Starting phenix.real_space_refine on Tue Mar 11 20:11:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9chv_45603/03_2025/9chv_45603.cif Found real_map, /net/cci-nas-00/data/ceres_data/9chv_45603/03_2025/9chv_45603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9chv_45603/03_2025/9chv_45603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9chv_45603/03_2025/9chv_45603.map" model { file = "/net/cci-nas-00/data/ceres_data/9chv_45603/03_2025/9chv_45603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9chv_45603/03_2025/9chv_45603.cif" } resolution = 3.95 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= 0.049 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 40 5.16 5 C 4277 2.51 5 N 1115 2.21 5 O 1212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6644 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 414, 2969 Classifications: {'peptide': 414} Incomplete info: {'truncation_to_alanine': 95} Link IDs: {'PTRANS': 9, 'TRANS': 404} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 383 Unresolved non-hydrogen angles: 496 Unresolved non-hydrogen dihedrals: 336 Unresolved non-hydrogen chiralities: 36 Planarities with less than four sites: {'GLN:plan1': 4, 'ARG:plan': 2, 'TYR:plan': 4, 'ASN:plan1': 6, 'TRP:plan': 4, 'ASP:plan': 3, 'PHE:plan': 11, 'GLU:plan': 4, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 204 Chain: "B" Number of atoms: 2810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2810 Classifications: {'peptide': 352} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 20, 'TRANS': 331} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "C" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 808 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 7, 'TRANS': 99} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'GLU%COO:oxt': 1} Unresolved non-hydrogen planarities: 19 Chain: "C" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 57 Unusual residues: {'FK5': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.48, per 1000 atoms: 0.82 Number of scatterers: 6644 At special positions: 0 Unit cell: (65.45, 85.85, 154.7, 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 40 16.00 O 1212 8.00 N 1115 7.00 C 4277 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 106 " - pdb=" SG CYS A 191 " distance=2.02 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: 1.56 Conformation dependent library (CDL) restraints added in 837.9 milliseconds 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1636 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 6 sheets defined 53.4% alpha, 4.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 33 through 61 removed outlier: 3.533A pdb=" N VAL A 54 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE A 55 " --> pdb=" O ASN A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 78 Processing helix chain 'A' and resid 80 through 85 Processing helix chain 'A' and resid 85 through 97 removed outlier: 3.637A pdb=" N PHE A 89 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY A 90 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ILE A 94 " --> pdb=" O GLY A 90 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LEU A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N MET A 96 " --> pdb=" O ALA A 92 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS A 97 " --> pdb=" O HIS A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 115 removed outlier: 4.384A pdb=" N GLU A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N PHE A 108 " --> pdb=" O PHE A 104 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N THR A 110 " --> pdb=" O CYS A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 137 removed outlier: 3.811A pdb=" N GLU A 122 " --> pdb=" O THR A 118 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER A 137 " --> pdb=" O PHE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.953A pdb=" N TYR A 141 " --> pdb=" O SER A 137 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N LEU A 145 " --> pdb=" O TYR A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 146 through 172 removed outlier: 3.691A pdb=" N ALA A 150 " --> pdb=" O THR A 146 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N VAL A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ILE A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A 160 " --> pdb=" O MET A 156 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N SER A 161 " --> pdb=" O VAL A 157 " (cutoff:3.500A) Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 197 through 207 removed outlier: 3.532A pdb=" N SER A 207 " --> pdb=" O SER A 203 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 