Starting phenix.real_space_refine on Thu Feb 13 05:17:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8fmz_29301/02_2025/8fmz_29301.cif Found real_map, /net/cci-nas-00/data/ceres_data/8fmz_29301/02_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_29301/02_2025/8fmz_29301.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8fmz_29301/02_2025/8fmz_29301.map" model { file = "/net/cci-nas-00/data/ceres_data/8fmz_29301/02_2025/8fmz_29301.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8fmz_29301/02_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/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: 2.28 Conformation dependent library (CDL) restraints added in 1.1 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: 1.07 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: 2.35 Time building geometry restraints manager: 2.71 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: 1.840 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: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.090 Process input model: 22.620 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.410 ------------------------------------------------------------------------------- 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 8953 Z= 0.263 Angle : 0.575 8.795 12142 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 *********************** 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 : 0.908 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: 1.2256 time to fit residues: 271.2299 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 : 0.957 ------------------------------------------------------------------------------- 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 = 0.180635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.123093 restraints weight = 8500.460| |-----------------------------------------------------------------------------| r_work (start): 0.3340 rms_B_bonded: 1.97 r_work: 0.3142 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8436 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 8953 Z= 0.348 Angle : 0.618 6.505 12142 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 *********************** 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 : 1.005 Fit side-chains REVERT: B 10 LYS cc_start: 0.8797 (mttt) cc_final: 0.8408 (mttt) REVERT: B 21 LYS cc_start: 0.8288 (tttm) cc_final: 0.7631 (ttpt) REVERT: B 24 ARG cc_start: 0.7079 (mtm-85) cc_final: 0.6731 (mtm-85) REVERT: B 120 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7410 (mt-10) REVERT: B 151 GLU cc_start: 0.6590 (mt-10) cc_final: 0.6239 (pt0) REVERT: B 152 LYS cc_start: 0.6620 (mttt) cc_final: 0.6381 (mttt) REVERT: B 195 LYS cc_start: 0.7668 (tttm) cc_final: 0.7303 (ttpp) REVERT: B 208 ARG cc_start: 0.7175 (mtm-85) cc_final: 0.6757 (ptt-90) REVERT: B 232 LYS cc_start: 0.8268 (ttmt) cc_final: 0.7986 (ttpt) REVERT: C 219 ARG cc_start: 0.8373 (mmm160) cc_final: 0.8116 (mtp180) REVERT: D 21 MET cc_start: 0.6297 (mtm) cc_final: 0.5471 (tmt) REVERT: E 7 SER cc_start: 0.8402 (t) cc_final: 0.8072 (p) REVERT: E 43 LYS cc_start: 0.8335 (mtpp) cc_final: 0.7820 (mtpm) REVERT: E 85 SER cc_start: 0.8608 (m) cc_final: 0.8297 (p) REVERT: A 248 PHE cc_start: 0.7278 (t80) cc_final: 0.6976 (t80) outliers start: 21 outliers final: 14 residues processed: 146 average time/residue: 1.4562 time to fit residues: 224.7315 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 : 0.942 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.9980 chunk 4 optimal weight: 0.6980 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 A 370 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.181919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.124110 restraints weight = 8653.637| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.04 r_work: 0.3179 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8953 Z= 0.204 Angle : 0.512 7.122 12142 Z= 0.279 Chirality : 0.042 0.140 1388 Planarity : 0.004 0.046 1531 Dihedral : 4.418 23.345 1217 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 2.87 % Allowed : 13.09 % 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: 1.57 (0.25), residues: 1098 helix: 2.58 (0.26), residues: 381 sheet: 0.69 (0.29), residues: 283 loop : -0.06 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 169 HIS 0.005 0.001 HIS B 82 PHE 0.017 0.001 PHE C 151 TYR 0.014 0.001 TYR E 178 ARG 0.008 0.000 ARG B 135 *********************** 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 150 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 0.796 Fit side-chains REVERT: B 10 LYS cc_start: 0.8667 (mttt) cc_final: 0.8299 (mttt) REVERT: B 21 LYS cc_start: 0.8336 (tttm) cc_final: 0.7719 (ttpt) REVERT: B 24 ARG cc_start: 0.6954 (mtm-85) cc_final: 0.6644 (mtm-85) REVERT: B 151 GLU cc_start: 0.6379 (mt-10) cc_final: 0.6049 (pt0) REVERT: B 195 LYS cc_start: 0.7481 (tttm) cc_final: 0.7142 (ttpp) REVERT: B 208 ARG cc_start: 0.7168 (mtm-85) cc_final: 0.6650 (ptt-90) REVERT: B 232 LYS cc_start: 0.8245 (ttmt) cc_final: 0.7945 (tttt) REVERT: B 241 ARG cc_start: 0.7215 (mtm-85) cc_final: 0.6871 (mmt-90) REVERT: C 61 MET cc_start: 0.9190 (OUTLIER) cc_final: 0.8905 (ppp) REVERT: C 217 MET cc_start: 0.8686 (pmm) cc_final: 0.8304 (pmm) REVERT: C 219 ARG cc_start: 0.8278 (mmm160) cc_final: 0.8001 (mtp180) REVERT: C 247 ASP cc_start: 0.7607 (m-30) cc_final: 0.7241 (m-30) REVERT: C 304 ARG cc_start: 0.8128 (ttp-170) cc_final: 0.7882 (ttp80) REVERT: D 21 MET cc_start: 0.6259 (mtm) cc_final: 0.5417 (tmt) REVERT: D 47 GLU cc_start: 0.7957 (OUTLIER) cc_final: 0.7757 (pt0) REVERT: E 7 SER cc_start: 0.8378 (t) cc_final: 0.8070 (p) REVERT: E 43 LYS cc_start: 0.8331 (mtpp) cc_final: 0.7731 (mtpm) REVERT: E 85 SER cc_start: 0.8627 (m) cc_final: 0.8274 (p) REVERT: A 121 MET cc_start: 0.5719 (tpp) cc_final: 0.5335 (ttp) REVERT: A 248 PHE cc_start: 0.7175 (t80) cc_final: 0.6907 (t80) outliers start: 27 outliers final: 10 residues processed: 138 average time/residue: 1.4632 time to fit residues: 213.3615 Evaluate side-chains 126 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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: 2.9990 chunk 3 optimal weight: 4.9990 chunk 42 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 7.9990 chunk 74 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 45 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3953 r_free = 0.3953 target = 0.177023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.120574 restraints weight = 8607.186| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.90 r_work: 0.3101 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2968 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 8953 Z= 0.462 Angle : 0.671 6.581 12142 Z= 0.362 Chirality : 0.048 0.164 1388 Planarity : 0.005 0.054 1531 Dihedral : 5.076 24.021 1217 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 3.72 % Allowed : 12.98 % Favored : 83.30 % 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: 1.14 (0.25), residues: 1098 helix: 2.18 (0.26), residues: 377 sheet: 0.44 (0.28), residues: 294 loop : -0.23 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 169 HIS 0.006 0.002 HIS E 35 PHE 0.027 0.002 PHE C 151 TYR 0.017 0.003 TYR E 103 ARG 0.009 0.001 ARG B 135 *********************** 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 156 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 121 time to evaluate : 0.971 Fit side-chains REVERT: B 10 LYS cc_start: 0.8781 (mttt) cc_final: 0.8369 (mttt) REVERT: B 21 LYS cc_start: 0.8384 (tttm) cc_final: 0.7741 (ttpt) REVERT: B 24 ARG cc_start: 0.7040 (mtm-85) cc_final: 0.6740 (mtm-85) REVERT: B 151 GLU cc_start: 0.6534 (mt-10) cc_final: 0.6228 (pt0) REVERT: B 195 LYS cc_start: 0.7646 (tttm) cc_final: 0.7293 (ttpp) REVERT: B 208 ARG cc_start: 0.7167 (mtm-85) cc_final: 0.6415 (mmm160) REVERT: B 232 LYS cc_start: 0.8374 (ttmt) cc_final: 0.8103 (ttpt) REVERT: B 241 ARG cc_start: 0.7302 (mtm-85) cc_final: 0.6952 (mmt-90) REVERT: C 217 MET cc_start: 0.8681 (pmm) cc_final: 0.8473 (pmm) REVERT: C 219 ARG cc_start: 0.8367 (mmm160) cc_final: 0.8067 (mtp180) REVERT: D 21 MET cc_start: 0.6457 (mtm) cc_final: 0.5614 (tmt) REVERT: E 7 SER cc_start: 0.8450 (t) cc_final: 0.8171 (p) REVERT: E 43 LYS cc_start: 0.8424 (mtpp) cc_final: 0.7839 (mtpm) REVERT: E 85 SER cc_start: 0.8651 (m) cc_final: 0.8351 (t) REVERT: A 61 ILE cc_start: 