Starting phenix.real_space_refine on Mon Mar 11 02:10:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erl_28554/03_2024/8erl_28554.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erl_28554/03_2024/8erl_28554.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erl_28554/03_2024/8erl_28554.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erl_28554/03_2024/8erl_28554.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erl_28554/03_2024/8erl_28554.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8erl_28554/03_2024/8erl_28554.pdb" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.008 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 36 5.16 5 C 4208 2.51 5 N 1130 2.21 5 O 1226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 6600 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3300 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 20, 'TRANS': 394} Chain breaks: 1 Chain: "B" Number of atoms: 3300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3300 Classifications: {'peptide': 415} Link IDs: {'PTRANS': 20, 'TRANS': 394} Chain breaks: 1 Time building chain proxies: 4.30, per 1000 atoms: 0.65 Number of scatterers: 6600 At special positions: 0 Unit cell: (76.56, 157.52, 58.96, 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 36 16.00 O 1226 8.00 N 1130 7.00 C 4208 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 70 " distance=2.03 Simple disulfide: pdb=" SG CYS A 294 " - pdb=" SG CYS A 305 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 313 " distance=2.03 Simple disulfide: pdb=" SG CYS A 448 " - pdb=" SG CYS A 468 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 70 " distance=2.03 Simple disulfide: pdb=" SG CYS B 294 " - pdb=" SG CYS B 305 " distance=2.03 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 313 " distance=2.03 Simple disulfide: pdb=" SG CYS B 448 " - pdb=" SG CYS B 468 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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: 3.88 Conformation dependent library (CDL) restraints added in 2.5 seconds 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1548 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 6 sheets defined 23.7% alpha, 17.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.16 Creating SS restraints... Processing helix chain 'A' and resid 94 through 106 Processing helix chain 'A' and resid 116 through 120 removed outlier: 3.826A pdb=" N ALA A 120 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 149 removed outlier: 4.393A pdb=" N LYS A 132 " --> pdb=" O ALA A 128 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LEU A 133 " --> pdb=" O GLY A 129 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET A 145 " --> pdb=" O PHE A 141 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP A 147 " --> pdb=" O ASN A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 175 Processing helix chain 'A' and resid 196 through 200 Processing helix chain 'A' and resid 202 through 206 removed outlier: 3.762A pdb=" N ALA A 206 " --> pdb=" O PRO A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 241 No H-bonds generated for 'chain 'A' and resid 239 through 241' Processing helix chain 'A' and resid 270 through 284 Processing helix chain 'A' and resid 296 through 303 Processing helix chain 'A' and resid 451 through 455 removed outlier: 3.964A pdb=" N SER A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR A 455 " --> pdb=" O LYS A 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 451 through 455' Processing helix chain 'B' and resid 94 through 106 Processing helix chain 'B' and resid 116 through 120 removed outlier: 3.826A pdb=" N ALA B 120 " --> pdb=" O LEU B 117 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 149 removed outlier: 4.393A pdb=" N LYS B 132 " --> pdb=" O ALA B 128 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N LEU B 133 " --> pdb=" O GLY B 129 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N MET B 145 " --> pdb=" O PHE B 141 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ALA B 146 " --> pdb=" O MET B 142 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ASP B 147 " --> pdb=" O ASN B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 175 Processing helix chain 'B' and resid 196 through 200 Processing helix chain 'B' and resid 202 through 206 removed outlier: 3.761A pdb=" N ALA B 206 " --> pdb=" O PRO B 203 " (cutoff:3.500A) Processing helix chain 'B' and resid 239 through 241 No H-bonds generated for 'chain 'B' and resid 239 through 241' Processing helix chain 'B' and resid 271 through 284 removed outlier: 3.696A pdb=" N PHE B 278 " --> pdb=" O SER B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 