Starting phenix.real_space_refine on Thu Feb 13 09:08:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8e3y_27873/02_2025/8e3y_27873.cif Found real_map, /net/cci-nas-00/data/ceres_data/8e3y_27873/02_2025/8e3y_27873.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8e3y_27873/02_2025/8e3y_27873.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8e3y_27873/02_2025/8e3y_27873.map" model { file = "/net/cci-nas-00/data/ceres_data/8e3y_27873/02_2025/8e3y_27873.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8e3y_27873/02_2025/8e3y_27873.cif" } resolution = 2.3 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= 0.002 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 60 5.16 5 C 5685 2.51 5 N 1559 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8966 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 1856 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 221, 1844 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 3 Conformer: "B" Number of residues, atoms: 221, 1844 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 3 bond proxies already assigned to first conformer: 1864 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 424 Classifications: {'peptide': 55} Link IDs: {'PTRANS': 4, 'TRANS': 50} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "P" Number of atoms: 221 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 221 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "R" Number of atoms: 2890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 372, 2890 Classifications: {'peptide': 372} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 14, 'TRANS': 357} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 129 Unresolved non-hydrogen angles: 169 Unresolved non-hydrogen dihedrals: 109 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 74 Chain: "P" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATYR A 358 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 358 " occ=0.50 Time building chain proxies: 6.15, per 1000 atoms: 0.69 Number of scatterers: 8966 At special positions: 0 Unit cell: (89.7, 99.45, 163.8, 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 60 16.00 O 1662 8.00 N 1559 7.00 C 5685 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 50 " - pdb=" SG CYS R 72 " distance=1.98 Simple disulfide: pdb=" SG CYS R 63 " - pdb=" SG CYS R 105 " distance=2.03 Simple disulfide: pdb=" SG CYS R 86 " - pdb=" SG CYS R 122 " distance=2.03 Simple disulfide: pdb=" SG CYS R 215 " - pdb=" SG CYS R 285 " 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: 2.51 Conformation dependent library (CDL) restraints added in 1.2 seconds 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 11 sheets defined 43.8% alpha, 19.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.13 Creating SS restraints... Processing helix chain 'A' and resid 12 through 39 removed outlier: 3.667A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 265 through 279 Processing helix chain 'A' and resid 293 through 300 Processing helix chain 'A' and resid 312 through 318 Processing helix chain 'A' and resid 331 through 352 removed outlier: 4.081A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER A 349 " --> pdb=" O PHE A 345 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N SER A 352 " --> pdb=" O ILE A 348 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'G' and resid 9 through 23 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 55 through 59 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.623A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 27 Processing helix chain 'R' and resid 37 through 54 removed outlier: 3.514A pdb=" N GLN R 41 " --> pdb=" O CYS R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 94 removed outlier: 4.149A pdb=" N PHE R 93 " --> pdb=" O ILE R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 121 removed outlier: 3.674A pdb=" N ILE R 120 " --> pdb=" O GLY R 116 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 127 removed outlier: 3.539A pdb=" N ASP R 126 " --> pdb=" O CYS R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 128 through 167 removed outlier: 3.709A pdb=" N VAL R 159 " --> pdb=" O ALA R 155 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE R 167 " --> pdb=" O ILE R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 168 through 171 Processing helix chain 'R' and resid 172 through 200 Processing helix chain 'R' and resid 205 through 210 removed outlier: 3.914A pdb=" N SER R 209 " --> pdb=" O SER R 205 " (cutoff:3.500A) Processing helix