Starting phenix.real_space_refine on Wed Feb 12 21:51:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s8o_24899/02_2025/7s8o_24899.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s8o_24899/02_2025/7s8o_24899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s8o_24899/02_2025/7s8o_24899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s8o_24899/02_2025/7s8o_24899.map" model { file = "/net/cci-nas-00/data/ceres_data/7s8o_24899/02_2025/7s8o_24899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s8o_24899/02_2025/7s8o_24899.cif" } resolution = 2.58 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= 0.002 sd= 0.027 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 62 5.16 5 C 5332 2.51 5 N 1407 2.21 5 O 1530 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 50 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8331 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 1893 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 1893 Classifications: {'peptide': 257} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 8, 'TRANS': 248} Chain breaks: 1 Unresolved non-hydrogen bonds: 160 Unresolved non-hydrogen angles: 203 Unresolved non-hydrogen dihedrals: 144 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'HIS:plan': 1, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 9, 'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 104 Chain: "B" Number of atoms: 1707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1707 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 2, 'TRANS': 215} Chain breaks: 2 Unresolved non-hydrogen bonds: 51 Unresolved non-hydrogen angles: 61 Unresolved non-hydrogen dihedrals: 41 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 35 Chain: "C" Number of atoms: 2564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2564 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 2, 'ARG:plan': 3, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "D" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 401 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 1743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1743 Classifications: {'peptide': 232} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 31 Chain: "R" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'8IU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.14, per 1000 atoms: 0.62 Number of scatterers: 8331 At special positions: 0 Unit cell: (91.91, 125.58, 121.94, 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 62 16.00 O 1530 8.00 N 1407 7.00 C 5332 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 168 " - pdb=" SG CYS R 180 " 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: 2.09 Conformation dependent library (CDL) restraints added in 992.2 milliseconds 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2048 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 36.7% alpha, 23.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'R' and resid 30 through 57 removed outlier: 3.967A pdb=" N VAL R 34 " --> pdb=" O THR R 30 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N PHE R 35 " --> pdb=" O LEU R 31 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL R 43 " --> pdb=" O PHE R 39 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N GLY R 44 " --> pdb=" O ILE R 40 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU R 45 " --> pdb=" O ALA R 41 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N VAL R 46 " --> pdb=" O LEU R 42 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY R 47 " --> pdb=" O VAL R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 64 through 95 removed outlier: 3.889A pdb=" N VAL R 68 " --> pdb=" O PHE R 64 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 133 removed outlier: 4.371A pdb=" N THR R 106 " --> pdb=" O PRO R 102 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR R 107 " --> pdb=" O SER R 103 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N LEU R 120 " --> pdb=" O GLY R 116 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N SER R 121 " --> pdb=" O LEU R 117 " (cutoff:3.500A) Processing helix chain 'R' and resid 133 through 139 Processing helix chain 'R' and resid 144 through 167 removed outlier: 3.715A pdb=" N PHE R 167 " --> pdb=" O LEU R 163 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 212 removed outlier: 3.645A pdb=" N GLY R 212 " --> pdb=" O ARG R 208 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 