215 removed outlier: 3.845A pdb=" N ILE A 214 " --> pdb=" O VAL A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 225 Processing helix chain 'A' and resid 226 through 231 removed outlier: 3.940A pdb=" N LEU A 230 " --> pdb=" O ALA A 226 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASP A 231 " --> pdb=" O LYS A 227 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 226 through 231' Processing helix chain 'A' and resid 236 through 246 Processing helix chain 'A' and resid 255 through 259 Processing helix chain 'A' and resid 270 through 278 Processing helix chain 'A' and resid 286 through 296 removed outlier: 3.825A pdb=" N ILE A 291 " --> pdb=" O PHE A 287 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N GLU A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 315 removed outlier: 3.932A pdb=" N LYS A 306 " --> pdb=" O ASP A 302 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N TYR A 314 " --> pdb=" O ALA A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 336 removed outlier: 4.501A pdb=" N LEU A 331 " --> pdb=" O LEU A 327 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N MET A 334 " --> pdb=" O VAL A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 356 removed outlier: 3.858A pdb=" N LEU A 344 " --> pdb=" O LYS A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 373 Processing helix chain 'A' and resid 377 through 381 removed outlier: 3.888A pdb=" N MET A 381 " --> pdb=" O HIS A 378 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 394 removed outlier: 3.858A pdb=" N ALA A 394 " --> pdb=" O GLU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 408 removed outlier: 4.477A pdb=" N THR A 406 " --> pdb=" O MET A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 409 through 421 removed outlier: 3.984A pdb=" N PHE A 413 " --> pdb=" O TRP A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 435 Processing helix chain 'A' and resid 436 through 445 removed outlier: 3.930A pdb=" N VAL A 440 " --> pdb=" O TRP A 436 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASN A 441 " --> pdb=" O ILE A 437 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N SER A 442 " --> pdb=" O GLY A 438 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N GLY A 443 " --> pdb=" O TYR A 439 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN A 445 " --> pdb=" O ASN A 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 451 removed outlier: 3.812A pdb=" N CYS A 450 " --> pdb=" O LEU A 447 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ARG A 451 " --> pdb=" O ILE A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 461 removed outlier: 3.659A pdb=" N ALA A 458 " --> pdb=" O ASP A 454 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 50 Processing helix chain 'B' and resid 56 through 73 removed outlier: 4.315A pdb=" N GLN B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.905A pdb=" N LYS B 99 " --> pdb=" O PHE B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 139 Processing helix chain 'B' and resid 153 through 159 Processing helix chain 'B' and resid 161 through 169 Processing helix chain 'B' and resid 170 through 182 removed outlier: 3.729A pdb=" N TYR B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 213 removed outlier: 4.025A pdb=" N LYS B 213 " --> pdb=" O ASP B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 230 removed outlier: 3.898A pdb=" N LEU B 230 " --> pdb=" O MET B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 271 Processing helix chain 'B' and resid 309 through 313 Processing helix chain 'B' and resid 347 through 369 Proline residue: B 354 - end of helix removed outlier: 4.360A pdb=" N GLU B 358 " --> pdb=" O PRO B 354 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN B 369 " --> pdb=" O VAL B 365 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 63 removed outlier: 3.512A pdb=" N GLU C 60 " --> pdb=" O ILE C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 64 through 66 No H-bonds generated for 'chain 'C' and resid 64 through 66' Processing sheet with id=AA1, first strand: chain 'A' and resid 253 through 254 Processing sheet with id=AA2, first strand: chain 'B' and resid 85 through 86 removed outlier: 6.528A pdb=" N THR B 85 " --> pdb=" O LEU B 113 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 189 through 190 removed outlier: 4.030A pdb=" N MET B 190 " --> pdb=" O PHE B 194 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N LEU B 195 " --> pdb=" O LEU B 277 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE B 276 " --> pdb=" O ILE B 302 " (cutoff:3.500A) removed outlier: 8.130A pdb=" N ILE B 304 " --> pdb=" O ILE B 