Starting phenix.real_space_refine on Sat Jun 7 11:32:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fmz_29301/06_2025/8fmz_29301.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fmz_29301/06_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_29301/06_2025/8fmz_29301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fmz_29301/06_2025/8fmz_29301.map" model { file = "/net/cci-nas-00/data/ceres_data/8fmz_29301/06_2025/8fmz_29301.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fmz_29301/06_2025/8fmz_29301.cif" } resolution = 2.59 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.159 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: {'GLU:plan': 1, 'ASP: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: {'GLU:plan': 1, 'ARG: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, 'GLU:plan': 1, 'ARG: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: 5.41, per 1000 atoms: 0.62 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: 2.29 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 0.93 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: 2.99 Time building geometry restraints manager: 2.69 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: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.500 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:37.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.190 ------------------------------------------------------------------------------- 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 : 6.51 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (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 TRP 0.016 0.001 TRP C 169 HIS 0.003 0.001 HIS A 348 PHE 0.014 0.001 PHE C 151 TYR 0.013 0.001 TYR E 178 ARG 0.002 0.000 ARG E 38 Details of bonding type rmsd hydrogen bonds : bond 0.12833 ( 467) hydrogen bonds : angle 5.39918 ( 1287) SS BOND : bond 0.00515 ( 2) SS BOND : angle 0.81194 ( 4) covalent geometry : bond 0.00398 ( 8953) covalent geometry : angle 0.57475 (12142) *********************** 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 : 0.909 Fit side-chains REVERT: B 10 LYS cc_start: 0.7671 (mttt) cc_final: 0.7282 (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: 0.6116 (mtm-85) REVERT: B 69 ILE cc_start: 0.8322 (OUTLIER) cc_final: 0.8092 (tt) 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: 0.6066 (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: 1.5848 time to fit residues: 351.1452 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 : 0.923 ------------------------------------------------------------------------------- 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 93 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 56 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 87 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 64 optimal weight: 0.2980 chunk 100 optimal weight: 10.0000 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 C 156 GLN 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.180637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.123095 restraints weight = 8500.396| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.97 r_work: 0.3141 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 8955 Z= 0.221 Angle : 0.618 6.505 12146 Z= 0.336 Chirality : 0.045 0.152 1388 Planarity : 0.005 0.047 1531 Dihedral : 4.796 23.747 1219 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.23 % Allowed : 10.43 % Favored : 87.