Starting phenix.real_space_refine on Sat Aug 23 00:08:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fmz_29301/08_2025/8fmz_29301.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fmz_29301/08_2025/8fmz_29301.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8fmz_29301/08_2025/8fmz_29301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fmz_29301/08_2025/8fmz_29301.map" model { file = "/net/cci-nas-00/data/ceres_data/8fmz_29301/08_2025/8fmz_29301.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fmz_29301/08_2025/8fmz_29301.cif" } resolution = 2.59 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= 0.159 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 55 5.16 5 C 5595 2.51 5 N 1492 2.21 5 O 1626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8768 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1795 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 6, 'TRANS': 214} Chain breaks: 3 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 6 Chain: "C" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2593 Classifications: {'peptide': 338} 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: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 380 Classifications: {'peptide': 51} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 46} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "E" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1754 Classifications: {'peptide': 230} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 219} Chain breaks: 2 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 280, 2188 Classifications: {'peptide': 280} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 270} Chain breaks: 3 Unresolved non-hydrogen bonds: 30 Unresolved non-hydrogen angles: 36 Unresolved non-hydrogen dihedrals: 26 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 21 Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 58 Classifications: {'peptide': 6} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 4} Time building chain proxies: 1.57, per 1000 atoms: 0.18 Number of scatterers: 8768 At special positions: 0 Unit cell: (88.88, 120.56, 131.12, 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 55 16.00 O 1626 8.00 N 1492 7.00 C 5595 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.04 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 225 " 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: 0.53 Conformation dependent library (CDL) restraints added in 312.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 14 sheets defined 39.5% alpha, 24.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'B' and resid 6 through 31 Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 94 through 101 removed outlier: 3.736A pdb=" N GLN B 98 " --> pdb=" O LYS B 95 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN B 101 " --> pdb=" O GLN B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 130 Processing helix chain 'B' and resid 131 through 135 removed outlier: 4.079A pdb=" N ARG B 135 " --> pdb=" O ARG B 132 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 156 Processing helix chain 'B' and resid 159 through 163 Processing helix chain 'B' and resid 164 through 170 removed outlier: 3.505A pdb=" N TYR B 170 " --> pdb=" O PHE B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 204 removed outlier: 3.738A pdb=" N PHE B 197 " --> pdb=" O ILE B 193 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N SER B 204 " --> pdb=" O ILE B 200 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 243 Processing helix chain 'C' and resid 4 through 25 Processing helix chain 'C' and resid 29 through 37 removed outlier: 4.078A pdb=" N THR C 34 " --> pdb=" O SER C 31 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N ASN C 35 " --> pdb=" O GLN C 32 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASN C 36 " --> pdb=" O ILE C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 132 removed outlier: 3.775A pdb=" N GLY C 131 " --> pdb=" O THR C 128 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASN C 132 " --> pdb=" O ARG C 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 128 through 132' Processing helix chain 'D' and resid 12 through 24 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'D' and resid 45 through 48 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.166A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 Processing helix chain 'A' and resid 52 through 56 removed outlier: 4.040A pdb=" N ASP A 56 " --> pdb=" O SER A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 90 Processing helix chain 'A' and resid 101 through 128 removed outlier: 3.679A pdb=" N HIS A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N MET A 121 " --> pdb=" O LEU A 117 " (cutoff:3.500A) Proline residue: A 122 - end of helix Processing helix chain 'A' and resid 137 through 173 Processing helix chain 'A' and resid 173 through 181 removed outlier: 3.579A pdb=" N THR A 179 " --> pdb=" O PHE A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 201 removed outlier: 3.543A pdb=" N ALA A 201 " --> pdb=" O SER A 197 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 206 Processing helix chain 'A' and resid 219 through 221 No H-bonds generated for 'chain 'A' and resid 219 through 221' Processing helix chain 'A' and resid 230 through 246 removed outlier: 3.618A pdb=" N VAL A 236 " --> pdb=" O ALA A 232 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 266 Processing helix chain 'A' and resid 304 through 334 Proline residue: A 323 - end of helix removed outlier: 