276 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N ARG B 278 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR B 303 " --> pdb=" O ARG B 288 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG B 288 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 319 through 324 removed outlier: 3.687A pdb=" N ASN B 329 " --> pdb=" O LYS B 322 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 2 through 3 removed outlier: 3.630A pdb=" N THR C 75 " --> pdb=" O GLN C 3 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 46 through 49 removed outlier: 3.827A pdb=" N PHE C 48 " --> pdb=" O CYS C 22 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N CYS C 22 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 7.688A pdb=" N THR C 21 " --> pdb=" O LEU C 106 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N LEU C 106 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N VAL C 23 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS C 25 " --> pdb=" O GLU C 102 " (cutoff:3.500A) 259 hydrogen bonds defined for protein. 738 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: 1.60 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1093 1.30 - 1.43: 1763 1.43 - 1.56: 3871 1.56 - 1.69: 2 1.69 - 1.81: 60 Bond restraints: 6789 Sorted by residual: bond pdb=" C THR A 164 " pdb=" O THR A 164 " ideal model delta sigma weight residual 1.236 1.338 -0.102 1.15e-02 7.56e+03 7.81e+01 bond pdb=" C TYR A 209 " pdb=" O TYR A 209 " ideal model delta sigma weight residual 1.236 1.338 -0.102 1.15e-02 7.56e+03 7.81e+01 bond pdb=" C VAL A 160 " pdb=" O VAL A 160 " ideal model delta sigma weight residual 1.237 1.323 -0.086 1.17e-02 7.31e+03 5.40e+01 bond pdb=" C SER A 161 " pdb=" O SER A 161 " ideal model delta sigma weight residual 1.237 1.312 -0.075 1.17e-02 7.31e+03 4.11e+01 bond pdb=" C VAL A 126 " pdb=" O VAL A 126 " ideal model delta sigma weight residual 1.237 1.301 -0.065 1.14e-02 7.69e+03 3.20e+01 ... (remaining 6784 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.46: 9002 4.46 - 8.92: 188 8.92 - 13.38: 30 13.38 - 17.85: 4 17.85 - 22.31: 1 Bond angle restraints: 9225 Sorted by residual: angle pdb=" N VAL A 206 " pdb=" CA VAL A 206 " pdb=" C VAL A 206 " ideal model delta sigma weight residual 111.45 133.76 -22.31 9.30e-01 1.16e+00 5.75e+02 angle pdb=" C VAL A 206 " pdb=" CA VAL A 206 " pdb=" CB VAL A 206 " ideal model delta sigma weight residual 111.92 96.50 15.42 1.31e+00 5.83e-01 1.39e+02 angle pdb=" N PHE A 208 " pdb=" CA PHE A 208 " pdb=" C PHE A 208 " ideal model delta sigma weight residual 112.68 97.55 15.13 1.33e+00 5.65e-01 1.29e+02 angle pdb=" C VAL A 213 " pdb=" N ILE A 214 " pdb=" CA ILE A 214 " ideal model delta sigma weight residual 120.56 133.54 -12.98 1.26e+00 6.30e-01 1.06e+02 angle pdb=" N LYS A 60 " pdb=" CA LYS A 60 " pdb=" C LYS A 60 " ideal model delta sigma weight residual 111.28 121.88 -10.60 1.09e+00 8.42e-01 9.45e+01 ... (remaining 9220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 3601 17.64 - 35.28: 330 35.28 - 52.92: 87 52.92 - 70.56: 13 70.56 - 88.20: 6 Dihedral angle restraints: 4037 sinusoidal: 1505 harmonic: 2532 Sorted by residual: dihedral pdb=" CB CYS A 106 " pdb=" SG CYS A 106 " pdb=" SG CYS A 191 " pdb=" CB CYS A 191 " ideal model delta sinusoidal sigma weight residual 93.00 169.43 -76.43 1 1.00e+01 1.00e-02 7.35e+01 dihedral pdb=" C VAL A 114 " pdb=" N VAL A 114 " pdb=" CA VAL A 114 " pdb=" CB VAL A 114 " ideal model delta harmonic sigma weight residual -122.00 -142.76 20.76 0 2.50e+00 1.60e-01 6.89e+01 dihedral pdb=" N VAL A 114 " pdb=" C VAL A 114 " pdb=" CA VAL A 114 " pdb=" CB VAL A 114 " ideal model delta harmonic sigma weight residual 123.40 141.76 -18.36 0 2.50e+00 1.60e-01 5.39e+01 ... (remaining 4034 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.155: 960 0.155 - 0.311: 65 0.311 - 0.466: 21 0.466 - 0.622: 7 0.622 - 0.777: 4 Chirality restraints: 1057 Sorted by residual: chirality pdb=" CA PRO A 211 " pdb=" N PRO A 211 " pdb=" C PRO A 211 " pdb=" CB PRO A 211 " both_signs ideal model delta sigma weight residual False 2.72 1.94 0.78 2.00e-01 2.50e+01 1.51e+01 chirality pdb=" CA VAL A 114 " pdb=" N VAL A 114 " pdb=" C VAL A 114 " pdb=" CB VAL A 114 " both_signs ideal model delta sigma weight residual False 2.44 1.71 0.73 2.00e-01 2.50e+01 1.34e+01 chirality pdb=" CA ALA A 128 " pdb=" N ALA A 128 " pdb=" C ALA A 128 " pdb=" CB ALA A 128 " both_signs ideal model delta sigma weight residual False 2.48 1.76 0.72 2.00e-01 2.50e+01 1.30e+01 ... (remaining 1054 not shown) Planarity restraints: 1184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 148 " 0.038 2.00e-02 2.50e+03 