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.25), residues: 1098 helix: 2.49 (0.26), residues: 376 sheet: 0.57 (0.28), residues: 307 loop : 0.02 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 169 HIS 0.006 0.002 HIS D 44 PHE 0.023 0.002 PHE C 151 TYR 0.015 0.002 TYR E 178 ARG 0.006 0.001 ARG B 135 Details of bonding type rmsd hydrogen bonds : bond 0.05000 ( 467) hydrogen bonds : angle 5.00482 ( 1287) SS BOND : bond 0.00901 ( 2) SS BOND : angle 1.35157 ( 4) covalent geometry : bond 0.00522 ( 8953) covalent geometry : angle 0.61801 (12142) *********************** 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 156 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 135 time to evaluate : 0.887 Fit side-chains REVERT: B 10 LYS cc_start: 0.8794 (mttt) cc_final: 0.8405 (mttt) REVERT: B 21 LYS cc_start: 0.8290 (tttm) cc_final: 0.7636 (ttpt) REVERT: B 24 ARG cc_start: 0.7083 (mtm-85) cc_final: 0.6735 (mtm-85) REVERT: B 120 GLU cc_start: 0.7735 (mt-10) cc_final: 0.7405 (mt-10) REVERT: B 151 GLU cc_start: 0.6553 (mt-10) cc_final: 0.6204 (pt0) REVERT: B 152 LYS cc_start: 0.6573 (mttt) cc_final: 0.6335 (mttt) REVERT: B 195 LYS cc_start: 0.7664 (tttm) cc_final: 0.7293 (ttpp) REVERT: B 208 ARG cc_start: 0.7171 (mtm-85) cc_final: 0.6758 (ptt-90) REVERT: B 232 LYS cc_start: 0.8272 (ttmt) cc_final: 0.7990 (ttpt) REVERT: C 219 ARG cc_start: 0.8371 (mmm160) cc_final: 0.8114 (mtp180) REVERT: D 21 MET cc_start: 0.6229 (mtm) cc_final: 0.5411 (tmt) REVERT: E 7 SER cc_start: 0.8404 (t) cc_final: 0.8070 (p) REVERT: E 43 LYS cc_start: 0.8332 (mtpp) cc_final: 0.7822 (mtpm) REVERT: E 85 SER cc_start: 0.8608 (m) cc_final: 0.8297 (p) REVERT: A 248 PHE cc_start: 0.7271 (t80) cc_final: 0.6967 (t80) outliers start: 21 outliers final: 14 residues processed: 146 average time/residue: 1.3906 time to fit residues: 214.7438 Evaluate side-chains 136 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 122 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 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 62 optimal weight: 5.9990 chunk 10 optimal weight: 0.9990 chunk 90 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 22 ASN ** B 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.4008 r_free = 0.4008 target = 0.181075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.123066 restraints weight = 8646.111| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.99 r_work: 0.3174 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8955 Z= 0.152 Angle : 0.528 6.968 12146 Z= 0.288 Chirality : 0.042 0.142 1388 Planarity : 0.004 0.046 1531 Dihedral : 4.495 23.449 1217 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.98 % Allowed : 12.98 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.51 (0.25), residues: 1098 helix: 2.53 (0.26), residues: 381 sheet: 0.67 (0.29), residues: 278 loop : -0.10 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.004 0.001 HIS E 35 PHE 0.018 0.001 PHE C 151 TYR 0.014 0.002 TYR E 178 ARG 0.007 0.000 ARG B 135 Details of bonding type rmsd hydrogen bonds : bond 0.04312 ( 467) hydrogen bonds : angle 4.76828 ( 1287) SS BOND : bond 0.00692 ( 2) SS BOND : angle 1.30986 ( 4) covalent geometry : bond 0.00347 ( 8953) covalent geometry : angle 0.52737 (12142) *********************** 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 149 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.886 Fit side-chains REVERT: B 10 LYS cc_start: 0.8658 (mttt) cc_final: 0.8277 (mttt) REVERT: B 21 LYS cc_start: 0.8319 (tttm) cc_final: 0.7670 (ttpt) REVERT: B 24 ARG cc_start: 0.6913 (mtm-85) cc_final: 0.6518 (mtm-85) REVERT: B 120 GLU cc_start: 0.7565 (mt-10) cc_final: 0.7346 (mt-10) REVERT: B 151 GLU cc_start: 0.6371 (mt-10) cc_final: 0.6045 (pt0) REVERT: B 195 LYS cc_start: 0.7491 (tttm) cc_final: 0.7123 (ttpp) REVERT: B 208 ARG cc_start: 0.7133 (mtm-85) cc_final: 0.6603 (ptt-90) REVERT: B 232 LYS cc_start: 0.8239 (ttmt) cc_final: 0.7971 (ttpt) REVERT: B 241 ARG cc_start: 0.7196 (mtm-85) cc_final: 0.6853 (mmt-90) REVERT: C 61 MET cc_start: 0.9179 (OUTLIER) cc_final: 0.8908 (ppp) REVERT: C 217 MET cc_start: 0.8674 (pmm) cc_final: 0.8285 (pmm) REVERT: C 219 ARG cc_start: 0.8250 (mmm160) cc_final: 0.7975 (mtp180) REVERT: C 304 ARG cc_start: 0.8131 (ttp-170) cc_final: 0.7893 (ttp80) REVERT: D 21 MET cc_start: 0.6331 (mtm) cc_final: 0.5455 (tmt) REVERT: D 47 GLU cc_start: 0.7976 (OUTLIER) cc_final: 0.7762 (pt0) REVERT: E 