Starting phenix.real_space_refine on Thu Nov 14 20:07:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlp_36403/11_2024/8jlp_36403.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlp_36403/11_2024/8jlp_36403.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlp_36403/11_2024/8jlp_36403.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlp_36403/11_2024/8jlp_36403.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlp_36403/11_2024/8jlp_36403.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jlp_36403/11_2024/8jlp_36403.cif" } resolution = 3.23 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= -0.001 sd= 0.041 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 58 5.16 5 C 4687 2.51 5 N 1267 2.21 5 O 1331 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7343 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1972 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2593 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 2310 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2310 Classifications: {'peptide': 285} Link IDs: {'PTRANS': 11, 'TRANS': 273} Chain breaks: 1 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'UJU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.49, per 1000 atoms: 0.61 Number of scatterers: 7343 At special positions: 0 Unit cell: (102.85, 132.6, 80.75, 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 58 16.00 O 1331 8.00 N 1267 7.00 C 4687 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.92 Conformation dependent library (CDL) restraints added in 1.1 seconds 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1746 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 10 sheets defined 46.6% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 13 through 40 removed outlier: 3.585A pdb=" N LYS A 32 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR A 40 " --> pdb=" O VAL A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 62 removed outlier: 4.023A pdb=" N ILE A 56 " --> pdb=" O GLY A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 239 removed outlier: 3.849A pdb=" N ASN A 239 " --> pdb=" O GLN A 236 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 removed outlier: 4.465A pdb=" N LEU A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 Processing helix chain 'A' and resid 307 through 311 removed outlier: 3.710A pdb=" N TYR A 311 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 332 through 349 removed outlier: 4.347A pdb=" N ARG A 336 " --> pdb=" O PRO A 332 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA A 337 " --> pdb=" O ARG A 333 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 387 removed outlier: 4.175A pdb=" N ARG A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N VAL A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N PHE A 376 " --> pdb=" O ILE A 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 30 through 37 Processing helix chain 'R' and resid 20 through 50 removed outlier: 3.673A pdb=" N HIS R 50 " --> pdb=" O VAL R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 76 Processing helix chain 'R' and resid 76 through 87 removed outlier: 3.632A pdb=" N SER R 80 " --> pdb=" O VAL R 76 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL R 82 " --> pdb=" O PRO R 78 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG R 83 " --> pdb=" O TYR R 79 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N SER R 84 " --> pdb=" O SER R 80 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ALA R 85 " --> pdb=" O MET R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 94 through 127 removed outlier: 3.552A pdb=" N ILE R 98 " --> pdb=" O VAL R 94 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE R 104 " --> pdb=" O THR R 100 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N MET R 105 " --> pdb=" O SER R 101 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASP R 127 " --> pdb=" O TYR R 123 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 131 removed outlier: 3.920A pdb=" N TYR R 131 " --> pdb=" O PRO R 128 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 128 through 131' Processing helix chain 'R' and resid 136 through 161 Proline residue: R 151 - end of helix removed outlier: 3.565A pdb=" N PHE R 154 " --> pdb=" O VAL R 150 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE R 159 " --> pdb=" O ALA R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 180 Processing helix chain 'R' and resid 187 through 199 Processing helix chain 'R' and resid 200 through 228 Processing helix chain 'R' and resid 247 through 274 Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 275 through 278 removed outlier: 3.847A pdb=" N HIS R 278 " --> pdb=" O PRO R 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 275 