7.14e-02 5.10e+01 pdb=" C ASN A 148 " -0.124 2.00e-02 2.50e+03 pdb=" O ASN A 148 " 0.044 2.00e-02 2.50e+03 pdb=" N LYS A 149 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 157 " 0.033 2.00e-02 2.50e+03 6.43e-02 4.13e+01 pdb=" C VAL A 157 " -0.111 2.00e-02 2.50e+03 pdb=" O VAL A 157 " 0.040 2.00e-02 2.50e+03 pdb=" N TRP A 158 " 0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 205 " 0.032 2.00e-02 2.50e+03 6.41e-02 4.11e+01 pdb=" C ILE A 205 " -0.111 2.00e-02 2.50e+03 pdb=" O ILE A 205 " 0.042 2.00e-02 2.50e+03 pdb=" N VAL A 206 " 0.037 2.00e-02 2.50e+03 ... (remaining 1181 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.66: 194 2.66 - 3.22: 6325 3.22 - 3.78: 9254 3.78 - 4.34: 12079 4.34 - 4.90: 18996 Nonbonded interactions: 46848 Sorted by model distance: nonbonded pdb=" O10 FK5 C 201 " pdb=" O9 FK5 C 201 " model vdw 2.106 3.040 nonbonded pdb=" OH TYR C 82 " pdb=" O3 FK5 C 201 " model vdw 2.214 3.040 nonbonded pdb=" OD1 ASP C 37 " pdb=" N SER C 38 " model vdw 2.259 3.120 nonbonded pdb=" O ASP C 11 " pdb=" NE2 GLN C 70 " model vdw 2.269 3.120 nonbonded pdb=" NH2 ARG A 272 " pdb=" O ARG A 312 " model vdw 2.315 3.120 ... (remaining 46843 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.240 Find NCS groups from input model: 0.090 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:4.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6366 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 : 0.009 0.102 6789 Z= 0.595 Angle : 1.526 22.306 9225 Z= 1.095 Chirality : 0.111 0.777 1057 Planarity : 0.009 0.142 1184 Dihedral : 15.276 88.197 2398 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 11.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 4.86 % Allowed : 3.95 % Favored : 91.20 % Cbeta Deviations : 4.03 % 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: -1.78 (0.29), residues: 861 helix: -0.41 (0.27), residues: 374 sheet: -3.30 (0.66), residues: 42 loop : -1.63 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.005 TRP A 109 HIS 0.011 0.001 HIS B 280 PHE 0.029 0.002 PHE B 181 TYR 0.033 0.002 TYR A 132 ARG 0.002 0.000 ARG B 331 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.759 Fit side-chains revert: symmetry clash REVERT: A 74 SER cc_start: 0.6572 (OUTLIER) cc_final: 0.6331 (t) REVERT: A 360 ASP cc_start: 0.6098 (p0) cc_final: 0.5089 (t0) REVERT: A 402 MET cc_start: 0.6873 (mtt) cc_final: 0.6662 (mtm) outliers start: 32 outliers final: 12 residues processed: 175 average time/residue: 0.1679 time to fit residues: 39.5888 Evaluate side-chains 106 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 74 SER Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 126 VAL Chi-restraints excluded: chain A residue 129 VAL Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 165 SER Chi-restraints excluded: chain A residue 211 PRO Chi-restraints excluded: chain A residue 404 THR Chi-restraints excluded: chain A residue 448 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 0.5980 chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 0.0010 chunk 34 optimal weight: 0.4980 chunk 67 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 40 optimal weight: 0.8980 chunk 50 optimal weight: 0.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 249 ASN A 337 ASN A 392 HIS ** A 445 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 271 ASN B 309 ASN B 326 ASN C 25 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.217245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.208332 restraints weight = 8787.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.208021 restraints weight = 15213.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.207703 restraints weight = 14125.334| |-----------------------------------------------------------------------------| r_work (final): 0.4445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6789 Z= 0.214 Angle : 0.684 12.049 9225 Z= 0.342 Chirality : 0.043 0.150 1057 Planarity : 0.004 0.034 1184 Dihedral : 7.028 57.769 993 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.88 % Allowed : 16.84 % Favored : 80.27 % 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: -1.54 (0.28), residues: 861 helix: -0.10 (0.26), residues: 404 sheet: -3.30 (0.58), residues: 61 loop : -1.57 (0.30), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 133 HIS 0.006 0.001 HIS A 93 PHE 0.019 0.001 PHE B 181 TYR 0.012 0.001 TYR B 340 ARG 0.002 0.000 ARG A 131 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.730 Fit side-chains revert: symmetry clash REVERT: A 360 ASP cc_start: 0.6539 (p0) cc_final: 0.5576 (t0) REVERT: B 346 MET cc_start: 0.7990 (mmt) cc_final: 