236 removed outlier: 3.637A pdb=" N LEU R 221 " --> pdb=" O PRO R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 236 through 250 removed outlier: 4.496A pdb=" N GLY R 240 " --> pdb=" O GLY R 236 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N LEU R 247 " --> pdb=" O TRP R 243 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N TRP R 248 " --> pdb=" O PHE R 244 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 259 removed outlier: 4.184A pdb=" N CYS R 258 " --> pdb=" O ASP R 254 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 281 Proline residue: R 276 - end of helix Processing helix chain 'B' and resid 6 through 31 Processing helix chain 'B' and resid 46 through 53 Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.546A pdb=" N LYS B 210 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N TRP B 211 " --> pdb=" O ARG B 208 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE B 215 " --> pdb=" O ILE B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 270 through 278 removed outlier: 3.544A pdb=" N PHE B 274 " --> pdb=" O LYS B 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.609A pdb=" N ILE B 285 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 309 Processing helix chain 'B' and resid 330 through 350 removed outlier: 3.944A pdb=" N ASP B 341 " --> pdb=" O ASP B 337 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL B 342 " --> pdb=" O ALA B 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 24 removed outlier: 3.510A pdb=" N LEU C 14 " --> pdb=" O GLU C 10 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS C 15 " --> pdb=" O ALA C 11 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ASN C 16 " --> pdb=" O GLU C 12 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLN C 17 " --> pdb=" O GLN C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'D' and resid 9 through 23 Processing helix chain 'D' and resid 29 through 43 Processing helix chain 'D' and resid 55 through 59 removed outlier: 3.876A pdb=" N ASN D 59 " --> pdb=" O ALA D 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.554A pdb=" N SER E 31 " --> pdb=" O ALA E 28 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.828A pdb=" N ASP E 90 " --> pdb=" O ARG E 87 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 87 through 91' Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 190 removed outlier: 6.914A pdb=" N LYS B 35 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ILE B 222 " --> pdb=" O LYS B 35 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU B 37 " --> pdb=" O ILE B 222 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N CYS B 224 " --> pdb=" O LEU B 37 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LEU B 39 " --> pdb=" O CYS B 224 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N ALA B 226 " --> pdb=" O LEU B 39 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ILE B 221 " --> pdb=" O ILE B 265 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N PHE B 267 " --> pdb=" O ILE B 221 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N PHE B 223 " --> pdb=" O PHE B 267 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ASN B 269 " --> pdb=" O PHE B 223 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 225 " --> pdb=" O ASN B 269 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 46 through 51 removed outlier: 3.954A pdb=" N ARG C 46 " --> pdb=" O ASN C 340 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE C 338 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N THR C 50 " --> pdb=" O LEU C 336 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N LEU C 336 " --> pdb=" O THR C 50 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 7.033A pdb=" N ALA C 73 " --> pdb=" O TYR C 59 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N MET C 61 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N VAL C 71 " --> pdb=" O MET C 61 " (cutoff:3.500A) removed outlier: 5.268A pdb=" N TRP C 63 " --> pdb=" O LEU C 69 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N LEU C 69 " --> pdb=" O TRP C 63 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER C 74 " --> pdb=" O LYS C 78 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN C 88 " --> pdb=" O ASP C 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.990A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 6.938A pdb=" N SER C 160 " --> pdb=" O SER C 147 