Starting phenix.real_space_refine on Wed Sep 17 07:20:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9chv_45603/09_2025/9chv_45603.cif Found real_map, /net/cci-nas-00/data/ceres_data/9chv_45603/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9chv_45603/09_2025/9chv_45603.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9chv_45603/09_2025/9chv_45603.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9chv_45603/09_2025/9chv_45603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9chv_45603/09_2025/9chv_45603.map" } resolution = 3.95 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'TRP:plan': 4, 'PHE:plan': 11, 'ASN:plan1': 6, 'GLU:plan': 4, 'ASP:plan': 3, 'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 4, 'ARG:plan': 2} 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: {'ARG:plan': 2, 'GLU:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 1} 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: {'ARG:plan': 2, 'GLU: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: 1.75, per 1000 atoms: 0.26 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: 0.64 Conformation dependent library (CDL) restraints added in 354.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.24 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: 0.96 Time building geometry restraints manager: 0.83 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: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.960 Find NCS groups from input model: 0.040 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.640 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.002 0.000 ARG B 331 TYR 0.033 0.002 TYR A 132 PHE 0.029 0.002 PHE B 181 TRP 0.046 0.005 TRP A 109 HIS 0.011 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.01059 ( 6789) covalent geometry : angle 1.54406 ( 9225) SS BOND : bond 0.00635 ( 1) SS BOND : angle 0.94528 ( 2) hydrogen bonds : bond 0.19809 ( 259) hydrogen bonds : angle 8.19128 ( 738) *********************** 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 : 0.281 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: 0.0811 time to fit residues: 19.3196 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 : 0.268 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.1980 chunk 53 optimal weight: 0.5980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.0970 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 0.0040 chunk 74 optimal weight: 0.1980 overall best weight: 0.2190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN A 392 HIS A 445 ASN 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 = 0.4543 r_free = 0.4543 target = 0.212608 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.199888 restraints weight = 8701.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.198925 restraints weight = 14972.599| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.198566 restraints weight = 14637.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.197915 restraints weight = 11825.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.197989 restraints weight = 11816.291| |-----------------------------------------------------------------------------| r_work (final): 0.4434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6518 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6790 Z= 0.126 Angle : 0.625 9.965 9227 Z= 0.318 Chirality : 0.042 0.167 1058 Planarity : 0.004 0.032 1183 Dihedral : 14.734 179.953 1054 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 2.43 % Allowed : 16.24 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.28), residues: 861 helix: -0.07 (0.26), residues: 403 sheet: -3.21 (0.58), residues: 61 loop : -1.58 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 172 TYR 0.013 0.001 TYR B 174 PHE 0.020 0.001 PHE B 181 TRP 0.020 0.002 TRP B 133 HIS 0.006 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00263 ( 6789) covalent geometry : angle 0.62358 ( 9225) SS BOND : bond 0.00105 ( 1) SS BOND : angle 2.74899 ( 2) hydrogen bonds : bond 0.03631 ( 259) hydrogen bonds : angle 4.69275 ( 738) *********************** 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 123 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 107 time to evaluate : 0.256 Fit side-chains REVERT: A 360 ASP cc_start: 0.6325 (p0) cc_final: 0.5368 (t0) REVERT: C 29 MET cc_start: 0.7416 (ttm) cc_final: 0.7210 (ttm) outliers start: 16 outliers final: 11 residues processed: 120 average time/residue: 0.0734 time to fit residues: 12.3805 Evaluate side-chains 92 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 81 time to evaluate : 0.264 ------------------------------------------------------------------------------- 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 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 372 VAL Chi-restraints excluded: chain A residue 417 ILE Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain B residue 367 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 chunk 71 optimal weight: 0.0470 chunk 26 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 4 optimal weight: 0.6980 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN A 338 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4535 r_free = 0.4535 target = 0.218013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.209577 restraints weight = 8812.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.195406 restraints weight = 14719.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.190859 restraints weight = 12903.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.191226 restraints weight = 14503.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.192127 restraints weight = 11519.563| |-----------------------------------------------------------------------------| r_work (final): 0.4227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.4271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 6790 Z= 0.154 Angle : 0.638 10.657 9227 Z= 0.326 Chirality : 0.043 0.146 1058 Planarity : 0.004 0.039 1183 Dihedral : 13.469 177.178 1042 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.19 % Allowed : 18.51 % Favored : 78.