0.7282 (mtt) REVERT: C 29 MET cc_start: 0.7717 (ttm) cc_final: 0.7436 (ttm) outliers start: 19 outliers final: 14 residues processed: 117 average time/residue: 0.1449 time to fit residues: 24.1790 Evaluate side-chains 99 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 124 LEU Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 85 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 61 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 70 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 56 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 3 optimal weight: 0.9990 chunk 83 optimal weight: 0.4980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4497 r_free = 0.4497 target = 0.212609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.203243 restraints weight = 8829.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.192456 restraints weight = 16621.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4157 r_free = 0.4157 target = 0.186158 restraints weight = 14574.759| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.4943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6789 Z= 0.265 Angle : 0.693 11.928 9225 Z= 0.350 Chirality : 0.044 0.147 1057 Planarity : 0.004 0.057 1184 Dihedral : 6.927 59.445 981 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.49 % Allowed : 18.51 % Favored : 78.00 % 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 (0.29), residues: 861 helix: 0.31 (0.27), residues: 401 sheet: -3.49 (0.59), residues: 63 loop : -1.55 (0.31), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 133 HIS 0.004 0.001 HIS A 93 PHE 0.017 0.002 PHE B 181 TYR 0.017 0.001 TYR B 323 ARG 0.008 0.001 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 97 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.7801 (ttt) cc_final: 0.7439 (ttp) REVERT: A 242 PHE cc_start: 0.7229 (t80) cc_final: 0.6990 (t80) REVERT: A 360 ASP cc_start: 0.7129 (p0) cc_final: 0.6193 (t0) REVERT: B 98 MET cc_start: 0.8374 (mmp) cc_final: 0.7952 (mmp) REVERT: B 346 MET cc_start: 0.8398 (mmt) cc_final: 0.8128 (mtt) outliers start: 23 outliers final: 13 residues processed: 111 average time/residue: 0.1540 time to fit residues: 23.9298 Evaluate side-chains 98 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 86 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 66 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 59 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 63 optimal weight: 0.0870 chunk 62 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 1 optimal weight: 6.9990 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 58 optimal weight: 0.5980 overall best weight: 0.7162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 HIS C 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4502 r_free = 0.4502 target = 0.212991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.204569 restraints weight = 8950.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.202820 restraints weight = 12781.458| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.200232 restraints weight = 13745.579| |-----------------------------------------------------------------------------| r_work (final): 0.4356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.5656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6789 Z= 0.221 Angle : 0.639 11.914 9225 Z= 0.316 Chirality : 0.042 0.140 1057 Planarity : 0.004 0.043 1184 Dihedral : 6.583 57.669 978 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.49 % Allowed : 20.33 % Favored : 76.18 % 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: -1.02 (0.29), residues: 861 helix: 0.45 (0.27), residues: 405 sheet: -3.06 (0.74), residues: 42 loop : -1.56 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 133 HIS 0.003 0.001 HIS B 48 PHE 0.023 0.001 PHE A 193 TYR 0.013 0.001 TYR B 174 ARG 0.002 0.000 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 87 time to evaluate : 0.736 Fit side-chains revert: symmetry clash REVERT: A 215 MET cc_start: 0.8310 (tmm) cc_final: 0.7735 (tmm) REVERT: A 360 ASP cc_start: 0.6884 (p0) cc_final: 0.5998 (t0) outliers start: 23 outliers final: 16 residues processed: 107 average time/residue: 0.1599 time to fit residues: 24.0392 Evaluate side-chains 96 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 136 THR Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain B residue 312 ASP Chi-restraints excluded: chain B residue 331 ARG Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 101 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 57 optimal weight: 0.5980 chunk 76 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 64 optimal weight: 3.9990 chunk 79 optimal weight: 0.5980 chunk 3 optimal weight: 0.1980 chunk 10 optimal weight: 9.9990 chunk 31 optimal weight: 0.0070 chunk 20 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 392 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.215190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.206126 restraints weight = 8838.