chain 'R' and resid 212 through 246 Processing helix chain 'R' and resid 250 through 253 Processing helix chain 'R' and resid 254 through 281 removed outlier: 4.431A pdb=" N VAL R 265 " --> pdb=" O ILE R 261 " (cutoff:3.500A) Proline residue: R 266 - end of helix Processing helix chain 'R' and resid 293 through 324 removed outlier: 4.002A pdb=" N ILE R 297 " --> pdb=" O LEU R 293 " (cutoff:3.500A) Proline residue: R 300 - end of helix removed outlier: 3.595A pdb=" N ARG R 324 " --> pdb=" O LEU R 320 " (cutoff:3.500A) Processing helix chain 'R' and resid 336 through 351 Proline residue: R 348 - end of helix Processing helix chain 'R' and resid 352 through 356 Processing helix chain 'R' and resid 365 through 375 removed outlier: 3.665A pdb=" N LYS R 369 " --> pdb=" O LYS R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 376 through 378 No H-bonds generated for 'chain 'R' and resid 376 through 378' Processing helix chain 'R' and resid 379 through 388 Processing helix chain 'R' and resid 392 through 407 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.424A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.691A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 9.336A pdb=" N ALA A 243 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N VAL A 247 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LEU A 46 " --> pdb=" O VAL A 247 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N ALA A 249 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.275A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N VAL A 287 " --> pdb=" O TYR A 360 " (cutoff:3.500A) removed outlier: 7.839A pdb=" N HIS A 362 " --> pdb=" O VAL A 287 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LEU A 289 " --> pdb=" O HIS A 362 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 5.260A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.833A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.031A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.671A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.512A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.659A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.700A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ASP B 303 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 11 removed outlier: 5.631A pdb=" N GLY N 10 " --> pdb=" O THR N 125 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'R' and resid 82 through 85 461 hydrogen bonds defined for protein. 1299 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: 2.90 Time building geometry restraints manager: 2.67 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: 2912 1.34 - 1.46: 1510 1.46 - 1.57: 4639 1.57 - 1.69: 0 1.69 - 1.81: 83 Bond restraints: 9144 Sorted by residual: bond pdb=" N VAL P 19 " pdb=" CA VAL P 19 " ideal model delta sigma weight residual 1.460 1.495 -0.036 1.21e-02 6.83e+03 8.77e+00 bond pdb=" N ILE R 177 " pdb=" CA ILE R 177 " ideal model delta sigma weight residual 1.460 1.496 -0.036 1.26e-02 6.30e+03 8.10e+00 bond pdb=" N VAL R 235 " pdb=" CA VAL R 235 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.71e+00 bond pdb=" N PHE R 93 " pdb=" CA PHE R 93 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.32e-02 5.74e+03 7.57e+00 bond pdb=" N LEU R 349 " pdb=" CA LEU R 349 " ideal model delta sigma weight residual 1.458 1.494 -0.037 1.33e-02 5.65e+03 7.54e+00 ... (remaining 9139 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.13: 11643 1.13 - 2.26: 530 2.26 - 3.39: 168 3.39 - 4.51: 21 4.51 - 5.64: 14 Bond angle restraints: 12376 Sorted by residual: angle pdb=" N ALA R 129 " pdb=" CA ALA R 129 " pdb=" C ALA R 129 " ideal model delta sigma weight residual 111.71 106.46 5.25 1.15e+00 7.56e-01 2.09e+01 angle pdb=" N LEU R 233 " pdb=" CA LEU R 233 " pdb=" C LEU R 233 " ideal model delta sigma weight residual 111.36 106.41 4.95 1.09e+00 8.42e-01 2.06e+01 angle pdb=" N PHE R 350 " pdb=" CA PHE R 350 " pdb=" C PHE R 350 " ideal model delta sigma weight residual 114.31 108.69 5.62 1.29e+00 6.01e-01 1.90e+01 angle pdb=" N PHE R 182 " pdb=" CA PHE R 182 " pdb=" C PHE R 182 " ideal model delta sigma weight residual 112.23 107.79 4.44 1.26e+00 6.30e-01 1.24e+01 angle pdb=" N LEU R 181 " pdb=" CA LEU R 181 " pdb=" C LEU R 181 " ideal model delta sigma weight residual 111.28 107.73 3.55 1.09e+00 8.42e-01 1.06e+01 ... (remaining 12371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.94: 4934 16.94 - 33.89: 410 33.89 - 50.83: 64 50.83 - 67.78: 12 67.78 - 84.72: 7 Dihedral angle restraints: 5427 sinusoidal: 2117 