3.552A pdb=" N ILE A 334 " --> pdb=" O MET A 330 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 370 removed outlier: 3.671A pdb=" N HIS A 348 " --> pdb=" O PHE A 344 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER A 362 " --> pdb=" O PHE A 358 " (cutoff:3.500A) Proline residue: A 366 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 69 through 76 removed outlier: 4.697A pdb=" N VAL B 86 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.499A pdb=" N GLY B 40 " --> pdb=" O VAL B 86 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA B 105 " --> pdb=" O ARG B 35 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N ILE B 106 " --> pdb=" O ILE B 140 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N PHE B 142 " --> pdb=" O ILE B 106 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE B 108 " --> pdb=" O PHE B 142 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ASN B 144 " --> pdb=" O PHE B 108 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL B 110 " --> pdb=" O ASN B 144 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.711A pdb=" N ARG C 49 " --> pdb=" O ILE C 338 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.701A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.974A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N ASN C 125 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.029A pdb=" N VAL C 135 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.566A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 192 removed outlier: 6.915A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N CYS C 218 " --> pdb=" O ASP C 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.669A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.625A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.550A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 6.161A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.017A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.017A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 130 Processing sheet with id=AB4, first strand: chain 'E' and resid 134 through 136 removed outlier: 3.556A pdb=" N GLU E 234 " --> pdb=" O VAL E 135 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N LEU E 162 " --> pdb=" O TYR E 178 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N TYR E 178 " --> pdb=" O LEU E 162 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 208 through 212 471 hydrogen bonds defined for protein. 1287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.06 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2822 1.34 - 1.46: 2052 1.46 - 1.58: 3998 1.58 - 1.69: 0 1.69 - 1.81: 81 Bond restraints: 8953 Sorted by residual: bond pdb=" N ASP C 291 " pdb=" CA ASP C 291 " ideal model delta sigma weight residual 1.457 1.493 -0.036 1.40e-02 5.10e+03 6.68e+00 bond pdb=" N ASP C 290 " pdb=" CA ASP C 290 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.32e-02 5.74e+03 5.59e+00 bond pdb=" N ASP C 186 " pdb=" CA ASP C 186 " ideal model delta sigma weight residual 1.456 1.486 -0.030 1.28e-02 6.10e+03 5.43e+00 bond pdb=" C ILE A 202 " pdb=" N PRO A 203 " ideal model delta sigma weight residual 1.335 1.353 -0.019 1.28e-02 6.10e+03 2.16e+00 bond pdb=" CA ASP C 290 " pdb=" C ASP C 290 " ideal model delta sigma weight residual 1.523 1.539 -0.017 1.41e-02 5.03e+03 1.42e+00 ... (remaining 8948 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 11926 1.76 - 3.52: 192 3.52 - 5.28: 18 5.28 - 7.04: 4 7.04 - 8.79: 2 Bond angle restraints: 12142 Sorted by residual: angle pdb=" N VAL C 187 " pdb=" CA VAL C 187 " pdb=" CB VAL C 187 " ideal model delta sigma weight residual 111.00 119.79 -8.79 1.14e+00 7.69e-01 5.95e+01 angle pdb=" N TYR C 289 " pdb=" CA TYR C 289 " pdb=" C TYR C 289 " ideal model delta sigma weight residual 109.81 118.54 -8.73 1.53e+00 4.27e-01 3.26e+01 angle pdb=" N VAL C 187 " pdb=" CA VAL C 187 " pdb=" C VAL C 187 " ideal model delta sigma weight residual 108.23 103.12 5.11 1.53e+00 4.27e-01 1.12e+01 angle pdb=" C ASP C 195 " pdb=" N THR C 196 " pdb=" CA THR C 196 " ideal model delta sigma weight residual 122.40 126.46 -4.06 1.45e+00 4.76e-01 7.84e+00 angle pdb=" CA ASP C 186 " pdb=" C ASP C 186 " pdb=" O ASP C 186 " ideal model delta sigma weight residual 120.92 117.93 2.99 1.14e+00 7.69e-01 6.87e+00 ... (remaining 12137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.83: 5047 15.83 - 31.67: 207 31.67 - 47.50: 27 47.50 - 63.34: 4 63.34 - 79.17: 2 Dihedral angle restraints: 5287 sinusoidal: 2020 harmonic: 3267 Sorted by residual: dihedral pdb=" CA TRP C 82 " pdb=" C TRP C 82 " pdb=" N ASP C 83 " pdb=" CA ASP C 83 " ideal model delta harmonic sigma weight residual 180.00 161.28 18.72 0 5.00e+00 4.00e-02 1.40e+01 dihedral pdb=" CA ARG E 179 " pdb=" C ARG E 179 " pdb=" N MET E 180 " pdb=" CA MET E 180 " ideal model delta harmonic sigma weight residual 180.00 162.26 17.74 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA PHE E 32 " pdb=" C PHE E 32 " pdb=" N GLY E 33 " pdb=" CA GLY E 33 " ideal model delta harmonic sigma weight residual 180.00 163.10 16.90 0 5.00e+00 4.00e-02 1.14e+01 ... (remaining 5284 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 991 0.041 - 0.082: 307 0.082 - 0.124: 86 0.124 - 0.165: 3 0.165 - 0.206: 1 Chirality restraints: 1388 Sorted by residual: chirality pdb=" CA TYR C 289 " pdb=" N TYR C 289 " pdb=" C TYR C 289 " pdb=" CB TYR C 289 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA VAL E 37 " pdb=" N VAL E 37 " pdb=" C VAL E 37 " pdb=" CB VAL E 37 