7 SER cc_start: 0.8383 (t) cc_final: 0.8056 (p) REVERT: E 43 LYS cc_start: 0.8357 (mtpp) cc_final: 0.7762 (mtpm) REVERT: E 85 SER cc_start: 0.8658 (m) cc_final: 0.8298 (p) REVERT: A 121 MET cc_start: 0.5648 (tpp) cc_final: 0.5216 (ttp) REVERT: A 248 PHE cc_start: 0.7201 (t80) cc_final: 0.6930 (t80) outliers start: 28 outliers final: 10 residues processed: 138 average time/residue: 1.4026 time to fit residues: 204.5719 Evaluate side-chains 125 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain C residue 61 MET Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain D residue 47 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 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 78 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 74 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 174 GLN A 103 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.178732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.122792 restraints weight = 8596.153| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.87 r_work: 0.3103 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 8955 Z= 0.209 Angle : 0.589 6.213 12146 Z= 0.320 Chirality : 0.045 0.152 1388 Planarity : 0.005 0.046 1531 Dihedral : 4.800 23.839 1217 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.09 % Allowed : 13.83 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.25), residues: 1098 helix: 2.37 (0.26), residues: 380 sheet: 0.54 (0.29), residues: 292 loop : -0.21 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 169 HIS 0.005 0.001 HIS E 35 PHE 0.022 0.002 PHE C 151 TYR 0.014 0.002 TYR E 103 ARG 0.008 0.001 ARG B 135 Details of bonding type rmsd hydrogen bonds : bond 0.04798 ( 467) hydrogen bonds : angle 4.94245 ( 1287) SS BOND : bond 0.00890 ( 2) SS BOND : angle 1.63881 ( 4) covalent geometry : bond 0.00492 ( 8953) covalent geometry : angle 0.58884 (12142) *********************** 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 152 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.907 Fit side-chains REVERT: B 10 LYS cc_start: 0.8817 (mttt) cc_final: 0.8423 (mttt) REVERT: B 21 LYS cc_start: 0.8383 (tttm) cc_final: 0.7776 (ttpt) REVERT: B 24 ARG cc_start: 0.7033 (mtm-85) cc_final: 0.6703 (mtm-85) REVERT: B 151 GLU cc_start: 0.6572 (mt-10) cc_final: 0.6250 (pt0) REVERT: B 195 LYS cc_start: 0.7668 (tttm) cc_final: 0.7301 (ttpp) REVERT: B 208 ARG cc_start: 0.7192 (mtm-85) cc_final: 0.6434 (mmm160) REVERT: B 232 LYS cc_start: 0.8333 (ttmt) cc_final: 0.8076 (ttpt) REVERT: C 217 MET cc_start: 0.8700 (pmm) cc_final: 0.8372 (pmm) REVERT: C 219 ARG cc_start: 0.8396 (mmm160) cc_final: 0.8113 (mtp180) REVERT: D 21 MET cc_start: 0.6476 (mtm) cc_final: 0.5696 (tmt) REVERT: E 7 SER cc_start: 0.8467 (t) cc_final: 0.8200 (p) REVERT: E 43 LYS cc_start: 0.8431 (mtpp) cc_final: 0.7857 (mtpm) REVERT: E 85 SER cc_start: 0.8698 (m) cc_final: 0.8354 (p) REVERT: A 248 PHE cc_start: 0.7337 (t80) cc_final: 0.7020 (t80) outliers start: 29 outliers final: 16 residues processed: 140 average time/residue: 1.4509 time to fit residues: 214.4720 Evaluate side-chains 129 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 113 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 146 LEU 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 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 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 45 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 83 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.178979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.121786 restraints weight = 8578.797| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.86 r_work: 0.3104 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2972 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8955 Z= 0.190 Angle : 0.568 8.173 12146 Z= 0.308 Chirality : 0.044 0.150 1388 Planarity : 0.005 0.047 1531 Dihedral : 4.719 23.498 1217 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.40 % Allowed : 14.57 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.25), residues: 1098 helix: 2.40 (0.26), residues: 380 sheet: 0.54 (0.28), residues: 292 loop : -0.24 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.005 0.001 HIS E 35 PHE 0.021 0.002 PHE C 151 TYR 0.013 0.002 TYR E 103 ARG 0.010 0.001 ARG B 135 Details of bonding type rmsd hydrogen bonds : bond 0.04560 ( 467) hydrogen bonds : angle 4.85709 ( 1287) SS BOND : bond 0.00841 ( 2) SS BOND : angle 1.61526 ( 4) covalent geometry : bond 0.00445 ( 8953) covalent geometry : angle 0.56751 (12142) *********************** 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 150 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 118 time to evaluate : 1.024 Fit side-chains REVERT: B 10 LYS cc_start: 0.8740 (mttt) cc_final: 0.8340 (mttt) REVERT: B 21 LYS cc_start: 0.8389 (tttm) cc_final: 0.7799 (ttpt) REVERT: B 24 ARG cc_start: 0.7052 (mtm-85) cc_final: 0.6713 (mtm-85) REVERT: B 132 ARG cc_start: 0.8607 (ptt-90) cc_final: 0.8225 (ptt-90) REVERT: B 135 ARG cc_start: 0.8502 (ptp-110) cc_final: 0.8244 (ptp-110) REVERT: B 151 GLU cc_start: 0.6645 (mt-10) cc_final: 0.6310 (pt0) REVERT: B 195 LYS cc_start: 0.7591 (tttm) cc_final: 0.7245 (ttpp) REVERT: B 208 ARG cc_start: 0.7164 (mtm-85) cc_final: 0.6391 (mmm160) REVERT: B 232 LYS cc_start: 0.8333 (ttmt) cc_final: 0.8073 (ttpt) REVERT: C 217 MET cc_start: 0.8705 (pmm) cc_final: 0.8383 (pmm) REVERT: C 219 ARG cc_start: 0.8388 (mmm160) cc_final: 0.8129 (mtp180) REVERT: D 21 MET cc_start: 0.6549 (mtm) cc_final: 0.5788 (tmt) REVERT: E 43 LYS cc_start: 0.8441 (mtpp) cc_final: 0.7856 (mtpm) REVERT: E 46 GLU cc_start: 0.8873 (OUTLIER) cc_final: 0.8525 (tt0) REVERT: E 85 SER cc_start: 0.8700 (m) cc_final: 0.8349 (p) REVERT: A 248 PHE cc_start: 0.7382 (t80) cc_final: 0.7073 (t80) outliers start: 32 outliers final: 21 residues processed: 137 average time/residue: 1.3759 time to fit residues: 199.8021 Evaluate side-chains 131 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 109 time to evaluate : 0.971 ------------------------------------------------------------------------------- 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 B residue 222 GLU 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 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 99 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 108 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 305 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.181978 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.127577 restraints weight = 8534.050| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.81 r_work: 0.3194 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8955 Z= 0.112 Angle : 0.493 7.155 12146 Z= 0.266 Chirality : 0.041 0.134 1388 Planarity : 0.004 0.046 1531 Dihedral : 4.261 22.441 1217 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.13 % Allowed : 15.96 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.26), residues: 1098 helix: 2.60 (0.27), residues: 380 sheet: 0.71 (0.29), residues: 285 loop : -0.17 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 211 HIS 0.004 0.001 HIS A 103 PHE 0.014 0.001 PHE C 151 TYR 0.013 0.001 TYR E 178 ARG 0.006 0.000 ARG C 96 Details of bonding type rmsd hydrogen bonds : bond 0.03728 ( 467) hydrogen bonds : angle 4.57005 ( 1287) SS BOND : bond 0.00522 ( 2) SS BOND : angle 1.34440 ( 4) covalent geometry : bond 0.00242 ( 8953) covalent geometry : angle 0.49202 (12142) *********************** 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 139 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 0.875 Fit side-chains REVERT: B 10 LYS cc_start: 0.8614 (mttt) cc_final: 0.8254 (mttt) REVERT: B 21 LYS cc_start: 0.8351 (tttm) cc_final: 0.7804 (ttpt) REVERT: B 24 ARG cc_start: 0.6962 (mtm-85) cc_final: 0.6714 (mtm-85) REVERT: B 135 ARG cc_start: 0.8365 (ptp-110) cc_final: 0.8165 (ptp-110) REVERT: B 151 GLU cc_start: 0.6637 (mt-10) cc_final: 0.6382 (pt0) REVERT: B 195 LYS cc_start: 0.7587 (tttm) cc_final: 0.7223 (ttpp) REVERT: B 208 ARG cc_start: 0.7154 (mtm-85) cc_final: 0.6635 (ptt-90) REVERT: B 222 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7542 (pt0) REVERT: B 232 LYS cc_start: 0.8297 (ttmt) cc_final: 0.8005 (tttt) REVERT: C 217 MET cc_start: 0.8710 (OUTLIER) cc_final: 0.8347 (pmm) REVERT: C 219 ARG cc_start: 0.8222 (mmm160) cc_final: 0.7940 (mtp180) REVERT: C 256 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7499 (mtp180) REVERT: C 293 ASN cc_start: 0.7992 (p0) cc_final: 0.7603 (p0) REVERT: D 21 MET cc_start: 0.6500 (mtm) cc_final: 0.5787 (tmt) REVERT: E 23 SER cc_start: 0.8542 (t) cc_final: 0.8328 (p) REVERT: E 43 LYS cc_start: 0.8377 (mtpp) cc_final: 0.7829 (mtpm) REVERT: E 85 SER cc_start: 0.8656 (m) cc_final: 0.8322 (p) REVERT: A 248 PHE cc_start: 0.7256 (t80) cc_final: 0.6954 (t80) outliers start: 20 outliers final: 9 residues processed: 129 average time/residue: 1.4498 time to fit residues: 197.4908 Evaluate side-chains 128 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 116 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 222 GLU 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 217 MET Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain D residue 37 LEU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 226 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 87 optimal weight: 9.9990 chunk 51 optimal weight: 6.9990 chunk 60 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 chunk 20 optimal weight: 0.7980 chunk 93 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 = 0.3997 r_free = 0.3997 target = 0.181527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.126405 restraints weight = 8624.028| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.88 r_work: 0.3174 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3040 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3040 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3581 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 : 0.506 8.046 12146 Z= 0.270 Chirality : 0.041 0.140 1388 Planarity : 0.004 0.046 1531 Dihedral : 4.272 22.704 1217 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.34 % Allowed : 15.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.26), residues: 1098 helix: 2.65 (0.27), residues: 379 sheet: 0.70 (0.29), residues: 287 loop : -0.13 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE C 151 TYR 0.012 0.001 TYR E 178 ARG 0.005 0.000 ARG B 135 Details of bonding type rmsd hydrogen bonds : bond 0.03805 ( 467) hydrogen bonds : angle 4.55823 ( 1287) SS BOND : bond 0.00571 ( 2) SS BOND : angle 1.30540 ( 4) covalent geometry : bond 0.00269 ( 8953) covalent geometry : angle 0.50520 (12142) *********************** 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 136 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.930 Fit side-chains REVERT: B 10 LYS cc_start: 0.8624 (mttt) cc_final: 0.8255 (mttt) REVERT: B 21 LYS cc_start: 0.8314 (tttm) cc_final: 0.7769 (ttpt) REVERT: B 24 ARG cc_start: 0.6955 (mtm-85) cc_final: 0.6682 (mtm-85) REVERT: B 132 ARG cc_start: 0.8559 (ptt-90) cc_final: 0.8240 (ptt-90) REVERT: B 151 GLU cc_start: 0.6629 (mt-10) cc_final: 0.6369 (pt0) REVERT: B 195 LYS cc_start: 0.7590 (tttm) cc_final: 0.7213 (ttpp) REVERT: B 232 LYS cc_start: 0.8303 (ttmt) cc_final: 0.8002 (tttt) REVERT: C 217 MET cc_start: 0.8698 (pmm) cc_final: 0.8383 (pmm) REVERT: C 219 ARG cc_start: 0.8217 (mmm160) cc_final: 0.7931 (mtp180) REVERT: C 256 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7508 (mtp180) REVERT: D 21 MET cc_start: 0.6449 (mtm) cc_final: 0.5770 (tmt) REVERT: E 23 SER cc_start: 0.8572 (t) cc_final: 0.8329 (p) REVERT: E 43 LYS cc_start: 0.8383 (mtpp) cc_final: 0.7851 (mtpm) REVERT: E 85 SER cc_start: 0.8668 (m) cc_final: 0.8330 (p) outliers start: 22 outliers final: 11 residues