0.5149 (tp) cc_final: 0.4919 (tp) REVERT: A 248 PHE cc_start: 0.7389 (t80) cc_final: 0.7090 (t80) outliers start: 35 outliers final: 21 residues processed: 141 average time/residue: 1.4269 time to fit residues: 212.9354 Evaluate side-chains 135 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 146 LEU Chi-restraints excluded: chain C residue 173 THR Chi-restraints excluded: chain C residue 196 THR 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 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: 0.5980 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 0.0030 chunk 74 optimal weight: 5.9990 chunk 39 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 46 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 83 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 overall best weight: 0.6190 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.182085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.126433 restraints weight = 8615.395| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.89 r_work: 0.3179 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8953 Z= 0.158 Angle : 0.487 7.678 12142 Z= 0.265 Chirality : 0.041 0.135 1388 Planarity : 0.004 0.046 1531 Dihedral : 4.301 22.555 1217 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.45 % Allowed : 15.32 % Favored : 82.23 % 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: 1.50 (0.25), residues: 1098 helix: 2.60 (0.27), residues: 380 sheet: 0.63 (0.29), residues: 284 loop : -0.16 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 211 HIS 0.004 0.001 HIS A 103 PHE 0.014 0.001 PHE C 151 TYR 0.014 0.001 TYR E 178 ARG 0.010 0.000 ARG B 135 *********************** 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 151 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 1.028 Fit side-chains REVERT: B 10 LYS cc_start: 0.8589 (mttt) cc_final: 0.8217 (mttt) REVERT: B 21 LYS cc_start: 0.8355 (tttm) cc_final: 0.7757 (ttpt) REVERT: B 24 ARG cc_start: 0.6995 (mtm-85) cc_final: 0.6753 (mtm-85) REVERT: B 135 ARG cc_start: 0.8340 (ptp-110) cc_final: 0.8127 (ptp-110) REVERT: B 145 LYS cc_start: 0.8234 (OUTLIER) cc_final: 0.7928 (mttp) REVERT: B 151 GLU cc_start: 0.6594 (mt-10) cc_final: 0.6314 (pt0) REVERT: B 195 LYS cc_start: 0.7605 (tttm) cc_final: 0.7243 (ttpp) REVERT: B 208 ARG cc_start: 0.7128 (mtm-85) cc_final: 0.6385 (mmm160) REVERT: B 222 GLU cc_start: 0.7772 (OUTLIER) cc_final: 0.7540 (pt0) REVERT: B 232 LYS cc_start: 0.8295 (ttmt) cc_final: 0.8049 (tttt) REVERT: C 61 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8889 (ppp) REVERT: C 217 MET cc_start: 0.8711 (pmm) cc_final: 0.8423 (pmm) REVERT: C 219 ARG cc_start: 0.8264 (mmm160) cc_final: 0.7973 (mtp180) REVERT: C 293 ASN cc_start: 0.8061 (p0) cc_final: 0.7621 (p0) REVERT: D 21 MET cc_start: 0.6508 (mtm) cc_final: 0.5766 (tmt) REVERT: D 47 GLU cc_start: 0.7959 (OUTLIER) cc_final: 0.7748 (pt0) REVERT: E 23 SER cc_start: 0.8567 (t) cc_final: 0.8282 (p) REVERT: E 43 LYS cc_start: 0.8384 (mtpp) cc_final: 0.7818 (mtpm) REVERT: E 85 SER cc_start: 0.8667 (m) cc_final: 0.8330 (p) REVERT: A 248 PHE cc_start: 0.7212 (t80) cc_final: 0.6895 (t80) outliers start: 23 outliers final: 10 residues processed: 141 average time/residue: 1.3908 time to fit residues: 207.8872 Evaluate side-chains 133 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 61 MET 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 D residue 47 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 362 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 99 optimal weight: 9.9990 chunk 40 optimal weight: 0.9990 chunk 47 optimal weight: 0.6980 chunk 108 optimal weight: 3.9990 chunk 103 optimal weight: 0.9990 chunk 5 optimal weight: 4.9990 chunk 71 optimal weight: 8.9990 chunk 32 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.4001 r_free = 0.4001 target = 0.181947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.126757 restraints weight = 8503.778| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 1.79 r_work: 0.3181 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3049 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.3492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8953 