296 through 303 Processing helix chain 'B' and resid 451 through 455 removed outlier: 3.964A pdb=" N SER B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N TYR B 455 " --> pdb=" O LYS B 452 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 451 through 455' Processing sheet with id=AA1, first strand: chain 'A' and resid 44 through 47 removed outlier: 4.704A pdb=" N VAL A 111 " --> pdb=" O ARG A 47 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LYS A 77 " --> pdb=" O ASN A 110 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N ILE A 112 " --> pdb=" O LYS A 77 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N PHE A 79 " --> pdb=" O ILE A 112 " (cutoff:3.500A) removed outlier: 9.158A pdb=" N VAL A 114 " --> pdb=" O PHE A 79 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N VAL A 81 " --> pdb=" O VAL A 114 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYR A 161 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N THR A 183 " --> pdb=" O VAL A 156 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU A 158 " --> pdb=" O THR A 183 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU A 185 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N GLY A 160 " --> pdb=" O LEU A 185 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N SER A 162 " --> pdb=" O PRO A 187 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU A 212 " --> pdb=" O GLY A 184 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ASP A 186 " --> pdb=" O LEU A 212 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL A 209 " --> pdb=" O VAL A 233 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N ILE A 235 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL A 211 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 5.610A pdb=" N ASP A 234 " --> pdb=" O MET A 331 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU A 333 " --> pdb=" O ASP A 234 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR A 236 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LYS A 330 " --> pdb=" O CYS A 294 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 395 through 398 removed outlier: 4.239A pdb=" N VAL A 436 " --> pdb=" O VAL A 445 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N VAL A 445 " --> pdb=" O VAL A 436 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 375 through 381 removed outlier: 5.731A pdb=" N GLU A 375 " --> pdb=" O GLY A 371 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N GLY A 371 " --> pdb=" O GLU A 375 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N GLU A 377 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 5.270A pdb=" N LEU A 369 " --> pdb=" O GLU A 377 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE A 367 " --> pdb=" O ILE A 379 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE A 365 " --> pdb=" O PHE A 381 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N TYR A 370 " --> pdb=" O MET A 407 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N MET A 407 " --> pdb=" O TYR A 370 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 44 through 47 removed outlier: 4.705A pdb=" N VAL B 111 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LYS B 77 " --> pdb=" O ASN B 110 " (cutoff:3.500A) removed outlier: 7.751A pdb=" N ILE B 112 " --> pdb=" O LYS B 77 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N PHE B 79 " --> pdb=" O ILE B 112 " (cutoff:3.500A) removed outlier: 9.156A pdb=" N VAL B 114 " --> pdb=" O PHE B 79 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL B 81 " --> pdb=" O VAL B 114 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N TYR B 161 " --> pdb=" O ILE B 82 " (cutoff:3.500A) removed outlier: 8.342A pdb=" N THR B 183 " --> pdb=" O VAL B 156 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU B 158 " --> pdb=" O THR B 183 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N LEU B 185 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N GLY B 160 " --> pdb=" O LEU B 185 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N SER B 162 " --> pdb=" O PRO B 187 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU B 212 " --> pdb=" O GLY B 184 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP B 186 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B 209 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N ILE B 235 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 7.396A pdb=" N VAL B 211 " --> pdb=" O ILE B 235 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N ASP B 234 " --> pdb=" O MET B 331 " (cutoff:3.500A) removed outlier: 7.269A pdb=" N LEU B 333 " --> pdb=" O ASP B 234 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N TYR B 236 