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.41e-01 chirality pdb=" CA ILE C 93 " pdb=" N ILE C 93 " pdb=" C ILE C 93 " pdb=" CB ILE C 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 1385 not shown) Planarity restraints: 1531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR C 289 " -0.011 2.00e-02 2.50e+03 2.16e-02 4.68e+00 pdb=" C TYR C 289 " 0.037 2.00e-02 2.50e+03 pdb=" O TYR C 289 " -0.014 2.00e-02 2.50e+03 pdb=" N ASP C 290 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " 0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO C 236 " -0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 226 " 0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO A 227 " -0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 227 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 227 " 0.020 5.00e-02 4.00e+02 ... (remaining 1528 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2006 2.79 - 3.32: 8111 3.32 - 3.85: 14475 3.85 - 4.37: 17461 4.37 - 4.90: 30600 Nonbonded interactions: 72653 Sorted by model distance: nonbonded pdb=" OE2 GLU C 260 " pdb=" OG1 THR C 263 " model vdw 2.264 3.040 nonbonded pdb=" O ASN A 241 " pdb=" OG SER A 245 " model vdw 2.267 3.040 nonbonded pdb=" OE2 GLU B 8 " pdb=" OH TYR E 163 " model vdw 2.269 3.040 nonbonded pdb=" O ASP A 230 " pdb=" OG1 THR A 233 " model vdw 2.273 3.040 nonbonded pdb=" NH1 ARG B 15 " pdb=" O VAL C 90 " model vdw 2.275 3.120 ... (remaining 72648 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=0.00 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: 0.860 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 7.170 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:5.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 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 : 0.004 0.036 8955 Z= 0.187 Angle : 0.575 8.795 12146 Z= 0.346 Chirality : 0.042 0.206 1388 Planarity : 0.004 0.044 1531 Dihedral : 8.857 79.171 3171 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.21 % Allowed : 3.51 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.58 (0.25), residues: 1098 helix: 2.54 (0.26), residues: 381 sheet: 0.65 (0.28), residues: 301 loop : 0.01 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 38 TYR 0.013 0.001 TYR E 178 PHE 0.014 0.001 PHE C 151 TRP 0.016 0.001 TRP C 169 HIS 0.003 0.001 HIS A 348 Details of bonding type rmsd covalent geometry : bond 0.00398 ( 8953) covalent geometry : angle 0.57475 (12142) SS BOND : bond 0.00515 ( 2) SS BOND : angle 0.81194 ( 4) hydrogen bonds : bond 0.12833 ( 467) hydrogen bonds : angle 5.39918 ( 1287) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 206 time to evaluate : 0.229 Fit side-chains REVERT: B 10 LYS cc_start: 0.7671 (mttt) cc_final: 0.7281 (mttt) REVERT: B 21 LYS cc_start: 0.7549 (tttm) cc_final: 0.6884 (ttpt) REVERT: B 24 ARG cc_start: 0.6542 (mtm-85) cc_final: 0.6115 (mtm-85) REVERT: B 69 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.8092 (tt) REVERT: B 73 LYS cc_start: 0.8448 (mttt) cc_final: 0.8069 (mtpm) REVERT: B 82 HIS cc_start: 0.7911 (t-170) cc_final: 0.7623 (t-90) REVERT: B 120 GLU cc_start: 0.7449 (mt-10) cc_final: 0.7068 (mt-10) REVERT: B 195 LYS cc_start: 0.7358 (tttm) cc_final: 0.7113 (ttpp) REVERT: B 208 ARG cc_start: 0.6845 (mtm-85) cc_final: 0.6567 (ptt-90) REVERT: C 101 MET cc_start: 0.8277 (mtt) cc_final: 0.8063 (mpp) REVERT: C 254 ASP cc_start: 0.7683 (t70) cc_final: 0.7377 (t0) REVERT: C 325 MET cc_start: 0.8036 (mmm) cc_final: 0.7719 (tpp) REVERT: D 21 MET cc_start: 0.6224 (mtm) cc_final: 0.5483 (tmm) REVERT: E 7 SER cc_start: 0.8016 (t) cc_final: 0.7605 (p) REVERT: E 46 GLU cc_start: 0.7617 (tt0) cc_final: 0.7169 (tt0) REVERT: E 85 SER cc_start: 0.8216 (m) cc_final: 0.7899 (t) REVERT: A 61 ILE cc_start: 0.5555 (tp) cc_final: 0.5323 (tp) REVERT: A 121 MET cc_start: 0.6297 (tpp) cc_final: 0.6067 (tpp) REVERT: A 248 PHE cc_start: 0.7530 (t80) cc_final: 0.7284 (t80) REVERT: A 361 SER cc_start: 0.7548 (t) cc_final: 0.7050 (p) outliers start: 2 outliers final: 0 residues processed: 207 average time/residue: 0.4872 time to fit residues: 107.3462 Evaluate side-chains 137 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 136 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 106 optimal weight: 4.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN C 62 HIS E 130 GLN E 174 GLN E 182 ASN A 52 ASN A 325 HIS ** A 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.180023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.123960 restraints weight = 8580.466| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 1.75 r_work: 0.3136 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.2715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 8955 Z= 0.241 Angle : 0.638 6.724 12146 Z= 0.346 Chirality : 0.046 0.155 1388 Planarity : 0.005 0.048 1531 Dihedral : 4.880 24.004 1219 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.34 % Allowed : 10.00 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.44 (0.25), residues: 1098 helix: 2.42 (0.26), residues: 376 sheet: 0.53 (0.28), residues: 308 loop : -0.00 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 135 TYR 0.015 0.002 TYR E 103 PHE 0.024 0.002 PHE C 151 TRP 0.012 0.002 TRP C 169 HIS 0.006 0.002 HIS D 44 Details of bonding type rmsd covalent geometry : bond 0.00570 ( 8953) covalent geometry : angle 0.63728 (12142) SS BOND : bond 0.00938 ( 2) SS BOND : angle 1.31639 ( 4) hydrogen bonds : bond 0.05180 ( 467) hydrogen bonds : angle 5.04915 ( 1287) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 135 time to evaluate : 0.323 Fit side-chains REVERT: B 10 LYS cc_start: 0.8809 (mttt) cc_final: 0.8424 (mttt) REVERT: B 21 LYS cc_start: 0.8309 (tttm) cc_final: 0.7671 (ttpt) REVERT: B 24 ARG cc_start: 0.7070 (mtm-85) cc_final: 0.6746 (mtm-85) REVERT: B 73 LYS cc_start: 0.8866 (mttt) cc_final: 0.8260 (mtpm) REVERT: B 120 GLU cc_start: 0.7699 (mt-10) cc_final: 0.7365 (mt-10) REVERT: B 151 GLU cc_start: 0.6599 (mt-10) cc_final: 0.6250 (pt0) REVERT: B 152 LYS cc_start: 0.6647 (mttt) cc_final: 0.6398 (mttt) REVERT: B 195 LYS cc_start: 0.7680 (tttm) cc_final: 0.7330 (ttpp) REVERT: B 208 ARG cc_start: 0.7194 (mtm-85) cc_final: 0.6781 (ptt-90) REVERT: B 232 LYS cc_start: 0.8306 (ttmt) cc_final: 0.8024 (ttpt) REVERT: C 219 ARG cc_start: 0.8377 (mmm160) cc_final: 0.8121 (mtp180) REVERT: D 21 MET cc_start: 0.6313 (mtm) cc_final: 0.5488 (tmt) REVERT: E 7 SER cc_start: 0.8383 (t) cc_final: 0.8129 (p) REVERT: E 43 LYS cc_start: 0.8391 (mtpp) cc_final: 0.7889 (mtpm) REVERT: E 85 SER cc_start: 0.8616 (m) cc_final: 0.8305 (p) REVERT: A 248 PHE cc_start: 0.7309 (t80) cc_final: 0.7009 (t80) outliers start: 22 outliers final: 15 residues processed: 146 average time/residue: 0.5954 time to fit residues: 91.8060 Evaluate side-chains 137 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 122 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 362 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 55 optimal weight: 5.9990 chunk 13 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 77 optimal weight: 0.6980 chunk 35 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 116 ASN C 266 HIS E 130 GLN E 167 GLN E 174 GLN A 370 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.178156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.123022 restraints weight = 8570.433| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.84 r_work: 0.3140 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 8955 Z= 0.217 Angle : 0.598 7.703 12146 Z= 0.325 Chirality : 0.045 0.153 1388 Planarity : 0.005 0.047 1531 Dihedral : 4.838 23.854 1217 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 3.51 % Allowed : 12.77 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.24 (0.25), residues: 1098 helix: 2.25 (0.26), residues: 382 sheet: 0.48 (0.28), residues: 297 loop : -0.20 (0.30), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 135 TYR 0.015 0.002 TYR E 103 PHE 0.023 0.002 PHE C 151 TRP 0.013 0.002 TRP C 169 HIS 0.004 0.001 HIS D 44 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 8953) covalent geometry : angle 0.59771 (12142) SS BOND : bond 0.00932 ( 2) SS BOND : angle 1.56081 ( 4) hydrogen bonds : bond 0.04908 ( 467) hydrogen bonds : angle 4.97297 ( 1287) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 129 time to evaluate : 0.226 Fit side-chains REVERT: B 10 LYS cc_start: 0.8721 (mttt) cc_final: 0.8316 (mttt) REVERT: B 21 LYS cc_start: 0.8306 (tttm) cc_final: 0.7683 (ttpt) REVERT: B 24 ARG cc_start: 0.7019 (mtm-85) cc_final: 0.6631 (mtm-85) REVERT: B 73 LYS cc_start: 0.8878 (mttt) cc_final: 0.8530 (mtpt) REVERT: B 82 HIS cc_start: 0.8172 (t-90) cc_final: 0.7944 (t70) REVERT: B 120 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7294 (mt-10) REVERT: B 151 GLU cc_start: 0.6389 (mt-10) cc_final: 0.6065 (pt0) REVERT: B 195 LYS cc_start: 0.7567 (tttm) cc_final: 0.7181 (ttpp) REVERT: B 208 ARG cc_start: 0.7156 (mtm-85) cc_final: 0.6427 (mmm160) REVERT: B 232 LYS cc_start: 0.8234 (ttmt) cc_final: 0.7949 (ttpt) REVERT: C 217 MET cc_start: 0.8709 (pmm) cc_final: 0.8411 (pmm) REVERT: C 219 ARG cc_start: 0.8303 (mmm160) cc_final: 0.8019 (mtp180) REVERT: D 21 MET cc_start: 0.6392 (mtm) cc_final: 0.5508 (tmt) REVERT: E 7 SER cc_start: 0.8407 (t) cc_final: 0.8123 (p) REVERT: E 43 LYS cc_start: 0.8369 (mtpp) cc_final: 0.7764 (mtpm) REVERT: E 85 SER cc_start: 0.8690 (m) cc_final: 0.8319 (p) REVERT: A 61 ILE cc_start: 0.5150 (tp) cc_final: 0.4924 (tp) REVERT: A 208 MET cc_start: 0.6166 (mmp) cc_final: 0.5965 (mmp) REVERT: A 248 PHE cc_start: 0.7332 (t80) cc_final: 0.6986 (t80) outliers start: 33 outliers final: 15 residues processed: 148 average time/residue: 0.5466 time to fit residues: 85.5399 Evaluate side-chains 133 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 118 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 362 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 3.9990 chunk 107 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 28 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 72 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 116 ASN A 103 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.177818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.121293 restraints weight = 8699.748| |-----------------------------------------------------------------------------| r_work (start): 0.3313 rms_B_bonded: 1.92 r_work: 0.3109 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2973 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2973 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.3378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 8955 Z= 0.221 Angle : 0.603 6.329 12146 Z= 0.327 Chirality : 0.045 0.155 1388 Planarity : 0.005 0.048 1531 Dihedral : 4.893 23.954 1217 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.94 % Allowed : 13.72 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.17 (0.25), residues: 1098 helix: 2.24 (0.26), residues: 381 sheet: 0.46 (0.28), residues: 292 loop : -0.29 (0.30), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 135 TYR 0.015 0.002 TYR E 103 PHE 0.023 0.002 PHE