Starting phenix.real_space_refine on Fri Nov 15 14:30:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jln_36401/11_2024/8jln_36401.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jln_36401/11_2024/8jln_36401.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jln_36401/11_2024/8jln_36401.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jln_36401/11_2024/8jln_36401.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jln_36401/11_2024/8jln_36401.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jln_36401/11_2024/8jln_36401.cif" } resolution = 3.24 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= 0.037 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: 5 Type Number sf(0) Gaussians I 1 10.91 5 S 68 5.16 5 C 5814 2.51 5 N 1560 2.21 5 O 1674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 9117 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1972 Classifications: {'peptide': 240} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 6, 'TRANS': 233} Chain breaks: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2593 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "R" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2322 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 11, 'TRANS': 274} Chain breaks: 1 Chain: "S" Number of atoms: 1767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1767 Classifications: {'peptide': 230} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "Y" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "R" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'UJF': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.81, per 1000 atoms: 0.64 Number of scatterers: 9117 At special positions: 0 Unit cell: (107.95, 118.15, 130.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) I 1 52.95 S 68 16.00 O 1674 8.00 N 1560 7.00 C 5814 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 182 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.21 Conformation dependent library (CDL) restraints added in 1.0 seconds 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 14 sheets defined 37.2% alpha, 18.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.04 Creating SS restraints... Processing helix chain 'A' and resid 13 through 38 Processing helix chain 'A' and resid 52 through 62 removed outlier: 3.978A pdb=" N ILE A 62 " --> pdb=" O LYS A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 removed outlier: 3.546A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 302 removed outlier: 4.086A pdb=" N LEU A 297 " --> pdb=" O LYS A 293 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N LEU A 302 " --> pdb=" O ALA A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 316 removed outlier: 3.864A pdb=" N ALA A 316 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.995A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 removed outlier: 3.623A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 29 through 35 removed outlier: 4.262A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 21 through 50 removed outlier: 3.891A pdb=" N HIS R 50 " --> pdb=" O VAL R 46 " (cutoff:3.500A) Processing helix chain 'R' and resid 56 through 76 Processing helix chain 'R' and resid 76 through 84 removed outlier: 3.503A pdb=" N SER R 80 " --> pdb=" O VAL R 76 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL R 82 " --> pdb=" O PRO R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 95 through 127 removed outlier: 3.914A pdb=" N THR R 100 " --> pdb=" O CYS R 96 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N SER R 101 " --> pdb=" O LYS R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 136 through 160 Proline residue: R 151 - end of helix Processing helix chain 'R' and resid 168 through 176 Processing helix chain 'R' and resid 178 through 182 Processing helix chain 'R' and resid 187 through 199 Processing helix chain 'R' and resid 199 through 