Starting phenix.real_space_refine on Wed Mar 12 20:36:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ikh_35512/03_2025/8ikh_35512_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ikh_35512/03_2025/8ikh_35512.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ikh_35512/03_2025/8ikh_35512.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ikh_35512/03_2025/8ikh_35512.map" model { file = "/net/cci-nas-00/data/ceres_data/8ikh_35512/03_2025/8ikh_35512_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ikh_35512/03_2025/8ikh_35512_neut.cif" } resolution = 3.3 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= 0.010 sd= 0.088 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 60 5.16 5 C 5376 2.51 5 N 1433 2.21 5 O 1534 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8403 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1675 Classifications: {'peptide': 217} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Unresolved non-hydrogen bonds: 74 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 5} Unresolved non-hydrogen planarities: 47 Chain: "B" Number of atoms: 2547 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2547 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLU:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "C" Number of atoms: 406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 406 Classifications: {'peptide': 53} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "R" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 2076 Classifications: {'peptide': 265} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 7, 'TRANS': 257} Chain breaks: 3 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "S" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1671 Classifications: {'peptide': 223} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 10, 'TRANS': 212} Chain breaks: 3 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 47 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 6, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 44 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'Q2L': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.39, per 1000 atoms: 0.64 Number of scatterers: 8403 At special positions: 0 Unit cell: (96.12, 128.16, 126.38, 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 60 16.00 O 1534 8.00 N 1433 7.00 C 5376 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.15 Conformation dependent library (CDL) restraints added in 986.5 milliseconds 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2042 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 13 sheets defined 37.1% alpha, 19.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 6 through 28 removed outlier: 3.768A pdb=" N GLU A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER A 16 " --> pdb=" O ALA A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 54 removed outlier: 4.238A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLN A 52 " --> pdb=" O THR A 48 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LYS A 54 " --> pdb=" O VAL A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 removed outlier: 3.701A pdb=" N TRP A 211 " --> pdb=" O ARG A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 242 through 255 Processing helix chain 'A' and resid 270 through 277 removed outlier: 3.807A pdb=" N PHE A 274 " --> pdb=" O LYS A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 278 through 281 removed outlier: 3.856A pdb=" N SER A 281 " --> pdb=" O ILE A 278 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 278 through 281' Processing helix chain 'A' and resid 282 through 287 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.700A pdb=" N ALA A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 352 removed outlier: 3.658A pdb=" N PHE A 334 " --> pdb=" O LYS A 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 22 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 128 through 132 removed outlier: 3.721A pdb=" N GLY B 131 " --> pdb=" O THR B 128 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ASN B 132 " --> pdb=" O ARG B 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 128 through 132' Processing helix chain 'B' and resid 279 through 282 Processing helix chain 'C' and resid 8 through 23 removed outlier: 3.617A pdb=" N GLN C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU C 19 " --> pdb=" O