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.198936 restraints weight = 14640.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.194529 restraints weight = 16440.040| |-----------------------------------------------------------------------------| r_work (final): 0.4316 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.6009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6789 Z= 0.164 Angle : 0.603 11.750 9225 Z= 0.294 Chirality : 0.040 0.132 1057 Planarity : 0.003 0.037 1184 Dihedral : 6.234 55.545 978 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.19 % Allowed : 22.46 % Favored : 74.36 % 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: -0.81 (0.30), residues: 861 helix: 0.62 (0.27), residues: 405 sheet: -2.68 (0.75), residues: 40 loop : -1.49 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 133 HIS 0.004 0.001 HIS B 280 PHE 0.015 0.001 PHE A 242 TYR 0.014 0.001 TYR B 174 ARG 0.001 0.000 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 89 time to evaluate : 0.682 Fit side-chains REVERT: A 215 MET cc_start: 0.8330 (tmm) cc_final: 0.7793 (tmm) REVERT: A 360 ASP cc_start: 0.7018 (p0) cc_final: 0.6154 (t0) REVERT: B 102 GLU cc_start: 0.7848 (tm-30) cc_final: 0.7577 (tm-30) outliers start: 21 outliers final: 13 residues processed: 104 average time/residue: 0.1466 time to fit residues: 21.6659 Evaluate side-chains 94 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 103 VAL Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain C residue 101 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 20 optimal weight: 0.7980 chunk 68 optimal weight: 6.9990 chunk 21 optimal weight: 0.6980 chunk 57 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 67 optimal weight: 0.5980 chunk 84 optimal weight: 0.0060 chunk 23 optimal weight: 0.8980 chunk 60 optimal weight: 0.0270 chunk 83 optimal weight: 0.0870 chunk 30 optimal weight: 0.5980 overall best weight: 0.2632 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.213734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.205399 restraints weight = 8450.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.202603 restraints weight = 12991.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4415 r_free = 0.4415 target = 0.198763 restraints weight = 14305.736| |-----------------------------------------------------------------------------| r_work (final): 0.4436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.6221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6789 Z= 0.143 Angle : 0.600 14.804 9225 Z= 0.284 Chirality : 0.040 0.122 1057 Planarity : 0.003 0.030 1184 Dihedral : 5.960 57.912 976 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 3.79 % Allowed : 22.00 % Favored : 74.20 % 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: -0.66 (0.30), residues: 861 helix: 0.70 (0.27), residues: 409 sheet: -2.59 (0.76), residues: 40 loop : -1.39 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 133 HIS 0.003 0.000 HIS B 280 PHE 0.012 0.001 PHE A 242 TYR 0.013 0.001 TYR B 131 ARG 0.002 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 86 time to evaluate : 0.751 Fit side-chains REVERT: A 215 MET cc_start: 0.8327 (tmm) cc_final: 0.7879 (tmm) REVERT: A 360 ASP cc_start: 0.6939 (p0) cc_final: 0.6214 (t0) REVERT: B 98 MET cc_start: 0.8031 (mmp) cc_final: 0.7446 (mmm) REVERT: B 246 HIS cc_start: 0.6063 (OUTLIER) cc_final: 0.5338 (t-90) REVERT: B 259 TYR cc_start: 0.7994 (p90) cc_final: 0.7672 (p90) outliers start: 25 outliers final: 17 residues processed: 105 average time/residue: 0.1572 time to fit residues: 23.2068 Evaluate side-chains 100 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 82 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 101 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 75 optimal weight: 0.5980 chunk 68 optimal weight: 5.9990 chunk 24 optimal weight: 0.5980 chunk 31 optimal weight: 0.0170 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 39 optimal weight: 0.2980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 ASN B 366 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.207509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.192217 restraints weight = 8593.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.189798 restraints weight = 18476.