232 Processing helix chain 'R' and resid 247 through 277 removed outlier: 4.439A pdb=" N CYS R 263 " --> pdb=" O VAL R 259 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N TRP R 264 " --> pdb=" O PHE R 260 " (cutoff:3.500A) Proline residue: R 266 - end of helix Proline residue: R 275 - end of helix Processing helix chain 'R' and resid 282 through 300 removed outlier: 3.559A pdb=" N ILE R 290 " --> pdb=" O ASN R 286 " (cutoff:3.500A) Processing helix chain 'R' and resid 300 through 305 removed outlier: 3.814A pdb=" N TYR R 304 " --> pdb=" O ASN R 300 " (cutoff:3.500A) Processing helix chain 'R' and resid 308 through 318 removed outlier: 3.572A pdb=" N MET R 318 " --> pdb=" O ALA R 314 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 4.338A pdb=" N SER S 31 " --> pdb=" O ALA S 28 " (cutoff:3.500A) Processing helix chain 'S' and resid 220 through 224 removed outlier: 4.118A pdb=" N VAL S 224 " --> pdb=" O ALA S 221 " (cutoff:3.500A) Processing helix chain 'Y' and resid 7 through 24 Processing helix chain 'Y' and resid 29 through 45 removed outlier: 4.060A pdb=" N ALA Y 33 " --> pdb=" O LYS Y 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 6.333A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N ASN A 292 " --> pdb=" O PHE A 246 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.617A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.577A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N LEU B 70 " --> pdb=" O TRP B 82 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER B 72 " --> pdb=" O ILE B 80 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N ILE B 80 " --> pdb=" O SER B 72 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.903A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL B 112 " --> pdb=" O TYR B 124 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 148 removed outlier: 3.607A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA B 167 " --> pdb=" O THR B 159 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR B 178 " --> pdb=" O LEU B 168 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 191 removed outlier: 3.754A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLY B 202 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA B 203 " --> pdb=" O SER B 207 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.671A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 275 through 277 removed outlier: 3.991A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 315 through 320 Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 8 removed outlier: 3.573A pdb=" N MET S 83 " --> pdb=" O ARG S 18 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 59 removed outlier: 6.567A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 141 removed outlier: 3.765A pdb=" N THR S 141 " --> pdb=" O ARG S 160 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ARG S 160 " --> pdb=" O THR S 141 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'S' and resid 174 through 176 Processing sheet with id=AB5, first strand: chain 'S' and resid 189 through 190 409 hydrogen bonds defined for protein. 1179 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.51 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.40: 3889 1.40 - 1.58: 5330 1.58 - 1.76: 0 1.76 - 1.93: 102 1.93 - 2.11: 1 Bond restraints: 9322 Sorted by residual: bond pdb=" N ASP R 103 " pdb=" CA ASP R 103 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.25e-02 6.40e+03 6.61e+00 bond pdb=" C01 UJF R 401 " pdb=" O01 UJF R 401 " ideal model delta sigma weight residual 1.370 1.396 -0.026 2.00e-02 2.50e+03 1.64e+00 bond pdb=" C ASP B 38 " pdb=" N PRO B 39 " ideal model delta sigma weight residual 1.330 1.345 -0.015 1.25e-02 6.40e+03 1.42e+00 bond pdb=" C07 UJF R 401 " pdb=" O02 UJF R 401 " ideal model delta sigma weight residual 1.379 1.402 -0.023 2.00e-02 2.50e+03 1.29e+00 bond pdb=" C THR R 102 " pdb=" N ASP