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N CYS C 149 " --> pdb=" O VAL C 158 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VAL C 158 " --> pdb=" O CYS C 149 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N PHE C 151 " --> pdb=" O GLN C 156 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N GLN C 156 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ILE C 157 " --> pdb=" O TRP C 169 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N THR C 165 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N THR C 178 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 5.860A 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: 6.935A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N LEU C 192 " --> pdb=" O LEU C 198 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N LEU C 198 " --> pdb=" O LEU C 192 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N PHE C 199 " --> pdb=" O TRP C 211 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ASP C 212 " --> pdb=" O CYS C 218 " (cutoff:3.500A) removed outlier: 6.371A 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: 6.581A pdb=" N CYS C 250 " --> pdb=" O THR C 263 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N THR C 263 " --> pdb=" O CYS C 250 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LEU C 252 " --> pdb=" O LEU C 261 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN C 259 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 273 through 278 removed outlier: 3.771A pdb=" N SER C 275 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.447A 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: 6.138A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA E 49 " --> pdb=" O TRP E 36 " (cutoff:3.500A) removed outlier: 6.134A pdb=" N ARG E 38 " --> pdb=" O TRP E 47 " (cutoff:3.500A) removed outlier: 5.213A pdb=" N TRP E 47 " --> pdb=" O ARG E 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.138A pdb=" N GLY E 10 " --> pdb=" O THR E 118 " (cutoff:3.500A) removed outlier: 4.573A 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 129 Processing sheet with id=AB4, first strand: chain 'E' and resid 135 through 136 removed outlier: 6.773A pdb=" N TRP E 164 " --> pdb=" O LEU E 176 " (cutoff:3.500A) 409 hydrogen bonds defined for protein. 1155 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: 2.62 Time building geometry restraints manager: 2.42 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: 2664 1.34 - 1.46: 1953 1.46 - 1.58: 3804 1.58 - 1.70: 1 1.70 - 1.81: 86 Bond restraints: 8508 Sorted by residual: bond pdb=" C03 8IU R 401 " pdb=" C04 8IU R 401 " ideal model delta sigma weight residual 1.528 1.320 0.208 2.00e-02 2.50e+03 1.09e+02 bond pdb=" C04 8IU R 401 " pdb=" N05 8IU R 401 " ideal model delta sigma weight residual 1.457 1.647 -0.190 2.00e-02 2.50e+03 9.07e+01 bond pdb=" C21 8IU R 401 " pdb=" N05 8IU R 401 " ideal model delta sigma weight residual 1.470 1.326 0.144 2.00e-02 2.50e+03 5.20e+01 bond pdb=" C03 8IU R 401 " pdb=" N02 8IU R 401 " ideal model delta sigma weight residual 1.448 1.557 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" N19 8IU R 401 " pdb=" N20 8IU R 401 " ideal model delta sigma weight residual 1.341 1.444 -0.103 2.00e-02 2.50e+03 2.63e+01 ... (remaining 8503 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 11344 2.15 - 4.30: 180 4.30 - 6.46: 32 6.46 - 8.61: 4 8.61 - 10.76: 1 Bond angle restraints: 11561 Sorted by residual: angle pdb=" CA LEU R 163 " pdb=" C LEU R 163 " pdb=" N GLU R 164 " ideal model delta sigma weight residual 118.14 122.91 -4.77 1.31e+00 5.83e-01 1.32e+01 angle pdb=" N LEU R 237 " pdb=" CA LEU R 237 " pdb=" C LEU R 237 " ideal model delta sigma weight residual 109.81 117.45 -7.64 2.21e+00 2.05e-01 1.19e+01 angle pdb=" N PRO E 224 " pdb=" CA PRO E 224 " pdb=" C PRO E 224 " ideal model delta sigma weight residual 112.10 120.22 -8.12 2.60e+00 1.48e-01 9.74e+00 angle pdb=" CA TYR E 178 " pdb=" CB TYR E 178 " pdb=" CG TYR E 178 " ideal model delta sigma weight residual 113.90 119.47 -5.57 1.80e+00 3.09e-01 9.56e+00 angle pdb=" CA LEU B 227 " pdb=" CB LEU B 227 " pdb=" CG LEU B 227 " ideal model delta sigma weight residual 116.30 127.06 -10.76 3.50e+00 8.16e-02 9.45e+00 ... (remaining 11556 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.88: 4521 16.88 - 33.76: 364 33.76 - 50.64: 76 50.64 - 67.51: 18 67.51 - 84.39: 7 Dihedral angle restraints: 4986 sinusoidal: 1811 