Starting phenix.real_space_refine on Tue Feb 11 20:40:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9chv_45603/02_2025/9chv_45603.cif Found real_map, /net/cci-nas-00/data/ceres_data/9chv_45603/02_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_45603/02_2025/9chv_45603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9chv_45603/02_2025/9chv_45603.map" model { file = "/net/cci-nas-00/data/ceres_data/9chv_45603/02_2025/9chv_45603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9chv_45603/02_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-5592/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: 5.14, per 1000 atoms: 0.77 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: 1.65 Conformation dependent library (CDL) restraints added in 944.5 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: 0.63 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: 1.90 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: 3.960 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 18.910 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.950 ------------------------------------------------------------------------------- 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 : 0.677 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: 0.1703 time to fit residues: 39.9932 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 : 0.858 ------------------------------------------------------------------------------- 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 = 0.217244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.208338 restraints weight = 8787.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.207995 restraints weight = 15179.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.207550 restraints weight = 14130.805| |-----------------------------------------------------------------------------| r_work (final): 0.4443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6730 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 : 0.746 Fit side-chains revert: symmetry clash REVERT: A 360 ASP cc_start: 0.6539 (p0) cc_final: 0.5578 (t0) REVERT: B 346 MET cc_start: 0.7991 (mmt) cc_final: 0.7283 (mtt) REVERT: C 29 MET cc_start: 0.7716 (ttm) cc_final: 0.7434 (ttm) outliers start: 19 outliers final: 14 residues processed: 117 average time/residue: 0.1523 time to fit residues: 25.2004 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 : 0.685 ------------------------------------------------------------------------------- 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: 1.9990 chunk 70 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 40 optimal weight: 5.9990 chunk 45 optimal weight: 0.8980 chunk 56 optimal weight: 0.4980 chunk 82 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 83 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4498 r_free = 0.4498 target = 0.212617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.203361 restraints weight = 8823.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.192414 restraints weight = 14883.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.186676 restraints weight = 13019.171| |-----------------------------------------------------------------------------| r_work (final): 0.4194 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.5186 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= 0.267 Angle : 0.700 11.887 9225 Z= 0.353 Chirality : 0.044 0.145 1057 Planarity : 0.004 0.064 1184 Dihedral : 6.943 59.098 981 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 3.34 % Allowed : 18.97 % Favored : 77.69 % 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: -1.22 (0.29), residues: 861 helix: 0.33 (0.27), residues: 402 sheet: -3.50 (0.58), residues: 63 loop : -1.52 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 133 HIS 0.004 0.001 HIS A 93 PHE 0.017 0.002 PHE B 181 TYR 0.018 0.001 TYR B 323 ARG 0.007 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 123 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.792 Fit side-chains revert: symmetry clash REVERT: A 242 PHE cc_start: 0.7289 (t80) cc_final: 0.7046 (t80) REVERT: A 360 ASP cc_start: 0.7158 (p0) cc_final: 0.6256 (t0) REVERT: B 98 MET cc_start: 0.8393 (mmp) cc_final: 0.8003 (mmp) REVERT: B 346 MET cc_start: 0.8455 (mmt) cc_final: 0.8179 (mtt) outliers start: 22 outliers final: 13 residues processed: 115 average time/residue: 0.1616 time to fit residues: 25.9496 Evaluate side-chains 97 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.765 ------------------------------------------------------------------------------- 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: 0.0570 chunk 6 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 chunk 63 optimal weight: 0.0770 chunk 62 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 overall best weight: 0.4856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.206883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.193912 restraints weight = 8715.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.192912 restraints weight = 16811.