R 103 " ideal model delta sigma weight residual 1.335 1.350 -0.015 1.34e-02 5.57e+03 1.20e+00 ... (remaining 9317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 12416 2.01 - 4.03: 166 4.03 - 6.04: 27 6.04 - 8.06: 9 8.06 - 10.07: 1 Bond angle restraints: 12619 Sorted by residual: angle pdb=" C LYS Y 20 " pdb=" N MET Y 21 " pdb=" CA MET Y 21 " ideal model delta sigma weight residual 121.58 114.90 6.68 1.95e+00 2.63e-01 1.18e+01 angle pdb=" N VAL R 176 " pdb=" CA VAL R 176 " pdb=" C VAL R 176 " ideal model delta sigma weight residual 112.98 108.92 4.06 1.25e+00 6.40e-01 1.06e+01 angle pdb=" N VAL R 94 " pdb=" CA VAL R 94 " pdb=" C VAL R 94 " ideal model delta sigma weight residual 111.81 109.08 2.73 8.60e-01 1.35e+00 1.01e+01 angle pdb=" C ASP R 103 " pdb=" N ILE R 104 " pdb=" CA ILE R 104 " ideal model delta sigma weight residual 120.55 125.28 -4.73 1.60e+00 3.91e-01 8.74e+00 angle pdb=" CA MET Y 21 " pdb=" CB MET Y 21 " pdb=" CG MET Y 21 " ideal model delta sigma weight residual 114.10 119.87 -5.77 2.00e+00 2.50e-01 8.31e+00 ... (remaining 12614 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.14: 4949 18.14 - 36.29: 478 36.29 - 54.43: 81 54.43 - 72.57: 10 72.57 - 90.72: 9 Dihedral angle restraints: 5527 sinusoidal: 2176 harmonic: 3351 Sorted by residual: dihedral pdb=" CA GLY A 225 " pdb=" C GLY A 225 " pdb=" N ALA A 226 " pdb=" CA ALA A 226 " ideal model delta harmonic sigma weight residual -180.00 -157.44 -22.56 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA TYR S 235 " pdb=" C TYR S 235 " pdb=" N PRO S 236 " pdb=" CA PRO S 236 " ideal model delta harmonic sigma weight residual 180.00 160.22 19.78 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA VAL A 224 " pdb=" C VAL A 224 " pdb=" N GLY A 225 " pdb=" CA GLY A 225 " ideal model delta harmonic sigma weight residual 180.00 161.17 18.83 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 5524 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 911 0.034 - 0.068: 326 0.068 - 0.102: 116 0.102 - 0.136: 46 0.136 - 0.170: 4 Chirality restraints: 1403 Sorted by residual: chirality pdb=" CA MET Y 21 " pdb=" N MET Y 21 " pdb=" C MET Y 21 " pdb=" CB MET Y 21 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.24e-01 chirality pdb=" CB ILE R 280 " pdb=" CA ILE R 280 " pdb=" CG1 ILE R 280 " pdb=" CG2 ILE R 280 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.16 2.00e-01 2.50e+01 6.08e-01 chirality pdb=" CB THR A 350 " pdb=" CA THR A 350 " pdb=" OG1 THR A 350 " pdb=" CG2 THR A 350 " both_signs ideal model delta sigma weight residual False 2.55 2.41 0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 1400 not shown) Planarity restraints: 1597 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 310 " -0.014 2.00e-02 2.50e+03 1.55e-02 6.03e+00 pdb=" CG TRP R 310 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP R 310 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP R 310 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP R 310 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP R 310 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP R 310 " -0.008 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 310 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 310 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP R 310 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR S 150 " 0.034 5.00e-02 4.00e+02 5.09e-02 4.15e+00 pdb=" N PRO S 151 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO S 151 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO S 151 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER S 106 " -0.029 5.00e-02 4.00e+02 4.42e-02 3.12e+00 pdb=" N PRO S 107 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO S 107 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO S 107 " -0.024 5.00e-02 4.00e+02 ... (remaining 1594 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1441 2.76 - 3.31: 