Starting phenix.real_space_refine on Thu Jun 5 19:02:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9chv_45603/06_2025/9chv_45603.cif Found real_map, /net/cci-nas-00/data/ceres_data/9chv_45603/06_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_45603/06_2025/9chv_45603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9chv_45603/06_2025/9chv_45603.map" model { file = "/net/cci-nas-00/data/ceres_data/9chv_45603/06_2025/9chv_45603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9chv_45603/06_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-5710/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: 5.64, per 1000 atoms: 0.85 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: 1.83 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.56 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: 1.67 Time building geometry restraints manager: 2.16 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=" C9 FK5 C 201 " pdb=" O4 FK5 C 201 " ideal model delta sigma weight residual 1.206 1.408 -0.202 2.00e-02 2.50e+03 1.02e+02 bond pdb=" C1 FK5 C 201 " pdb=" O2 FK5 C 201 " ideal model delta sigma weight residual 1.211 1.408 -0.197 2.00e-02 2.50e+03 9.74e+01 bond pdb=" C22 FK5 C 201 " pdb=" O9 FK5 C 201 " ideal model delta sigma weight residual 1.215 1.409 -0.194 2.00e-02 2.50e+03 9.40e+01 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 ... (remaining 6784 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.46: 8991 4.46 - 8.92: 201 8.92 - 13.38: 28 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 - 35.82: 3972 35.82 - 71.65: 108 71.65 - 107.47: 10 107.47 - 143.30: 4 143.30 - 179.12: 4 Dihedral angle restraints: 4098 sinusoidal: 1566 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 4095 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.155: 957 0.155 - 0.311: 69 0.311 - 0.466: 21 0.466 - 0.622: 7 0.622 - 0.777: 4 Chirality restraints: 1058 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 1055 not shown) Planarity restraints: 1183 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C26 FK5 C 201 " 0.127 2.00e-02 2.50e+03 1.39e-01 2.41e+02 pdb=" C27 FK5 C 201 " -0.049 2.00e-02 2.50e+03 pdb=" C28 FK5 C 201 " -0.218 2.00e-02 2.50e+03 pdb=" C29 FK5 C 201 " 0.171 2.00e-02 2.50e+03 pdb=" C42 FK5 C 201 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C18 FK5 C 201 " 0.063 2.00e-02 2.50e+03 6.84e-02 5.85e+01 pdb=" C19 FK5 C 201 " -0.022 2.00e-02 2.50e+03 pdb=" C20 FK5 C 201 " -0.108 2.00e-02 2.50e+03 pdb=" C21 FK5 C 201 " 0.084 2.00e-02 2.50e+03 pdb=" C37 FK5 C 201 " -0.018 2.00e-02 2.50e+03 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 ... (remaining 1180 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.390 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.310 Find NCS groups from input model: 0.100 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: 0.000 Load rotamer database and sin/cos tables:3.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.290 ------------------------------------------------------------------------------- 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 : 0.011 0.202 6790 Z= 0.702 Angle : 1.544 22.306 9227 Z= 1.098 Chirality : 0.112 0.777 1058 Planarity : 0.010 0.142 1183 Dihedral : 18.200 179.122 2459 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 Details of bonding type rmsd hydrogen bonds : bond 0.19809 ( 259) hydrogen bonds : angle 8.19128 ( 738) SS BOND : bond 0.00635 ( 1) SS BOND : angle 0.94528 ( 2) covalent geometry : bond 0.01059 ( 6789) covalent geometry : angle 1.54406 ( 9225) *********************** 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 : 0.698 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: 0.1861 time to fit residues: 44.1167 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 : 0.721 ------------------------------------------------------------------------------- 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 = 0.4512 r_free = 0.4512 target = 0.209059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.196631 restraints weight = 8538.