harmonic: 3175 Sorted by residual: dihedral pdb=" CA ARG E 206 " pdb=" C ARG E 206 " pdb=" N LEU E 207 " pdb=" CA LEU E 207 " ideal model delta harmonic sigma weight residual -180.00 -157.85 -22.15 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" CA ASN B 347 " pdb=" C ASN B 347 " pdb=" N LEU B 348 " pdb=" CA LEU B 348 " ideal model delta harmonic sigma weight residual 180.00 158.06 21.94 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA CYS R 95 " pdb=" C CYS R 95 " pdb=" N SER R 96 " pdb=" CA SER R 96 " ideal model delta harmonic sigma weight residual -180.00 -158.44 -21.56 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 4983 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 863 0.038 - 0.076: 352 0.076 - 0.113: 96 0.113 - 0.151: 29 0.151 - 0.189: 3 Chirality restraints: 1343 Sorted by residual: chirality pdb=" CA PRO E 224 " pdb=" N PRO E 224 " pdb=" C PRO E 224 " pdb=" CB PRO E 224 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 8.93e-01 chirality pdb=" CA LEU R 237 " pdb=" N LEU R 237 " pdb=" C LEU R 237 " pdb=" CB LEU R 237 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.52e-01 chirality pdb=" CA ASN B 347 " pdb=" N ASN B 347 " pdb=" C ASN B 347 " pdb=" CB ASN B 347 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.15e-01 ... (remaining 1340 not shown) Planarity restraints: 1449 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL E 135 " 0.044 5.00e-02 4.00e+02 6.75e-02 7.29e+00 pdb=" N PRO E 136 " -0.117 5.00e-02 4.00e+02 pdb=" CA PRO E 136 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 136 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLN R 242 " 0.010 2.00e-02 2.50e+03 1.98e-02 3.94e+00 pdb=" C GLN R 242 " -0.034 2.00e-02 2.50e+03 pdb=" O GLN R 242 " 0.013 2.00e-02 2.50e+03 pdb=" N TRP R 243 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL R 123 " 0.010 2.00e-02 2.50e+03 1.94e-02 3.76e+00 pdb=" C VAL R 123 " -0.034 2.00e-02 2.50e+03 pdb=" O VAL R 123 " 0.013 2.00e-02 2.50e+03 pdb=" N SER R 124 " 0.011 2.00e-02 2.50e+03 ... (remaining 1446 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 67 2.66 - 3.22: 7178 3.22 - 3.78: 11683 3.78 - 4.34: 15805 4.34 - 4.90: 28160 Nonbonded interactions: 62893 Sorted by model distance: nonbonded pdb=" OD1 ASP R 75 " pdb=" OG SER R 272 " model vdw 2.102 3.040 nonbonded pdb=" OG1 THR C 128 " pdb=" O GLU C 130 " model vdw 2.213 3.040 nonbonded pdb=" OH TYR R 113 " pdb=" O GLY R 236 " model vdw 2.259 3.040 nonbonded pdb=" O ASP C 333 " pdb=" OG SER C 334 " model vdw 2.310 3.040 nonbonded pdb=" O SER E 106 " pdb=" OG SER E 106 " model vdw 2.334 3.040 ... (remaining 62888 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 0.320 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 21.790 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.550 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 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 : 0.007 0.208 8508 Z= 0.438 Angle : 0.718 10.761 11561 Z= 0.386 Chirality : 0.046 0.189 1343 Planarity : 0.005 0.068 1449 Dihedral : 13.522 84.393 2935 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.26), residues: 1083 helix: 2.11 (0.28), residues: 359 sheet: 0.95 (0.31), residues: 292 loop : -2.12 (0.25), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 82 HIS 0.005 0.001 HIS C 91 PHE 0.020 0.002 PHE R 232 TYR 0.029 0.002 TYR E 178 ARG 0.007 0.001 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 162 time to evaluate : 0.913 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 1.2082 time to fit residues: 208.1546 Evaluate side-chains 148 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 83 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 97 optimal weight: 5.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 75 GLN C 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.119088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.102223 restraints weight = 11562.956| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.69 r_work: 0.3256 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8508 Z= 0.210 Angle : 0.580 7.201 11561 Z= 0.309 Chirality : 0.042 0.170 1343 Planarity : 0.004 0.049 1449 Dihedral : 5.047 41.136 1193 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 1.73 % Allowed : 10.15 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.26), residues: 1083 helix: 2.77 (0.28), residues: 364 sheet: 1.21 (0.31), residues: 274 loop : -1.94 