8896 3.31 - 3.86: 15061 3.86 - 4.41: 17457 4.41 - 4.96: 30913 Nonbonded interactions: 73768 Sorted by model distance: nonbonded pdb=" OE2 GLU B 260 " pdb=" OG1 THR B 263 " model vdw 2.216 3.040 nonbonded pdb=" O ILE B 123 " pdb=" OG SER B 136 " model vdw 2.231 3.040 nonbonded pdb=" OE1 GLU A 21 " pdb=" OG SER S 52 " model vdw 2.243 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.273 3.040 nonbonded pdb=" OH TYR A 318 " pdb=" OD2 ASP A 343 " model vdw 2.288 3.040 ... (remaining 73763 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.050 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 23.020 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 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 : 0.002 0.032 9322 Z= 0.152 Angle : 0.637 10.073 12619 Z= 0.365 Chirality : 0.043 0.170 1403 Planarity : 0.004 0.051 1597 Dihedral : 14.364 90.715 3358 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 0.00 % Allowed : 0.20 % Favored : 99.80 % 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: -0.14 (0.25), residues: 1136 helix: 1.76 (0.27), residues: 396 sheet: -0.03 (0.34), residues: 246 loop : -1.73 (0.26), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP R 310 HIS 0.004 0.001 HIS S 35 PHE 0.020 0.001 PHE S 80 TYR 0.014 0.001 TYR S 103 ARG 0.006 0.000 ARG R 23 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.813 Fit side-chains REVERT: B 42 ARG cc_start: 0.7311 (ptm-80) cc_final: 0.6910 (tmt170) REVERT: R 262 ILE cc_start: 0.7961 (tt) cc_final: 0.7675 (tt) REVERT: S 20 LEU cc_start: 0.6905 (mt) cc_final: 0.6616 (mt) REVERT: Y 21 MET cc_start: 0.5427 (pmm) cc_final: 0.4650 (mtp) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1890 time to fit residues: 40.6756 Evaluate side-chains 127 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 6.9990 chunk 85 optimal weight: 20.0000 chunk 47 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 57 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 88 optimal weight: 20.0000 chunk 34 optimal weight: 0.6980 chunk 53 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 35 ASN B 110 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 50 HIS S 35 HIS S 183 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 9322 Z= 0.436 Angle : 0.735 9.344 12619 Z= 0.387 Chirality : 0.050 0.175 1403 Planarity : 0.005 0.052 1597 Dihedral : 6.052 72.148 1264 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.69 % Favored : 93.31 % Rotamer: Outliers : 1.62 % Allowed : 9.40 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.68 (0.24), residues: 1136 helix: 1.27 (0.25), residues: 397 sheet: -0.44 (0.33), residues: 251 loop : -1.95 (0.25), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP R 310 HIS 0.008 0.002 HIS B 311 PHE 0.033 0.003 PHE R 165 TYR 0.019 0.002 TYR S 103 ARG 0.006 0.001 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 1.037 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.6886 (tt0) cc_final: 0.6642 (tm-30) REVERT: B 42 ARG cc_start: 0.7577 (ptm-80) cc_final: 0.7078 (tmt170) REVERT: B 153 ASP cc_start: 0.8221 (t0) cc_final: 0.8000 (t0) REVERT: B 212 ASP cc_start: 0.7635 (t0) cc_final: 0.7201 (p0) REVERT: B 247 ASP cc_start: 0.8234 (t70) cc_final: 0.7912 (t0) REVERT: R 50 HIS cc_start: 0.7353 (OUTLIER) cc_final: 0.7149 (p90) REVERT: R 91 PHE cc_start: 0.8341 (m-80) cc_final: 0.8050 (m-80) REVERT: S 20 LEU cc_start: 0.6916 (mt) cc_final: 0.6631 (mt) REVERT: S 172 THR cc_start: 0.7910 (m) cc_final: 0.7470 (t) REVERT: S 233 LEU cc_start: 0.4600 (tp) cc_final: 0.4332 (tp) outliers start: 16 outliers final: 13 residues processed: 146 average time/residue: 0.1971 time to fit residues: 41.4913 Evaluate side-chains 145 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 70 LEU Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 200 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 50 HIS Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain S residue 99 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 6.9990 chunk 31 optimal weight: 0.5980 chunk 85 optimal weight: 30.0000 chunk 69 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 111 optimal weight: 0.9980 chunk 91 optimal weight: 0.0170 chunk 101 optimal weight: 20.0000 chunk 35 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 54 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS R 20 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9322 Z= 0.156 Angle : 0.563 11.077 12619 Z= 0.292 Chirality : 0.042 0.151 1403 Planarity : 0.004 0.051 1597 Dihedral : 5.747 73.369 1264 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.01 % Allowed : 13.75 % Favored : 85.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.24), residues: 1136 helix: 1.53 (0.25), residues: 404 sheet: -0.39 (0.33), residues: 257 loop : -1.86 (0.25), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP R 310 HIS 0.010 0.001 HIS R 50 PHE 0.022 0.001 PHE S 80 TYR 0.015 0.001 TYR S 190 ARG 0.002 0.000 ARG A 232 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 129 time to evaluate : 1.491 Fit side-chains revert: symmetry clash REVERT: A 209 GLU cc_start: 0.6904 (tt0) cc_final: 0.6645 (tm-30) REVERT: B 42 ARG cc_start: 0.7590 (ptm-80) cc_final: 0.7164 (tmt170) REVERT: B 138 GLU cc_start: 0.7414 (mm-30) cc_final: 0.7141 (mm-30) REVERT: B 153 ASP cc_start: 0.7707 (t0) cc_final: 0.7503 (t0) REVERT: B 212 ASP cc_start: 0.7576 (t0) cc_final: 0.7152 (p0) REVERT: B 247 ASP cc_start: 0.8175 (t70) cc_final: 0.7759 (t0) REVERT: R 69 ASP cc_start: 0.7470 (m-30) cc_final: 0.7201 (m-30) REVERT: S 20 LEU cc_start: 0.7024 (mt) cc_final: 0.6713 (mt) REVERT: S 172 THR cc_start: 0.7901 (m) cc_final: 0.7310 (t) outliers start: 10 outliers final: 7 residues processed: 135 average time/residue: 0.1961 time to fit residues: 38.6519 Evaluate side-chains 131 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 193 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 103 optimal weight: 8.9990 chunk 109 optimal weight: 5.9990 chunk 97 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 90 optimal weight: 6.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 362 HIS ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS R 50 HIS S 35 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 9322 Z= 0.422 Angle : 0.686 8.929 12619 Z= 0.365 Chirality : 0.048 0.245 1403 Planarity : 0.005 0.051 1597 Dihedral : 6.081 81.640 1264 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.63 % Allowed : 15.98 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.72 (0.24), residues: 1136 helix: 1.33 (0.25), residues: 391 sheet: -0.51 (0.34), residues: 251 loop : -2.00 (0.24), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 310 HIS 0.006 0.001 HIS R 63 PHE 0.036 0.002 PHE R 165 TYR 0.018 0.002 TYR A 37 ARG 0.005 0.001 ARG A 228 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.7041 (tt0) cc_final: 0.6732 (tm-30) REVERT: B 42 ARG cc_start: 0.7719 (ptm-80) cc_final: 0.7288 (tmt170) REVERT: B 153 ASP cc_start: 0.8192 (t0) cc_final: 0.7923 (t0) REVERT: B 247 ASP cc_start: 0.8268 (t70) cc_final: 0.7709 (t0) REVERT: R 69 ASP cc_start: 0.7708 (m-30) cc_final: 0.7483 (m-30) REVERT: R 165 PHE cc_start: 0.8424 (p90) cc_final: 0.8094 (p90) REVERT: S 20 LEU cc_start: 0.7058 (mt) cc_final: 0.6742 (mt) REVERT: S 172 THR cc_start: 0.7908 (m) cc_final: 0.7324 (t) REVERT: Y 38 MET cc_start: 0.7805 (ttm) cc_final: 0.7574 (mtt) outliers start: 26 outliers final: 22 residues processed: 148 average time/residue: 0.1954 time to fit residues: 41.9868 Evaluate side-chains 146 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 68 VAL Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain R residue 250 VAL Chi-restraints excluded: chain R residue 271 THR Chi-restraints excluded: chain R residue 298 THR Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 