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.29), residues: 861 helix: 0.24 (0.26), residues: 406 sheet: -3.19 (0.59), residues: 61 loop : -1.51 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 172 TYR 0.018 0.001 TYR B 323 PHE 0.024 0.001 PHE B 345 TRP 0.013 0.001 TRP B 133 HIS 0.004 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 6789) covalent geometry : angle 0.63735 ( 9225) SS BOND : bond 0.00230 ( 1) SS BOND : angle 1.51039 ( 2) hydrogen bonds : bond 0.04468 ( 259) hydrogen bonds : angle 4.22828 ( 738) *********************** 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 119 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 98 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 360 ASP cc_start: 0.6989 (p0) cc_final: 0.6079 (t0) REVERT: A 381 MET cc_start: 0.8459 (OUTLIER) cc_final: 0.8087 (mtp) REVERT: B 178 MET cc_start: 0.8092 (mmt) cc_final: 0.7280 (mmm) REVERT: B 272 ASN cc_start: 0.7540 (t0) cc_final: 0.7338 (t0) REVERT: C 29 MET cc_start: 0.7716 (ttm) cc_final: 0.7486 (ttm) outliers start: 21 outliers final: 14 residues processed: 113 average time/residue: 0.0719 time to fit residues: 11.4714 Evaluate side-chains 103 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 88 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 77 CYS 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 257 GLU 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 381 MET Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 440 VAL Chi-restraints excluded: chain B residue 302 ILE 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 80 optimal weight: 0.4980 chunk 38 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 81 optimal weight: 0.4980 chunk 23 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 3 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 337 ASN A 338 ASN B 193 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.215212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.207019 restraints weight = 8882.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.195322 restraints weight = 14941.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.190561 restraints weight = 14827.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.191639 restraints weight = 12989.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.191503 restraints weight = 10567.559| |-----------------------------------------------------------------------------| r_work (final): 0.4240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7365 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6790 Z= 0.142 Angle : 0.615 10.118 9227 Z= 0.313 Chirality : 0.042 0.137 1058 Planarity : 0.004 0.051 1183 Dihedral : 13.521 179.851 1037 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 3.79 % Allowed : 19.58 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.08 (0.29), residues: 861 helix: 0.41 (0.27), residues: 407 sheet: -3.24 (0.59), residues: 61 loop : -1.47 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 172 TYR 0.011 0.001 TYR B 323 PHE 0.022 0.001 PHE A 193 TRP 0.010 0.001 TRP B 351 HIS 0.002 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 6789) covalent geometry : angle 0.61487 ( 9225) SS BOND : bond 0.00206 ( 1) SS BOND : angle 0.95840 ( 2) hydrogen bonds : bond 0.03729 ( 259) hydrogen bonds : angle 4.06548 ( 738) *********************** 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 120 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 95 time to evaluate : 0.266 Fit side-chains REVERT: A 242 PHE cc_start: 0.7154 (t80) cc_final: 0.6864 (t80) REVERT: A 360 ASP cc_start: 0.7080 (p0) cc_final: 0.6220 (t0) REVERT: B 98 MET cc_start: 0.8431 (mmp) cc_final: 0.8120 (mmp) outliers start: 25 outliers final: 16 residues processed: 113 average time/residue: 0.0667 time to fit residues: 10.8521 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 : 0.179 ------------------------------------------------------------------------------- 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 135 ILE Chi-restraints excluded: chain A residue 136 THR 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 372 VAL Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 28 LEU Chi-restraints excluded: chain B residue 280 HIS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 5 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 84 optimal weight: 0.4980 chunk 48 optimal weight: 0.5980 chunk 12 optimal weight: 0.0980 chunk 14 optimal weight: 6.9990 chunk 74 optimal weight: 0.0970 chunk 67 optimal weight: 0.0870 chunk 66 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 overall best weight: 0.2756 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 344 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.219828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.211760 restraints weight = 8958.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.196395 restraints weight = 14974.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.192314 restraints weight = 13894.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.192611 restraints weight = 11785.