harmonic: 3310 Sorted by residual: dihedral pdb=" CB CYS R 50 " pdb=" SG CYS R 50 " pdb=" SG CYS R 72 " pdb=" CB CYS R 72 " ideal model delta sinusoidal sigma weight residual -86.00 -145.03 59.03 1 1.00e+01 1.00e-02 4.66e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual -86.00 -127.78 41.78 1 1.00e+01 1.00e-02 2.44e+01 dihedral pdb=" CB CYS R 86 " pdb=" SG CYS R 86 " pdb=" SG CYS R 122 " pdb=" CB CYS R 122 " ideal model delta sinusoidal sigma weight residual 93.00 133.96 -40.96 1 1.00e+01 1.00e-02 2.35e+01 ... (remaining 5424 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1013 0.045 - 0.091: 262 0.091 - 0.136: 74 0.136 - 0.182: 13 0.182 - 0.227: 7 Chirality restraints: 1369 Sorted by residual: chirality pdb=" CA ASN R 175 " pdb=" N ASN R 175 " pdb=" C ASN R 175 " pdb=" CB ASN R 175 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CA ILE R 177 " pdb=" N ILE R 177 " pdb=" C ILE R 177 " pdb=" CB ILE R 177 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA LEU R 233 " pdb=" N LEU R 233 " pdb=" C LEU R 233 " pdb=" CB LEU R 233 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 1366 not shown) Planarity restraints: 1583 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR G 52 " 0.038 5.00e-02 4.00e+02 5.77e-02 5.33e+00 pdb=" N PRO G 53 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO G 53 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO G 53 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 331 " -0.033 5.00e-02 4.00e+02 5.11e-02 4.18e+00 pdb=" N PRO A 332 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 332 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 332 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER R 334 " 0.027 5.00e-02 4.00e+02 4.15e-02 2.76e+00 pdb=" N PRO R 335 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO R 335 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 335 " 0.023 5.00e-02 4.00e+02 ... (remaining 1580 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1594 2.77 - 3.30: 8672 3.30 - 3.83: 15280 3.83 - 4.37: 18618 4.37 - 4.90: 31213 Nonbonded interactions: 75377 Sorted by model distance: nonbonded pdb=" O PRO R 300 " pdb=" OG1 THR R 303 " model vdw 2.237 3.040 nonbonded pdb=" NH1 ARG A 228 " pdb=" OD1 ASP B 186 " model vdw 2.259 3.120 nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.271 3.040 nonbonded pdb=" OE2 GLU A 230 " pdb=" OG SER N 112 " model vdw 2.288 3.040 nonbonded pdb=" OD1 ASP B 228 " pdb=" OH TYR N 117 " model vdw 2.303 3.040 ... (remaining 75372 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=0.50 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: 2.090 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: 0.000 Extract box with map and model: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 24.500 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 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 0.037 9144 Z= 0.206 Angle : 0.599 5.643 12376 Z= 0.404 Chirality : 0.047 0.227 1369 Planarity : 0.004 0.058 1583 Dihedral : 12.649 84.724 3276 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.11 % Allowed : 0.53 % Favored : 99.36 % 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: 1.26 (0.25), residues: 1124 helix: 2.05 (0.25), residues: 445 sheet: 0.50 (0.33), residues: 224 loop : -0.15 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.013 0.001 HIS A 220 PHE 0.013 0.001 PHE A 212 TYR 0.011 0.001 TYR R 388 ARG 0.005 0.000 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 165 time to evaluate : 1.061 Fit side-chains REVERT: B 6 GLN cc_start: 0.7495 (pp30) cc_final: 0.7293 (pp30) REVERT: G 20 LYS cc_start: 0.8426 (mtmt) cc_final: 0.7861 (mtmt) REVERT: R 252 ARG cc_start: 0.6712 (tpt90) cc_final: 0.6467 (tpt170) outliers start: 1 outliers final: 0 residues processed: 166 average time/residue: 1.6332 time to fit residues: 285.6280 Evaluate side-chains 139 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 ASN B 176 GLN B 237 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN R 321 GLN R 353 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.140280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.086584 restraints weight = 20839.717| |-----------------------------------------------------------------------------| r_work (start): 0.2986 rms_B_bonded: 3.25 r_work: 0.2824 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2691 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2690 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2690 r_free = 0.2690 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2690 