45 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 75 optimal weight: 0.7980 chunk 0 optimal weight: 7.9990 chunk 55 optimal weight: 0.9980 chunk 98 optimal weight: 6.9990 chunk 27 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9322 Z= 0.158 Angle : 0.557 10.260 12619 Z= 0.289 Chirality : 0.042 0.162 1403 Planarity : 0.004 0.051 1597 Dihedral : 5.753 81.187 1264 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.62 % Allowed : 18.20 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.25), residues: 1136 helix: 1.65 (0.26), residues: 398 sheet: -0.35 (0.33), residues: 257 loop : -1.89 (0.25), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP R 310 HIS 0.004 0.001 HIS B 225 PHE 0.022 0.001 PHE R 165 TYR 0.015 0.001 TYR S 190 ARG 0.002 0.000 ARG R 222 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.839 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.6933 (tt0) cc_final: 0.6674 (tm-30) REVERT: B 42 ARG cc_start: 0.7705 (ptm-80) cc_final: 0.7324 (tmt170) REVERT: B 153 ASP cc_start: 0.7657 (t0) cc_final: 0.7407 (t0) REVERT: B 247 ASP cc_start: 0.8222 (t70) cc_final: 0.7648 (t0) REVERT: R 69 ASP cc_start: 0.7356 (m-30) cc_final: 0.7083 (m-30) REVERT: R 165 PHE cc_start: 0.8316 (p90) cc_final: 0.7990 (p90) REVERT: S 20 LEU cc_start: 0.7066 (mt) cc_final: 0.6731 (mt) REVERT: S 172 THR cc_start: 0.7900 (m) cc_final: 0.7375 (t) REVERT: S 230 MET cc_start: 0.5806 (tmm) cc_final: 0.5581 (tmm) outliers start: 16 outliers final: 12 residues processed: 138 average time/residue: 0.1796 time to fit residues: 36.2533 Evaluate side-chains 135 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 123 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 193 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 0.8980 chunk 21 optimal weight: 9.9990 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 109 optimal weight: 4.9990 chunk 90 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 266 HIS S 35 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9322 Z= 0.203 Angle : 0.567 8.561 12619 Z= 0.292 Chirality : 0.043 0.197 1403 Planarity : 0.004 0.049 1597 Dihedral : 5.749 84.683 1264 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.22 % Allowed : 17.90 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.25), residues: 1136 helix: 1.76 (0.26), residues: 395 sheet: -0.35 (0.33), residues: 257 loop : -1.83 (0.25), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP R 310 HIS 0.004 0.001 HIS S 35 PHE 0.021 0.001 PHE S 80 TYR 0.016 0.001 TYR A 37 ARG 0.002 0.000 ARG B 46 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.6936 (tt0) cc_final: 0.6676 (tm-30) REVERT: B 42 ARG cc_start: 0.7748 (ptm-80) cc_final: 0.7346 (tmt170) REVERT: B 153 ASP cc_start: 0.7859 (t0) cc_final: 0.7640 (t0) REVERT: B 247 ASP cc_start: 0.8176 (t70) cc_final: 0.7593 (t0) REVERT: B 256 ARG cc_start: 0.8028 (mtp180) cc_final: 0.7807 (mtp180) REVERT: R 23 ARG cc_start: 0.8290 (mpt-90) cc_final: 0.8060 (mpt-90) REVERT: R 69 ASP cc_start: 0.7514 (m-30) cc_final: 0.7250 (m-30) REVERT: R 262 ILE cc_start: 0.8760 (tp) cc_final: 0.8337 (tp) REVERT: S 172 THR cc_start: 0.7892 (m) cc_final: 0.7384 (t) outliers start: 22 outliers final: 18 residues processed: 142 average time/residue: 0.2047 time to fit residues: 41.1408 Evaluate side-chains 144 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 92 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 50 optimal weight: 7.9990 chunk 67 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9322 Z= 0.198 Angle : 0.575 10.075 12619 Z= 0.294 Chirality : 0.043 0.183 1403 Planarity : 0.004 0.050 1597 Dihedral : 5.749 85.862 1264 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 2.02 % Allowed : 18.91 % Favored : 79.