processed: 128 average time/residue: 1.6386 time to fit residues: 221.5835 Evaluate side-chains 125 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 113 time to evaluate : 0.772 ------------------------------------------------------------------------------- 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 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 256 ARG Chi-restraints excluded: chain D residue 37 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 13 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 85 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 99 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4002 r_free = 0.4002 target = 0.182010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.126602 restraints weight = 8671.361| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.86 r_work: 0.3182 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3051 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.3628 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= 0.116 Angle : 0.500 7.118 12146 Z= 0.267 Chirality : 0.041 0.153 1388 Planarity : 0.004 0.046 1531 Dihedral : 4.210 22.470 1217 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.13 % Allowed : 16.28 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.26), residues: 1098 helix: 2.67 (0.27), residues: 380 sheet: 0.71 (0.29), residues: 286 loop : -0.06 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE C 151 TYR 0.012 0.001 TYR E 178 ARG 0.010 0.000 ARG B 135 Details of bonding type rmsd hydrogen bonds : bond 0.03716 ( 467) hydrogen bonds : angle 4.52007 ( 1287) SS BOND : bond 0.00524 ( 2) SS BOND : angle 1.27568 ( 4) covalent geometry : bond 0.00257 ( 8953) covalent geometry : angle 0.49951 (12142) *********************** 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 135 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 1.048 Fit side-chains REVERT: B 10 LYS cc_start: 0.8631 (mttt) cc_final: 0.8276 (mttt) REVERT: B 21 LYS cc_start: 0.8343 (tttm) cc_final: 0.7811 (ttpt) REVERT: B 24 ARG cc_start: 0.6979 (mtm-85) cc_final: 0.6711 (mtm-85) REVERT: B 132 ARG cc_start: 0.8544 (ptt-90) cc_final: 0.8177 (ptt-90) REVERT: B 135 ARG cc_start: 0.8286 (ptp-110) cc_final: 0.8027 (ptp-110) REVERT: B 151 GLU cc_start: 0.6686 (mt-10) cc_final: 0.6393 (pt0) REVERT: B 195 LYS cc_start: 0.7592 (tttm) cc_final: 0.7226 (ttpp) REVERT: B 232 LYS cc_start: 0.8309 (ttmt) cc_final: 0.8012 (tttt) REVERT: C 217 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8383 (pmm) REVERT: C 219 ARG cc_start: 0.8152 (mmm160) cc_final: 0.7940 (mtp180) REVERT: C 256 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7489 (mtp180) REVERT: D 21 MET cc_start: 0.6460 (mtm) cc_final: 0.5787 (tmt) REVERT: E 23 SER cc_start: 0.8558 (t) cc_final: 0.8326 (p) REVERT: E 43 LYS cc_start: 0.8384 (mtpp) cc_final: 0.7861 (mtpm) REVERT: E 85 SER cc_start: 0.8715 (m) cc_final: 0.8396 (p) outliers start: 20 outliers final: 13 residues processed: 127 average time/residue: 1.8172 time to fit residues: 243.9734 Evaluate side-chains 126 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.985 ------------------------------------------------------------------------------- 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 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 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 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 253 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 33 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 87 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 61 optimal weight: 0.0970 chunk 74 optimal weight: 2.9990 chunk 94 optimal weight: 0.4980 overall best weight: 0.6778 ------------------------------------------------------------------------------- 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 = 0.4010 r_free = 0.4010 target = 0.182845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.126971 