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9144 Z= 0.266 Angle : 0.564 8.437 12376 Z= 0.307 Chirality : 0.044 0.141 1369 Planarity : 0.004 0.051 1583 Dihedral : 4.313 22.346 1244 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.17 % Allowed : 9.32 % Favored : 89.51 % 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: 1.67 (0.25), residues: 1124 helix: 2.59 (0.24), residues: 445 sheet: 0.66 (0.33), residues: 223 loop : -0.12 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 339 HIS 0.024 0.001 HIS A 357 PHE 0.014 0.002 PHE R 382 TYR 0.030 0.002 TYR R 146 ARG 0.006 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.983 Fit side-chains REVERT: A 17 LYS cc_start: 0.7899 (OUTLIER) cc_final: 0.7478 (ptmm) REVERT: A 314 GLU cc_start: 0.7948 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: B 134 ARG cc_start: 0.8239 (ptp90) cc_final: 0.7994 (ptp90) REVERT: B 197 ARG cc_start: 0.8850 (mmm-85) cc_final: 0.8633 (mmm160) REVERT: B 266 HIS cc_start: 0.8647 (t-170) cc_final: 0.8434 (t-170) REVERT: B 270 ILE cc_start: 0.9209 (pt) cc_final: 0.8989 (pp) REVERT: G 17 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8214 (mm-30) REVERT: G 20 LYS cc_start: 0.8644 (mtmt) cc_final: 0.8377 (mtmt) REVERT: N 43 LYS cc_start: 0.8518 (mttm) cc_final: 0.8153 (mttp) REVERT: R 252 ARG cc_start: 0.7055 (tpt90) cc_final: 0.6614 (tpt170) outliers start: 11 outliers final: 3 residues processed: 151 average time/residue: 1.5163 time to fit residues: 241.5702 Evaluate side-chains 144 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 139 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain B residue 25 CYS Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain R residue 159 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 99 optimal weight: 1.9990 chunk 78 optimal weight: 40.0000 chunk 96 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 71 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 80 optimal weight: 30.0000 chunk 49 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 390 GLN B 237 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.141008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.088555 restraints weight = 20269.942| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 3.35 r_work: 0.2808 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work: 0.2673 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 9144 Z= 0.249 Angle : 0.540 7.248 12376 Z= 0.295 Chirality : 0.043 0.137 1369 Planarity : 0.004 0.049 1583 Dihedral : 4.405 22.179 1244 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.27 % Allowed : 10.49 % Favored : 88.24 % 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: 1.68 (0.25), residues: 1124 helix: 2.59 (0.24), residues: 445 sheet: 0.76 (0.33), residues: 231 loop : -0.19 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 256 HIS 0.021 0.002 HIS A 357 PHE 0.014 0.002 PHE R 382 TYR 0.027 0.002 TYR R 146 ARG 0.006 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 144 time to evaluate : 0.801 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.7984 (OUTLIER) cc_final: 0.7580 (ptmm) REVERT: A 20 ARG cc_start: 0.8007 (mtm-85) cc_final: 0.7767 (mtm-85) REVERT: A 59 GLN cc_start: 0.8360 (tp40) cc_final: 0.7737 (mm-40) REVERT: A 314 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7114 (mp0) REVERT: B 270 ILE cc_start: 0.9244 (pt) cc_final: 0.9028 (pp) REVERT: G 20 LYS cc_start: 0.8663 (mtmt) cc_final: 0.8425 (mtmt) REVERT: N 43 LYS cc_start: 0.8627 (mttm) cc_final: 0.8396 (mttp) REVERT: R 252 ARG cc_start: 0.7000 (tpt90) cc_final: 0.6548 (tpt170) REVERT: R 338 ARG cc_start: 0.7007 (tpt170) cc_final: 0.6626 (tpt170) outliers start: 12 outliers final: 3 residues processed: 147 average time/residue: 1.5616 time to fit residues: 241.8302 Evaluate side-chains 145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 140 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain R residue 159 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 86 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 107 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN B 237 ASN ** G 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN R 363 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.139356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.085354 restraints weight = 14854.732| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.40 r_work: 0.2805 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2678 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2678 