A 419 ********************** 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 160 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 147 time to evaluate : 1.795 Fit side-chains REVERT: B 140 GLU cc_start: 0.6921 (OUTLIER) cc_final: 0.6534 (mt-10) REVERT: E 140 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6547 (mt-10) outliers start: 13 outliers final: 7 residues processed: 159 average time/residue: 1.4130 time to fit residues: 245.9070 Evaluate side-chains 146 residues out of total 1464 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 137 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 137 THR Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain B residue 374 ASN Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain C residue 137 THR Chi-restraints excluded: chain C residue 162 VAL Chi-restraints excluded: chain D residue 374 ASN Chi-restraints excluded: chain E residue 140 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 174 random chunks: chunk 42 optimal weight: 9.9990 chunk 127 optimal weight: 0.8980 chunk 20 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 138 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 141 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 25 optimal weight: 9.9990 chunk 121 optimal weight: 6.9990 chunk 7 optimal weight: 0.9980 overall best weight: 4.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN ** B 450 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 205 GLN D 205 GLN E 205 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.106118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.093788 restraints weight = 24610.984| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.42 r_work: 0.3606 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.4527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 14070 Z= 0.314 Angle : 0.560 7.180 18996 Z= 0.302 Chirality : 0.044 0.132 2052 Planarity : 0.005 0.059 2454 Dihedral : 4.367 21.361 1944 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 0.75 % Allowed : 16.87 % 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: 1.89 (0.21), residues: 1740 helix: 2.19 (0.17), residues: 936 sheet: -0.60 (0.29), residues: 288 loop : 0.80 (0.29), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 385 HIS 0.009 0.001 HIS A 450 PHE 0.028 0.002 PHE C 220 TYR 0.012 0.001 TYR B 382 ARG 0.005 0.001 ARG A 419 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6815.57 seconds wall clock time: 120 minutes 13.18 seconds (7213.18 seconds total)