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.195540 restraints weight = 14410.861| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.195179 restraints weight = 14019.878| |-----------------------------------------------------------------------------| r_work (final): 0.4412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6788 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6790 Z= 0.147 Angle : 0.664 10.241 9227 Z= 0.339 Chirality : 0.044 0.159 1058 Planarity : 0.004 0.033 1183 Dihedral : 14.926 179.789 1054 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.88 % Allowed : 16.69 % Favored : 80.42 % 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: -1.59 (0.28), residues: 861 helix: -0.15 (0.26), residues: 405 sheet: -3.30 (0.58), residues: 61 loop : -1.59 (0.30), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 133 HIS 0.006 0.001 HIS B 280 PHE 0.020 0.001 PHE B 181 TYR 0.012 0.001 TYR B 340 ARG 0.004 0.000 ARG B 172 Details of bonding type rmsd hydrogen bonds : bond 0.03895 ( 259) hydrogen bonds : angle 4.75042 ( 738) SS BOND : bond 0.00214 ( 1) SS BOND : angle 2.56695 ( 2) covalent geometry : bond 0.00326 ( 6789) covalent geometry : angle 0.66269 ( 9225) *********************** 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 120 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 101 time to evaluate : 0.781 Fit side-chains revert: symmetry clash REVERT: B 289 MET cc_start: 0.6748 (mtt) cc_final: 0.6440 (mtt) REVERT: B 346 MET cc_start: 0.7983 (mmt) cc_final: 0.7320 (mtt) REVERT: C 29 MET cc_start: 0.7685 (ttm) cc_final: 0.7420 (ttm) outliers start: 19 outliers final: 13 residues processed: 115 average time/residue: 0.1523 time to fit residues: 24.9224 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 : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 25 HIS 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: 3.9990 chunk 41 optimal weight: 0.0980 chunk 70 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 82 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 3 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN A 445 ASN C 20 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4516 r_free = 0.4516 target = 0.215295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.206158 restraints weight = 8812.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.196153 restraints weight = 14387.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.189877 restraints weight = 12798.101| |-----------------------------------------------------------------------------| r_work (final): 0.4217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6790 Z= 0.151 Angle : 0.627 7.142 9227 Z= 0.322 Chirality : 0.042 0.150 1058 Planarity : 0.004 0.049 1183 Dihedral : 13.685 178.763 1040 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 2.73 % Allowed : 19.42 % Favored : 77.85 % 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: 0.27 (0.27), residues: 407 sheet: -3.16 (0.62), residues: 61 loop : -1.54 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 133 HIS 0.033 0.002 HIS C 25 PHE 0.015 0.001 PHE B 181 TYR 0.016 0.001 TYR B 323 ARG 0.005 0.000 ARG B 172 Details of bonding type rmsd hydrogen bonds : bond 0.04236 ( 259) hydrogen bonds : angle 4.30673 ( 738) SS BOND : bond 0.00177 ( 1) SS BOND : angle 1.49275 ( 2) covalent geometry : bond 0.00347 ( 6789) covalent geometry : angle 0.62705 ( 9225) *********************** 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: 18 poor density : 102 time to evaluate : 0.761 Fit side-chains revert: symmetry clash REVERT: A 242 PHE cc_start: 0.7087 (t80) cc_final: 0.6688 (t80) REVERT: A 360 ASP cc_start: 0.7087 (p0) cc_final: 0.6092 (t0) REVERT: B 178 MET cc_start: 0.8108 (mmt) cc_final: 0.7112 (mmm) REVERT: B 346 MET cc_start: 0.8340 (mmt) cc_final: 0.7919 (mtt) REVERT: C 29 MET cc_start: 0.7722 (ttm) cc_final: 0.7500 (ttm) outliers start: 18 outliers final: 13 residues processed: 113 average time/residue: 0.1538 time to fit residues: 24.8746 Evaluate side-chains 105 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 92 time to evaluate : 0.762 ------------------------------------------------------------------------------- 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 322 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 440 VAL Chi-restraints excluded: chain B residue 302 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 367 VAL Chi-restraints excluded: chain C residue 38 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 59 optimal weight: 0.1980 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 63 optimal weight: 0.0770 chunk 62 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.4523 r_free = 0.4523 target = 0.215438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.207164 restraints weight = 8900.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 72)----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.198961 restraints weight = 14724.