C 151 TRP 0.013 0.002 TRP C 169 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00523 ( 8953) covalent geometry : angle 0.60233 (12142) SS BOND : bond 0.00914 ( 2) SS BOND : angle 1.63471 ( 4) hydrogen bonds : bond 0.04898 ( 467) hydrogen bonds : angle 4.98167 ( 1287) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 122 time to evaluate : 0.356 Fit side-chains REVERT: B 21 LYS cc_start: 0.8357 (tttm) cc_final: 0.7747 (ttpt) REVERT: B 24 ARG cc_start: 0.7007 (mtm-85) cc_final: 0.6676 (mtm-85) REVERT: B 73 LYS cc_start: 0.8923 (mttt) cc_final: 0.8623 (mtpt) REVERT: B 151 GLU cc_start: 0.6536 (mt-10) cc_final: 0.6221 (pt0) REVERT: B 195 LYS cc_start: 0.7629 (tttm) cc_final: 0.7263 (ttpp) REVERT: B 208 ARG cc_start: 0.7189 (mtm-85) cc_final: 0.6427 (mmm160) REVERT: B 232 LYS cc_start: 0.8318 (ttmt) cc_final: 0.8047 (ttpt) REVERT: C 217 MET cc_start: 0.8697 (pmm) cc_final: 0.8406 (pmm) REVERT: C 219 ARG cc_start: 0.8369 (mmm160) cc_final: 0.8081 (mtp180) REVERT: D 21 MET cc_start: 0.6500 (mtm) cc_final: 0.5694 (tmt) REVERT: E 7 SER cc_start: 0.8450 (t) cc_final: 0.8191 (p) REVERT: E 43 LYS cc_start: 0.8426 (mtpp) cc_final: 0.7850 (mtpm) REVERT: E 132 THR cc_start: 0.7641 (OUTLIER) cc_final: 0.7415 (m) REVERT: E 211 ASP cc_start: 0.7847 (t0) cc_final: 0.7635 (t0) REVERT: A 61 ILE cc_start: 0.5141 (tp) cc_final: 0.4917 (tp) REVERT: A 248 PHE cc_start: 0.7356 (t80) cc_final: 0.7050 (t80) outliers start: 37 outliers final: 25 residues processed: 145 average time/residue: 0.5345 time to fit residues: 82.0472 Evaluate side-chains 142 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 116 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 25 SER Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 242 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 362 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 0 optimal weight: 4.9990 chunk 109 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 chunk 85 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 76 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 91 optimal weight: 7.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 116 ASN E 167 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.180497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.128498 restraints weight = 8601.528| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 1.84 r_work: 0.3161 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3030 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8414 moved from start: 0.3441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8955 Z= 0.131 Angle : 0.509 7.839 12146 Z= 0.276 Chirality : 0.042 0.140 1388 Planarity : 0.004 0.047 1531 Dihedral : 4.473 23.154 1217 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.98 % Allowed : 15.00 % Favored : 82.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.40 (0.25), residues: 1098 helix: 2.54 (0.27), residues: 379 sheet: 0.50 (0.29), residues: 285 loop : -0.17 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 135 TYR 0.013 0.001 TYR E 178 PHE 0.016 0.001 PHE C 151 TRP 0.014 0.001 TRP C 169 HIS 0.005 0.001 HIS A 103 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 8953) covalent geometry : angle 0.50843 (12142) SS BOND : bond 0.00618 ( 2) SS BOND : angle 1.38590 ( 4) hydrogen bonds : bond 0.04031 ( 467) hydrogen bonds : angle 4.70079 ( 1287) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 124 time to evaluate : 0.226 Fit side-chains REVERT: B 10 LYS cc_start: 0.8568 (mttm) cc_final: 0.8248 (mttt) REVERT: B 21 LYS cc_start: 0.8372 (tttm) cc_final: 0.7830 (ttpt) REVERT: B 24 ARG cc_start: 0.7000 (mtm-85) cc_final: 0.6747 (mtm-85) REVERT: B 73 LYS cc_start: 0.8879 (mttt) cc_final: 0.8597 (mtpt) REVERT: B 135 ARG cc_start: 0.8438 (ptp-110) cc_final: 0.8198 (ptp-110) REVERT: B 151 GLU cc_start: 0.6579 (mt-10) cc_final: 0.6294 (pt0) REVERT: B 195 LYS cc_start: 0.7557 (tttm) cc_final: 0.7184 (ttpp) REVERT: B 208 ARG cc_start: 0.7161 (mtm-85) cc_final: 0.6406 (mmm160) REVERT: B 222 GLU cc_start: 0.7784 (OUTLIER) cc_final: 0.7553 (pt0) REVERT: B 232 LYS cc_start: 0.8319 (ttmt) cc_final: 0.8068 (tttt) REVERT: C 52 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8057 (mtt90) REVERT: C 101 MET cc_start: 0.9087 (mtp) cc_final: 0.8874 (mtp) REVERT: C 217 MET cc_start: 0.8731 (OUTLIER) cc_final: 0.8397 (pmm) REVERT: C 219 ARG cc_start: 0.8262 (mmm160) cc_final: 0.7990 (mtp180) REVERT: D 21 MET cc_start: 0.6563 (mtm) cc_final: 0.5850 (tmt) REVERT: E 23 SER cc_start: 0.8615 (t) cc_final: 0.8325 (p) REVERT: E 43 LYS cc_start: 0.8387 (mtpp) cc_final: 0.7826 (mtpm) REVERT: E 46 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8397 (tt0) REVERT: E 85 SER cc_start: 0.8693 (m) cc_final: 0.8343 (p) REVERT: A 61 ILE cc_start: 0.5186 (tp) cc_final: 0.4979 (tp) REVERT: A 208 MET cc_start: 0.5963 (mmp) cc_final: 0.5630 (mmm) REVERT: A 248 PHE cc_start: 0.7248 (t80) cc_final: 0.6937 (t80) REVERT: A 267 MET cc_start: 0.6639 (mpt) cc_final: 0.6430 (mpt) REVERT: A 352 MET cc_start: 0.7999 (mtp) cc_final: 0.7795 (mtm) outliers start: 28 outliers final: 14 residues processed: 138 average time/residue: 0.5579 time to fit residues: 81.2313 Evaluate side-chains 133 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 115 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 362 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 5.9990 chunk 32 optimal weight: 0.9980 chunk 23 optimal weight: 7.