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 248 HIS 0.003 0.001 HIS R 261 PHE 0.013 0.001 PHE R 232 TYR 0.020 0.002 TYR E 178 ARG 0.002 0.000 ARG E 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 0.864 Fit side-chains REVERT: R 167 PHE cc_start: 0.7685 (m-80) cc_final: 0.7281 (m-10) REVERT: C 23 LYS cc_start: 0.8140 (tmmt) cc_final: 0.7719 (ttmt) REVERT: C 57 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8220 (ptmt) outliers start: 15 outliers final: 5 residues processed: 151 average time/residue: 1.2190 time to fit residues: 196.6262 Evaluate side-chains 150 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 144 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 81 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 48 ASN C 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.117493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.100720 restraints weight = 11735.392| |-----------------------------------------------------------------------------| r_work (start): 0.3331 rms_B_bonded: 1.70 r_work: 0.3232 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3099 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8508 Z= 0.231 Angle : 0.584 7.191 11561 Z= 0.309 Chirality : 0.042 0.175 1343 Planarity : 0.004 0.043 1449 Dihedral : 4.787 35.356 1193 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.54 % Allowed : 12.57 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.95 (0.26), residues: 1083 helix: 2.95 (0.28), residues: 362 sheet: 1.29 (0.31), residues: 268 loop : -1.91 (0.25), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP R 248 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.002 PHE R 232 TYR 0.023 0.002 TYR E 178 ARG 0.004 0.000 ARG C 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.996 Fit side-chains REVERT: R 54 LEU cc_start: 0.7560 (mp) cc_final: 0.7358 (mt) REVERT: R 237 LEU cc_start: 0.8055 (OUTLIER) cc_final: 0.7377 (mp) REVERT: B 252 SER cc_start: 0.8389 (t) cc_final: 0.8057 (p) REVERT: C 20 ASP cc_start: 0.7802 (m-30) cc_final: 0.7586 (m-30) REVERT: C 57 LYS cc_start: 0.8711 (OUTLIER) cc_final: 0.8229 (ptmt) REVERT: C 164 THR cc_start: 0.8026 (m) cc_final: 0.7725 (p) outliers start: 22 outliers final: 10 residues processed: 161 average time/residue: 1.1599 time to fit residues: 199.3435 Evaluate side-chains 163 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 45 optimal weight: 0.6980 chunk 104 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 105 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 132 ASN C 340 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.114096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.097594 restraints weight = 11598.748| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.67 r_work: 0.3180 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3045 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 8508 Z= 0.430 Angle : 0.715 10.418 11561 Z= 0.375 Chirality : 0.048 0.224 1343 Planarity : 0.004 0.050 1449 Dihedral : 5.259 42.013 1193 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.77 % Allowed : 14.99 % Favored : 82.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.26), residues: 1083 helix: 2.69 (0.28), residues: 362 sheet: 1.14 (0.31), residues: 266 loop : -2.05 (0.25), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 248 HIS 0.006 0.002 HIS E 35 PHE 0.023 0.002 PHE R 232 TYR 0.032 0.003 TYR E 178 ARG 0.004 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.926 Fit side-chains REVERT: R 237 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7399 (mp) REVERT: B 252 SER cc_start: 0.8414 (t) cc_final: 0.8142 (p) REVERT: C 20 ASP cc_start: 0.7859 (m-30) cc_final: 0.7642 (m-30) REVERT: C 22 ARG cc_start: 0.8297 (ptp-170) cc_final: 0.8078 (ptp-170) REVERT: C 57 LYS cc_start: 0.8769 (OUTLIER) cc_final: 0.8315 (ptmt) REVERT: C 164 THR cc_start: 0.8184 (m) cc_final: 0.7904 (p) REVERT: C 198 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8265 (pp) outliers start: 24 outliers final: 11 residues processed: 177 average time/residue: 1.0839 time to fit residues: 205.5978 Evaluate side-chains 182 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 168 time to evaluate : 0.