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LYS B 330 " --> pdb=" O CYS B 294 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 395 through 398 removed outlier: 4.238A pdb=" N VAL B 436 " --> pdb=" O VAL B 445 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N VAL B 445 " --> pdb=" O VAL B 436 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 375 through 381 removed outlier: 5.730A pdb=" N GLU B 375 " --> pdb=" O GLY B 371 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N GLY B 371 " --> pdb=" O GLU B 375 " (cutoff:3.500A) removed outlier: 5.578A pdb=" N GLU B 377 " --> pdb=" O LEU B 369 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N LEU B 369 " --> pdb=" O GLU B 377 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE B 367 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N PHE B 365 " --> pdb=" O PHE B 381 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N TYR B 370 " --> pdb=" O MET B 407 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N MET B 407 " --> pdb=" O TYR B 370 " (cutoff:3.500A) 172 hydrogen bonds defined for protein. 468 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: 3.11 Time building geometry restraints manager: 4.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2071 1.34 - 1.46: 1655 1.46 - 1.59: 2998 1.59 - 1.71: 0 1.71 - 1.83: 52 Bond restraints: 6776 Sorted by residual: bond pdb=" C VAL A 95 " pdb=" N PRO A 96 " ideal model delta sigma weight residual 1.336 1.361 -0.025 1.20e-02 6.94e+03 4.38e+00 bond pdb=" C VAL B 95 " pdb=" N PRO B 96 " ideal model delta sigma weight residual 1.336 1.361 -0.025 1.20e-02 6.94e+03 4.22e+00 bond pdb=" CB TRP A 412 " pdb=" CG TRP A 412 " ideal model delta sigma weight residual 1.498 1.551 -0.053 3.10e-02 1.04e+03 2.89e+00 bond pdb=" CB TRP B 412 " pdb=" CG TRP B 412 " ideal model delta sigma weight residual 1.498 1.550 -0.052 3.10e-02 1.04e+03 2.79e+00 bond pdb=" CB PHE B 79 " pdb=" CG PHE B 79 " ideal model delta sigma weight residual 1.502 1.539 -0.037 2.30e-02 1.89e+03 2.59e+00 ... (remaining 6771 not shown) Histogram of bond angle deviations from ideal: 95.02 - 103.13: 52 103.13 - 111.25: 2472 111.25 - 119.37: 3080 119.37 - 127.48: 3460 127.48 - 135.60: 112 Bond angle restraints: 9176 Sorted by residual: angle pdb=" CA LEU B 102 " pdb=" CB LEU B 102 " pdb=" CG LEU B 102 " ideal model delta sigma weight residual 116.30 134.78 -18.48 3.50e+00 8.16e-02 2.79e+01 angle pdb=" CA LEU A 102 " pdb=" CB LEU A 102 " pdb=" CG LEU A 102 " ideal model delta sigma weight residual 116.30 134.76 -18.46 3.50e+00 8.16e-02 2.78e+01 angle pdb=" CG1 ILE A 320 " pdb=" CB ILE A 320 " pdb=" CG2 ILE A 320 " ideal model delta sigma weight residual 110.70 95.02 15.68 3.00e+00 1.11e-01 2.73e+01 angle pdb=" CG1 ILE B 320 " pdb=" CB ILE B 320 " pdb=" CG2 ILE B 320 " ideal model delta sigma weight residual 110.70 95.04 15.66 3.00e+00 1.11e-01 2.72e+01 angle pdb=" CA LEU B 277 " pdb=" CB LEU B 277 " pdb=" CG LEU B 277 " ideal model delta sigma weight residual 116.30 133.94 -17.64 3.50e+00 8.16e-02 2.54e+01 ... (remaining 9171 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.79: 3541 17.79 - 35.57: 392 35.57 - 53.35: 84 53.35 - 71.14: 12 71.14 - 88.92: 9 Dihedral angle restraints: 4038 sinusoidal: 1626 harmonic: 2412 Sorted by residual: dihedral pdb=" CB CYS B 448 " pdb=" SG CYS B 448 " pdb=" SG CYS B 468 " pdb=" CB CYS B 468 " ideal model delta sinusoidal sigma weight residual -86.00 -172.57 86.57 1 1.00e+01 1.00e-02 9.03e+01 dihedral pdb=" CB CYS A 448 " pdb=" SG CYS A 448 " pdb=" SG CYS A 468 " pdb=" CB CYS A 468 " ideal model delta sinusoidal sigma weight residual -86.00 -172.53 86.53 1 1.00e+01 1.00e-02 9.02e+01 dihedral pdb=" CB CYS B 294 " pdb=" SG CYS B 294 " pdb=" SG CYS B 305 " pdb=" CB CYS B 305 " ideal model delta sinusoidal sigma weight residual 93.00 41.28 51.72 1 1.00e+01 1.00e-02 3.65e+01 ... (remaining 4035 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 715 0.062 - 0.124: 196 0.124 - 0.186: 57 0.186 - 0.248: 8 0.248 - 0.311: 4 Chirality restraints: 980 Sorted by residual: chirality pdb=" CG LEU B 333 " pdb=" CB LEU B 333 " pdb=" CD1 LEU B 333 " pdb=" CD2 LEU B 333 " both_signs ideal model delta sigma weight residual False -2.59 -2.90 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CG LEU A 333 " pdb=" CB LEU A 333 " pdb=" CD1 LEU A 333 " pdb=" CD2 LEU A 333 " both_signs ideal model delta sigma weight residual False -2.59 -2.90 0.31 2.00e-01 2.50e+01 2.41e+00 chirality pdb=" CB ILE B 320 " pdb=" CA ILE B 320 " pdb=" CG1 ILE B 320 " pdb=" CG2 ILE B 320 " both_signs ideal model delta sigma weight residual False 2.64 2.93 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (remaining 