restraints weight = 8626.907| |-----------------------------------------------------------------------------| r_work (start): 0.3396 rms_B_bonded: 1.81 r_work: 0.3186 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3054 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8955 Z= 0.108 Angle : 0.497 9.323 12146 Z= 0.263 Chirality : 0.041 0.149 1388 Planarity : 0.004 0.045 1531 Dihedral : 4.112 22.056 1217 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.91 % Allowed : 16.91 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.26), residues: 1098 helix: 2.70 (0.27), residues: 380 sheet: 0.73 (0.29), residues: 286 loop : -0.03 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 PHE 0.014 0.001 PHE C 151 TYR 0.012 0.001 TYR E 178 ARG 0.009 0.000 ARG B 135 Details of bonding type rmsd hydrogen bonds : bond 0.03566 ( 467) hydrogen bonds : angle 4.46943 ( 1287) SS BOND : bond 0.00477 ( 2) SS BOND : angle 1.25411 ( 4) covalent geometry : bond 0.00234 ( 8953) covalent geometry : angle 0.49695 (12142) *********************** 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 132 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 114 time to evaluate : 0.990 Fit side-chains REVERT: B 10 LYS cc_start: 0.8597 (mttt) cc_final: 0.8261 (mttt) REVERT: B 21 LYS cc_start: 0.8348 (tttm) cc_final: 0.7818 (ttpt) REVERT: B 24 ARG cc_start: 0.7004 (mtm-85) cc_final: 0.6726 (mtm-85) REVERT: B 132 ARG cc_start: 0.8542 (ptt-90) cc_final: 0.8220 (ptt-90) REVERT: B 151 GLU cc_start: 0.6752 (mt-10) cc_final: 0.6465 (pt0) REVERT: B 195 LYS cc_start: 0.7566 (tttm) cc_final: 0.7231 (ttpp) REVERT: B 208 ARG cc_start: 0.7424 (mtm110) cc_final: 0.6577 (mmm160) REVERT: B 232 LYS cc_start: 0.8315 (ttmt) cc_final: 0.8028 (tttt) REVERT: C 217 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8323 (pmm) REVERT: C 219 ARG cc_start: 0.8130 (mmm160) cc_final: 0.7903 (mtp180) REVERT: C 256 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7459 (mtp180) REVERT: D 21 MET cc_start: 0.6449 (mtm) cc_final: 0.5779 (tmt) REVERT: E 43 LYS cc_start: 0.8383 (mtpp) cc_final: 0.7864 (mtpm) REVERT: E 85 SER cc_start: 0.8721 (m) cc_final: 0.8406 (p) REVERT: A 330 MET cc_start: 0.7750 (ttp) cc_final: 0.7465 (ptm) outliers start: 18 outliers final: 16 residues processed: 125 average time/residue: 1.4913 time to fit residues: 196.7594 Evaluate side-chains 126 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 1.002 ------------------------------------------------------------------------------- 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 210 ILE Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 146 LEU 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 D residue 47 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 180 MET 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 253 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 91 optimal weight: 0.6980 chunk 108 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 31 optimal weight: 0.0070 chunk 14 optimal weight: 0.9980 chunk 96 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 3 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 19 optimal weight: 0.0980 chunk 102 optimal weight: 6.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 293 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.184004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.132184 restraints weight = 8631.368| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.80 r_work: 0.3224 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3094 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.3746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8955 Z= 0.098 Angle : 0.483 9.611 12146 Z= 0.254 Chirality : 0.040 0.146 1388 Planarity : 0.004 0.045 1531 Dihedral : 3.973 21.605 1217 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.81 % Allowed : 17.02 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.26), residues: 1098 