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.192932 restraints weight = 15703.625| |-----------------------------------------------------------------------------| r_work (final): 0.4369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7123 moved from start: 0.5617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6789 Z= 0.176 Angle : 0.612 11.815 9225 Z= 0.301 Chirality : 0.041 0.140 1057 Planarity : 0.003 0.042 1184 Dihedral : 6.446 58.790 978 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.19 % Allowed : 21.55 % Favored : 75.27 % 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: -0.93 (0.29), residues: 861 helix: 0.48 (0.27), residues: 408 sheet: -2.83 (0.75), residues: 42 loop : -1.51 (0.31), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 133 HIS 0.003 0.001 HIS B 48 PHE 0.014 0.001 PHE A 193 TYR 0.013 0.001 TYR B 174 ARG 0.001 0.000 ARG B 27 *********************** 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 111 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.725 Fit side-chains revert: symmetry clash REVERT: A 215 MET cc_start: 0.8229 (tmm) cc_final: 0.7766 (tmm) REVERT: A 242 PHE cc_start: 0.6928 (t80) cc_final: 0.6676 (t80) REVERT: A 360 ASP cc_start: 0.6899 (p0) cc_final: 0.6071 (t0) outliers start: 21 outliers final: 11 residues processed: 103 average time/residue: 0.1498 time to fit residues: 21.9686 Evaluate side-chains 94 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 154 ILE Chi-restraints excluded: chain A residue 223 PHE Chi-restraints excluded: chain A residue 254 SER 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 28 LEU 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: 0.6980 chunk 76 optimal weight: 3.9990 chunk 56 optimal weight: 0.2980 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 3 optimal weight: 0.2980 chunk 10 optimal weight: 10.0000 chunk 31 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 71 optimal weight: 0.0570 chunk 55 optimal weight: 0.2980 overall best weight: 0.2898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.218067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.206606 restraints weight = 8853.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.202112 restraints weight = 16021.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.200037 restraints weight = 16651.012| |-----------------------------------------------------------------------------| r_work (final): 0.4373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7134 moved from start: 0.5913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6789 Z= 0.152 Angle : 0.609 13.965 9225 Z= 0.291 Chirality : 0.040 0.125 1057 Planarity : 0.003 0.033 1184 Dihedral : 6.074 59.888 976 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 3.19 % Allowed : 21.85 % Favored : 74.96 % 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: -0.74 (0.30), residues: 861 helix: 0.68 (0.27), residues: 408 sheet: -2.52 (0.71), residues: 50 loop : -1.45 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 133 HIS 0.002 0.000 HIS B 280 PHE 0.011 0.001 PHE B 181 TYR 0.013 0.001 TYR A 132 ARG 0.002 0.000 ARG A 272 *********************** 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 111 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 90 time to evaluate : 0.788 Fit side-chains REVERT: A 242 PHE cc_start: 0.7168 (t80) cc_final: 0.6917 (t80) REVERT: A 360 ASP cc_start: 0.7157 (p0) cc_final: 0.6304 (t0) outliers start: 21 outliers final: 14 residues processed: 106 average time/residue: 0.1647 time to fit residues: 24.8093 Evaluate side-chains 98 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 84 time to evaluate : 0.729 ------------------------------------------------------------------------------- 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 169 ILE Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 264 LEU 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 103 VAL Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 367 VAL 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: 0.8980 chunk 68 optimal weight: 5.9990 chunk 21 optimal weight: 0.5980 chunk 57 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 84 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 83 optimal weight: 0.1980 chunk 30 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.210659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.202649 restraints weight = 8431.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.198830 restraints weight = 12865.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.195176 restraints weight = 15343.355| |-----------------------------------------------------------------------------| r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 0.6212 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= 0.185 Angle : 0.620 11.982 9225 Z= 0.299 Chirality : 0.040 0.125 1057 Planarity : 0.003 0.031 1184 Dihedral : 6.158 59.963 976 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.70 % Allowed : 21.40 % Favored : 73.90 % 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: -0.71 (0.30), residues: 861 helix: 0.70 (0.27), residues: 407 sheet: -2.53 (0.73), residues: 50 loop : -1.42 (0.31), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 133 HIS 0.002 0.001 HIS A 93 PHE 0.013 0.001 PHE A 193 TYR 0.009 0.001 TYR B 174 ARG 0.003 0.000 ARG B 172 *********************** 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: 31 poor density : 80 time to evaluate : 0.720 Fit side-chains REVERT: A 215 MET cc_start: 0.8316 (tmm) cc_final: 0.8085 (tmm) REVERT: A 360 ASP cc_start: 0.7082 (p0) cc_final: 0.6101 (t0) REVERT: B 98 MET cc_start: 0.8271 (mmp) cc_final: 0.7863 (mmp) REVERT: B 246 HIS cc_start: 0.6038 (OUTLIER) cc_final: 0.5245 (t-90) outliers start: 31 outliers final: 18 residues processed: 109 average time/residue: 0.1447 time to fit residues: 22.5096 Evaluate side-chains 96 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 77 time to evaluate : 0.746 ------------------------------------------------------------------------------- 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 169 ILE Chi-restraints excluded: chain A residue 223 PHE 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 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 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: 0.7980 chunk 68 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 31 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 78 optimal weight: 2.9990 chunk 42 optimal weight: 0.0050 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 overall best weight: 0.