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 120 LEU Chi-restraints excluded: chain R residue 237 LEU Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain C residue 57 LYS Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 2 optimal weight: 1.9990 chunk 73 optimal weight: 1.9990 chunk 47 optimal weight: 0.0010 chunk 74 optimal weight: 0.0770 chunk 58 optimal weight: 1.9990 chunk 88 optimal weight: 0.3980 chunk 70 optimal weight: 1.9990 chunk 90 optimal weight: 0.6980 chunk 84 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 0.3980 overall best weight: 0.3144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 48 ASN C 132 ASN C 155 ASN C 340 ASN E 167 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.119882 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.103319 restraints weight = 11651.641| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.69 r_work: 0.3277 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3147 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 8508 Z= 0.133 Angle : 0.509 6.332 11561 Z= 0.271 Chirality : 0.040 0.143 1343 Planarity : 0.004 0.039 1449 Dihedral : 4.355 24.174 1193 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.54 % Allowed : 16.26 % Favored : 81.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.02 (0.26), residues: 1083 helix: 3.18 (0.28), residues: 360 sheet: 1.27 (0.31), residues: 267 loop : -1.96 (0.25), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 243 HIS 0.002 0.001 HIS C 91 PHE 0.011 0.001 PHE B 189 TYR 0.013 0.001 TYR R 222 ARG 0.005 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.956 Fit side-chains REVERT: B 252 SER cc_start: 0.8358 (t) cc_final: 0.8001 (p) REVERT: C 20 ASP cc_start: 0.7834 (m-30) cc_final: 0.7586 (m-30) REVERT: C 164 THR cc_start: 0.8018 (m) cc_final: 0.7683 (p) outliers start: 22 outliers final: 7 residues processed: 163 average time/residue: 1.1095 time to fit residues: 193.3421 Evaluate side-chains 163 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 156 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 249 ILE Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 234 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 6 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 96 optimal weight: 0.3980 chunk 81 optimal weight: 3.9990 chunk 32 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 105 optimal weight: 2.9990 chunk 7 optimal weight: 0.0770 overall best weight: 1.2542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 48 ASN C 132 ASN C 259 GLN C 340 ASN E 130 GLN E 167 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.115323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.098762 restraints weight = 11587.067| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 1.69 r_work: 0.3201 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.2433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8508 Z= 0.318 Angle : 0.638 8.307 11561 Z= 0.335 Chirality : 0.044 0.200 1343 Planarity : 0.004 0.044 1449 Dihedral : 4.821 33.999 1193 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.19 % Allowed : 18.57 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.26), residues: 1083 helix: 3.00 (0.28), residues: 362 sheet: 1.25 (0.31), residues: 264 loop : -1.87 (0.25), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP R 248 HIS 0.005 0.001 HIS E 35 PHE 0.020 0.002 PHE R 232 TYR 0.029 0.002 TYR E 178 ARG 0.006 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.938 Fit side-chains REVERT: R 54 LEU cc_start: 0.7563 (mp) cc_final: 0.7355 (mt) REVERT: B 252 SER cc_start: 0.8355 (t) cc_final: 0.8066 (p) REVERT: C 20 ASP cc_start: 0.7853 (m-30) cc_final: 0.7632 (m-30) REVERT: C 164 THR cc_start: 0.8174 (m) cc_final: 0.7886 (p) REVERT: C 198 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8186 (pp) REVERT: E 6 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8314 (mp0) outliers start: 19 outliers final: 13 residues processed: 173 average time/residue: 1.1309 time to fit residues: 209.0221 Evaluate side-chains 177 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 198 LEU Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain C residue 254 ASP Chi-restraints excluded: chain E residue 6 GLU Chi-restraints excluded: chain E residue 115 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 54 optimal weight: 0.8980 chunk 98 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 40 optimal weight: 0.0370 chunk 33 optimal weight: 0.0570 chunk 18 optimal weight: 0.7980 chunk 50 optimal weight: 1.9990 chunk 102 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 24 optimal weight: 0.9980 overall