Z= 0.165 Angle : 0.493 7.582 12142 Z= 0.264 Chirality : 0.041 0.136 1388 Planarity : 0.004 0.045 1531 Dihedral : 4.230 22.567 1217 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.55 % Allowed : 15.74 % 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: 1.61 (0.26), residues: 1098 helix: 2.65 (0.26), residues: 380 sheet: 0.74 (0.29), residues: 280 loop : -0.09 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 169 HIS 0.003 0.001 HIS A 103 PHE 0.015 0.001 PHE C 151 TYR 0.012 0.001 TYR E 178 ARG 0.007 0.000 ARG C 96 *********************** 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 141 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 1.019 Fit side-chains REVERT: B 10 LYS cc_start: 0.8608 (mttt) cc_final: 0.8253 (mttt) REVERT: B 21 LYS cc_start: 0.8359 (tttm) cc_final: 0.7814 (ttpt) REVERT: B 24 ARG cc_start: 0.6992 (mtm-85) cc_final: 0.6736 (mtm-85) REVERT: B 48 THR cc_start: 0.7803 (OUTLIER) cc_final: 0.7432 (p) REVERT: B 135 ARG cc_start: 0.8373 (ptp-110) cc_final: 0.8141 (ptp-110) REVERT: B 145 LYS cc_start: 0.8208 (OUTLIER) cc_final: 0.7896 (mttp) REVERT: B 151 GLU cc_start: 0.6644 (mt-10) cc_final: 0.6389 (pt0) REVERT: B 195 LYS cc_start: 0.7596 (tttm) cc_final: 0.7231 (ttpp) REVERT: B 222 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7569 (pt0) REVERT: B 232 LYS cc_start: 0.8301 (ttmt) cc_final: 0.8003 (tttt) REVERT: C 61 MET cc_start: 0.9129 (OUTLIER) cc_final: 0.8907 (ppp) REVERT: C 205 ASP cc_start: 0.7392 (OUTLIER) cc_final: 0.6684 (m-30) REVERT: C 217 MET cc_start: 0.8695 (OUTLIER) cc_final: 0.8338 (pmm) REVERT: C 219 ARG cc_start: 0.8219 (mmm160) cc_final: 0.7929 (mtp180) REVERT: C 247 ASP cc_start: 0.7528 (m-30) cc_final: 0.6694 (m-30) REVERT: C 256 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7492 (mtp180) REVERT: D 21 MET cc_start: 0.6448 (mtm) cc_final: 0.5761 (tmt) REVERT: D 47 GLU cc_start: 0.7941 (OUTLIER) cc_final: 0.7722 (pt0) REVERT: E 23 SER cc_start: 0.8596 (t) cc_final: 0.8367 (p) REVERT: E 43 LYS cc_start: 0.8345 (mtpp) cc_final: 0.7791 (mtpm) REVERT: E 85 SER cc_start: 0.8672 (m) cc_final: 0.8346 (p) REVERT: A 248 PHE cc_start: 0.7225 (t80) cc_final: 0.6959 (t80) outliers start: 24 outliers final: 12 residues processed: 129 average time/residue: 1.5148 time to fit residues: 206.8819 Evaluate side-chains 132 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 112 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 145 LYS Chi-restraints excluded: chain B residue 209 HIS Chi-restraints excluded: chain B residue 216 THR Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 61 MET 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 D residue 37 LEU Chi-restraints excluded: chain D residue 47 GLU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain A residue 131 VAL Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 244 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 87 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 60 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 4 optimal weight: 0.0470 chunk 45 optimal weight: 1.9990 chunk 74 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 overall best weight: 1.1684 ------------------------------------------------------------------------------- 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 = 0.3991 r_free = 0.3991 target = 0.180897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.124823 restraints weight = 8619.376| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 1.76 r_work: 0.3157 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8423 moved from start: 0.3559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8953 Z= 0.206 Angle : 0.520 9.106 12142 Z= 0.277 Chirality : 0.042 0.138 1388 Planarity : 0.004 0.044 1531 Dihedral : 4.344 23.093 1217 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.19 % Allowed : 15.