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 86 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.179797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.124155 restraints weight = 8560.940| |-----------------------------------------------------------------------------| r_work (start): 0.3354 rms_B_bonded: 1.78 r_work: 0.3139 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8955 Z= 0.152 Angle : 0.528 7.039 12146 Z= 0.286 Chirality : 0.042 0.142 1388 Planarity : 0.004 0.047 1531 Dihedral : 4.539 23.344 1217 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.87 % Allowed : 15.00 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.41 (0.26), residues: 1098 helix: 2.50 (0.27), residues: 379 sheet: 0.50 (0.28), residues: 292 loop : -0.13 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 96 TYR 0.014 0.002 TYR B 212 PHE 0.018 0.001 PHE C 151 TRP 0.013 0.001 TRP C 169 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00350 ( 8953) covalent geometry : angle 0.52776 (12142) SS BOND : bond 0.00711 ( 2) SS BOND : angle 1.46047 ( 4) hydrogen bonds : bond 0.04223 ( 467) hydrogen bonds : angle 4.73307 ( 1287) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.235 Fit side-chains REVERT: B 10 LYS cc_start: 0.8626 (mttm) cc_final: 0.8319 (mttt) REVERT: B 21 LYS cc_start: 0.8371 (tttm) cc_final: 0.7813 (ttpt) REVERT: B 24 ARG cc_start: 0.7009 (mtm-85) cc_final: 0.6739 (mtm-85) REVERT: B 73 LYS cc_start: 0.8912 (mttt) cc_final: 0.8617 (mtpt) REVERT: B 132 ARG cc_start: 0.8556 (ptt-90) cc_final: 0.8240 (ptt-90) REVERT: B 151 GLU cc_start: 0.6622 (mt-10) cc_final: 0.6349 (pt0) REVERT: B 195 LYS cc_start: 0.7552 (tttm) cc_final: 0.7169 (ttpp) REVERT: B 208 ARG cc_start: 0.7156 (mtm-85) cc_final: 0.6362 (mmm160) REVERT: B 222 GLU cc_start: 0.7813 (OUTLIER) cc_final: 0.7591 (pt0) REVERT: B 232 LYS cc_start: 0.8338 (ttmt) cc_final: 0.8094 (ttpt) REVERT: C 52 ARG cc_start: 0.8549 (OUTLIER) cc_final: 0.8103 (mtt90) REVERT: C 217 MET cc_start: 0.8737 (OUTLIER) cc_final: 0.8399 (pmm) REVERT: C 219 ARG cc_start: 0.8306 (mmm160) cc_final: 0.8026 (mtp180) REVERT: D 21 MET cc_start: 0.6422 (mtm) cc_final: 0.5728 (tmt) REVERT: E 23 SER cc_start: 0.8606 (t) cc_final: 0.8346 (p) REVERT: E 43 LYS cc_start: 0.8419 (mtpp) cc_final: 0.7851 (mtpm) REVERT: E 46 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8510 (tt0) REVERT: E 85 SER cc_start: 0.8707 (m) cc_final: 0.8350 (p) REVERT: E 211 ASP cc_start: 0.7794 (t0) cc_final: 0.7569 (t0) REVERT: A 248 PHE cc_start: 0.7323 (t80) cc_final: 0.7046 (t80) REVERT: A 267 MET cc_start: 0.6593 (mpt) cc_final: 0.6381 (mpt) REVERT: A 352 MET cc_start: 0.8024 (mtp) cc_final: 0.7814 (mtm) outliers start: 27 outliers final: 16 residues processed: 138 average time/residue: 0.5779 time to fit residues: 84.1785 Evaluate side-chains 137 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 253 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 23 optimal weight: 7.9990 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 28 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 92 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 95 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 103 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 116 ASN E 167 GLN A 305 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.179200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.125959 restraints weight = 8623.847| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.91 r_work: 0.3131 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3000 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8439 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8955 Z= 0.170 Angle : 0.555 6.792 12146 Z= 0.298 Chirality : 0.043 0.164 1388 Planarity : 0.004 0.047 1531 Dihedral : 4.644 23.548 1217 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 3.51 % Allowed : 14.68 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.34 (0.25), residues: 1098 helix: 2.43 (0.26), residues: 380 sheet: 0.46 (0.28), residues: 293 loop : -0.16 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 135 TYR 0.015 0.002 TYR B 212 PHE 0.019 0.002 PHE C 151 TRP 0.013 0.001 TRP C 169 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00395 ( 8953) covalent geometry : angle 0.55389 (12142) SS BOND : bond 0.00779 ( 2) SS BOND : angle 1.58027 ( 4) hydrogen bonds : bond 0.04358 ( 467) hydrogen bonds : angle 4.79805 ( 1287) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 115 time to evaluate : 0.261 Fit side-chains REVERT: B 10 LYS cc_start: 0.8620 (mttm) cc_final: 0.8304 (mttt) REVERT: B 21 LYS cc_start: 0.8357 (tttm) cc_final: 0.7792 (ttpt) REVERT: B 24 ARG cc_start: 0.6998 (mtm-85) cc_final: 0.6734 (mtm-85) REVERT: B 73 LYS cc_start: 0.8910 (mttt) cc_final: 0.8617 (mtpt) REVERT: B 132 ARG cc_start: 0.8571 (ptt-90) cc_final: 0.8205 (ptt-90) REVERT: B 135 ARG cc_start: 0.8374 (ptp-110) cc_final: 0.8141 (ptp-110) REVERT: B 151 GLU cc_start: 0.6649 (mt-10) cc_final: 0.6394 (pt0) REVERT: B 195 LYS cc_start: 0.7536 (tttm) cc_final: 0.7166 (ttpp) REVERT: B 208 ARG cc_start: 0.7192 (mtm-85) cc_final: 0.6425 (mmm160) REVERT: B 222 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7578 (pt0) REVERT: B 232 LYS cc_start: 0.8298 (ttmt) cc_final: 0.8044 (ttpt) REVERT: C 52 ARG cc_start: 0.8540 (OUTLIER) cc_final: 0.8095 (mtt90) REVERT: C 217 MET cc_start: 0.8720 (OUTLIER) cc_final: 0.8373 (pmm) REVERT: C 219 ARG cc_start: 0.8330 (mmm160) cc_final: 0.8051 (mtp180) REVERT: C 256 ARG cc_start: 0.8296 (OUTLIER) cc_final: 0.7574 (mtp180) REVERT: D 21 MET cc_start: 0.6461 (mtm) cc_final: 0.5763 (tmt) REVERT: E 23 SER cc_start: 0.8609 (t) cc_final: 0.8325 (p) REVERT: E 43 LYS cc_start: 0.8412 (mtpp) cc_final: 0.7845 (mtpm) REVERT: E 46 GLU cc_start: 0.8840 (OUTLIER) cc_final: 0.8470 (tt0) REVERT: A 248 PHE cc_start: 0.7336 (t80) cc_final: 0.7022 (t80) REVERT: A 352 MET cc_start: 0.8026 (mtp) cc_final: 0.7820 (mtm) outliers start: 33 outliers final: 20 residues processed: 131 average time/residue: 0.6367 time to fit residues: 87.7131 Evaluate side-chains 138 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 253 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 57 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 87 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.180468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.123276 restraints weight = 8665.634| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 1.92 r_work: 0.3146 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8955 Z= 0.132 Angle : 0.521 9.363 12146 Z= 0.278 Chirality : 0.042 0.151 1388 Planarity : 0.004 0.047 1531 Dihedral : 4.435 23.139 1217 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 2.98 % Allowed : 15.32 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.45 (0.26), residues: 1098 helix: 2.55 (0.27), residues: 380 sheet: 0.56 (0.28), residues: 287 loop : -0.17 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 135 TYR 0.013 0.001 TYR B 212 PHE 0.016 0.001 PHE C 151 TRP 0.013 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8953) covalent geometry : angle 0.52045 (12142) SS BOND : bond 0.00632 ( 2) SS BOND : angle 1.43533 ( 4) hydrogen bonds : bond 0.03968 ( 467) hydrogen bonds : angle 4.68226 ( 1287) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 115 time to evaluate : 0.245 Fit side-chains REVERT: B 10 LYS cc_start: 0.8579 (mttm) cc_final: 0.8274 (mttt) REVERT: B 21 LYS cc_start: 0.8337 (tttm) cc_final: 0.7775 (ttpt) REVERT: B 24 ARG cc_start: 0.6989 (mtm-85) cc_final: 0.6723 (mtm-85) REVERT: B 73 LYS cc_start: 0.8895 (mttt) cc_final: 0.8591 (mtpt) REVERT: B 132 ARG cc_start: 0.8561 (ptt-90) cc_final: 0.8212 (ptt-90) REVERT: B 151 GLU cc_start: 0.6685 (mt-10) cc_final: 0.6422 (pt0) REVERT: B 195 LYS cc_start: 0.7573 (tttm) cc_final: 0.7204 (ttpp) REVERT: B 208 ARG cc_start: 0.7154 (mtm-85) cc_final: 0.6389 (mmm160) REVERT: B 232 LYS cc_start: 0.8307 (ttmt) cc_final: 0.8011 (tttt) REVERT: C 52 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.8090 (mtt90) REVERT: C 217 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8390 (pmm) REVERT: C 219 ARG cc_start: 0.8299 (mmm160) cc_final: 0.8004 (mtp180) REVERT: C 256 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7456 (mtp180) REVERT: C 336 LEU cc_start: 0.8799 (OUTLIER) cc_final: 0.8215 (mt) REVERT: D 21 MET cc_start: 0.6490 (mtm) cc_final: 0.5805 (tmt) REVERT: E 23 SER cc_start: 0.8566 (t) cc_final: 0.8302 (p) REVERT: E 43 LYS cc_start: 0.8393 (mtpp) cc_final: 0.7821 (mtpm) REVERT: E 46 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.8521 (tt0) REVERT: E 85 SER cc_start: 0.8701 (m) cc_final: 0.8334 (p) outliers start: 28 outliers final: 19 residues processed: 130 average time/residue: 0.6161 time to fit residues: 84.1169 Evaluate side-chains 137 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 113 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain C residue 336 LEU Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 253 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 90 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 14 optimal weight: 4.9990 chunk 86 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 6 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3956 r_free = 0.3956 target = 0.177456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.120195 restraints weight = 8623.940| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.90 r_work: 0.3099 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 8955 Z= 0.238 Angle : 0.624 9.718 12146 Z= 0.332 Chirality : 0.045 0.160 1388 Planarity : 0.005 0.047 1531 Dihedral : 4.896 23.670 1217 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.30 % Allowed : 15.00 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.16 (0.25), residues: 1098 helix: 2.23 (0.26), residues: 381 sheet: 0.39 (0.28), residues: 294 loop : -0.26 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 96 TYR 0.017 0.002 TYR B 212 PHE 0.023 0.002 PHE C 151 TRP 0.011 0.002 TRP C 169 HIS 0.005 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00566 ( 8953) covalent geometry : angle 0.62369 (12142) SS BOND : bond 0.00923 ( 2) SS BOND : angle 1.74478 ( 4) hydrogen bonds : bond 0.04905 ( 467) hydrogen bonds : angle 4.95661 ( 1287) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 113 time to evaluate : 0.278 Fit side-chains REVERT: B 21 LYS cc_start: 0.8357 (tttm) cc_final: 0.7761 (ttpt) REVERT: B 24 ARG cc_start: 0.7043 (mtm-85) cc_final: 0.6755 (mtm-85) REVERT: B 73 LYS cc_start: 0.8942 (mttt) cc_final: 0.8604 (mtpt) REVERT: B 132 ARG cc_start: 0.8518 (ptt-90) cc_final: 0.8254 (ptt-90) REVERT: B 151 GLU cc_start: 0.6657 (mt-10) cc_final: 0.6407 (pt0) REVERT: B 195 LYS cc_start: 0.7601 (tttm) cc_final: 0.7215 (ttpp) REVERT: B 208 ARG cc_start: 0.7230 (mtm-85) cc_final: 0.6447 (mmm160) REVERT: B 232 LYS cc_start: 0.8341 (ttmt) cc_final: 0.8085 (ttpt) REVERT: C 52 ARG cc_start: 0.8598 (OUTLIER) cc_final: 0.8144 (mtt90) REVERT: C 219 ARG cc_start: 0.8383 (mmm160) cc_final: 0.8120 (mtp180) REVERT: C 256 ARG cc_start: 0.8323 (OUTLIER) cc_final: 0.7984 (mtm180) REVERT: D 21 MET cc_start: 0.6460 (mtm) cc_final: 0.5752 (tmt) REVERT: E 43 