LEU C 15 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N LYS C 20 " --> pdb=" O VAL C 16 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N MET C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 removed outlier: 3.707A pdb=" N ALA C 33 " --> pdb=" O LYS C 29 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS C 44 " --> pdb=" O TYR C 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 114 through 116 No H-bonds generated for 'chain 'R' and resid 114 through 116' Processing helix chain 'R' and resid 117 through 142 Processing helix chain 'R' and resid 150 through 172 removed outlier: 3.767A pdb=" N HIS R 154 " --> pdb=" O ARG R 150 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR R 172 " --> pdb=" O VAL R 168 " (cutoff:3.500A) Processing helix chain 'R' and resid 185 through 220 removed outlier: 3.611A pdb=" N PHE R 189 " --> pdb=" O SER R 185 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE R 218 " --> pdb=" O ARG R 214 " (cutoff:3.500A) Processing helix chain 'R' and resid 223 through 228 Processing helix chain 'R' and resid 234 through 250 removed outlier: 3.546A pdb=" N TRP R 241 " --> pdb=" O PHE R 237 " (cutoff:3.500A) Processing helix chain 'R' and resid 272 through 279 Processing helix chain 'R' and resid 281 through 312 removed outlier: 4.171A pdb=" N LEU R 286 " --> pdb=" O VAL R 282 " (cutoff:3.500A) Processing helix chain 'R' and resid 336 through 366 removed outlier: 3.692A pdb=" N ARG R 340 " --> pdb=" O ARG R 336 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N LEU R 347 " --> pdb=" O LYS R 343 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ILE R 348 " --> pdb=" O THR R 344 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY R 357 " --> pdb=" O ILE R 353 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 372 through 388 removed outlier: 3.987A pdb=" N MET R 384 " --> pdb=" O ALA R 380 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N LEU R 385 " --> pdb=" O PHE R 381 " (cutoff:3.500A) Processing helix chain 'R' and resid 388 through 401 Proline residue: R 394 - end of helix removed outlier: 4.304A pdb=" N SER R 401 " --> pdb=" O TYR R 397 " (cutoff:3.500A) Processing helix chain 'R' and resid 401 through 408 removed outlier: 4.028A pdb=" N ARG R 405 " --> pdb=" O SER R 401 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 32 removed outlier: 3.509A pdb=" N PHE S 32 " --> pdb=" O PHE S 29 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.230A pdb=" N VAL A 34 " --> pdb=" O LYS A 197 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE A 199 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N LEU A 36 " --> pdb=" O PHE A 199 " (cutoff:3.500A) removed outlier: 8.283A pdb=" N VAL A 201 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 7.981A pdb=" N LEU A 38 " --> pdb=" O VAL A 201 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.593A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.204A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 5.072A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 5.894A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.629A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N SER B 161 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.022A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N PHE B 199 " --> pdb=" O TRP B 211 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ALA B 208 " --> pdb=" O THR B 221 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N THR B 221 " --> pdb=" O ALA B 208 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU B 210 " --> pdb=" O ARG B 219 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.525A pdb=" N ALA B 231 " --> pdb=" O GLY B 244 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N LEU B 252 " --> pdb=" O MET B 262 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.548A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277 removed outlier: 6.324A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.760A pdb=" N GLN S 3 " --> pdb=" O SER S 25 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG S 18 " --> pdb=" O MET S 83 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 46 through 51 removed outlier: 6.724A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 46 through 51 removed outlier: 6.724A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 144 through 148 Processing sheet with id=AB4, first strand: chain 'S' and resid 166 through 167 372 hydrogen bonds defined for protein. 