977 not shown) Planarity restraints: 1174 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG B 273 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.23e+00 pdb=" C ARG B 273 " -0.050 2.00e-02 2.50e+03 pdb=" O ARG B 273 " 0.019 2.00e-02 2.50e+03 pdb=" N SER B 274 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 79 " 0.016 2.00e-02 2.50e+03 2.02e-02 7.17e+00 pdb=" CG PHE B 79 " -0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE B 79 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 79 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE B 79 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE B 79 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE B 79 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 79 " -0.016 2.00e-02 2.50e+03 2.02e-02 7.12e+00 pdb=" CG PHE A 79 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 PHE A 79 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 79 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 79 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 79 " 0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 79 " -0.001 2.00e-02 2.50e+03 ... (remaining 1171 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1885 2.82 - 3.34: 5895 3.34 - 3.86: 11272 3.86 - 4.38: 12283 4.38 - 4.90: 20881 Nonbonded interactions: 52216 Sorted by model distance: nonbonded pdb=" NE2 GLN B 457 " pdb=" O GLY B 459 " model vdw 2.296 2.520 nonbonded pdb=" NE2 GLN A 457 " pdb=" O GLY A 459 " model vdw 2.296 2.520 nonbonded pdb=" O ALA B 128 " pdb=" OG1 THR B 131 " model vdw 2.299 2.440 nonbonded pdb=" O ALA A 128 " pdb=" OG1 THR A 131 " model vdw 2.299 2.440 nonbonded pdb=" O ASN B 73 " pdb=" OG SER B 76 " model vdw 2.337 2.440 ... (remaining 52211 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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 group one per residue 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: 2.700 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: 7.200 Check model and map are aligned: 0.100 Set scattering table: 0.060 Process input model: 28.730 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 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 : 0.005 0.053 6776 Z= 0.358 Angle : 1.277 18.484 9176 Z= 0.623 Chirality : 0.065 0.311 980 Planarity : 0.006 0.042 1174 Dihedral : 15.420 88.923 2466 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 4.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 0.27 % Allowed : 23.08 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.82 (0.24), residues: 822 helix: -2.63 (0.29), residues: 156 sheet: -1.66 (0.35), residues: 206 loop : -3.01 (0.23), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.005 TRP A 420 HIS 0.028 0.003 HIS A 83 PHE 0.047 0.002 PHE B 79 TYR 0.026 0.002 TYR A 124 ARG 0.013 0.001 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 90 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.9184 (tpm170) cc_final: 0.8844 (tpt90) REVERT: A 272 GLU cc_start: 0.8864 (OUTLIER) cc_final: 0.8345 (mp0) REVERT: A 365 PHE cc_start: 0.8462 (m-80) cc_final: 0.7838 (m-10) REVERT: A 453 MET cc_start: 0.8235 (pmm) cc_final: 0.6581 (mmm) REVERT: B 409 LYS cc_start: 0.8138 (tptm) cc_final: 0.7652 (tptp) REVERT: B 453 MET cc_start: 0.8261 (pmm) cc_final: 0.6675 (mmm) REVERT: B 464 ILE cc_start: 0.9099 (pt) cc_final: 0.8870 (mm) outliers start: 2 outliers final: 1 residues processed: 92 average time/residue: 0.1714 time to fit residues: 21.8837 Evaluate side-chains 87 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 85 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 268 LYS Chi-restraints excluded: chain A residue 272 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 0.0970 chunk 21 optimal weight: 3.9990 chunk 41 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 74 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 271 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 6776 Z= 0.187 Angle : 0.674 10.987 9176 Z= 0.334 Chirality : 0.044 0.201 980 Planarity : 0.004 0.061 1174 Dihedral : 5.799 57.169 905 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 3.71 % Allowed : 20.05 % Favored : 76.