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.22 (0.25), residues: 1136 helix: 1.79 (0.26), residues: 395 sheet: -0.23 (0.33), residues: 255 loop : -1.80 (0.25), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP R 310 HIS 0.004 0.001 HIS B 225 PHE 0.019 0.001 PHE A 212 TYR 0.018 0.001 TYR A 318 ARG 0.004 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.048 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.6974 (tt0) cc_final: 0.6684 (tm-30) REVERT: B 42 ARG cc_start: 0.7764 (ptm-80) cc_final: 0.7388 (tmt170) REVERT: B 153 ASP cc_start: 0.7725 (t0) cc_final: 0.7481 (t0) REVERT: B 247 ASP cc_start: 0.8165 (t70) cc_final: 0.7600 (t0) REVERT: B 256 ARG cc_start: 0.7971 (mtp180) cc_final: 0.7766 (mtp85) REVERT: R 23 ARG cc_start: 0.8293 (mpt-90) cc_final: 0.8061 (mpt-90) REVERT: R 69 ASP cc_start: 0.7504 (m-30) cc_final: 0.7226 (m-30) REVERT: R 262 ILE cc_start: 0.8741 (tp) cc_final: 0.8325 (tp) REVERT: S 172 THR cc_start: 0.7883 (m) cc_final: 0.7405 (t) REVERT: Y 21 MET cc_start: 0.6419 (pmm) cc_final: 0.5008 (mtp) outliers start: 20 outliers final: 18 residues processed: 139 average time/residue: 0.1975 time to fit residues: 39.3553 Evaluate side-chains 144 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 126 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 311 HIS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 85 optimal weight: 0.0060 chunk 99 optimal weight: 1.9990 chunk 104 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 overall best weight: 1.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 9322 Z= 0.253 Angle : 0.604 9.318 12619 Z= 0.311 Chirality : 0.044 0.176 1403 Planarity : 0.004 0.049 1597 Dihedral : 5.858 87.970 1264 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 2.43 % Allowed : 18.91 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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 (0.25), residues: 1136 helix: 1.72 (0.26), residues: 395 sheet: -0.26 (0.33), residues: 256 loop : -1.85 (0.25), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP R 310 HIS 0.005 0.001 HIS B 225 PHE 0.022 0.002 PHE A 212 TYR 0.021 0.002 TYR A 318 ARG 0.003 0.000 ARG A 333 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.6926 (tt0) cc_final: 0.6618 (tm-30) REVERT: B 42 ARG cc_start: 0.7822 (ptm-80) cc_final: 0.7454 (tmt170) REVERT: B 153 ASP cc_start: 0.7993 (t0) cc_final: 0.7749 (t0) REVERT: B 247 ASP cc_start: 0.8159 (t70) cc_final: 0.7596 (t0) REVERT: R 23 ARG cc_start: 0.8300 (mpt-90) cc_final: 0.7977 (mpt-90) REVERT: R 69 ASP cc_start: 0.7543 (m-30) cc_final: 0.7278 (m-30) REVERT: S 172 THR cc_start: 0.7865 (m) cc_final: 0.7387 (t) REVERT: Y 21 MET cc_start: 0.6398 (pmm) cc_final: 0.5044 (mtp) outliers start: 24 outliers final: 20 residues processed: 140 average time/residue: 0.2003 time to fit residues: 40.1562 Evaluate side-chains 145 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain S residue 214 LEU Chi-restraints excluded: chain Y residue 41 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 5.9990 chunk 104 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 44 optimal weight: 7.9990 chunk 79 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 107 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9322 Z= 0.249 Angle : 0.605 10.888 12619 Z= 0.310 Chirality : 0.044 0.167 1403 Planarity : 0.004 0.051 1597 Dihedral : 5.896 89.347 1264 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.22 % Allowed : 20.02 % Favored : 77.