1059 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: 2.46 Time building geometry restraints manager: 2.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1336 1.30 - 1.43: 2289 1.43 - 1.56: 4856 1.56 - 1.69: 0 1.69 - 1.81: 87 Bond restraints: 8568 Sorted by residual: bond pdb=" N11 Q2L R 501 " pdb=" O12 Q2L R 501 " ideal model delta sigma weight residual 1.207 1.402 -0.195 2.00e-02 2.50e+03 9.49e+01 bond pdb=" N ARG R 145 " pdb=" CA ARG R 145 " ideal model delta sigma weight residual 1.459 1.412 0.047 1.06e-02 8.90e+03 1.98e+01 bond pdb=" CA ARG R 145 " pdb=" C ARG R 145 " ideal model delta sigma weight residual 1.524 1.494 0.030 7.00e-03 2.04e+04 1.90e+01 bond pdb=" N ASN R 256 " pdb=" CA ASN R 256 " ideal model delta sigma weight residual 1.457 1.510 -0.052 1.29e-02 6.01e+03 1.65e+01 bond pdb=" CA ASP R 272 " pdb=" CB ASP R 272 " ideal model delta sigma weight residual 1.533 1.480 0.054 1.51e-02 4.39e+03 1.26e+01 ... (remaining 8563 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 11371 1.73 - 3.46: 176 3.46 - 5.19: 34 5.19 - 6.92: 19 6.92 - 8.65: 5 Bond angle restraints: 11605 Sorted by residual: angle pdb=" C SER R 144 " pdb=" N ARG R 145 " pdb=" CA ARG R 145 " ideal model delta sigma weight residual 122.44 115.29 7.15 1.19e+00 7.06e-01 3.61e+01 angle pdb=" N VAL S 48 " pdb=" CA VAL S 48 " pdb=" C VAL S 48 " ideal model delta sigma weight residual 113.71 108.67 5.04 9.50e-01 1.11e+00 2.82e+01 angle pdb=" N TRP R 279 " pdb=" CA TRP R 279 " pdb=" C TRP R 279 " ideal model delta sigma weight residual 112.57 106.96 5.61 1.13e+00 7.83e-01 2.46e+01 angle pdb=" C GLU R 273 " pdb=" N THR R 274 " pdb=" CA THR R 274 " ideal model delta sigma weight residual 120.44 114.08 6.36 1.36e+00 5.41e-01 2.19e+01 angle pdb=" C CYS R 107 " pdb=" N PHE R 108 " pdb=" CA PHE R 108 " ideal model delta sigma weight residual 121.26 113.88 7.38 1.59e+00 3.96e-01 2.16e+01 ... (remaining 11600 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 4426 16.00 - 32.00: 481 32.00 - 47.99: 123 47.99 - 63.99: 19 63.99 - 79.99: 5 Dihedral angle restraints: 5054 sinusoidal: 1900 harmonic: 3154 Sorted by residual: dihedral pdb=" C ASP R 272 " pdb=" N ASP R 272 " pdb=" CA ASP R 272 " pdb=" CB ASP R 272 " ideal model delta harmonic sigma weight residual -122.60 -109.32 -13.28 0 2.50e+00 1.60e-01 2.82e+01 dihedral pdb=" N ASP R 272 " pdb=" C ASP R 272 " pdb=" CA ASP R 272 " pdb=" CB ASP R 272 " ideal model delta harmonic sigma weight residual 122.80 112.02 10.78 0 2.50e+00 1.60e-01 1.86e+01 dihedral pdb=" C LEU R 165 " pdb=" N LEU R 165 " pdb=" CA LEU R 165 " pdb=" CB LEU R 165 " ideal model delta harmonic sigma weight residual -122.60 -112.40 -10.20 0 2.50e+00 1.60e-01 1.66e+01 ... (remaining 5051 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1198 0.065 - 0.129: 139 0.129 - 0.194: 5 0.194 - 0.258: 4 0.258 - 0.323: 1 Chirality restraints: 1347 Sorted by residual: chirality pdb=" CA ASP R 272 " pdb=" N ASP R 272 " pdb=" C ASP R 272 " pdb=" CB ASP R 272 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.60e+00 chirality pdb=" CA ASN R 256 " pdb=" N ASN R 256 " pdb=" C ASN R 256 " pdb=" CB ASN R 256 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.27e+00 chirality pdb=" CA CYS R 107 " pdb=" N CYS R 107 " pdb=" C CYS R 107 " pdb=" CB CYS R 107 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.20e+00 ... (remaining 1344 not shown) Planarity restraints: 1447 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 165 " 0.014 2.00e-02 2.50e+03 2.75e-02 7.59e+00 pdb=" C LEU R 165 " -0.048 2.00e-02 2.50e+03 pdb=" O LEU R 165 " 0.018 2.00e-02 2.50e+03 pdb=" N GLY R 166 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE B 235 " -0.035 5.00e-02 4.00e+02 5.37e-02 4.61e+00 pdb=" N PRO B 236 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO B 236 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO B 236 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASN R 256 " 0.010 2.00e-02 2.50e+03 2.10e-02 4.39e+00 pdb=" C ASN R 256 " -0.036 2.00e-02 2.50e+03 pdb=" O ASN R 256 " 0.014 2.00e-02 2.50e+03 pdb=" N CYS R 257 " 0.012 2.00e-02 2.50e+03 ... (remaining 1444 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 473 2.73 - 3.28: 8073 3.28 - 3.82: 13117 3.82 - 4.36: 14548 4.36 - 4.90: 26352 Nonbonded