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.26), residues: 822 helix: -1.62 (0.34), residues: 168 sheet: -1.57 (0.36), residues: 208 loop : -2.55 (0.25), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 423 HIS 0.007 0.001 HIS B 83 PHE 0.012 0.001 PHE A 278 TYR 0.022 0.001 TYR B 124 ARG 0.004 0.000 ARG B 336 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 73 time to evaluate : 0.776 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 MET cc_start: 0.9628 (mpp) cc_final: 0.9411 (ppp) REVERT: A 272 GLU cc_start: 0.8842 (OUTLIER) cc_final: 0.8519 (mp0) REVERT: A 407 MET cc_start: 0.8904 (ppp) cc_final: 0.8442 (ppp) REVERT: B 407 MET cc_start: 0.8875 (ppp) cc_final: 0.8455 (ppp) REVERT: B 409 LYS cc_start: 0.8417 (tptm) cc_final: 0.8088 (tptt) outliers start: 27 outliers final: 18 residues processed: 92 average time/residue: 0.1523 time to fit residues: 20.0130 Evaluate side-chains 89 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 70 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 TRP Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 386 VAL Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 424 TRP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 94 TRP Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 465 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 74 optimal weight: 0.0370 chunk 80 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 73 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 59 optimal weight: 5.9990 overall best weight: 1.1664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 6776 Z= 0.172 Angle : 0.630 11.472 9176 Z= 0.310 Chirality : 0.043 0.127 980 Planarity : 0.003 0.043 1174 Dihedral : 5.032 47.452 901 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 15.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 4.26 % Allowed : 19.92 % Favored : 75.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.80 (0.26), residues: 822 helix: -0.54 (0.39), residues: 152 sheet: -1.52 (0.35), residues: 210 loop : -2.57 (0.25), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 423 HIS 0.003 0.001 HIS A 83 PHE 0.011 0.001 PHE B 215 TYR 0.019 0.001 TYR A 124 ARG 0.009 0.001 ARG B 217 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 70 time to evaluate : 0.805 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 TRP cc_start: 0.7942 (t-100) cc_final: 0.7548 (t-100) REVERT: A 272 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8555 (mp0) REVERT: A 333 LEU cc_start: 0.8847 (mt) cc_final: 0.8601 (mt) REVERT: A 365 PHE cc_start: 0.8248 (m-10) cc_final: 0.8016 (m-10) REVERT: A 407 MET cc_start: 0.8995 (ppp) cc_final: 0.8034 (ppp) REVERT: A 464 ILE cc_start: 0.9183 (pt) cc_final: 0.8940 (mm) REVERT: B 333 LEU cc_start: 0.8908 (mt) cc_final: 0.8673 (mt) REVERT: B 407 MET cc_start: 0.8898 (ppp) cc_final: 0.8312 (ppp) REVERT: B 409 LYS cc_start: 0.8426 (tptm) cc_final: 0.8102 (tptp) outliers start: 31 outliers final: 22 residues processed: 91 average time/residue: 0.1472 time to fit residues: 19.5474 Evaluate side-chains 94 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 71 time to evaluate : 0.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 267 VAL Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 424 TRP Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 466 VAL Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 194 TYR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 465 PHE Chi-restraints excluded: chain B residue 466 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 35 optimal weight: 6.9990 chunk 50 optimal weight: 0.7980 chunk 74 optimal weight: 0.0470 chunk 79 optimal weight: 0.1980 chunk 39 optimal weight: 5.9990 chunk 70 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 overall best weight: 0.6082 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 58 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.2321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 6776 Z= 0.132 Angle : 0.606 14.069 9176 Z= 0.290 Chirality : 0.042 0.127 980 Planarity : 0.003 0.028 1174 Dihedral : 4.679 39.387 901 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 3.57 % Allowed : 21.98 % Favored : 74.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.26), residues: 822 helix: -0.05 (0.40), residues: 152 sheet: -1.36 (0.38), residues: 184 loop : -2.46 (0.24), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 412 HIS 0.003 0.001 HIS A 83 PHE 0.014 0.001 PHE A 79 TYR 0.018 0.001 TYR A 124 ARG 0.004 0.000 ARG B 217 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 74 time to evaluate : 0.907 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 TRP cc_start: 0.7972 (t-100) cc_final: 0.7619 (t-100) REVERT: A 272 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8483 (mp0) REVERT: A 407 MET cc_start: 0.9023 (ppp) cc_final: 0.8114 (ppp) REVERT: B 407 MET cc_start: 0.8943 (ppp) cc_final: 0.8161 (ppp) outliers start: 26 outliers final: 21 residues processed: 92 average time/residue: 0.1584 time to fit residues: 21.4102 Evaluate side-chains 97 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 75 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 424 TRP Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 194 TYR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 465 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 1.9990 chunk 44 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 32 optimal weight: 0.0870 chunk 67 optimal weight: 3.9990 chunk 54 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 20 optimal weight: 0.0270 overall best weight: 1.4222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 6776 Z= 0.189 Angle : 0.615 11.632 9176 Z= 0.304 Chirality : 0.042 0.129 980 Planarity : 0.003 0.027 1174 Dihedral : 4.799 36.274 901 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 20.