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.214867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.205732 restraints weight = 8809.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.204354 restraints weight = 13779.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.203271 restraints weight = 15225.077| |-----------------------------------------------------------------------------| r_work (final): 0.4409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.6588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6789 Z= 0.202 Angle : 0.633 11.743 9225 Z= 0.306 Chirality : 0.040 0.130 1057 Planarity : 0.003 0.030 1184 Dihedral : 6.149 59.405 976 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.10 % Allowed : 23.07 % 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: -0.65 (0.30), residues: 861 helix: 0.76 (0.27), residues: 408 sheet: -2.66 (0.78), residues: 40 loop : -1.43 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 133 HIS 0.002 0.001 HIS B 280 PHE 0.013 0.001 PHE A 242 TYR 0.011 0.001 TYR B 174 ARG 0.003 0.000 ARG B 172 *********************** 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 107 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 80 time to evaluate : 0.778 Fit side-chains REVERT: A 360 ASP cc_start: 0.6996 (p0) cc_final: 0.6217 (t0) REVERT: B 98 MET cc_start: 0.8145 (mmp) cc_final: 0.7884 (mmp) REVERT: B 246 HIS cc_start: 0.6140 (OUTLIER) cc_final: 0.5351 (t-90) outliers start: 27 outliers final: 19 residues processed: 102 average time/residue: 0.1553 time to fit residues: 22.6566 Evaluate side-chains 94 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.735 ------------------------------------------------------------------------------- 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 103 VAL 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: 0.9980 chunk 21 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 chunk 51 optimal weight: 0.0870 chunk 39 optimal weight: 0.4980 chunk 58 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 28 optimal weight: 0.5980 chunk 64 optimal weight: 9.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.214512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.205563 restraints weight = 8848.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.203909 restraints weight = 13744.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.202107 restraints weight = 15403.488| |-----------------------------------------------------------------------------| r_work (final): 0.4389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.6768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6789 Z= 0.193 Angle : 0.630 11.726 9225 Z= 0.304 Chirality : 0.041 0.130 1057 Planarity : 0.003 0.037 1184 Dihedral : 6.112 59.263 976 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 3.95 % Allowed : 22.31 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.30), residues: 861 helix: 0.91 (0.28), residues: 400 sheet: -2.66 (0.77), residues: 40 loop : -1.43 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 133 HIS 0.002 0.001 HIS B 280 PHE 0.013 0.001 PHE A 193 TYR 0.007 0.001 TYR B 118 ARG 0.002 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 102 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 76 time to evaluate : 0.734 Fit side-chains REVERT: A 215 MET cc_start: 0.8315 (tmm) cc_final: 0.7904 (tmm) REVERT: A 242 PHE cc_start: 0.7044 (t80) cc_final: 0.6841 (t80) REVERT: A 360 ASP cc_start: 0.6932 (p0) cc_final: 0.6129 (t0) REVERT: A 375 LEU cc_start: 0.7978 (mp) cc_final: 0.7587 (mp) REVERT: B 98 MET cc_start: 0.8180 (mmp) cc_final: 0.7890 (mmp) REVERT: B 246 HIS cc_start: 0.6118 (OUTLIER) cc_final: 0.5323 (t-90) outliers start: 26 outliers final: 22 residues processed: 98 average time/residue: 0.1414 time to fit residues: 20.2803 Evaluate side-chains 95 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 72 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 103 VAL 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 65 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 79 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 1 optimal weight: 5.9990 chunk 47 optimal weight: 0.2980 chunk 74 optimal weight: 0.7980 chunk 43 optimal weight: 0.4980 chunk 83 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 72 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4483 r_free = 0.4483 target = 0.205239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.192467 restraints weight = 8674.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.191448 restraints weight = 13723.