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.193096 restraints weight = 11050.717| |-----------------------------------------------------------------------------| r_work (final): 0.4234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.5669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6790 Z= 0.103 Angle : 0.566 8.350 9227 Z= 0.285 Chirality : 0.041 0.245 1058 Planarity : 0.003 0.041 1183 Dihedral : 13.201 179.717 1037 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.73 % Allowed : 21.55 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.81 (0.29), residues: 861 helix: 0.59 (0.27), residues: 410 sheet: -2.50 (0.70), residues: 50 loop : -1.46 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 172 TYR 0.019 0.001 TYR B 323 PHE 0.012 0.001 PHE B 345 TRP 0.007 0.001 TRP B 133 HIS 0.001 0.000 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 6789) covalent geometry : angle 0.56561 ( 9225) SS BOND : bond 0.00071 ( 1) SS BOND : angle 0.47473 ( 2) hydrogen bonds : bond 0.03020 ( 259) hydrogen bonds : angle 3.84451 ( 738) *********************** 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 108 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 0.285 Fit side-chains REVERT: A 360 ASP cc_start: 0.7198 (p0) cc_final: 0.6515 (t0) REVERT: B 259 TYR cc_start: 0.8101 (p90) cc_final: 0.7884 (p90) outliers start: 18 outliers final: 13 residues processed: 103 average time/residue: 0.0695 time to fit residues: 10.3693 Evaluate side-chains 95 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.306 ------------------------------------------------------------------------------- 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 258 PHE Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 280 HIS Chi-restraints excluded: chain B residue 342 LEU Chi-restraints excluded: chain C residue 38 SER 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 83 optimal weight: 0.2980 chunk 56 optimal weight: 0.4980 chunk 52 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 62 optimal weight: 0.0060 chunk 6 optimal weight: 3.9990 overall best weight: 0.3996 ------------------------------------------------------------------------------- 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 = 0.4566 r_free = 0.4566 target = 0.213376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.204960 restraints weight = 8603.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4479 r_free = 0.4479 target = 0.204230 restraints weight = 13493.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4471 r_free = 0.4471 target = 0.203735 restraints weight = 13207.574| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4463 r_free = 0.4463 target = 0.203022 restraints weight = 11243.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4462 r_free = 0.4462 target = 0.203062 restraints weight = 10442.302| |-----------------------------------------------------------------------------| r_work (final): 0.4519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7043 moved from start: 0.6003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 6790 Z= 0.109 Angle : 0.551 8.464 9227 Z= 0.278 Chirality : 0.041 0.202 1058 Planarity : 0.003 0.038 1183 Dihedral : 13.252 179.843 1037 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.64 % Allowed : 21.55 % Favored : 74.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.30), residues: 861 helix: 0.69 (0.27), residues: 410 sheet: -2.54 (0.70), residues: 50 loop : -1.37 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 172 TYR 0.011 0.001 TYR A 132 PHE 0.012 0.001 PHE A 193 TRP 0.007 0.001 TRP B 231 HIS 0.002 0.000 HIS A 392 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 6789) covalent geometry : angle 0.55078 ( 9225) SS BOND : bond 0.00015 ( 1) SS BOND : angle 0.34925 ( 2) hydrogen bonds : bond 0.03225 ( 259) hydrogen bonds : angle 3.78001 ( 738) *********************** 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 107 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 83 time to evaluate : 0.253 Fit side-chains REVERT: A 215 MET cc_start: 0.8360 (tmm) cc_final: 0.8142 (tmm) REVERT: A 242 PHE cc_start: 0.7074 (t80) cc_final: 0.6810 (t80) REVERT: A 360 ASP cc_start: 0.7063 (p0) cc_final: 0.6153 (t0) REVERT: B 98 MET cc_start: 0.7976 (mmp) cc_final: 0.7347 (mmm) REVERT: B 246 HIS cc_start: 0.5976 (OUTLIER) cc_final: 0.5269 (t-90) outliers start: 24 outliers final: 15 residues processed: 104 average time/residue: 0.0735 time to fit residues: 10.8522 Evaluate side-chains 92 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 76 time to evaluate : 0.266 ------------------------------------------------------------------------------- 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 258 PHE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 55 LEU 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 38 SER 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 21 optimal weight: 0.3980 chunk 69 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 50 optimal weight: 0.3980 chunk 68 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 52 optimal weight: 0.5980 chunk 78 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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** B 315 ASN B 366 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.214940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.205653 restraints weight = 8858.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.203721 restraints weight = 13493.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.202566 restraints weight = 16943.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.201760 restraints weight = 13257.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.201578 restraints weight = 13498.582| |-----------------------------------------------------------------------------| r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.6440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6790 Z= 0.134 Angle : 0.605 8.578 9227 Z= 0.304 Chirality : 0.042 0.190 1058 Planarity : 0.004 0.035 1183 Dihedral : 13.410 179.803 1037 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 4.10 % Allowed : 22.