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.26), residues: 1098 helix: 2.65 (0.26), residues: 379 sheet: 0.67 (0.29), residues: 282 loop : -0.07 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 169 HIS 0.004 0.001 HIS E 35 PHE 0.017 0.001 PHE C 151 TYR 0.015 0.002 TYR B 212 ARG 0.007 0.000 ARG C 96 *********************** 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 144 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 114 time to evaluate : 0.935 Fit side-chains REVERT: B 10 LYS cc_start: 0.8678 (mttt) cc_final: 0.8310 (mttt) REVERT: B 21 LYS cc_start: 0.8359 (tttm) cc_final: 0.7814 (ttpt) REVERT: B 24 ARG cc_start: 0.7024 (mtm-85) cc_final: 0.6754 (mtm-85) REVERT: B 132 ARG cc_start: 0.8557 (ptt-90) cc_final: 0.8199 (ptt-90) REVERT: B 151 GLU cc_start: 0.6679 (mt-10) cc_final: 0.6421 (pt0) REVERT: B 195 LYS cc_start: 0.7565 (tttm) cc_final: 0.7194 (ttpp) REVERT: B 208 ARG cc_start: 0.7408 (mtm110) cc_final: 0.6610 (mmm160) REVERT: B 222 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7613 (pt0) REVERT: B 232 LYS cc_start: 0.8315 (ttmt) cc_final: 0.8016 (tttt) REVERT: C 61 MET cc_start: 0.9171 (OUTLIER) cc_final: 0.8957 (ppp) REVERT: C 205 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7086 (m-30) REVERT: C 217 MET cc_start: 0.8704 (OUTLIER) cc_final: 0.8380 (pmm) REVERT: C 219 ARG cc_start: 0.8251 (mmm160) cc_final: 0.7958 (mtp180) REVERT: C 256 ARG cc_start: 0.8253 (OUTLIER) cc_final: 0.7523 (mtp180) REVERT: D 21 MET cc_start: 0.6464 (mtm) cc_final: 0.5794 (tmt) REVERT: E 23 SER cc_start: 0.8590 (t) cc_final: 0.8355 (p) REVERT: E 43 LYS cc_start: 0.8405 (mtpp) cc_final: 0.7852 (mtpm) REVERT: E 85 SER cc_start: 0.8676 (m) cc_final: 0.8357 (p) REVERT: A 204 MET cc_start: 0.5583 (tpp) cc_final: 0.5343 (tpt) REVERT: A 248 PHE cc_start: 0.7313 (t80) cc_final: 0.7093 (t80) outliers start: 30 outliers final: 16 residues processed: 130 average time/residue: 1.5201 time to fit residues: 208.5590 Evaluate side-chains 133 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 48 THR 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 216 THR Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 61 MET 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 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 244 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 13 optimal weight: 0.0020 chunk 46 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 0.2980 chunk 1 optimal weight: 0.9990 chunk 85 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 52 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.183060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.127355 restraints weight = 8675.430| |-----------------------------------------------------------------------------| r_work (start): 0.3395 rms_B_bonded: 1.92 r_work: 0.3177 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3046 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8953 Z= 0.150 Angle : 0.480 7.625 12142 Z= 0.256 Chirality : 0.041 0.147 1388 Planarity : 0.004 0.044 1531 Dihedral : 4.096 22.187 1217 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.02 % Allowed : 16.28 % 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: 1.72 (0.26), residues: 1098 helix: 2.77 (0.26), residues: 379 sheet: 0.81 (0.29), residues: 284 loop : -0.07 (0.31), residues: 435 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 0.013 0.001 PHE C 151 TYR 0.012 0.001 TYR E 178 ARG 0.005 0.000 ARG C 96 *********************** 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 134 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 115 time to evaluate : 1.023 Fit side-chains REVERT: B 10 LYS cc_start: 0.8603 (mttt) cc_final: 0.8255 (mttt) REVERT: B 21 LYS cc_start: 0.8350 (tttm) cc_final: 0.7808 (ttpt) REVERT: B 24 ARG cc_start: 0.7018 (mtm-85) cc_final: 0.6752 (mtm-85) REVERT: B 132 ARG cc_start: 0.8530 (ptt-90) cc_final: 0.8243 (ptt-90) REVERT: B 151 GLU cc_start: 0.6740 (mt-10) cc_final: 0.6474 (pt0) REVERT: B 195 LYS cc_start: 0.7622 (tttm) cc_final: 0.7265 (ttpp) REVERT: B 208 ARG cc_start: 0.7419 (mtm110) cc_final: 0.6574 (mmm160) REVERT: B 222 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7618 (pt0) REVERT: B 232 LYS cc_start: 0.8320 (ttmt) cc_final: 0.8023 (tttt) REVERT: C 205 ASP cc_start: 0.7442 (OUTLIER) cc_final: 0.6852 (m-30) REVERT: C 217 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8398 (pmm) REVERT: C 219 ARG cc_start: 0.8156 (mmm160) cc_final: 0.7922 (mtp180) REVERT: C 256 ARG cc_start: 0.8192 (OUTLIER) cc_final: 0.7383 (mtp180) REVERT: D 21 MET cc_start: 0.6466 (mtm) cc_final: 0.5785 (tmt) REVERT: E 23 SER cc_start: 0.8577 (t) cc_final: 0.8340 (p) REVERT: E 43 LYS cc_start: 0.8369 (mtpp) cc_final: 0.7822 (mtpm) REVERT: E 85 SER cc_start: 0.8719 (m) cc_final: 0.8401 (p) REVERT: A 204 MET cc_start: 0.5620 (tpp) cc_final: 0.5349 (tpt) outliers start: 19 outliers final: 14 residues processed: 126 average time/residue: 1.5053 time to fit residues: 200.7798 Evaluate side-chains 129 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 111 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 THR 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 B residue 216 THR 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 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 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.7980 chunk 92 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 87 optimal weight: 9.9990 chunk 0 optimal weight: 4.9990 chunk 49 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 61 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.182226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.126505 restraints weight = 8615.334| |-----------------------------------------------------------------------------| r_work (start): 0.3389 rms_B_bonded: 1.87 r_work: 0.3171 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8953 Z= 0.170 Angle : 0.497 7.216 12142 Z= 0.263 Chirality : 0.041 0.143 1388 Planarity : 0.004 0.044 1531 Dihedral : 4.156 22.665 1217 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.45 % Allowed : 16.06 % 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 (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: 1.71 (0.26), residues: 1098 helix: 2.75 (0.26), residues: 379 sheet: 0.82 (0.29), residues: 281 loop : -0.07 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 B 212 ARG 0.006 0.000 ARG C 96 *********************** 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 137 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 1.012 Fit side-chains REVERT: B 10 LYS cc_start: 0.8653 (mttt) cc_final: 0.8306 (mttt) REVERT: B 21 LYS cc_start: 0.8344 (tttm) cc_final: 0.7796 (ttpt) REVERT: B 24 ARG cc_start: 0.7003 (mtm-85) cc_final: 0.6718 (mtm-85) REVERT: B 132 ARG cc_start: 0.8498 (ptt-90) cc_final: 0.8213 (ptt-90) REVERT: B 151 GLU cc_start: 0.6726 (mt-10) cc_final: 0.6440 (pt0) REVERT: B 195 LYS cc_start: 0.7602 (tttm) cc_final: 0.7237 (ttpp) REVERT: B 208 ARG cc_start: 0.7406 (mtm110) cc_final: 0.6566 (mmm160) REVERT: B 222 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.7610 (pt0) REVERT: B 232 LYS cc_start: 0.8320 (ttmt) cc_final: 0.8027 (tttt) REVERT: C 61 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8924 (ppp) REVERT: C 205 ASP cc_start: 0.7389 (OUTLIER) cc_final: 0.6714 (m-30) REVERT: C 217 MET cc_start: 0.8654 (OUTLIER) cc_final: 0.8299 (pmm) REVERT: C 219 ARG cc_start: 0.8173 (mmm160) cc_final: 0.7950 (mtp180) REVERT: C 256 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7398 (mtp180) REVERT: D 21 MET cc_start: 0.6393 (mtm) cc_final: 0.5696 (tmt) REVERT: E 23 SER cc_start: 0.8564 (t) cc_final: 0.8356 (p) REVERT: E 43 LYS cc_start: 0.8401 (mtpp) cc_final: 0.7871 (mtpm) REVERT: E 85 SER cc_start: 0.8713 (m) cc_final: 0.8396 (p) REVERT: A 204 MET cc_start: 0.5583 (tpp) cc_final: 0.5316 (tpt) REVERT: A 330 MET cc_start: 0.7835 (ttp) cc_final: 0.7498 (ptm) outliers start: 23 outliers final: 16 residues processed: 126 average time/residue: 1.4688 time to fit residues: 195.9891 Evaluate side-chains 133 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 48 THR 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 61 MET 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 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 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 91 optimal weight: 0.7980 chunk 108 optimal weight: 0.6980 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 96 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 ASN E 167 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.182585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.125084 restraints weight = 