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.193805 restraints weight = 17605.113| |-----------------------------------------------------------------------------| r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6790 Z= 0.134 Angle : 0.609 12.238 9227 Z= 0.305 Chirality : 0.042 0.139 1058 Planarity : 0.004 0.048 1183 Dihedral : 13.420 179.833 1037 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.95 % Allowed : 18.97 % Favored : 77.09 % 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: -1.05 (0.29), residues: 861 helix: 0.45 (0.27), residues: 410 sheet: -3.27 (0.60), residues: 63 loop : -1.45 (0.31), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 133 HIS 0.002 0.001 HIS B 48 PHE 0.019 0.001 PHE A 193 TYR 0.012 0.001 TYR B 323 ARG 0.002 0.000 ARG A 272 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 259) hydrogen bonds : angle 4.02477 ( 738) SS BOND : bond 0.00142 ( 1) SS BOND : angle 0.82899 ( 2) covalent geometry : bond 0.00305 ( 6789) covalent geometry : angle 0.60860 ( 9225) *********************** 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 119 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 93 time to evaluate : 0.806 Fit side-chains REVERT: A 242 PHE cc_start: 0.7207 (t80) cc_final: 0.6922 (t80) REVERT: A 360 ASP cc_start: 0.7113 (p0) cc_final: 0.6236 (t0) REVERT: B 98 MET cc_start: 0.8170 (mmm) cc_final: 0.7194 (mmm) REVERT: C 29 MET cc_start: 0.7784 (ttm) cc_final: 0.7580 (ttm) outliers start: 26 outliers final: 14 residues processed: 112 average time/residue: 0.1693 time to fit residues: 26.7021 Evaluate side-chains 100 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.791 ------------------------------------------------------------------------------- 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 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 280 HIS Chi-restraints excluded: chain B residue 367 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: 4.9990 chunk 56 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 chunk 3 optimal weight: 0.0170 chunk 10 optimal weight: 10.0000 chunk 31 optimal weight: 4.9990 chunk 20 optimal weight: 0.0070 chunk 71 optimal weight: 0.0570 chunk 55 optimal weight: 0.0470 overall best weight: 0.1452 ------------------------------------------------------------------------------- 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 = 0.4571 r_free = 0.4571 target = 0.221993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.213215 restraints weight = 8834.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.203756 restraints weight = 13641.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.197192 restraints weight = 12278.732| |-----------------------------------------------------------------------------| r_work (final): 0.4299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.5567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 6790 Z= 0.095 Angle : 0.547 11.155 9227 Z= 0.275 Chirality : 0.040 0.130 1058 Planarity : 0.003 0.040 1183 Dihedral : 13.149 179.978 1037 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.43 % Allowed : 20.94 % Favored : 76.63 % 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: -0.73 (0.30), residues: 861 helix: 0.70 (0.27), residues: 409 sheet: -2.48 (0.70), residues: 50 loop : -1.48 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 133 HIS 0.002 0.000 HIS B 198 PHE 0.011 0.001 PHE B 181 TYR 0.019 0.001 TYR B 323 ARG 0.002 0.000 ARG A 272 Details of bonding type rmsd hydrogen bonds : bond 0.02720 ( 259) hydrogen bonds : angle 3.77230 ( 738) SS BOND : bond 0.00046 ( 1) SS BOND : angle 0.36981 ( 2) covalent geometry : bond 0.00203 ( 6789) covalent geometry : angle 0.54659 ( 9225) *********************** 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 106 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.710 Fit side-chains REVERT: A 242 PHE cc_start: 0.7131 (t80) cc_final: 0.6800 (t80) REVERT: A 360 ASP cc_start: 0.7379 (p0) cc_final: 0.6457 (t0) REVERT: B 98 MET cc_start: 0.8139 (mmm) cc_final: 0.7431 (mmm) outliers start: 16 outliers final: 12 residues processed: 102 average time/residue: 0.1515 time to fit residues: 21.9860 Evaluate side-chains 93 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.793 ------------------------------------------------------------------------------- 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 264 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 342 LEU 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: 0.0270 chunk 68 optimal weight: 6.9990 chunk 21 optimal weight: 0.0000 chunk 57 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 60 optimal weight: 0.0060 chunk 83 optimal weight: 0.6980 chunk 30 optimal weight: 0.1980 overall best weight: 0.1858 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4585 r_free = 0.4585 target = 0.215547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.202900 restraints weight = 8447.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.200829 restraints weight = 15585.