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.69 (0.30), residues: 861 helix: 0.74 (0.27), residues: 408 sheet: -2.76 (0.70), residues: 50 loop : -1.41 (0.31), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 172 TYR 0.017 0.001 TYR B 323 PHE 0.010 0.001 PHE B 181 TRP 0.010 0.001 TRP B 231 HIS 0.002 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 6789) covalent geometry : angle 0.60463 ( 9225) SS BOND : bond 0.00036 ( 1) SS BOND : angle 0.34777 ( 2) hydrogen bonds : bond 0.03693 ( 259) hydrogen bonds : angle 3.89588 ( 738) *********************** 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: 27 poor density : 83 time to evaluate : 0.304 Fit side-chains REVERT: A 215 MET cc_start: 0.8461 (tmm) cc_final: 0.7895 (tmm) REVERT: A 360 ASP cc_start: 0.7003 (p0) cc_final: 0.5985 (t0) REVERT: B 98 MET cc_start: 0.7866 (mmp) cc_final: 0.7271 (mmm) REVERT: B 246 HIS cc_start: 0.6046 (OUTLIER) cc_final: 0.5332 (t-90) outliers start: 27 outliers final: 17 residues processed: 106 average time/residue: 0.0684 time to fit residues: 10.3954 Evaluate side-chains 95 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 0.242 ------------------------------------------------------------------------------- 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 258 PHE Chi-restraints excluded: chain A residue 352 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain B residue 13 THR Chi-restraints excluded: chain B residue 55 LEU 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 38 SER 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 12 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 31 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 62 optimal weight: 0.0000 chunk 49 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 = 0.208896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.200118 restraints weight = 8528.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.199024 restraints weight = 13858.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.197922 restraints weight = 15008.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.197176 restraints weight = 12944.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.197162 restraints weight = 12069.192| |-----------------------------------------------------------------------------| r_work (final): 0.4421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.6778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6790 Z= 0.143 Angle : 0.611 7.039 9227 Z= 0.308 Chirality : 0.042 0.179 1058 Planarity : 0.004 0.034 1183 Dihedral : 13.499 179.874 1037 Min Nonbonded Distance : 2.318 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 4.55 % Allowed : 22.00 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.30), residues: 861 helix: 0.73 (0.27), residues: 408 sheet: -2.85 (0.76), residues: 40 loop : -1.37 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 308 TYR 0.012 0.001 TYR B 323 PHE 0.015 0.001 PHE A 242 TRP 0.012 0.001 TRP B 231 HIS 0.002 0.001 HIS A 93 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 6789) covalent geometry : angle 0.61065 ( 9225) SS BOND : bond 0.00043 ( 1) SS BOND : angle 0.27981 ( 2) hydrogen bonds : bond 0.03866 ( 259) hydrogen bonds : angle 3.97184 ( 738) *********************** 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 106 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 76 time to evaluate : 0.279 Fit side-chains REVERT: A 263 GLU cc_start: 0.7025 (mp0) cc_final: 0.6794 (mt-10) REVERT: A 360 ASP cc_start: 0.6978 (p0) cc_final: 0.6200 (t0) REVERT: B 246 HIS cc_start: 0.6106 (OUTLIER) cc_final: 0.5348 (t-90) outliers start: 30 outliers final: 20 residues processed: 102 average time/residue: 0.0710 time to fit residues: 10.3618 Evaluate side-chains 92 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 71 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 VAL Chi-restraints excluded: chain A residue 77 CYS 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 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 B residue 13 THR Chi-restraints excluded: chain B residue 55 LEU 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 38 SER 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 77 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 64 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 74 optimal weight: 0.8980 chunk 41 optimal weight: 0.0770 chunk 57 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.6338 ------------------------------------------------------------------------------- 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 = 0.4503 r_free = 0.4503 target = 0.213864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4423 r_free = 0.4423 target = 0.205466 restraints weight = 8869.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.203035 restraints weight = 12863.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.200731 restraints weight = 15458.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.200182 restraints weight = 13481.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.200166 restraints weight = 11835.498| |-----------------------------------------------------------------------------| r_work (final): 0.4376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.7060 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= 0.133 Angle : 0.622 7.245 9227 Z= 0.310 Chirality : 0.042 0.164 1058 Planarity : 0.004 0.037 1183 Dihedral : 13.453 179.845 1037 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.64 % Allowed : 22.