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.190525 restraints weight = 18207.123| |-----------------------------------------------------------------------------| r_work (final): 0.4347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7198 moved from start: 0.6485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6789 Z= 0.181 Angle : 0.615 12.580 9225 Z= 0.297 Chirality : 0.041 0.279 1057 Planarity : 0.003 0.027 1184 Dihedral : 6.067 56.923 976 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 5.01 % Allowed : 22.15 % Favored : 72.84 % 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: -0.63 (0.30), residues: 861 helix: 0.82 (0.28), residues: 401 sheet: -2.67 (0.79), residues: 40 loop : -1.42 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 133 HIS 0.004 0.001 HIS B 280 PHE 0.011 0.001 PHE A 217 TYR 0.011 0.001 TYR B 174 ARG 0.001 0.000 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 83 time to evaluate : 0.778 Fit side-chains REVERT: A 215 MET cc_start: 0.8429 (tmm) cc_final: 0.8213 (tmm) REVERT: A 360 ASP cc_start: 0.6962 (p0) cc_final: 0.6194 (t0) REVERT: B 98 MET cc_start: 0.7875 (mmp) cc_final: 0.7282 (mmm) REVERT: B 246 HIS cc_start: 0.6095 (OUTLIER) cc_final: 0.5408 (t-90) outliers start: 33 outliers final: 19 residues processed: 110 average time/residue: 0.1512 time to fit residues: 23.7326 Evaluate side-chains 98 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 78 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 101 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 76 optimal weight: 0.2980 chunk 51 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 48 optimal weight: 0.0980 chunk 57 optimal weight: 0.5980 chunk 28 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.207873 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.195348 restraints weight = 8612.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.193863 restraints weight = 13621.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.192828 restraints weight = 14072.094| |-----------------------------------------------------------------------------| r_work (final): 0.4365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.6702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6789 Z= 0.170 Angle : 0.621 11.711 9225 Z= 0.298 Chirality : 0.041 0.256 1057 Planarity : 0.003 0.037 1184 Dihedral : 6.065 57.578 976 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.79 % Allowed : 23.52 % Favored : 72.69 % 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: -0.57 (0.30), residues: 861 helix: 0.93 (0.28), residues: 400 sheet: -2.91 (0.77), residues: 40 loop : -1.43 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 133 HIS 0.004 0.001 HIS B 280 PHE 0.015 0.001 PHE A 287 TYR 0.016 0.001 TYR B 323 ARG 0.001 0.000 ARG A 308 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 75 time to evaluate : 0.843 Fit side-chains revert: symmetry clash REVERT: A 360 ASP cc_start: 0.6928 (p0) cc_final: 0.6131 (t0) REVERT: B 98 MET cc_start: 0.7916 (mmp) cc_final: 0.7576 (mmm) REVERT: B 246 HIS cc_start: 0.6129 (OUTLIER) cc_final: 0.5461 (t-90) REVERT: B 346 MET cc_start: 0.8631 (mtt) cc_final: 0.8378 (mtt) outliers start: 25 outliers final: 21 residues processed: 95 average time/residue: 0.1499 time to fit residues: 20.8018 Evaluate side-chains 98 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 289 GLU Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 101 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 65 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 48 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 47 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 83 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.204668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.192923 restraints weight = 8657.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.191584 restraints weight = 12980.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.190369 restraints weight = 13710.957| |-----------------------------------------------------------------------------| r_work (final): 0.4343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.6965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6789 Z= 0.227 Angle : 0.666 11.771 9225 Z= 0.324 Chirality : 0.042 0.247 1057 Planarity : 0.004 0.033 1184 Dihedral : 6.307 59.566 976 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 4.40 % Allowed : 23.67 % Favored : 71.93 % 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: -0.59 (0.30), residues: 861 helix: 0.93 (0.28), residues: 395 sheet: -2.94 (0.76), residues: 40 loop : -1.42 