interactions: 62563 Sorted by model distance: nonbonded pdb=" O TRP R 255 " pdb=" OD1 ASN R 256 " model vdw 2.194 3.040 nonbonded pdb=" O GLY S 8 " pdb=" OG1 THR S 115 " model vdw 2.221 3.040 nonbonded pdb=" O CYS B 103 " pdb=" NH2 ARG B 150 " model vdw 2.234 3.120 nonbonded pdb=" O LEU R 165 " pdb=" N VAL R 168 " model vdw 2.249 3.120 nonbonded pdb=" O GLY S 112 " pdb=" OG SER S 172 " model vdw 2.256 3.040 ... (remaining 62558 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: 0.990 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: 0.370 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.000 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.050 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 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 0.195 8568 Z= 0.253 Angle : 0.614 8.646 11605 Z= 0.339 Chirality : 0.043 0.323 1347 Planarity : 0.003 0.054 1447 Dihedral : 14.347 79.989 3012 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.23 % Allowed : 0.68 % Favored : 99.10 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.27), residues: 1057 helix: 1.72 (0.29), residues: 372 sheet: -0.17 (0.34), residues: 264 loop : -0.93 (0.30), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 339 HIS 0.008 0.001 HIS R 154 PHE 0.017 0.001 PHE S 227 TYR 0.009 0.001 TYR S 102 ARG 0.004 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 0.821 Fit side-chains REVERT: B 17 GLN cc_start: 0.8646 (tm-30) cc_final: 0.8352 (tm-30) REVERT: B 273 ILE cc_start: 0.8539 (mp) cc_final: 0.8300 (mp) REVERT: R 353 ILE cc_start: 0.7864 (tp) cc_final: 0.7597 (tp) outliers start: 2 outliers final: 1 residues processed: 132 average time/residue: 0.1963 time to fit residues: 36.3743 Evaluate side-chains 105 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 104 time to evaluate : 1.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 273 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 0.0470 chunk 43 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 50 optimal weight: 0.9980 chunk 62 optimal weight: 5.9990 chunk 97 optimal weight: 0.0010 overall best weight: 0.3684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 220 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4274 r_free = 0.4274 target = 0.188158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.153419 restraints weight = 12217.754| |-----------------------------------------------------------------------------| r_work (start): 0.3893 rms_B_bonded: 2.25 r_work: 0.3680 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3557 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 8568 Z= 0.129 Angle : 0.489 7.096 11605 Z= 0.253 Chirality : 0.040 0.200 1347 Planarity : 0.003 0.054 1447 Dihedral : 4.488 35.810 1189 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.24 % Allowed : 7.67 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.27), residues: 1057 helix: 1.56 (0.28), residues: 385 sheet: -0.04 (0.34), residues: 259 loop : -0.98 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP R 279 HIS 0.008 0.001 HIS R 154 PHE 0.014 0.001 PHE S 80 TYR 0.008 0.001 TYR S 102 ARG 0.003 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 113 time to evaluate : 0.981 Fit side-chains REVERT: B 17 GLN cc_start: 0.8717 (tm-30) cc_final: 0.8299 (tm-30) REVERT: C 18 GLN cc_start: 0.8582 (tp40) cc_final: 0.8185 (tp-100) REVERT: C 21 MET cc_start: 0.8669 (tpp) cc_final: 0.8111 (ttt) REVERT: R 110 VAL cc_start: 0.5320 (OUTLIER) cc_final: 0.4944 (m) REVERT: R 183 LYS cc_start: 0.7247 (mmtm) cc_final: 0.6635 (mtmt) REVERT: R 353 ILE cc_start: 0.7865 (tp) cc_final: 0.7575 (tp) REVERT: S 159 ASN cc_start: 0.7721 (t0) cc_final: 0.7098 (t0) REVERT: S 217 CYS cc_start: 0.2108 (p) cc_final: 0.1569 (t) REVERT: S 218 MET cc_start: 0.1619 (ptp) cc_final: 0.1124 (ptp) outliers start: 11 outliers final: 8 residues processed: 120 average time/residue: 0.1977 time to fit residues: 33.2653 Evaluate side-chains 117 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 337 ASP Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 403 ASP Chi-restraints excluded: chain S residue 117 LEU Chi-restraints excluded: chain S residue 225 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 67 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 47 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS C 18 GLN ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.177128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.140673 restraints weight = 12294.853| |-----------------------------------------------------------------------------| r_work (start): 0.3748 rms_B_bonded: 2.40 r_work: 0.3505 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work: 0.3379 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7859 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 8568 Z= 0.352 Angle : 0.642 6.588 11605 Z= 0.334 Chirality : 0.045 0.162 1347 Planarity : 0.004 0.052 1447 Dihedral : 4.936 33.887 1186 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.03 % Allowed : 11.61 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.26), residues: 1057 helix: 1.27 (0.28), residues: 379 sheet: -0.18 (0.32), residues: 268 loop : -1.31 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP S 36 HIS 0.011 0.001 HIS R 154 PHE 0.034 0.002 PHE B 199 TYR 0.019 0.002 TYR B 105 ARG 0.007 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.920 Fit side-chains REVERT: B 17 GLN cc_start: 0.8636 (tm-30) cc_final: 0.8220 (tm-30) REVERT: C 18 GLN cc_start: 0.8542 (tp-100) cc_final: 0.8324 (tp40) REVERT: C 21 MET cc_start: 0.8808 (tpp) cc_final: 0.8134 (ttt) REVERT: R 116 GLN cc_start: 0.6392 (OUTLIER) cc_final: 0.5934 (mp10) REVERT: R 353 ILE cc_start: 0.7878 (tp) cc_final: 0.7666 (tp) REVERT: S 90 ASP cc_start: 0.7642 (m-30) cc_final: 0.7358 (m-30) outliers start: 18 outliers final: 13 residues processed: 113 average time/residue: 0.2572 time to fit residues: 39.5487 Evaluate side-chains 110 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain R residue 116 GLN Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 384 MET Chi-restraints excluded: chain R residue 403 ASP Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 93 optimal weight: 6.9990 chunk 61 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 chunk 74 optimal weight: 0.0670 chunk 87 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 overall best weight: 1.1122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 HIS ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.180203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.144950 restraints weight = 12192.660| |-----------------------------------------------------------------------------| r_work (start): 0.3800 rms_B_bonded: 2.52 r_work: 0.3536 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7675 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8568 Z= 0.177 Angle : 0.519 9.410 11605 Z= 0.269 Chirality : 0.041 0.165 1347 Planarity : 0.003 0.052 1447 Dihedral : 4.361 26.669 1186 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.48 % Allowed : 14.21 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.27), residues: 1057 helix: 1.48 (0.29), residues: 379 sheet: -0.18 (0.32), residues: 270 loop : -1.28 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP S 36 HIS 0.010 0.001 HIS R 154 PHE 0.019 0.001 PHE B 199 TYR 0.009 0.001 TYR S 102 ARG 0.005 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.965 Fit side-chains REVERT: B 17 GLN cc_start: 0.8629 (tm-30) cc_final: 0.8199 (tm-30) REVERT: C 18 GLN cc_start: 0.8524 (tp-100) cc_final: 0.7956 (tp-100) REVERT: C 21 MET cc_start: 0.8733 (tpp) cc_final: 0.8094 (ttt) REVERT: R 110 VAL cc_start: 0.4986 (OUTLIER) cc_final: 0.4776 (t) REVERT: R 116 GLN cc_start: 0.6320 (OUTLIER) cc_final: 0.5777 (mp10) REVERT: R 353 ILE cc_start: 0.7719 (tp) cc_final: 0.7491 (tp) REVERT: S 70 ILE cc_start: 0.6835 (OUTLIER) cc_final: 0.5734 (tt) REVERT: S 90 ASP cc_start: 0.7629 (m-30) cc_final: 0.7339 (m-30) REVERT: S 96 CYS cc_start: 0.8093 (p) cc_final: 0.7786 (t) REVERT: S 151 LYS cc_start: 0.6649 (mmtm) cc_final: 0.5152 (pttt) outliers start: 22 outliers final: 10 residues processed: 116 average time/residue: 0.2237 time to fit residues: 35.3799 Evaluate side-chains 114 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 101 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain R residue 110 VAL Chi-restraints excluded: chain R residue 116 GLN Chi-restraints excluded: chain R residue 403 ASP Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 97 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 63 optimal weight: 7.9990 chunk 79 optimal weight: 0.3980 chunk 36 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 21 optimal weight: 7.9990 chunk 70 optimal weight: 