through 278' Processing helix chain 'R' and resid 282 through 304 removed outlier: 3.848A pdb=" N ASN R 286 " --> pdb=" O PRO R 282 " (cutoff:3.500A) Proline residue: R 301 - end of helix removed outlier: 3.659A pdb=" N TYR R 304 " --> pdb=" O ASN R 300 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 319 removed outlier: 3.507A pdb=" N ARG R 312 " --> pdb=" O TYR R 308 " (cutoff:3.500A) Processing helix chain 'Y' and resid 7 through 24 Processing helix chain 'Y' and resid 29 through 45 removed outlier: 3.502A pdb=" N ALA Y 33 " --> pdb=" O LYS Y 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 45 removed outlier: 3.721A pdb=" N LEU A 45 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 243 through 245 removed outlier: 6.522A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.617A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N SER B 331 " --> pdb=" O PHE B 335 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.790A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.617A pdb=" N ALA B 104 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA B 113 " --> pdb=" O ALA B 104 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.748A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LEU B 152 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 191 removed outlier: 7.100A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.092A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 275 through 277 removed outlier: 3.924A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 293 through 294 363 hydrogen bonds defined for protein. 1059 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.04 Time building geometry restraints manager: 2.14 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: 2373 1.34 - 1.46: 1768 1.46 - 1.58: 3278 1.58 - 1.70: 0 1.70 - 1.82: 86 Bond restraints: 7505 Sorted by residual: bond pdb=" N1 UJU R 401 " pdb=" N2 UJU R 401 " ideal model delta sigma weight residual 1.316 1.351 -0.035 2.00e-02 2.50e+03 3.00e+00 bond pdb=" C16 UJU R 401 " pdb=" C4 UJU R 401 " ideal model delta sigma weight residual 1.416 1.383 0.033 2.00e-02 2.50e+03 2.76e+00 bond pdb=" C12 UJU R 401 " pdb=" C13 UJU R 401 " ideal model delta sigma weight residual 1.536 1.507 0.029 2.00e-02 2.50e+03 2.17e+00 bond pdb=" C10 UJU R 401 " pdb=" C11 UJU R 401 " ideal model delta sigma weight residual 1.547 1.518 0.029 2.00e-02 2.50e+03 2.12e+00 bond pdb=" CG GLU A 344 " pdb=" CD GLU A 344 " ideal model delta sigma weight residual 1.516 1.481 0.035 2.50e-02 1.60e+03 2.00e+00 ... (remaining 7500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 9960 1.91 - 3.83: 162 3.83 - 5.74: 25 5.74 - 7.66: 9 7.66 - 9.57: 1 Bond angle restraints: 10157 Sorted by residual: angle pdb=" N GLU A 344 " pdb=" CA GLU A 344 " pdb=" CB GLU A 344 " ideal model delta sigma weight residual 110.28 116.05 -5.77 1.55e+00 4.16e-01 1.39e+01 angle pdb=" CA GLU A 344 " pdb=" CB GLU A 344 " pdb=" CG GLU A 344 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 angle pdb=" C ILE B 81 " pdb=" N TRP B 82 " pdb=" CA TRP B 82 " ideal model delta sigma weight residual 122.64 127.90 -5.26 1.70e+00 3.46e-01 9.56e+00 angle pdb=" N VAL B 90 " pdb=" CA VAL B 90 " pdb=" C VAL B 90 " ideal model delta sigma weight residual 112.96 109.96 3.00 1.00e+00 1.00e+00 8.98e+00 angle pdb=" C ASP Y 48 " pdb=" CA ASP Y 48 " pdb=" CB ASP Y 48 " ideal model delta sigma weight residual 111.20 109.14 2.06 7.10e-01 1.98e+00 8.42e+00 ... (remaining 10152 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 3997 17.86 - 35.71: 374 35.71 - 53.57: 78 53.57 - 71.42: 14 71.42 - 89.28: 9 Dihedral angle restraints: 4472 sinusoidal: 1778 harmonic: 2694 Sorted by residual: dihedral pdb=" CB GLU A 370 " pdb=" CG GLU A 370 " pdb=" CD GLU A 370 " pdb=" OE1 GLU A 370 " ideal model delta sinusoidal sigma weight residual 0.00 -89.28 89.28 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CA ARG A 228 " pdb=" C ARG A 228 " pdb=" N ASP A 229 " pdb=" CA ASP A 229 " ideal model delta harmonic sigma weight residual -180.00 -163.88 -16.12 0 5.00e+00 4.00e-02 1.04e+01 dihedral pdb=" CA ASP A 368 " pdb=" CB ASP A 368 " pdb=" CG ASP A 368 " pdb=" OD1 ASP A 368 " ideal model delta sinusoidal sigma weight residual -30.00 -83.36 53.36 1 2.00e+01 2.50e-03 9.68e+00 ... (remaining 4469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 694 0.032 - 0.063: 299 0.063 - 0.095: 95 0.095 - 0.127: 44 0.127 - 0.158: 4 Chirality restraints: 1136 Sorted by residual: chirality pdb=" CA GLU A 344 " pdb=" N GLU A 344 " pdb=" C GLU A 344 " pdb=" CB GLU A 344 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA VAL B 307 " pdb=" N VAL B 307 " pdb=" C VAL B 307 " pdb=" CB VAL B 307 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.47e-01 