r_free = 0.2678 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2678 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9144 Z= 0.353 Angle : 0.584 6.495 12376 Z= 0.320 Chirality : 0.045 0.146 1369 Planarity : 0.005 0.053 1583 Dihedral : 4.631 22.135 1244 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.69 % Allowed : 11.12 % Favored : 87.18 % 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: 1.61 (0.25), residues: 1124 helix: 2.47 (0.24), residues: 445 sheet: 0.85 (0.33), residues: 229 loop : -0.23 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 256 HIS 0.021 0.002 HIS A 357 PHE 0.018 0.002 PHE R 222 TYR 0.025 0.002 TYR R 146 ARG 0.004 0.000 ARG R 277 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 1.116 Fit side-chains revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7567 (ptmm) REVERT: A 59 GLN cc_start: 0.8370 (tp40) cc_final: 0.7778 (mm-40) REVERT: A 314 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: G 17 GLU cc_start: 0.8399 (mm-30) cc_final: 0.8098 (mm-30) REVERT: G 20 LYS cc_start: 0.8677 (mtmt) cc_final: 0.8363 (mtmt) REVERT: N 43 LYS cc_start: 0.8689 (mttm) cc_final: 0.8469 (mttp) REVERT: N 89 GLU cc_start: 0.8682 (pm20) cc_final: 0.8419 (pm20) REVERT: R 252 ARG cc_start: 0.6952 (tpt90) cc_final: 0.6494 (tpt170) REVERT: R 338 ARG cc_start: 0.7039 (tpt170) cc_final: 0.6569 (tpp-160) outliers start: 16 outliers final: 3 residues processed: 143 average time/residue: 1.6856 time to fit residues: 253.0929 Evaluate side-chains 144 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 139 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain R residue 159 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 49 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 73 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN N 3 GLN N 84 ASN R 178 HIS R 363 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.139152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.083749 restraints weight = 27282.053| |-----------------------------------------------------------------------------| r_work (start): 0.2946 rms_B_bonded: 3.10 r_work: 0.2789 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2662 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2662 r_free = 0.2662 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2662 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.2180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9144 Z= 0.222 Angle : 0.526 6.203 12376 Z= 0.288 Chirality : 0.042 0.138 1369 Planarity : 0.004 0.049 1583 Dihedral : 4.425 21.191 1244 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.48 % Allowed : 12.18 % Favored : 86.33 % 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: 1.70 (0.25), residues: 1124 helix: 2.59 (0.24), residues: 445 sheet: 0.87 (0.33), residues: 229 loop : -0.22 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 256 HIS 0.013 0.001 HIS A 357 PHE 0.014 0.001 PHE R 222 TYR 0.021 0.001 TYR R 146 ARG 0.007 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 1.076 Fit side-chains REVERT: A 17 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7578 (ptmm) REVERT: A 59 GLN cc_start: 0.8341 (tp40) cc_final: 0.7746 (mm-40) REVERT: B 266 HIS cc_start: 0.8581 (t-170) cc_final: 0.8352 (t-170) REVERT: G 17 GLU cc_start: 0.8450 (mm-30) cc_final: 0.8164 (mm-30) REVERT: G 20 LYS cc_start: 0.8701 (mtmt) cc_final: 0.8340 (mtmt) REVERT: N 43 LYS cc_start: 0.8695 (mttm) cc_final: 0.8469 (mttp) REVERT: N 89 GLU cc_start: 0.8688 (pm20) cc_final: 0.8404 (pm20) REVERT: R 252 ARG cc_start: 0.6945 (tpt90) cc_final: 0.6469 (tpt170) REVERT: R 338 ARG cc_start: 0.7083 (tpt170) cc_final: 0.6619 (tpp-160) outliers start: 14 outliers final: 4 residues processed: 149 average time/residue: 1.6738 time to fit residues: 262.4745 Evaluate side-chains 145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 140 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain R residue 159 VAL Chi-restraints excluded: chain R residue 271 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 39 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 chunk 109 optimal weight: 4.9990 chunk 97 optimal weight: 0.0670 chunk 96 optimal weight: 0.9990 chunk 53 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 overall best weight: 0.7322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 3 GLN R 363 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.140563 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.087377 restraints weight = 22482.471| |-----------------------------------------------------------------------------| r_work (start): 0.3005 rms_B_bonded: 3.30 r_work: 0.2837 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2834 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2834 r_free = 0.2834 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2834 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9144 Z= 0.169 Angle : 0.498 6.820 12376 Z= 0.272 Chirality : 0.041 0.133 1369 Planarity : 0.004 0.049 1583 Dihedral : 4.240 20.209 1244 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.95 % Allowed : 13.77 % Favored : 85.28 % 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: 1.71 (0.25), residues: 1124 helix: 2.65 (0.24), residues: 445 sheet: 0.83 (0.33), residues: 228 loop : -0.25 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 256 HIS 0.009 0.001 HIS A 357 PHE 0.013 0.001 PHE R 382 TYR 0.021 0.001 TYR R 146 ARG 0.005 0.000 ARG A 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 140 time to evaluate : 1.106 Fit side-chains REVERT: A 17 LYS cc_start: 0.7986 (OUTLIER) cc_final: 0.7566 (ptmm) REVERT: A 59 GLN cc_start: 0.8257 (tp40) cc_final: 0.7655 (mm-40) REVERT: A 314 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.6988 (mp0) REVERT: B 197 ARG cc_start: 0.8652 (mmm160) cc_final: 0.8384 (mtp180) REVERT: B 266 HIS cc_start: 0.8461 (t-170) cc_final: 0.8202 (t-170) REVERT: G 17 GLU cc_start: 0.8351 (mm-30) cc_final: 0.7975 (mm-30) REVERT: G 20 LYS cc_start: 0.8636 (mtmt) cc_final: 0.8242 (mtmt) REVERT: N 43 LYS cc_start: 0.8586 (mttm) cc_final: 0.8363 (mttp) REVERT: R 252 ARG cc_start: 0.6959 (tpt90) cc_final: 0.6497 (tpt170) REVERT: R 338 ARG cc_start: 0.6879 (tpt170) cc_final: 0.6539 (tpt170) outliers start: 9 outliers final: 2 residues processed: 141 average time/residue: 1.6657 time to fit residues: 246.8892 Evaluate side-chains 143 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 139 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain R residue 159 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 87 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 101 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 108 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 92 optimal weight: 0.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN N 3 GLN N 84 ASN R 363 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.142142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.090168 restraints weight = 20289.306| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.25 r_work: 0.2838 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2708 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9144 Z= 0.184 Angle : 0.503 7.406 12376 Z= 0.275 Chirality : 0.041 0.134 1369 Planarity : 0.004 0.049 1583 Dihedral : 4.217 20.585 1244 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.17 % Allowed : 13.77 % Favored : 85.06 % 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: 1.74 (0.25), residues: 1124 helix: 2.71 (0.24), residues: 445 sheet: 0.84 (0.33), residues: 229 loop : -0.27 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP R 256 HIS 0.010 0.001 HIS A 357 PHE 0.013 0.001 PHE R 222 TYR 0.021 0.001 TYR R 146 ARG 0.008 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.988 Fit side-chains REVERT: A 17 LYS cc_start: 0.7932 (OUTLIER) cc_final: 0.7501 (ptmm) REVERT: A 59 GLN cc_start: 0.8303 (tp40) cc_final: 0.7688 (mm-40) REVERT: A 314 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7120 (mp0) REVERT: B 197 ARG cc_start: 0.8786 (mmm160) cc_final: 0.8542 (mtp180) REVERT: B 266 HIS cc_start: 0.8560 (t-170) cc_final: 0.8339 (t-170) REVERT: G 17 GLU cc_start: 0.8406 (mm-30) cc_final: 0.8085 (mm-30) REVERT: G 20 LYS cc_start: 0.8653 (mtmt) cc_final: 0.8250 (mtmt) REVERT: G 21 MET cc_start: 0.8491 (tpp) cc_final: 0.7912 (tmt) REVERT: N 43 LYS cc_start: 0.8640 (mttm) cc_final: 0.8410 (mttp) REVERT: N 89 GLU cc_start: 0.8697 (pm20) cc_final: 0.8409 (pm20) REVERT: R 252 ARG cc_start: 0.6968 (tpt90) cc_final: 0.6399 (tpt90) REVERT: R 338 ARG cc_start: 0.6979 (tpt170) cc_final: 0.6531 (tpp-160) outliers start: 11 outliers final: 2 residues processed: 145 average time/residue: 1.6425 time to fit residues: 250.7898 Evaluate side-chains 143 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 139 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain R residue 159 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 41 optimal weight: 3.9990 chunk 108 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 96 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 chunk 30 