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.200181 restraints weight = 15712.126| |-----------------------------------------------------------------------------| r_work (final): 0.4483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.5780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 6790 Z= 0.092 Angle : 0.540 10.453 9227 Z= 0.267 Chirality : 0.039 0.126 1058 Planarity : 0.003 0.036 1183 Dihedral : 13.085 179.669 1037 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.03 % Allowed : 21.40 % Favored : 75.57 % 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: -0.55 (0.30), residues: 861 helix: 0.93 (0.28), residues: 402 sheet: -2.48 (0.70), residues: 50 loop : -1.42 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 133 HIS 0.002 0.000 HIS B 280 PHE 0.014 0.001 PHE A 193 TYR 0.017 0.001 TYR B 323 ARG 0.002 0.000 ARG A 131 Details of bonding type rmsd hydrogen bonds : bond 0.02626 ( 259) hydrogen bonds : angle 3.66610 ( 738) SS BOND : bond 0.00001 ( 1) SS BOND : angle 0.07320 ( 2) covalent geometry : bond 0.00197 ( 6789) covalent geometry : angle 0.54044 ( 9225) *********************** 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: 20 poor density : 91 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: A 242 PHE cc_start: 0.6953 (t80) cc_final: 0.6728 (t80) REVERT: A 245 LEU cc_start: 0.7833 (OUTLIER) cc_final: 0.7383 (tt) REVERT: A 360 ASP cc_start: 0.7247 (p0) cc_final: 0.6309 (t0) REVERT: B 246 HIS cc_start: 0.5974 (OUTLIER) cc_final: 0.5395 (t-90) outliers start: 20 outliers final: 14 residues processed: 107 average time/residue: 0.1608 time to fit residues: 24.4460 Evaluate side-chains 102 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 86 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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 245 LEU Chi-restraints excluded: chain A residue 254 SER Chi-restraints excluded: chain A residue 264 LEU 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 80 ILE Chi-restraints excluded: chain B residue 135 LEU Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 342 LEU 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: 0.8980 chunk 31 optimal weight: 0.0470 chunk 54 optimal weight: 0.6980 chunk 30 optimal weight: 0.5980 chunk 7 optimal weight: 0.6980 chunk 78 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 3.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- 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 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.216756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.207550 restraints weight = 8783.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.205758 restraints weight = 14520.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.204535 restraints weight = 16237.290| |-----------------------------------------------------------------------------| r_work (final): 0.4389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.6185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6790 Z= 0.125 Angle : 0.585 9.188 9227 Z= 0.294 Chirality : 0.042 0.283 1058 Planarity : 0.003 0.035 1183 Dihedral : 13.348 179.922 1037 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % 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: -0.54 (0.30), residues: 861 helix: 0.94 (0.28), residues: 402 sheet: -2.74 (0.70), residues: 50 loop : -1.38 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 133 HIS 0.002 0.000 HIS A 93 PHE 0.031 0.001 PHE A 387 TYR 0.014 0.001 TYR B 323 ARG 0.002 0.000 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.03611 ( 259) hydrogen bonds : angle 3.83612 ( 738) SS BOND : bond 0.00049 ( 1) SS BOND : angle 0.24352 ( 2) covalent geometry : bond 0.00290 ( 6789) covalent geometry : angle 0.58464 ( 9225) *********************** 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 110 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 84 time to evaluate : 0.808 Fit side-chains REVERT: A 360 ASP cc_start: 0.6837 (p0) cc_final: 0.5952 (t0) REVERT: B 98 MET cc_start: 0.8027 (mmp) cc_final: 0.7436 (mmm) REVERT: B 246 HIS cc_start: 0.6033 (OUTLIER) cc_final: 0.5396 (t-90) outliers start: 26 outliers final: 15 residues processed: 104 average time/residue: 0.1612 time to fit residues: 24.8091 Evaluate side-chains 97 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 81 time to evaluate : 0.769 ------------------------------------------------------------------------------- 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 80 ILE 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 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: 0.3980 chunk 76 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 39 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 12 optimal weight: 0.0980 chunk 48 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 64 optimal weight: 0.0370 overall best weight: 0.3458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 445 ASN ** B 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.219037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.211275 restraints weight = 8827.