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 ... (remaining 1133 not shown) Planarity restraints: 1284 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C4 UJU R 401 " 0.060 2.00e-02 2.50e+03 6.75e-02 5.70e+01 pdb=" C5 UJU R 401 " -0.025 2.00e-02 2.50e+03 pdb=" C6 UJU R 401 " 0.081 2.00e-02 2.50e+03 pdb=" N3 UJU R 401 " -0.109 2.00e-02 2.50e+03 pdb=" O1 UJU R 401 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY R 254 " 0.010 2.00e-02 2.50e+03 2.02e-02 4.10e+00 pdb=" C GLY R 254 " -0.035 2.00e-02 2.50e+03 pdb=" O GLY R 254 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE R 255 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 380 " 0.009 2.00e-02 2.50e+03 1.85e-02 3.43e+00 pdb=" C ARG A 380 " -0.032 2.00e-02 2.50e+03 pdb=" O ARG A 380 " 0.012 2.00e-02 2.50e+03 pdb=" N ASP A 381 " 0.011 2.00e-02 2.50e+03 ... (remaining 1281 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 819 2.75 - 3.29: 7379 3.29 - 3.82: 11904 3.82 - 4.36: 13635 4.36 - 4.90: 23697 Nonbonded interactions: 57434 Sorted by model distance: nonbonded pdb=" NE1 TRP R 264 " pdb=" OD1 ASN R 296 " model vdw 2.209 3.120 nonbonded pdb=" OH TYR B 145 " pdb=" OD2 ASP B 186 " model vdw 2.212 3.040 nonbonded pdb=" O ARG A 333 " pdb=" NH1 ARG A 333 " model vdw 2.246 3.120 nonbonded pdb=" O CYS B 103 " pdb=" NH1 ARG B 150 " model vdw 2.300 3.120 nonbonded pdb=" ND2 ASN B 119 " pdb=" O THR B 143 " model vdw 2.307 3.120 ... (remaining 57429 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.700 Set stop_for_unknowns flag: 0.010 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 19.880 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6875 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7505 Z= 0.222 Angle : 0.635 9.570 10157 Z= 0.341 Chirality : 0.042 0.158 1136 Planarity : 0.004 0.068 1284 Dihedral : 14.931 89.276 2723 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: -0.31 (0.28), residues: 909 helix: 1.41 (0.27), residues: 383 sheet: -0.75 (0.44), residues: 139 loop : -1.68 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 82 HIS 0.005 0.001 HIS B 183 PHE 0.013 0.002 PHE R 165 TYR 0.014 0.001 TYR A 339 ARG 0.004 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.808 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 119 average time/residue: 0.1970 time to fit residues: 31.5414 Evaluate side-chains 91 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 91 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 23 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 36 optimal weight: 0.2980 chunk 70 optimal weight: 0.8980 chunk 27 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 88 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6962 moved from start: 0.0995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7505 Z= 0.283 Angle : 0.636 7.588 10157 Z= 0.335 Chirality : 0.044 0.141 1136 Planarity : 0.004 0.050 1284 Dihedral : 6.943 84.703 1021 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 1.76 % Allowed : 9.56 % Favored : 88.68 % 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: -0.21 (0.29), residues: 909 helix: 1.46 (0.26), residues: 396 sheet: -1.05 (0.40), residues: 172 loop : -1.54 (0.34), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 82 HIS 0.004 0.001 HIS Y 44 PHE 0.022 0.002 PHE R 154 TYR 0.017 0.001 TYR A 37 ARG 0.003 0.000 ARG A 283 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 100 time to evaluate : 0.824 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 10 residues processed: 109 average time/residue: 0.1998 time to fit residues: 29.8605 Evaluate side-chains 104 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 224 ILE Chi-restraints excluded: chain R residue 259 VAL Chi-restraints excluded: chain R residue 297 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 68 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 81 optimal weight: 0.0970 chunk 88 optimal weight: 7.9990 chunk 72 optimal weight: 0.9990 chunk 27 optimal weight: 20.0000 chunk 65 optimal weight: 0.7980 chunk 80 optimal weight: 0.6980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 88 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6856 moved from start: 0.1226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7505 Z= 0.152 Angle : 0.535 8.589 10157 Z= 0.283 Chirality : 0.041 0.154 1136 Planarity : 0.004 0.050 1284 Dihedral : 6.318 78.335 1021 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 1.64 % Allowed : 12.45 % Favored : 85.91 % 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: 0.12 (0.29), residues: 909 helix: 1.78 (0.27), residues: 396 sheet: -0.87 (0.42), residues: 154 loop : -1.45 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.001 HIS B 183 PHE 0.020 0.001 PHE R 154 TYR 0.009 0.001 