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.190936 restraints weight = 13583.065| |-----------------------------------------------------------------------------| r_work (final): 0.4348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.7029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6789 Z= 0.201 Angle : 0.649 11.708 9225 Z= 0.314 Chirality : 0.041 0.130 1057 Planarity : 0.003 0.033 1184 Dihedral : 6.095 59.573 976 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 4.10 % Allowed : 22.61 % Favored : 73.29 % 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: -0.62 (0.30), residues: 861 helix: 0.87 (0.28), residues: 405 sheet: -2.70 (0.75), residues: 40 loop : -1.49 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 133 HIS 0.003 0.001 HIS B 280 PHE 0.012 0.001 PHE A 242 TYR 0.015 0.001 TYR A 70 ARG 0.003 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 103 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 76 time to evaluate : 0.961 Fit side-chains REVERT: A 215 MET cc_start: 0.8335 (tmm) cc_final: 0.8062 (tmm) REVERT: A 360 ASP cc_start: 0.6919 (p0) cc_final: 0.6166 (t0) REVERT: A 375 LEU cc_start: 0.7974 (mp) cc_final: 0.7545 (mp) REVERT: B 98 MET cc_start: 0.8121 (mmp) cc_final: 0.7836 (mmp) REVERT: B 246 HIS cc_start: 0.6117 (OUTLIER) cc_final: 0.5349 (t-90) REVERT: B 328 MET cc_start: 0.8307 (tpt) cc_final: 0.7770 (tpt) outliers start: 27 outliers final: 23 residues processed: 98 average time/residue: 0.1491 time to fit residues: 21.0904 Evaluate side-chains 97 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 80 ILE Chi-restraints excluded: chain B residue 103 VAL 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: 3.9990 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 chunk 2 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 10.0000 chunk 11 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 ASN C 20 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.196629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.184422 restraints weight = 8763.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.183422 restraints weight = 13054.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4253 r_free = 0.4253 target = 0.182211 restraints weight = 12431.989| |-----------------------------------------------------------------------------| r_work (final): 0.4290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.7325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 6789 Z= 0.392 Angle : 0.780 12.421 9225 Z= 0.388 Chirality : 0.045 0.153 1057 Planarity : 0.004 0.038 1184 Dihedral : 6.779 56.279 976 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 3.64 % Allowed : 23.37 % Favored : 72.99 % 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: -0.98 (0.29), residues: 861 helix: 0.59 (0.27), residues: 402 sheet: -3.41 (0.80), residues: 35 loop : -1.64 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 231 HIS 0.005 0.001 HIS B 198 PHE 0.033 0.002 PHE A 287 TYR 0.013 0.001 TYR B 169 ARG 0.004 0.000 ARG A 308 ********************** 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 97 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 73 time to evaluate : 0.713 Fit side-chains REVERT: A 215 MET cc_start: 0.8616 (tmm) cc_final: 0.8364 (tmm) REVERT: A 360 ASP cc_start: 0.7013 (p0) cc_final: 0.6117 (t0) REVERT: B 98 MET cc_start: 0.8129 (mmp) cc_final: 0.7744 (mmp) REVERT: B 246 HIS cc_start: 0.6237 (OUTLIER) cc_final: 0.5402 (t-90) REVERT: B 346 MET cc_start: 0.8660 (mtt) cc_final: 0.8140 (mtt) outliers start: 24 outliers final: 19 residues processed: 96 average time/residue: 0.1582 time to fit residues: 21.4363 Evaluate side-chains 90 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 70 time to evaluate : 0.709 ------------------------------------------------------------------------------- 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 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 103 VAL 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 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 35 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 43 optimal weight: 0.2980 chunk 30 optimal weight: 0.5980 chunk 81 optimal weight: 0.1980 chunk 38 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4463 r_free = 0.4463 target = 0.203244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.190898 restraints weight = 8584.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.188468 restraints weight = 13002.468| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.185812 restraints weight = 13187.055| |-----------------------------------------------------------------------------| r_work (final): 0.4294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.7482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6789 Z= 0.207 Angle : 0.687 11.835 9225 Z= 0.333 Chirality : 0.041 0.151 1057 Planarity : 0.004 0.036 1184 Dihedral : 6.196 56.742 976 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.03 % Allowed : 25.19 % Favored : 71.78 % 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: -0.82 (0.30), residues: 861 helix: 0.70 (0.27), residues: 406 sheet: -2.72 (0.78), residues: 40 loop : -1.61 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 351 HIS 0.004 0.001 HIS B 280 PHE 0.014 0.001 PHE A 193 TYR 0.013 0.001 TYR A 70 ARG 0.002 0.000 ARG B 72 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2092.49 seconds wall clock time: 38 minutes 41.06 seconds (2321.06 seconds total)