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 5.77 % Allowed : 19.92 % Favored : 74.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.27), residues: 822 helix: -0.02 (0.41), residues: 152 sheet: -1.62 (0.36), residues: 200 loop : -2.42 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 412 HIS 0.003 0.001 HIS A 271 PHE 0.022 0.001 PHE A 365 TYR 0.017 0.001 TYR A 124 ARG 0.002 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 73 time to evaluate : 0.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 TRP cc_start: 0.7948 (t-100) cc_final: 0.7613 (t-100) REVERT: A 272 GLU cc_start: 0.8988 (OUTLIER) cc_final: 0.8652 (mp0) REVERT: A 407 MET cc_start: 0.9089 (ppp) cc_final: 0.8228 (ppp) REVERT: B 85 TRP cc_start: 0.7759 (t-100) cc_final: 0.7487 (t-100) REVERT: B 407 MET cc_start: 0.8994 (ppp) cc_final: 0.8132 (ppp) outliers start: 42 outliers final: 28 residues processed: 103 average time/residue: 0.1558 time to fit residues: 22.5589 Evaluate side-chains 98 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 69 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 94 TRP Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 272 GLU Chi-restraints excluded: chain A residue 274 SER Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 424 TRP Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 94 TRP Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 194 TYR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 386 VAL Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 417 TYR Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 465 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 79 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 76 optimal weight: 0.9980 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6776 Z= 0.316 Angle : 0.718 12.350 9176 Z= 0.368 Chirality : 0.045 0.172 980 Planarity : 0.004 0.031 1174 Dihedral : 5.462 33.661 901 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 31.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 6.32 % Allowed : 21.57 % Favored : 72.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.28), residues: 822 helix: -0.08 (0.43), residues: 152 sheet: -1.95 (0.39), residues: 162 loop : -2.36 (0.25), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.003 TRP B 412 HIS 0.005 0.001 HIS B 271 PHE 0.020 0.002 PHE A 278 TYR 0.016 0.002 TYR A 124 ARG 0.004 0.001 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 68 time to evaluate : 0.683 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 TRP cc_start: 0.7953 (t-100) cc_final: 0.7462 (t-100) REVERT: A 407 MET cc_start: 0.9107 (ppp) cc_final: 0.8176 (ppp) REVERT: B 85 TRP cc_start: 0.7677 (t-100) cc_final: 0.7221 (t-100) REVERT: B 333 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8550 (mt) REVERT: B 407 MET cc_start: 0.9028 (ppp) cc_final: 0.8149 (ppp) outliers start: 46 outliers final: 33 residues processed: 102 average time/residue: 0.1408 time to fit residues: 20.3821 Evaluate side-chains 99 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 65 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 94 TRP Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 424 TRP Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 94 TRP Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 161 TYR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 194 TYR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 333 LEU Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 417 TYR Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 465 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 0.0370 chunk 45 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 chunk 44 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 49 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 HIS ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7907 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6776 Z= 0.164 Angle : 0.667 14.284 9176 Z= 0.321 Chirality : 0.044 0.135 980 Planarity : 0.003 0.028 1174 Dihedral : 4.821 19.673 898 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 22.