TYR A 339 ARG 0.002 0.000 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.724 Fit side-chains REVERT: A 60 MET cc_start: 0.7180 (mpp) cc_final: 0.6947 (mpp) REVERT: A 289 LEU cc_start: 0.8081 (OUTLIER) cc_final: 0.7864 (tt) outliers start: 13 outliers final: 7 residues processed: 106 average time/residue: 0.1939 time to fit residues: 28.1130 Evaluate side-chains 101 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 224 ILE Chi-restraints excluded: chain R residue 297 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 chunk 77 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 225 HIS B 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6883 moved from start: 0.1427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7505 Z= 0.170 Angle : 0.538 8.084 10157 Z= 0.281 Chirality : 0.041 0.145 1136 Planarity : 0.003 0.049 1284 Dihedral : 6.122 76.789 1021 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.01 % Allowed : 14.59 % Favored : 83.40 % 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: 0.19 (0.29), residues: 909 helix: 1.83 (0.27), residues: 396 sheet: -0.82 (0.42), residues: 154 loop : -1.39 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS R 55 PHE 0.016 0.001 PHE R 154 TYR 0.011 0.001 TYR A 37 ARG 0.003 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 100 time to evaluate : 0.598 Fit side-chains REVERT: B 225 HIS cc_start: 0.5092 (OUTLIER) cc_final: 0.4308 (m-70) outliers start: 16 outliers final: 9 residues processed: 110 average time/residue: 0.1466 time to fit residues: 22.4702 Evaluate side-chains 105 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 95 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 224 ILE Chi-restraints excluded: chain R residue 297 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 74 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 44 optimal weight: 0.4980 chunk 78 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 29 optimal weight: 4.9990 chunk 17 optimal weight: 20.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6881 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7505 Z= 0.168 Angle : 0.550 9.896 10157 Z= 0.285 Chirality : 0.042 0.223 1136 Planarity : 0.003 0.048 1284 Dihedral : 6.025 75.379 1021 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 3.27 % Allowed : 15.09 % Favored : 81.64 % 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: 0.24 (0.29), residues: 909 helix: 1.86 (0.27), residues: 396 sheet: -0.77 (0.42), residues: 154 loop : -1.37 (0.33), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 PHE 0.015 0.001 PHE A 290 TYR 0.010 0.001 TYR A 339 ARG 0.003 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 95 time to evaluate : 0.839 Fit side-chains REVERT: A 244 ILE cc_start: 0.7776 (OUTLIER) cc_final: 0.7360 (mt) REVERT: R 194 THR cc_start: 0.8393 (OUTLIER) cc_final: 0.8131 (m) outliers start: 26 outliers final: 15 residues processed: 113 average time/residue: 0.1977 time to fit residues: 30.8642 Evaluate side-chains 109 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 92 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 123 TYR Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 224 ILE Chi-restraints excluded: chain R residue 297 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 0.0770 chunk 7 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 0.0980 chunk 83 optimal weight: 2.9990 chunk 9 optimal weight: 0.0980 chunk 49 optimal weight: 0.9990 overall best weight: 0.4340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6839 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7505 Z= 0.142 Angle : 0.526 10.470 10157 Z= 0.273 Chirality : 0.041 0.146 1136 Planarity : 0.003 0.048 1284 Dihedral : 5.733 70.066 1021 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 3.02 % Allowed : 15.22 % Favored : 81.76 % 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: 0.33 (0.29), residues: 909 helix: 2.04 (0.27), residues: 388 sheet: -0.71 (0.42), residues: 150 loop : -1.40 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.002 0.001 HIS R 55 PHE 0.012 0.001 PHE A 290 TYR 0.009 0.001 TYR A 339 ARG 0.003 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 100 time to evaluate : 0.771 Fit side-chains REVERT: A 221 MET cc_start: 0.6483 (mmt) cc_final: 0.6141 (mmt) REVERT: A 244 ILE cc_start: 0.7712 (OUTLIER) cc_final: 0.7319 (mt) REVERT: A 289 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7796 (tt) REVERT: B 99 TRP cc_start: 0.6282 (m100) cc_final: 0.5915 (m100) REVERT: B 134 ARG cc_start: 0.7506 (ptp-110) cc_final: 0.7246 (ptp-110) REVERT: R 194 THR cc_start: 0.8305 (OUTLIER) cc_final: 0.8049 (m) outliers start: 24 outliers final: 14 residues processed: 114 average time/residue: 0.1995 time to fit residues: 