0.0370 chunk 13 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 50 optimal weight: 0.2980 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 91 HIS ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.181811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.146879 restraints weight = 12157.377| |-----------------------------------------------------------------------------| r_work (start): 0.3821 rms_B_bonded: 2.46 r_work: 0.3567 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8568 Z= 0.141 Angle : 0.485 8.539 11605 Z= 0.251 Chirality : 0.040 0.150 1347 Planarity : 0.003 0.051 1447 Dihedral : 4.063 21.779 1186 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.59 % Allowed : 15.33 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.27), residues: 1057 helix: 1.54 (0.28), residues: 385 sheet: -0.22 (0.32), residues: 265 loop : -1.24 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP S 36 HIS 0.010 0.001 HIS R 154 PHE 0.016 0.001 PHE B 199 TYR 0.008 0.001 TYR R 296 ARG 0.004 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.928 Fit side-chains REVERT: B 17 GLN cc_start: 0.8612 (tm-30) cc_final: 0.8226 (tm-30) REVERT: B 283 ARG cc_start: 0.7982 (tpt-90) cc_final: 0.7569 (tpt170) REVERT: C 18 GLN cc_start: 0.8432 (tp-100) cc_final: 0.7841 (tp-100) REVERT: C 21 MET cc_start: 0.8746 (tpp) cc_final: 0.8098 (ttt) REVERT: R 116 GLN cc_start: 0.6206 (OUTLIER) cc_final: 0.5589 (mp10) REVERT: R 353 ILE cc_start: 0.7731 (tp) cc_final: 0.7510 (tp) REVERT: S 34 MET cc_start: 0.6663 (OUTLIER) cc_final: 0.6325 (ttt) REVERT: S 70 ILE cc_start: 0.6622 (OUTLIER) cc_final: 0.5588 (tt) REVERT: S 90 ASP cc_start: 0.7608 (m-30) cc_final: 0.7305 (m-30) REVERT: S 151 LYS cc_start: 0.6740 (mmtm) cc_final: 0.5230 (pttt) outliers start: 23 outliers final: 14 residues processed: 121 average time/residue: 0.2329 time to fit residues: 38.3649 Evaluate side-chains 117 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 100 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 116 GLN Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 403 ASP Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 71 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 70 optimal weight: 6.9990 chunk 77 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 21 optimal weight: 7.9990 chunk 31 optimal weight: 0.0010 chunk 44 optimal weight: 5.9990 overall best weight: 0.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.181880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.146506 restraints weight = 12108.939| |-----------------------------------------------------------------------------| r_work (start): 0.3813 rms_B_bonded: 2.44 r_work: 0.3580 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8568 Z= 0.143 Angle : 0.484 9.256 11605 Z= 0.250 Chirality : 0.040 0.187 1347 Planarity : 0.003 0.050 1447 Dihedral : 3.938 19.681 1186 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 2.48 % Allowed : 16.46 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.27), residues: 1057 helix: 1.58 (0.28), residues: 385 sheet: -0.21 (0.32), residues: 265 loop : -1.24 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 36 HIS 0.009 0.001 HIS R 154 PHE 0.016 0.001 PHE B 199 TYR 0.008 0.001 TYR R 296 ARG 0.006 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 104 time to evaluate : 0.959 Fit side-chains REVERT: B 10 GLU cc_start: 0.7300 (tp30) cc_final: 0.7098 (tp30) REVERT: B 14 LEU cc_start: 0.7787 (OUTLIER) cc_final: 0.7544 (mm) REVERT: B 17 GLN cc_start: 0.8620 (tm-30) cc_final: 0.8215 (tm-30) REVERT: B 283 ARG cc_start: 0.7970 (tpt-90) cc_final: 0.7621 (tpt170) REVERT: C 18 GLN cc_start: 0.8456 (tp-100) cc_final: 0.7855 (tp-100) REVERT: C 21 MET cc_start: 0.8727 (tpp) cc_final: 0.8058 (ttt) REVERT: R 116 GLN cc_start: 0.6120 (OUTLIER) cc_final: 0.5536 (mp10) REVERT: R 353 ILE cc_start: 0.7710 (tp) cc_final: 0.7477 (tp) REVERT: S 34 MET cc_start: 0.6674 (OUTLIER) cc_final: 0.6317 (ttt) REVERT: S 90 ASP cc_start: 0.7565 (m-30) cc_final: 0.7256 (m-30) REVERT: S 151 LYS cc_start: 0.6813 (mmtm) cc_final: 0.5331 (pttt) outliers start: 22 outliers final: 15 residues processed: 119 average time/residue: 0.2131 time to fit residues: 34.6354 Evaluate side-chains 119 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain R residue 116 GLN Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 403 