LYS cc_start: 0.8479 (mtpp) cc_final: 0.7915 (mtpt) REVERT: E 46 GLU cc_start: 0.8878 (OUTLIER) cc_final: 0.8517 (tt0) REVERT: E 85 SER cc_start: 0.8649 (m) cc_final: 0.8339 (t) REVERT: E 211 ASP cc_start: 0.7781 (t0) cc_final: 0.7413 (t0) outliers start: 31 outliers final: 25 residues processed: 131 average time/residue: 0.6210 time to fit residues: 85.6678 Evaluate side-chains 140 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 112 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 128 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 76 LYS Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 116 THR Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 253 ILE Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 372 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 103 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 102 optimal weight: 0.6980 chunk 101 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 chunk 25 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 90 optimal weight: 10.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.180729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.124960 restraints weight = 8569.692| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.86 r_work: 0.3175 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.3742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8955 Z= 0.121 Angle : 0.515 8.605 12146 Z= 0.274 Chirality : 0.041 0.153 1388 Planarity : 0.004 0.047 1531 Dihedral : 4.419 22.744 1217 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.34 % Allowed : 16.06 % Favored : 81.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.39 (0.26), residues: 1098 helix: 2.54 (0.27), residues: 380 sheet: 0.53 (0.29), residues: 285 loop : -0.23 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 96 TYR 0.014 0.001 TYR E 178 PHE 0.015 0.001 PHE C 151 TRP 0.015 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00270 ( 8953) covalent geometry : angle 0.51414 (12142) SS BOND : bond 0.00566 ( 2) SS BOND : angle 1.39230 ( 4) hydrogen bonds : bond 0.03895 ( 467) hydrogen bonds : angle 4.67997 ( 1287) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 113 time to evaluate : 0.248 Fit side-chains REVERT: B 10 LYS cc_start: 0.8553 (mttm) cc_final: 0.8239 (mttt) REVERT: B 21 LYS cc_start: 0.8334 (tttm) cc_final: 0.7785 (ttpt) REVERT: B 24 ARG cc_start: 0.6990 (mtm-85) cc_final: 0.6729 (mtm-85) REVERT: B 73 LYS cc_start: 0.8878 (mttt) cc_final: 0.8594 (mtpt) REVERT: B 132 ARG cc_start: 0.8522 (ptt-90) cc_final: 0.8234 (ptt-90) REVERT: B 151 GLU cc_start: 0.6683 (mt-10) cc_final: 0.6391 (pt0) REVERT: B 195 LYS cc_start: 0.7558 (tttm) cc_final: 0.7203 (ttpp) REVERT: B 208 ARG cc_start: 0.7185 (mtm-85) cc_final: 0.6418 (mmm160) REVERT: B 232 LYS cc_start: 0.8306 (ttmt) cc_final: 0.8009 (tttt) REVERT: C 52 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.8084 (mtt90) REVERT: C 217 MET cc_start: 0.8649 (pmm) cc_final: 0.8433 (pmm) REVERT: C 219 ARG cc_start: 0.8259 (mmm160) cc_final: 0.7961 (mtp180) REVERT: C 256 ARG cc_start: 0.8238 (OUTLIER) cc_final: 0.7545 (mtp180) REVERT: D 21 MET cc_start: 0.6484 (mtm) cc_final: 0.5819 (tmt) REVERT: E 23 SER cc_start: 0.8547 (t) cc_final: 0.8295 (p) REVERT: E 43 LYS cc_start: 0.8403 (mtpp) cc_final: 0.7850 (mtpm) REVERT: E 85 SER cc_start: 0.8689 (m) cc_final: 0.8338 (p) REVERT: A 330 MET cc_start: 0.7745 (ttp) cc_final: 0.7382 (ptm) outliers start: 22 outliers final: 19 residues processed: 125 average time/residue: 0.6023 time to fit residues: 79.1751 Evaluate side-chains 130 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 120 GLU Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 65 THR Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 196 THR Chi-restraints excluded: chain C residue 205 ASP Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain A residue 121 MET Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 244 MET Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 253 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 16 optimal weight: 0.9990 chunk 37 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 35 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 chunk 30 optimal weight: 0.4980 chunk 68 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN B 116 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.181491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.129938 restraints weight = 8526.439| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.62 r_work: 0.3197 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8955 Z= 0.115 Angle : 0.501 8.660 12146 Z= 0.266 Chirality : 0.041 0.154 1388 Planarity : 0.004 0.047 1531 Dihedral : 4.249 22.701 1217 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.13 % Allowed : 16.38 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % 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: 1.54 (0.26), residues: 1098 helix: 2.63 (0.26), residues: 380 sheet: 0.70 (0.29), residues: 283 loop : -0.17 (0.31), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 96 TYR 0.013 0.001 TYR E 178 PHE 0.014 0.001 PHE C 151 TRP 0.014 0.001 TRP C 211 HIS 0.004 0.001 HIS A 103 Details of bonding type rmsd covalent geometry : bond 0.00253 ( 8953) covalent geometry : angle 0.50074 (12142) SS BOND : bond 0.00550 ( 2) SS BOND : angle 1.41228 ( 4) hydrogen bonds : bond 0.03722 ( 467) hydrogen bonds : angle 4.57666 ( 1287) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3693.17 seconds wall clock time: 63 minutes 23.60 seconds (3803.60 seconds total)