31.1725 Evaluate side-chains 114 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 123 TYR Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 224 ILE Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain R residue 297 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 0.0020 chunk 49 optimal weight: 5.9990 chunk 73 optimal weight: 6.9990 chunk 48 optimal weight: 0.5980 chunk 86 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 40 optimal weight: 0.0000 chunk 53 optimal weight: 4.9990 chunk 34 optimal weight: 0.8980 chunk 51 optimal weight: 0.7980 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 36 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6819 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7505 Z= 0.144 Angle : 0.534 10.510 10157 Z= 0.275 Chirality : 0.041 0.144 1136 Planarity : 0.003 0.048 1284 Dihedral : 5.455 63.984 1021 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.02 % Allowed : 16.86 % Favored : 80.13 % 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: 0.33 (0.29), residues: 909 helix: 2.03 (0.27), residues: 385 sheet: -0.64 (0.43), residues: 147 loop : -1.38 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 82 HIS 0.003 0.001 HIS R 113 PHE 0.011 0.001 PHE B 241 TYR 0.009 0.001 TYR A 339 ARG 0.003 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.838 Fit side-chains REVERT: A 244 ILE cc_start: 0.7691 (OUTLIER) cc_final: 0.7326 (mt) REVERT: A 289 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7779 (tt) REVERT: B 99 TRP cc_start: 0.6208 (m100) cc_final: 0.5834 (m100) REVERT: R 90 TYR cc_start: 0.4593 (OUTLIER) cc_final: 0.4150 (m-10) REVERT: R 194 THR cc_start: 0.8314 (OUTLIER) cc_final: 0.8047 (m) outliers start: 24 outliers final: 18 residues processed: 112 average time/residue: 0.1962 time to fit residues: 29.8428 Evaluate side-chains 115 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 93 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain R residue 51 PHE Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 123 TYR Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain R residue 297 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 16 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 8 optimal weight: 0.1980 chunk 68 optimal weight: 0.0470 chunk 78 optimal weight: 0.8980 chunk 83 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6822 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7505 Z= 0.146 Angle : 0.545 11.833 10157 Z= 0.280 Chirality : 0.041 0.142 1136 Planarity : 0.003 0.048 1284 Dihedral : 5.281 60.004 1021 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.14 % Allowed : 17.11 % Favored : 79.75 % 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: 0.35 (0.29), residues: 909 helix: 2.05 (0.27), residues: 385 sheet: -0.66 (0.42), residues: 147 loop : -1.36 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 82 HIS 0.003 0.001 HIS R 55 PHE 0.011 0.001 PHE B 241 TYR 0.009 0.001 TYR A 339 ARG 0.003 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 94 time to evaluate : 0.884 Fit side-chains REVERT: A 20 ARG cc_start: 0.7164 (tpp-160) cc_final: 0.6776 (mmm160) REVERT: A 221 MET cc_start: 0.6583 (mmt) cc_final: 0.6249 (mmt) REVERT: A 244 ILE cc_start: 0.7679 (OUTLIER) cc_final: 0.7301 (mt) REVERT: B 99 TRP cc_start: 0.6210 (m100) cc_final: 0.5861 (m100) REVERT: R 90 TYR cc_start: 0.4677 (OUTLIER) cc_final: 0.4212 (m-10) REVERT: R 194 THR cc_start: 0.8325 (OUTLIER) cc_final: 0.8025 (m) outliers start: 25 outliers final: 20 residues processed: 112 average time/residue: 0.1964 time to fit residues: 30.0504 Evaluate side-chains 116 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 93 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 349 SER Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain R residue 51 PHE Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 123 TYR Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain R residue 297 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 1.9990 chunk 83 optimal weight: 0.0270 chunk 48 optimal weight: 0.0170 chunk 35 optimal weight: 0.3980 chunk 63 optimal weight: 0.0870 chunk 24 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 85 optimal weight: 0.0770 chunk 52 optimal weight: 0.7980 overall best weight: 0.1212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN B 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6770 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7505 Z= 0.136 Angle : 0.538 11.791 10157 Z= 0.275 Chirality : 0.040 0.139 1136 Planarity : 0.003 0.048 1284 Dihedral : 4.859 49.878 1021 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.77 % Allowed : 17.74 % Favored : 79.50 % 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: 0.40 (0.29), residues: 