best weight: 0.4176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 48 ASN C 132 ASN C 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.118709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.102124 restraints weight = 11755.967| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 1.69 r_work: 0.3262 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3132 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 8508 Z= 0.145 Angle : 0.526 8.082 11561 Z= 0.276 Chirality : 0.040 0.152 1343 Planarity : 0.004 0.038 1449 Dihedral : 4.279 23.659 1193 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 2.08 % Allowed : 20.30 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.02 (0.26), residues: 1083 helix: 3.16 (0.28), residues: 363 sheet: 1.37 (0.32), residues: 251 loop : -1.91 (0.25), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 243 HIS 0.002 0.001 HIS E 35 PHE 0.012 0.001 PHE B 189 TYR 0.015 0.001 TYR E 178 ARG 0.005 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.881 Fit side-chains REVERT: B 252 SER cc_start: 0.8374 (t) cc_final: 0.8054 (p) REVERT: C 20 ASP cc_start: 0.7865 (m-30) cc_final: 0.7620 (m-30) REVERT: C 22 ARG cc_start: 0.8281 (ptp-170) cc_final: 0.8000 (mtm180) REVERT: C 164 THR cc_start: 0.8065 (m) cc_final: 0.7748 (p) outliers start: 18 outliers final: 9 residues processed: 162 average time/residue: 1.1176 time to fit residues: 193.4975 Evaluate side-chains 161 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 234 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 45 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 0.6980 chunk 44 optimal weight: 0.9990 chunk 55 optimal weight: 0.0670 chunk 50 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 48 ASN B 22 ASN C 132 ASN C 340 ASN E 130 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.117971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.101401 restraints weight = 11772.056| |-----------------------------------------------------------------------------| r_work (start): 0.3349 rms_B_bonded: 1.69 r_work: 0.3249 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3117 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8508 Z= 0.175 Angle : 0.541 9.375 11561 Z= 0.284 Chirality : 0.041 0.161 1343 Planarity : 0.004 0.038 1449 Dihedral : 4.299 24.138 1193 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.19 % Allowed : 20.18 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.15 (0.26), residues: 1083 helix: 3.28 (0.28), residues: 362 sheet: 1.35 (0.31), residues: 262 loop : -1.85 (0.25), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP R 243 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE B 189 TYR 0.018 0.001 TYR E 178 ARG 0.006 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 156 time to evaluate : 0.981 Fit side-chains REVERT: B 252 SER cc_start: 0.8348 (t) cc_final: 0.8027 (p) REVERT: C 20 ASP cc_start: 0.7846 (m-30) cc_final: 0.7604 (m-30) REVERT: C 22 ARG cc_start: 0.8256 (ptp-170) cc_final: 0.7993 (mtm180) REVERT: C 164 THR cc_start: 0.8068 (m) cc_final: 0.7756 (p) outliers start: 19 outliers final: 12 residues processed: 164 average time/residue: 1.1218 time to fit residues: 196.6202 Evaluate side-chains 163 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 151 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 143 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 80 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 98 optimal weight: 0.7980 chunk 65 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 57 optimal weight: 0.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 48 ASN B 22 ASN C 132 ASN C 340 ASN E 130 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.116398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.099804 restraints weight = 11802.113| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 1.69 r_work: 0.3223 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3091 rms_B_bonded: 3.64 restraints_weight: 0.2500 r_work (final): 0.3091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8058 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 8508 Z= 0.234 Angle : 0.589 10.009 11561 Z= 0.308 Chirality : 0.042 0.179 1343 Planarity : 0.004 0.040 1449 Dihedral : 4.527 28.332 1193 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.54 % Allowed : 19.72 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.07 (0.26), residues: 1083 