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.35 (0.25), residues: 1136 helix: 1.68 (0.26), residues: 395 sheet: -0.33 (0.33), residues: 258 loop : -1.86 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP R 310 HIS 0.005 0.001 HIS B 225 PHE 0.023 0.001 PHE A 212 TYR 0.022 0.001 TYR A 318 ARG 0.004 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 1.170 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.6923 (tt0) cc_final: 0.6631 (tm-30) REVERT: B 42 ARG cc_start: 0.7877 (ptm-80) cc_final: 0.7455 (tmt170) REVERT: B 153 ASP cc_start: 0.7845 (t0) cc_final: 0.7584 (t0) REVERT: B 247 ASP cc_start: 0.8155 (t70) cc_final: 0.7588 (t0) REVERT: R 23 ARG cc_start: 0.8313 (mpt-90) cc_final: 0.7999 (mpt-90) REVERT: R 69 ASP cc_start: 0.7510 (m-30) cc_final: 0.7236 (m-30) REVERT: S 172 THR cc_start: 0.7851 (m) cc_final: 0.7379 (t) REVERT: Y 21 MET cc_start: 0.6246 (pmm) cc_final: 0.5125 (mtm) REVERT: Y 38 MET cc_start: 0.7776 (ttm) cc_final: 0.7558 (mtt) outliers start: 22 outliers final: 19 residues processed: 142 average time/residue: 0.2113 time to fit residues: 43.6173 Evaluate side-chains 145 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 126 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 284 ASP Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 112 optimal weight: 2.9990 chunk 103 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9322 Z= 0.227 Angle : 0.599 11.143 12619 Z= 0.305 Chirality : 0.043 0.163 1403 Planarity : 0.004 0.049 1597 Dihedral : 5.905 89.598 1264 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 1.82 % Allowed : 20.73 % Favored : 77.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.32 (0.25), residues: 1136 helix: 1.71 (0.26), residues: 395 sheet: -0.29 (0.33), residues: 258 loop : -1.87 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP R 310 HIS 0.005 0.001 HIS B 225 PHE 0.028 0.001 PHE A 212 TYR 0.022 0.002 TYR A 318 ARG 0.004 0.000 ARG A 333 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2272 Ramachandran restraints generated. 1136 Oldfield, 0 Emsley, 1136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 209 GLU cc_start: 0.6895 (tt0) cc_final: 0.6585 (tm-30) REVERT: B 42 ARG cc_start: 0.7902 (ptm-80) cc_final: 0.7499 (tmt170) REVERT: B 153 ASP cc_start: 0.7918 (t0) cc_final: 0.7672 (t0) REVERT: B 247 ASP cc_start: 0.8173 (t70) cc_final: 0.7606 (t0) REVERT: R 23 ARG cc_start: 0.8307 (mpt-90) cc_final: 0.8035 (mpt-90) REVERT: R 69 ASP cc_start: 0.7505 (m-30) cc_final: 0.7231 (m-30) REVERT: S 146 SER cc_start: 0.5235 (m) cc_final: 0.4674 (t) REVERT: Y 21 MET cc_start: 0.6246 (pmm) cc_final: 0.5094 (mtm) outliers start: 18 outliers final: 18 residues processed: 137 average time/residue: 0.1943 time to fit residues: 38.7383 Evaluate side-chains 142 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 124 time to evaluate : 1.073 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain A residue 334 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 195 ASP Chi-restraints excluded: chain B residue 320 VAL Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 46 VAL Chi-restraints excluded: chain R residue 74 CYS Chi-restraints excluded: chain R residue 76 VAL Chi-restraints excluded: chain R residue 94 VAL Chi-restraints excluded: chain R residue 193 LEU Chi-restraints excluded: chain S residue 214 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 89 optimal weight: 7.9990 chunk 37 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 35 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.208711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.133244 restraints weight = 9238.707| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 3.20 r_work: 0.3391 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9322 Z= 0.203 Angle : 0.588 11.596 12619 Z= 0.298 Chirality : 0.043 0.157 1403 Planarity : 0.004 0.051 1597 Dihedral : 5.864 89.463 1264 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.92 % Allowed : 20.73 % Favored : 77.35 % 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: -0.26 (0.25), residues: 1136 helix: 1.79 (0.26), residues: 395 sheet: -0.24 (0.33), residues: 256 loop : -1.86 (0.25), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.002 TRP R 310 HIS 0.004 0.001 HIS B 225 PHE 0.026 0.001 PHE A 212 TYR 0.022 0.001 TYR A 318 ARG 0.004 0.000 ARG A 333 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2217.65 seconds wall clock time: 41 minutes 10.02 seconds (2470.02 seconds total)