909 helix: 2.10 (0.27), residues: 385 sheet: -0.59 (0.42), residues: 147 loop : -1.36 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.002 0.000 HIS R 55 PHE 0.011 0.001 PHE B 241 TYR 0.008 0.001 TYR A 339 ARG 0.002 0.000 ARG B 134 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 96 time to evaluate : 0.841 Fit side-chains REVERT: A 20 ARG cc_start: 0.7099 (tpp-160) cc_final: 0.6750 (mmm160) REVERT: A 244 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7339 (mp) REVERT: B 99 TRP cc_start: 0.6147 (m100) cc_final: 0.5780 (m100) REVERT: R 90 TYR cc_start: 0.4686 (OUTLIER) cc_final: 0.4190 (m-10) REVERT: R 194 THR cc_start: 0.8303 (OUTLIER) cc_final: 0.8018 (m) outliers start: 22 outliers final: 15 residues processed: 112 average time/residue: 0.1973 time to fit residues: 30.1026 Evaluate side-chains 106 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 88 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 103 CYS Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain R residue 51 PHE Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 90 TYR Chi-restraints excluded: chain R residue 123 TYR Chi-restraints excluded: chain R residue 194 THR Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain R residue 297 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 chunk 89 optimal weight: 0.7980 chunk 82 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 56 optimal weight: 6.9990 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 0.0170 overall best weight: 0.9622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 294 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6863 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7505 Z= 0.187 Angle : 0.597 12.200 10157 Z= 0.300 Chirality : 0.042 0.154 1136 Planarity : 0.003 0.047 1284 Dihedral : 5.194 56.984 1021 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.26 % Allowed : 18.99 % Favored : 78.74 % 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: 0.35 (0.29), residues: 909 helix: 2.05 (0.27), residues: 389 sheet: -0.67 (0.43), residues: 138 loop : -1.37 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.003 0.001 HIS R 55 PHE 0.012 0.001 PHE R 51 TYR 0.013 0.001 TYR A 37 ARG 0.004 0.000 ARG A 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1818 Ramachandran restraints generated. 909 Oldfield, 0 Emsley, 909 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 93 time to evaluate : 0.793 Fit side-chains REVERT: A 20 ARG cc_start: 0.7131 (tpp-160) cc_final: 0.6834 (mmm160) REVERT: A 244 ILE cc_start: 0.7668 (OUTLIER) cc_final: 0.7247 (mt) REVERT: B 99 TRP cc_start: 0.6223 (m100) cc_final: 0.5882 (m100) outliers start: 18 outliers final: 15 residues processed: 107 average time/residue: 0.2016 time to fit residues: 29.3391 Evaluate side-chains 107 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 91 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 294 GLN Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 344 GLU Chi-restraints excluded: chain A residue 372 ILE Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 250 CYS Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain R residue 51 PHE Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 274 ASP Chi-restraints excluded: chain R residue 297 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.9990 chunk 10 optimal weight: 40.0000 chunk 19 optimal weight: 0.2980 chunk 71 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 73 optimal weight: 0.8980 chunk 9 optimal weight: 0.0060 chunk 13 optimal weight: 0.3980 chunk 62 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** 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 = 0.4835 r_free = 0.4835 target = 0.253321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.197531 restraints weight = 8134.525| |-----------------------------------------------------------------------------| r_work (start): 0.4374 rms_B_bonded: 3.26 r_work: 0.4133 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7109 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 7505 Z= 0.285 Angle : 0.965 59.200 10157 Z= 0.558 Chirality : 0.042 0.284 1136 Planarity : 0.003 0.047 1284 Dihedral : 5.198 56.910 1021 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 2.14 % Allowed : 19.12 % Favored : 78.74 % Cbeta Deviations : 0.11 % 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: 0.34 (0.29), residues: 909 helix: 2.03 (0.27), residues: 389 sheet: -0.68 (0.43), residues: 138 loop : -1.37 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.004 0.001 HIS A 220 PHE 0.013 0.001 PHE B 199 TYR 0.013 0.001 TYR A 37 ARG 0.002 0.000 ARG A 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1856.19 seconds wall clock time: 40 minutes 31.75 seconds (2431.75 seconds total)