helix: 2.77 (0.27), residues: 381 sheet: 0.79 (0.29), residues: 285 loop : 0.01 (0.31), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 211 HIS 0.003 0.001 HIS B 82 PHE 0.013 0.001 PHE B 74 TYR 0.012 0.001 TYR E 178 ARG 0.008 0.000 ARG C 96 Details of bonding type rmsd hydrogen bonds : bond 0.03396 ( 467) hydrogen bonds : angle 4.37982 ( 1287) SS BOND : bond 0.00426 ( 2) SS BOND : angle 1.26049 ( 4) covalent geometry : bond 0.00208 ( 8953) covalent geometry : angle 0.48222 (12142) ********************** 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 132 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 115 time to evaluate : 3.535 Fit side-chains REVERT: B 21 LYS cc_start: 0.8331 (tttm) cc_final: 0.7806 (ttpt) REVERT: B 24 ARG cc_start: 0.6994 (mtm-85) cc_final: 0.6682 (mtm-85) REVERT: B 132 ARG cc_start: 0.8485 (ptt-90) cc_final: 0.8203 (ptt-90) REVERT: B 151 GLU cc_start: 0.6781 (mt-10) cc_final: 0.6472 (pt0) REVERT: B 195 LYS cc_start: 0.7577 (tttm) cc_final: 0.7225 (ttpp) REVERT: B 208 ARG cc_start: 0.7320 (mtm110) cc_final: 0.6520 (mmm160) REVERT: B 232 LYS cc_start: 0.8301 (ttmt) cc_final: 0.8002 (tttt) REVERT: C 217 MET cc_start: 0.8624 (OUTLIER) cc_final: 0.8343 (pmm) REVERT: C 219 ARG cc_start: 0.8059 (mmm160) cc_final: 0.7842 (mtp180) REVERT: C 256 ARG cc_start: 0.8163 (OUTLIER) cc_final: 0.7394 (mtp180) REVERT: D 21 MET cc_start: 0.6389 (mtm) cc_final: 0.5709 (tmt) REVERT: E 43 LYS cc_start: 0.8353 (mtpp) cc_final: 0.7850 (mtpm) REVERT: E 85 SER cc_start: 0.8707 (m) cc_final: 0.8395 (p) REVERT: A 208 MET cc_start: 0.5688 (mmp) cc_final: 0.5153 (mmm) REVERT: A 330 MET cc_start: 0.7600 (ttp) cc_final: 0.7377 (ptm) outliers start: 17 outliers final: 12 residues processed: 128 average time/residue: 1.6856 time to fit residues: 228.9051 Evaluate side-chains 126 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.998 ------------------------------------------------------------------------------- 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 C residue 114 CYS Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 217 MET Chi-restraints excluded: chain C residue 256 ARG Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 12 VAL Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain E residue 185 SER Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 65 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 6 optimal weight: 0.7980 chunk 103 optimal weight: 4.9990 chunk 5 optimal weight: 8.9990 chunk 86 optimal weight: 6.9990 chunk 39 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 167 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.177560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.124024 restraints weight = 8679.640| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.96 r_work: 0.3100 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2965 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8453 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 8955 Z= 0.258 Angle : 0.651 10.412 12146 Z= 0.343 Chirality : 0.046 0.172 1388 Planarity : 0.005 0.046 1531 Dihedral : 4.849 23.323 1217 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.81 % Allowed : 17.23 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.88 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.25), residues: 1098 helix: 2.30 (0.26), residues: 381 sheet: 0.43 (0.28), residues: 298 loop : -0.14 (0.31), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 297 HIS 0.006 0.002 HIS E 35 PHE 0.025 0.002 PHE C 151 TYR 0.020 0.002 TYR B 212 ARG 0.009 0.001 ARG C 96 Details of bonding type rmsd hydrogen bonds : bond 0.04945 ( 467) hydrogen bonds : angle 4.90931 ( 1287) SS BOND : bond 0.00974 ( 2) SS BOND : angle 1.72758 ( 4) covalent geometry : bond 0.00615 ( 8953) covalent geometry : angle 0.64998 (12142) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9572.49 seconds wall clock time: 167 minutes 50.57 seconds (10070.57 seconds total)