helix: 3.19 (0.28), residues: 362 sheet: 1.42 (0.32), residues: 252 loop : -1.89 (0.25), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 82 HIS 0.004 0.001 HIS E 35 PHE 0.015 0.001 PHE R 232 TYR 0.024 0.002 TYR E 178 ARG 0.006 0.000 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 151 time to evaluate : 0.869 Fit side-chains REVERT: B 252 SER cc_start: 0.8358 (t) cc_final: 0.8066 (p) REVERT: C 20 ASP cc_start: 0.7845 (m-30) cc_final: 0.7604 (m-30) REVERT: C 164 THR cc_start: 0.8123 (m) cc_final: 0.7825 (p) REVERT: C 246 ASP cc_start: 0.8078 (m-30) cc_final: 0.7841 (m-30) outliers start: 22 outliers final: 14 residues processed: 161 average time/residue: 1.1378 time to fit residues: 195.4737 Evaluate side-chains 163 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 84 ILE Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 143 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 99 optimal weight: 0.1980 chunk 70 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 48 ASN B 22 ASN C 132 ASN C 340 ASN E 130 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.117077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.100530 restraints weight = 11560.563| |-----------------------------------------------------------------------------| r_work (start): 0.3336 rms_B_bonded: 1.67 r_work: 0.3236 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8045 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8508 Z= 0.207 Angle : 0.564 10.040 11561 Z= 0.296 Chirality : 0.042 0.171 1343 Planarity : 0.004 0.040 1449 Dihedral : 4.431 26.849 1193 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.85 % Allowed : 20.42 % Favored : 77.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.11 (0.26), residues: 1083 helix: 3.20 (0.28), residues: 362 sheet: 1.37 (0.31), residues: 262 loop : -1.87 (0.25), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 243 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE R 232 TYR 0.021 0.002 TYR E 178 ARG 0.006 0.000 ARG C 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 148 time to evaluate : 0.961 Fit side-chains REVERT: B 252 SER cc_start: 0.8354 (t) cc_final: 0.8060 (p) REVERT: C 20 ASP cc_start: 0.7833 (m-30) cc_final: 0.7595 (m-30) REVERT: C 164 THR cc_start: 0.8091 (m) cc_final: 0.7793 (p) REVERT: C 246 ASP cc_start: 0.8029 (m-30) cc_final: 0.7794 (m-30) outliers start: 16 outliers final: 14 residues processed: 156 average time/residue: 1.1113 time to fit residues: 185.3572 Evaluate side-chains 160 residues out of total 946 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 54 LEU Chi-restraints excluded: chain R residue 77 LEU Chi-restraints excluded: chain R residue 192 ILE Chi-restraints excluded: chain R residue 226 LEU Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 303 ILE Chi-restraints excluded: chain C residue 52 ARG Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 189 SER Chi-restraints excluded: chain C residue 207 SER Chi-restraints excluded: chain C residue 234 PHE Chi-restraints excluded: chain E residue 115 THR Chi-restraints excluded: chain E residue 143 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 42 optimal weight: 0.9990 chunk 81 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 3 optimal weight: 6.9990 chunk 63 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 56 optimal weight: 0.9980 chunk 10 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 48 ASN C 132 ASN C 340 ASN E 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.117846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.101227 restraints weight = 11803.014| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 1.69 r_work: 0.3247 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8508 Z= 0.182 Angle : 0.547 9.797 11561 Z= 0.287 Chirality : 0.041 0.165 1343 Planarity : 0.004 0.039 1449 Dihedral : 4.329 25.091 1193 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 2.42 % Allowed : 20.07 % Favored : 77.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 1.16 (0.26), residues: 1083 helix: 3.23 (0.28), residues: 363 sheet: 1.37 (0.31), residues: 262 loop : -1.82 (0.25), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 243 HIS 0.003 0.001 HIS E 35 PHE 0.012 0.001 PHE B 189 TYR 0.018 0.001 TYR E 178 ARG 0.006 0.000 ARG C 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6962.32 seconds wall clock time: 123 minutes 23.46 seconds (7403.46 seconds total)