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN N 3 GLN N 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.142662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.091395 restraints weight = 17745.924| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 3.16 r_work: 0.2851 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2708 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2708 r_free = 0.2708 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2708 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9144 Z= 0.169 Angle : 0.497 9.714 12376 Z= 0.271 Chirality : 0.041 0.134 1369 Planarity : 0.004 0.049 1583 Dihedral : 4.160 20.209 1244 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.53 % Allowed : 15.04 % Favored : 84.43 % 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: 1.74 (0.25), residues: 1124 helix: 2.74 (0.24), residues: 445 sheet: 0.83 (0.33), residues: 228 loop : -0.30 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP R 256 HIS 0.009 0.001 HIS A 357 PHE 0.024 0.001 PHE R 382 TYR 0.021 0.001 TYR R 146 ARG 0.007 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 141 time to evaluate : 1.110 Fit side-chains REVERT: A 17 LYS cc_start: 0.7928 (OUTLIER) cc_final: 0.7502 (ptmm) REVERT: A 59 GLN cc_start: 0.8299 (tp40) cc_final: 0.7675 (mm-40) REVERT: A 314 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7128 (mp0) REVERT: B 197 ARG cc_start: 0.8779 (mmm160) cc_final: 0.8550 (mtp180) REVERT: B 266 HIS cc_start: 0.8562 (t-170) cc_final: 0.8339 (t-170) REVERT: G 17 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8105 (mm-30) REVERT: G 20 LYS cc_start: 0.8678 (mtmt) cc_final: 0.8278 (mtmt) REVERT: G 21 MET cc_start: 0.8552 (tpp) cc_final: 0.7955 (tmt) REVERT: N 43 LYS cc_start: 0.8622 (mttm) cc_final: 0.8401 (mttp) REVERT: N 89 GLU cc_start: 0.8709 (pm20) cc_final: 0.8472 (pm20) REVERT: R 252 ARG cc_start: 0.6979 (tpt90) cc_final: 0.6395 (tpt90) REVERT: R 338 ARG cc_start: 0.6926 (tpt170) cc_final: 0.6553 (tpt170) outliers start: 5 outliers final: 2 residues processed: 143 average time/residue: 1.6482 time to fit residues: 248.0622 Evaluate side-chains 142 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 138 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain R residue 159 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 45 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 83 optimal weight: 9.9990 chunk 104 optimal weight: 0.9990 chunk 50 optimal weight: 0.8980 chunk 82 optimal weight: 50.0000 chunk 8 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN N 3 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.141784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.088878 restraints weight = 19153.888| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 3.31 r_work: 0.2825 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2825 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2824 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2824 r_free = 0.2824 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2824 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9144 Z= 0.208 Angle : 0.521 9.664 12376 Z= 0.282 Chirality : 0.042 0.135 1369 Planarity : 0.004 0.049 1583 Dihedral : 4.247 20.512 1244 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.85 % Allowed : 15.25 % Favored : 83.90 % 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: 1.73 (0.25), residues: 1124 helix: 2.71 (0.24), residues: 445 sheet: 0.86 (0.33), residues: 229 loop : -0.30 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP R 256 HIS 0.011 0.001 HIS A 357 PHE 0.022 0.001 PHE R 382 TYR 0.021 0.001 TYR R 146 ARG 0.008 0.000 ARG B 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 1.088 Fit side-chains REVERT: A 17 LYS cc_start: 0.8002 (OUTLIER) cc_final: 0.7589 (ptmm) REVERT: A 59 GLN cc_start: 0.8258 (tp40) cc_final: 0.7648 (mm-40) REVERT: A 314 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7043 (mp0) REVERT: G 17 GLU cc_start: 0.8357 (mm-30) cc_final: 0.8008 (mm-30) REVERT: G 20 LYS cc_start: 0.8721 (mtmt) cc_final: 0.8306 (mtmt) REVERT: G 21 MET cc_start: 0.8511 (tpp) cc_final: 0.7964 (tmt) REVERT: N 43 LYS cc_start: 0.8616 (mttm) cc_final: 0.8402 (mttp) REVERT: N 89 GLU cc_start: 0.8650 (pm20) cc_final: 0.8371 (pm20) REVERT: R 252 ARG cc_start: 0.6954 (tpt90) cc_final: 0.6482 (tpt170) REVERT: R 338 ARG cc_start: 0.6978 (tpt170) cc_final: 0.6548 (tpp-160) outliers start: 8 outliers final: 3 residues processed: 142 average time/residue: 1.6475 time to fit residues: 246.8388 