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.200436 restraints weight = 12953.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.194884 restraints weight = 14939.917| |-----------------------------------------------------------------------------| r_work (final): 0.4284 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.6441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 6790 Z= 0.106 Angle : 0.575 9.331 9227 Z= 0.285 Chirality : 0.041 0.256 1058 Planarity : 0.003 0.033 1183 Dihedral : 13.203 179.598 1037 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 3.49 % Allowed : 22.91 % Favored : 73.60 % 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: -0.42 (0.30), residues: 861 helix: 0.99 (0.28), residues: 404 sheet: -2.78 (0.75), residues: 40 loop : -1.30 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 133 HIS 0.002 0.000 HIS B 280 PHE 0.028 0.001 PHE A 387 TYR 0.011 0.001 TYR B 323 ARG 0.002 0.000 ARG B 172 Details of bonding type rmsd hydrogen bonds : bond 0.02932 ( 259) hydrogen bonds : angle 3.74783 ( 738) SS BOND : bond 0.00003 ( 1) SS BOND : angle 0.20518 ( 2) covalent geometry : bond 0.00243 ( 6789) covalent geometry : angle 0.57501 ( 9225) *********************** 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 107 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.616 Fit side-chains REVERT: A 360 ASP cc_start: 0.7135 (p0) cc_final: 0.6369 (t0) REVERT: A 375 LEU cc_start: 0.8027 (mp) cc_final: 0.7672 (mp) REVERT: B 98 MET cc_start: 0.7966 (mmp) cc_final: 0.7414 (mmm) REVERT: B 246 HIS cc_start: 0.5866 (OUTLIER) cc_final: 0.5277 (t-90) outliers start: 23 outliers final: 15 residues processed: 99 average time/residue: 0.1550 time to fit residues: 21.8803 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 : 0.701 ------------------------------------------------------------------------------- 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 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 101 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 65 optimal weight: 0.9980 chunk 31 optimal weight: 5.9990 chunk 79 optimal weight: 0.0030 chunk 48 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 74 optimal weight: 0.7980 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 0.3980 chunk 19 optimal weight: 0.9990 chunk 72 optimal weight: 0.6980 overall best weight: 0.5790 ------------------------------------------------------------------------------- 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 = 0.4502 r_free = 0.4502 target = 0.206838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.195666 restraints weight = 8662.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.193223 restraints weight = 14670.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.190431 restraints weight = 14518.982| |-----------------------------------------------------------------------------| r_work (final): 0.4341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.6663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6790 Z= 0.128 Angle : 0.600 8.705 9227 Z= 0.299 Chirality : 0.042 0.244 1058 Planarity : 0.003 0.032 1183 Dihedral : 13.346 179.775 1037 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 3.34 % Allowed : 23.22 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.30), residues: 861 helix: 1.07 (0.28), residues: 400 sheet: -2.82 (0.76), residues: 40 loop : -1.33 (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 150 PHE 0.028 0.001 PHE A 387 TYR 0.014 0.001 TYR B 131 ARG 0.001 0.000 ARG A 308 Details of bonding type rmsd hydrogen bonds : bond 0.03656 ( 259) hydrogen bonds : angle 3.90921 ( 738) SS BOND : bond 0.00036 ( 1) SS BOND : angle 0.22142 ( 2) covalent geometry : bond 0.00304 ( 6789) covalent geometry : angle 0.60050 ( 9225) *********************** 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 97 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 75 time to evaluate : 0.767 Fit side-chains REVERT: A 360 ASP cc_start: 0.7021 (p0) cc_final: 0.6190 (t0) REVERT: A 375 LEU cc_start: 0.7837 (mp) cc_final: 0.7445 (mp) REVERT: B 98 MET cc_start: 0.7983 (mmp) cc_final: 0.7726 (mmm) REVERT: B 246 HIS cc_start: 0.5975 (OUTLIER) cc_final: 0.5371 (t-90) outliers start: 22 outliers final: 18 residues processed: 93 average time/residue: 0.1888 time to fit residues: 25.6720 Evaluate side-chains 93 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 74 time to evaluate : 1.079 ------------------------------------------------------------------------------- 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 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 367 VAL Chi-restraints excluded: chain C residue 63 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 40 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 28 optimal weight: 0.3980 chunk 2 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 63 optimal weight: 0.1980 chunk 11 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 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 315 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.209149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.200487 restraints weight = 8637.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.195344 restraints weight = 14317.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.191014 restraints weight = 13186.863| |-----------------------------------------------------------------------------| r_work (final): 0.4365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.6969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6790 Z= 0.126 Angle : 0.606 8.861 9227 Z= 0.302 Chirality : 0.041 0.238 1058 Planarity : 0.003 0.038 1183 Dihedral : 13.346 179.934 1037 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.03 % Allowed : 23.37 % Favored : 73.60 % 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: -0.41 (0.30), residues: 861 helix: 1.03 (0.28), residues: 402 sheet: -2.81 (0.77), residues: 40 loop : -1.32 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 231 HIS 0.002 0.001 HIS B 280 PHE 0.027 0.001 PHE A 387 TYR 0.011 0.001 TYR B 323 ARG 0.002 0.000 ARG B 172 Details of bonding type rmsd hydrogen bonds : bond 0.03481 ( 259) hydrogen bonds : angle 3.92284 ( 738) SS BOND : bond 0.00004 ( 1) SS BOND : angle 0.18041 ( 2) covalent geometry : bond 0.00298 ( 6789) covalent geometry : angle 0.60605 ( 9225) ********************** 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 94 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 74 time to evaluate : 0.866 Fit side-chains revert: symmetry clash REVERT: A 242 PHE cc_start: 0.7055 (t80) cc_final: 0.6823 (t80) REVERT: A 360 ASP cc_start: 0.6966 (p0) cc_final: 0.6192 (t0) REVERT: A 375 LEU cc_start: 0.7975 (mp) cc_final: 0.7569 (mp) REVERT: B 98 MET cc_start: 0.7986 (mmp) cc_final: 0.7751 (mmm) REVERT: B 246 HIS cc_start: 0.5984 (OUTLIER) cc_final: 0.5342 (t-90) outliers start: 20 outliers final: 17 residues processed: 90 average time/residue: 0.1920 time to fit residues: 24.2440 Evaluate side-chains 89 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 367 VAL Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 63 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: 0.7980 chunk 20 optimal weight: 0.0050 chunk 41 optimal weight: 0.0050 chunk 3 optimal weight: 0.0980 chunk 43 optimal weight: 0.9980 chunk 30 optimal weight: 0.9980 chunk 81 optimal weight: 0.0870 chunk 38 optimal weight: 0.2980 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 0.3980 chunk 77 optimal weight: 4.9990 overall best weight: 0.0986 ------------------------------------------------------------------------------- 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 = 0.4586 r_free = 0.4586 target = 0.222473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.214407 restraints weight = 8816.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.213716 restraints weight = 13141.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.212957 restraints weight = 14312.568| |-----------------------------------------------------------------------------| r_work (final): 0.4478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6956 moved from start: 0.7130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6790 Z= 0.096 Angle : 0.558 9.555 9227 Z= 0.275 Chirality : 0.040 0.224 1058 Planarity : 0.003 0.033 1183 Dihedral : 13.045 179.913 1037 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 2.88 % Allowed : 23.52 % Favored : 73.60 % 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: -0.30 (0.30), residues: 861 helix: 1.13 (0.28), residues: 405 sheet: -2.76 (0.77), residues: 40 loop : -1.29 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 133 HIS 0.003 0.000 HIS B 280 PHE 0.024 0.001 PHE A 387 TYR 0.014 0.001 TYR B 131 ARG 0.002 0.000 ARG A 151 Details of bonding type rmsd hydrogen bonds : bond 0.02394 ( 259) hydrogen bonds : angle 3.71710 ( 738) SS BOND : bond 0.00035 ( 1) SS BOND : angle 0.35998 ( 2) covalent geometry : bond 0.00215 ( 6789) covalent geometry : angle 0.55846 ( 9225) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2623.22 seconds wall clock time: 47 minutes 12.80 seconds (2832.80 seconds total)