8607.579| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.85 r_work: 0.3193 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8379 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8953 Z= 0.167 Angle : 0.497 9.005 12142 Z= 0.262 Chirality : 0.041 0.142 1388 Planarity : 0.004 0.045 1531 Dihedral : 4.131 22.529 1217 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.45 % Allowed : 15.85 % 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: 1.75 (0.26), residues: 1098 helix: 2.79 (0.26), residues: 379 sheet: 0.85 (0.29), residues: 281 loop : -0.06 (0.31), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 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 B 212 ARG 0.008 0.000 ARG C 96 ********************** 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 134 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 111 time to evaluate : 1.144 Fit side-chains REVERT: B 10 LYS cc_start: 0.8635 (mttt) cc_final: 0.8286 (mttt) REVERT: B 21 LYS cc_start: 0.8335 (tttm) cc_final: 0.7788 (ttpt) REVERT: B 24 ARG cc_start: 0.6995 (mtm-85) cc_final: 0.6708 (mtm-85) REVERT: B 132 ARG cc_start: 0.8465 (ptt-90) cc_final: 0.8178 (ptt-90) REVERT: B 151 GLU cc_start: 0.6723 (mt-10) cc_final: 0.6457 (pt0) REVERT: B 195 LYS cc_start: 0.7587 (tttm) cc_final: 0.7222 (ttpp) REVERT: B 208 ARG cc_start: 0.7389 (mtm110) cc_final: 0.6579 (mmm160) REVERT: B 222 GLU cc_start: 0.7812 (OUTLIER) cc_final: 0.7594 (pt0) REVERT: B 232 LYS cc_start: 0.8308 (ttmt) cc_final: 0.8016 (tttt) REVERT: C 61 MET cc_start: 0.9135 (OUTLIER) cc_final: 0.8922 (ppp) REVERT: C 205 ASP cc_start: 0.7363 (OUTLIER) cc_final: 0.6606 (m-30) REVERT: C 217 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8318 (pmm) REVERT: C 219 ARG cc_start: 0.8131 (mmm160) cc_final: 0.7894 (mtp180) REVERT: C 256 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7401 (mtp180) REVERT: D 21 MET cc_start: 0.6400 (mtm) cc_final: 0.5711 (tmt) REVERT: E 23 SER cc_start: 0.8543 (t) cc_final: 0.8338 (p) REVERT: E 43 LYS cc_start: 0.8387 (mtpp) cc_final: 0.7854 (mtpm) REVERT: E 85 SER cc_start: 0.8703 (m) cc_final: 0.8392 (p) REVERT: A 204 MET cc_start: 0.5558 (tpp) cc_final: 0.5289 (tpt) REVERT: A 330 MET cc_start: 0.7762 (ttp) cc_final: 0.7468 (ptm) outliers start: 23 outliers final: 17 residues processed: 124 average time/residue: 1.4940 time to fit residues: 196.6438 Evaluate side-chains 132 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 110 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 48 THR 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 216 THR Chi-restraints excluded: chain B residue 222 GLU Chi-restraints excluded: chain C residue 61 MET 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 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 244 MET 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 65 optimal weight: 0.0770 chunk 20 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 6 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 5 optimal weight: 0.6980 chunk 86 optimal weight: 7.9990 chunk 39 optimal weight: 0.0570 chunk 68 optimal weight: 0.3980 chunk 82 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 overall best weight: 0.4458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.184416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.126519 restraints weight = 8699.250| |-----------------------------------------------------------------------------| r_work (start): 0.3376 rms_B_bonded: 1.83 r_work: 0.3232 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 8953 Z= 0.133 Angle : 0.476 9.084 12142 Z= 0.250 Chirality : 0.040 0.141 1388 Planarity : 0.004 0.045 1531 Dihedral : 3.950 21.747 1217 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.91 % Allowed : 16.70 % Favored : 81.38 % 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: 1.83 (0.26), residues: 1098 helix: 2.84 (0.27), residues: 380 sheet: 0.95 (0.29), residues: 278 loop : -0.04 (0.31), residues: 440 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 0.012 0.001 PHE B 74 TYR 0.012 0.001 TYR E 178 ARG 0.009 0.000 ARG C 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8570.42 seconds wall clock time: 151 minutes 38.01 seconds (9098.01 seconds total)