Evaluate side-chains 144 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 139 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain R residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 34 optimal weight: 1.9990 chunk 80 optimal weight: 30.0000 chunk 5 optimal weight: 2.9990 chunk 52 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN N 3 GLN N 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.141089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.088639 restraints weight = 20423.690| |-----------------------------------------------------------------------------| r_work (start): 0.2999 rms_B_bonded: 3.11 r_work: 0.2817 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2680 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2680 r_free = 0.2680 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2680 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9144 Z= 0.237 Angle : 0.542 9.457 12376 Z= 0.294 Chirality : 0.043 0.136 1369 Planarity : 0.004 0.049 1583 Dihedral : 4.358 21.174 1244 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.53 % Allowed : 15.68 % Favored : 83.79 % 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: 1.71 (0.25), residues: 1124 helix: 2.68 (0.24), residues: 445 sheet: 0.86 (0.33), residues: 229 loop : -0.29 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP R 256 HIS 0.012 0.001 HIS A 357 PHE 0.021 0.001 PHE R 382 TYR 0.021 0.001 TYR R 146 ARG 0.009 0.000 ARG B 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2248 Ramachandran restraints generated. 1124 Oldfield, 0 Emsley, 1124 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 142 time to evaluate : 1.088 Fit side-chains REVERT: A 17 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7542 (ptmm) REVERT: A 59 GLN cc_start: 0.8336 (tp40) cc_final: 0.7728 (mm-40) REVERT: A 314 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7198 (mp0) REVERT: B 215 GLU cc_start: 0.8728 (mp0) cc_final: 0.8200 (mp0) REVERT: G 17 GLU cc_start: 0.8449 (mm-30) cc_final: 0.8147 (mm-30) REVERT: G 20 LYS cc_start: 0.8735 (mtmt) cc_final: 0.8344 (mtmt) REVERT: G 21 MET cc_start: 0.8607 (tpp) cc_final: 0.7945 (tmt) REVERT: N 43 LYS cc_start: 0.8690 (mttm) cc_final: 0.8294 (mttp) REVERT: N 89 GLU cc_start: 0.8728 (pm20) cc_final: 0.8432 (pm20) REVERT: R 252 ARG cc_start: 0.6940 (tpt90) cc_final: 0.6369 (tpt90) REVERT: R 338 ARG cc_start: 0.7010 (tpt170) cc_final: 0.6563 (tpp-160) outliers start: 5 outliers final: 3 residues processed: 144 average time/residue: 1.6248 time to fit residues: 246.2090 Evaluate side-chains 145 residues out of total 978 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 140 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LYS Chi-restraints excluded: chain A residue 55 THR Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain P residue 11 SER Chi-restraints excluded: chain R residue 159 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 95 optimal weight: 7.9990 chunk 19 optimal weight: 0.4980 chunk 46 optimal weight: 0.9980 chunk 94 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 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 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN N 3 GLN N 82 GLN N 84 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.140868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.088454 restraints weight = 19014.219| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.96 r_work: 0.2848 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2718 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2716 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2716 r_free = 0.2716 target_work(ls_wunit_k1) = 0.068 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2716 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.2243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9144 Z= 0.178 Angle : 0.516 9.393 12376 Z= 0.279 Chirality : 0.041 0.135 1369 Planarity : 0.004 0.049 1583 Dihedral : 4.201 20.098 1244 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.53 % Allowed : 15.89 % Favored : 83.58 % 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: 1.71 (0.25), residues: 1124 helix: 2.72 (0.24), residues: 445 sheet: 0.84 (0.33), residues: 228 loop : -0.33 (0.29), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP R 256 HIS 0.009 0.001 HIS A 357 PHE 0.023 0.001 PHE R 382 TYR 0.020 0.001 TYR R 146 ARG 0.010 0.000 ARG B 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11749.46 seconds wall clock time: 206 minutes 23.18 seconds (12383.18 seconds total)