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.64 (0.30), residues: 861 helix: 0.78 (0.27), residues: 406 sheet: -2.87 (0.75), residues: 40 loop : -1.41 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 172 TYR 0.010 0.001 TYR B 323 PHE 0.015 0.001 PHE A 242 TRP 0.011 0.001 TRP B 231 HIS 0.002 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00318 ( 6789) covalent geometry : angle 0.62182 ( 9225) SS BOND : bond 0.00010 ( 1) SS BOND : angle 0.20542 ( 2) hydrogen bonds : bond 0.03680 ( 259) hydrogen bonds : angle 3.94269 ( 738) *********************** 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: 24 poor density : 73 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: A 242 PHE cc_start: 0.7177 (t80) cc_final: 0.6971 (t80) REVERT: A 360 ASP cc_start: 0.6999 (p0) cc_final: 0.6219 (t0) REVERT: B 98 MET cc_start: 0.7850 (mmp) cc_final: 0.7237 (mmm) REVERT: B 246 HIS cc_start: 0.6043 (OUTLIER) cc_final: 0.5314 (t-90) outliers start: 24 outliers final: 19 residues processed: 93 average time/residue: 0.0646 time to fit residues: 8.9345 Evaluate side-chains 91 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 71 time to evaluate : 0.339 ------------------------------------------------------------------------------- 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 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 B residue 13 THR Chi-restraints excluded: chain B residue 55 LEU 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 38 SER 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 57 optimal weight: 0.5980 chunk 33 optimal weight: 0.0970 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 chunk 10 optimal weight: 0.0980 chunk 15 optimal weight: 5.9990 chunk 72 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 56 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 315 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4524 r_free = 0.4524 target = 0.215811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4442 r_free = 0.4442 target = 0.207230 restraints weight = 8836.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4432 r_free = 0.4432 target = 0.206329 restraints weight = 12912.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.205623 restraints weight = 12487.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.204614 restraints weight = 12084.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.204258 restraints weight = 12096.719| |-----------------------------------------------------------------------------| r_work (final): 0.4418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7139 moved from start: 0.7173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6790 Z= 0.113 Angle : 0.594 7.555 9227 Z= 0.295 Chirality : 0.041 0.157 1058 Planarity : 0.003 0.033 1183 Dihedral : 13.294 179.814 1037 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 3.34 % Allowed : 22.91 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.51 (0.30), residues: 861 helix: 0.98 (0.28), residues: 400 sheet: -2.85 (0.76), residues: 40 loop : -1.41 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 27 TYR 0.010 0.001 TYR B 323 PHE 0.013 0.001 PHE A 242 TRP 0.010 0.001 TRP B 231 HIS 0.003 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 6789) covalent geometry : angle 0.59379 ( 9225) SS BOND : bond 0.00030 ( 1) SS BOND : angle 0.13737 ( 2) hydrogen bonds : bond 0.03270 ( 259) hydrogen bonds : angle 3.85197 ( 738) ********************** 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 98 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 76 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: A 263 GLU cc_start: 0.6726 (mp0) cc_final: 0.6440 (mt-10) REVERT: A 360 ASP cc_start: 0.6911 (p0) cc_final: 0.6228 (t0) REVERT: B 98 MET cc_start: 0.7825 (mmp) cc_final: 0.7254 (mmm) REVERT: B 246 HIS cc_start: 0.6103 (OUTLIER) cc_final: 0.5459 (t-90) REVERT: C 106 LEU cc_start: 0.7979 (tt) cc_final: 0.7705 (tt) outliers start: 22 outliers final: 19 residues processed: 93 average time/residue: 0.0670 time to fit residues: 9.0637 Evaluate side-chains 95 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 75 time to evaluate : 0.312 ------------------------------------------------------------------------------- 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 258 PHE Chi-restraints excluded: chain A residue 264 LEU 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 B residue 13 THR Chi-restraints excluded: chain B residue 55 LEU 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 38 SER 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 63 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 67 optimal weight: 2.9990 chunk 25 optimal weight: 0.0370 chunk 35 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 34 optimal weight: 0.1980 chunk 24 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.5458 ------------------------------------------------------------------------------- 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 = 0.4520 r_free = 0.4520 target = 0.215343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.206829 restraints weight = 8799.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.204557 restraints weight = 13466.302| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.202035 restraints weight = 15216.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.201513 restraints weight = 14963.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.201340 restraints weight = 14326.774| |-----------------------------------------------------------------------------| r_work (final): 0.4391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.7334 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 : 0.621 7.947 9227 Z= 0.310 Chirality : 0.042 0.155 1058 Planarity : 0.004 0.035 1183 Dihedral : 13.319 179.097 1037 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 3.03 % Allowed : 23.82 % Favored : 73.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.48 (0.30), residues: 861 helix: 0.96 (0.28), residues: 401 sheet: -2.81 (0.77), residues: 40 loop : -1.34 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 72 TYR 0.010 0.001 TYR B 323 PHE 0.015 0.001 PHE A 287 TRP 0.010 0.001 TRP B 231 HIS 0.003 0.001 HIS B 280 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6789) covalent geometry : angle 0.62123 ( 9225) SS BOND : bond 0.00008 ( 1) SS BOND : angle 0.13020 ( 2) hydrogen bonds : bond 0.03590 ( 259) hydrogen bonds : angle 3.89405 ( 738) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1194.23 seconds wall clock time: 21 minutes 20.69 seconds (1280.69 seconds total)