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 4.53 % Allowed : 23.49 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.28), residues: 822 helix: 0.20 (0.44), residues: 152 sheet: -1.84 (0.37), residues: 192 loop : -2.21 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 412 HIS 0.005 0.001 HIS A 83 PHE 0.021 0.001 PHE A 365 TYR 0.016 0.001 TYR A 124 ARG 0.002 0.000 ARG B 217 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 71 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: A 85 TRP cc_start: 0.8062 (t-100) cc_final: 0.7385 (t-100) REVERT: A 116 TRP cc_start: 0.8008 (t-100) cc_final: 0.7633 (t-100) REVERT: A 136 GLN cc_start: 0.9797 (mt0) cc_final: 0.9554 (mp10) REVERT: A 145 MET cc_start: 0.9711 (pmm) cc_final: 0.9495 (pmm) REVERT: A 331 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7654 (mtp) REVERT: A 407 MET cc_start: 0.9091 (ppp) cc_final: 0.8147 (ppp) REVERT: B 116 TRP cc_start: 0.8045 (t-100) cc_final: 0.7832 (t-100) REVERT: B 136 GLN cc_start: 0.9784 (mt0) cc_final: 0.9505 (mt0) REVERT: B 331 MET cc_start: 0.7967 (OUTLIER) cc_final: 0.7643 (mtp) REVERT: B 407 MET cc_start: 0.8983 (ppp) cc_final: 0.8047 (ppp) outliers start: 33 outliers final: 27 residues processed: 95 average time/residue: 0.1409 time to fit residues: 19.4808 Evaluate side-chains 99 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 70 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 424 TRP Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 194 TYR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 376 SER Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 417 TYR Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 465 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 75 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6776 Z= 0.181 Angle : 0.650 13.515 9176 Z= 0.315 Chirality : 0.043 0.131 980 Planarity : 0.003 0.028 1174 Dihedral : 4.743 18.435 898 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 22.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 4.40 % Allowed : 23.35 % Favored : 72.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.28), residues: 822 helix: 0.24 (0.44), residues: 152 sheet: -1.85 (0.37), residues: 192 loop : -2.18 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 412 HIS 0.004 0.001 HIS A 83 PHE 0.012 0.001 PHE A 44 TYR 0.016 0.001 TYR A 124 ARG 0.002 0.000 ARG B 47 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 69 time to evaluate : 0.714 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 TRP cc_start: 0.8112 (t-100) cc_final: 0.7460 (t-100) REVERT: A 136 GLN cc_start: 0.9799 (mt0) cc_final: 0.9560 (mp10) REVERT: B 407 MET cc_start: 0.9071 (ppp) cc_final: 0.8112 (ppp) outliers start: 32 outliers final: 29 residues processed: 91 average time/residue: 0.1429 time to fit residues: 19.1710 Evaluate side-chains 97 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 68 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 194 TYR Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 373 VAL Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 417 TYR Chi-restraints excluded: chain A residue 424 TRP Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 156 VAL Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 194 TYR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 373 VAL Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 417 TYR Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 436 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 77 optimal weight: 0.0040 chunk 47 optimal weight: 1.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 358 ASN B 363 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.3831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 6776 Z= 0.153 Angle : 0.659 15.045 9176 Z= 0.311 Chirality : 0.043 0.135 980 Planarity : 0.003 0.028 1174 Dihedral : 4.546 18.527 898 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 19.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 3.57 % Allowed : 23.76 % Favored : 72.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.41 (0.28), residues: 822 helix: 0.25 (0.43), residues: 152 sheet: -1.85 (0.38), residues: 188 loop : -2.19 (0.26), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 412 HIS 0.005 0.001 HIS A 83 PHE 0.021 0.001 PHE A 365 TYR 0.016 0.001 TYR A 124 ARG 0.002 0.000 ARG B 273 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 71 time to evaluate : 0.