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 133 HIS 0.006 0.001 HIS B 280 PHE 0.018 0.001 PHE A 287 TYR 0.014 0.001 TYR B 323 ARG 0.005 0.000 ARG B 172 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 360 ASP cc_start: 0.6931 (p0) cc_final: 0.6077 (t0) REVERT: B 246 HIS cc_start: 0.6105 (OUTLIER) cc_final: 0.5376 (t-90) outliers start: 29 outliers final: 21 residues processed: 99 average time/residue: 0.1402 time to fit residues: 20.4839 Evaluate side-chains 93 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 71 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 365 VAL Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 100 ASP Chi-restraints excluded: chain C residue 101 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 40 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 28 optimal weight: 0.6980 chunk 2 optimal weight: 0.0670 chunk 32 optimal weight: 0.0000 chunk 63 optimal weight: 0.4980 chunk 11 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 overall best weight: 0.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4565 r_free = 0.4565 target = 0.213244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.202611 restraints weight = 8624.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.200993 restraints weight = 15724.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.199079 restraints weight = 14099.678| |-----------------------------------------------------------------------------| r_work (final): 0.4436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.7082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 6789 Z= 0.156 Angle : 0.619 11.676 9225 Z= 0.295 Chirality : 0.041 0.234 1057 Planarity : 0.003 0.030 1184 Dihedral : 6.011 59.594 976 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.49 % Allowed : 24.43 % Favored : 72.08 % 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: -0.48 (0.30), residues: 861 helix: 1.01 (0.28), residues: 401 sheet: -2.77 (0.76), residues: 40 loop : -1.41 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 133 HIS 0.005 0.001 HIS B 280 PHE 0.013 0.001 PHE A 193 TYR 0.013 0.001 TYR B 323 ARG 0.002 0.000 ARG B 172 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 77 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: A 360 ASP cc_start: 0.6988 (p0) cc_final: 0.6175 (t0) REVERT: B 98 MET cc_start: 0.7826 (mmp) cc_final: 0.7618 (mmm) REVERT: B 246 HIS cc_start: 0.6102 (OUTLIER) cc_final: 0.5464 (t-90) REVERT: B 367 VAL cc_start: 0.7998 (OUTLIER) cc_final: 0.7753 (p) outliers start: 23 outliers final: 18 residues processed: 94 average time/residue: 0.1387 time to fit residues: 18.9636 Evaluate side-chains 93 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 120 SER Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 154 ILE Chi-restraints excluded: chain A residue 169 ILE Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 258 PHE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain A residue 419 HIS Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 101 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 0.0980 chunk 41 optimal weight: 0.0670 chunk 3 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 81 optimal weight: 0.0000 chunk 38 optimal weight: 0.5980 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 overall best weight: 0.2722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 315 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4554 r_free = 0.4554 target = 0.218795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.210242 restraints weight = 8756.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.206417 restraints weight = 12240.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.202300 restraints weight = 14693.836| |-----------------------------------------------------------------------------| r_work (final): 0.4403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.7264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 6789 Z= 0.159 Angle : 0.633 11.745 9225 Z= 0.302 Chirality : 0.041 0.232 1057 Planarity : 0.003 0.032 1184 Dihedral : 5.864 57.140 976 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 3.03 % Allowed : 24.89 % Favored : 72.08 % 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: -0.38 (0.30), residues: 861 helix: 1.10 (0.28), residues: 401 sheet: -2.62 (0.78), residues: 40 loop : -1.37 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 133 HIS 0.004 0.001 HIS B 280 PHE 0.015 0.001 PHE B 181 TYR 0.016 0.001 TYR B 323 ARG 0.002 0.000 ARG B 172 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2131.85 seconds wall clock time: 37 minutes 51.45 seconds (2271.45 seconds total)