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 GLN cc_start: 0.9803 (mt0) cc_final: 0.9559 (mp10) REVERT: B 116 TRP cc_start: 0.8070 (t-100) cc_final: 0.7671 (t-100) REVERT: B 136 GLN cc_start: 0.9789 (mt0) cc_final: 0.9518 (mt0) REVERT: B 407 MET cc_start: 0.9033 (ppp) cc_final: 0.8015 (ppp) outliers start: 26 outliers final: 21 residues processed: 91 average time/residue: 0.1470 time to fit residues: 19.3723 Evaluate side-chains 91 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 70 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 424 TRP Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 465 PHE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 465 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 81 optimal weight: 0.5980 chunk 75 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 50 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 51 optimal weight: 0.3980 chunk 69 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.3844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6776 Z= 0.153 Angle : 0.686 14.650 9176 Z= 0.321 Chirality : 0.043 0.127 980 Planarity : 0.003 0.031 1174 Dihedral : 4.501 18.049 898 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 20.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.76 % Favored : 91.24 % Rotamer: Outliers : 3.57 % Allowed : 24.45 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.28), residues: 822 helix: 0.25 (0.43), residues: 152 sheet: -1.85 (0.36), residues: 192 loop : -2.16 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 412 HIS 0.004 0.001 HIS A 83 PHE 0.011 0.001 PHE A 44 TYR 0.017 0.001 TYR A 124 ARG 0.002 0.000 ARG A 336 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1644 Ramachandran restraints generated. 822 Oldfield, 0 Emsley, 822 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 71 time to evaluate : 0.784 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 TRP cc_start: 0.8192 (t-100) cc_final: 0.7447 (t-100) REVERT: A 136 GLN cc_start: 0.9803 (mt0) cc_final: 0.9561 (mp10) REVERT: B 90 MET cc_start: 0.8096 (ppp) cc_final: 0.7193 (ppp) REVERT: B 116 TRP cc_start: 0.8048 (t-100) cc_final: 0.7613 (t-100) REVERT: B 136 GLN cc_start: 0.9790 (mt0) cc_final: 0.9545 (mp10) REVERT: B 407 MET cc_start: 0.9023 (ppp) cc_final: 0.7994 (ppp) outliers start: 26 outliers final: 24 residues processed: 91 average time/residue: 0.1481 time to fit residues: 19.5740 Evaluate side-chains 95 residues out of total 728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 71 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 THR Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 161 TYR Chi-restraints excluded: chain A residue 166 HIS Chi-restraints excluded: chain A residue 284 ASN Chi-restraints excluded: chain A residue 331 MET Chi-restraints excluded: chain A residue 336 ARG Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 379 ILE Chi-restraints excluded: chain A residue 398 THR Chi-restraints excluded: chain A residue 405 LEU Chi-restraints excluded: chain A residue 424 TRP Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain B residue 37 PHE Chi-restraints excluded: chain B residue 159 LEU Chi-restraints excluded: chain B residue 166 HIS Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 331 MET Chi-restraints excluded: chain B residue 336 ARG Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 398 THR Chi-restraints excluded: chain B residue 424 TRP Chi-restraints excluded: chain B residue 436 VAL Chi-restraints excluded: chain B residue 465 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 6.9990 chunk 65 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 8 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 3 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.067203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.049727 restraints weight = 30333.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.051738 restraints weight = 19911.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.053042 restraints weight = 14908.200| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6776 Z= 0.179 Angle : 0.683 14.491 9176 Z= 0.323 Chirality : 0.043 0.127 980 Planarity : 0.003 0.031 1174 Dihedral : 4.554 17.809 898 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 23.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.00 % Favored : 91.00 % Rotamer: Outliers : 3.85 % Allowed : 24.18 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.32 (0.28), residues: 822 helix: 0.27 (0.43), residues: 152 sheet: -1.80 (0.36), residues: 196 loop : -2.09 (0.27), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 412 HIS 0.004 0.001 HIS A 83 PHE 0.021 0.001 PHE A 365 TYR 0.016 0.001 TYR A 124 ARG 0.002 0.000 ARG B 47 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1533.29 seconds wall clock time: 29 minutes 13.58 seconds (1753.58 seconds total)