ASP Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 74 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 88 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 106 optimal weight: 6.9990 chunk 56 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 8 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 91 HIS ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.175952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.140399 restraints weight = 12165.000| |-----------------------------------------------------------------------------| r_work (start): 0.3744 rms_B_bonded: 2.57 r_work: 0.3481 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 8568 Z= 0.319 Angle : 0.613 10.081 11605 Z= 0.317 Chirality : 0.043 0.206 1347 Planarity : 0.004 0.048 1447 Dihedral : 4.639 23.267 1186 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.04 % Allowed : 16.80 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.26), residues: 1057 helix: 1.36 (0.28), residues: 381 sheet: -0.38 (0.31), residues: 270 loop : -1.51 (0.29), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP S 36 HIS 0.013 0.002 HIS R 154 PHE 0.028 0.002 PHE B 199 TYR 0.013 0.002 TYR B 264 ARG 0.007 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 100 time to evaluate : 0.944 Fit side-chains REVERT: B 17 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8176 (tm-30) REVERT: B 234 PHE cc_start: 0.8747 (OUTLIER) cc_final: 0.8312 (m-80) REVERT: C 18 GLN cc_start: 0.8503 (tp-100) cc_final: 0.7929 (tp-100) REVERT: C 21 MET cc_start: 0.8797 (tpp) cc_final: 0.8077 (ttt) REVERT: R 116 GLN cc_start: 0.6277 (OUTLIER) cc_final: 0.5699 (mp10) REVERT: R 353 ILE cc_start: 0.7997 (tp) cc_final: 0.7684 (tp) REVERT: S 34 MET cc_start: 0.6888 (OUTLIER) cc_final: 0.6560 (ttt) REVERT: S 70 ILE cc_start: 0.7023 (OUTLIER) cc_final: 0.5876 (tt) REVERT: S 90 ASP cc_start: 0.7737 (m-30) cc_final: 0.7411 (m-30) REVERT: S 151 LYS cc_start: 0.6989 (mmtm) cc_final: 0.5901 (pttt) outliers start: 27 outliers final: 19 residues processed: 118 average time/residue: 0.2058 time to fit residues: 33.6450 Evaluate side-chains 119 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 96 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 LEU Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain R residue 116 GLN Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 287 LEU Chi-restraints excluded: chain R residue 384 MET Chi-restraints excluded: chain R residue 403 ASP Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 5 optimal weight: 2.9990 chunk 62 optimal weight: 0.9980 chunk 79 optimal weight: 0.4980 chunk 54 optimal weight: 7.9990 chunk 71 optimal weight: 0.0030 chunk 57 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 91 HIS B 142 HIS ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 256 ASN S 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.180569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.145894 restraints weight = 12173.789| |-----------------------------------------------------------------------------| r_work (start): 0.3809 rms_B_bonded: 2.45 r_work: 0.3557 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7641 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 8568 Z= 0.141 Angle : 0.498 9.029 11605 Z= 0.257 Chirality : 0.040 0.186 1347 Planarity : 0.003 0.051 1447 Dihedral : 4.108 23.536 1186 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.59 % Allowed : 17.14 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.27), residues: 1057 helix: 1.59 (0.28), residues: 379 sheet: -0.24 (0.32), residues: 266 loop : -1.31 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 36 HIS 0.009 0.001 HIS R 154 PHE 0.014 0.001 PHE B 199 TYR 0.008 0.001 TYR R 296 ARG 0.007 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 101 time to evaluate : 0.991 Fit side-chains REVERT: B 17 GLN cc_start: 0.8616 (tm-30) cc_final: 0.8252 (tm-30) REVERT: B 234 PHE cc_start: 0.8574 (OUTLIER) cc_final: 0.8090 (m-80) REVERT: B 283 ARG cc_start: 0.8006 (tpt-90) cc_final: 0.7690 (tpt170) REVERT: C 18 GLN cc_start: 0.8473 (tp-100) cc_final: 0.7884 (tp-100) REVERT: C 21 MET cc_start: 0.8776 (tpp) cc_final: 0.7956 (ttt) REVERT: R 116 GLN cc_start: 0.6179 (OUTLIER) cc_final: 0.5623 (mp10) REVERT: R 353 ILE cc_start: 0.7887 (tp) cc_final: 0.7618 (tp) REVERT: S 34 MET cc_start: 0.6761 (OUTLIER) cc_final: 0.6435 (ttt) REVERT: S 70 ILE cc_start: 0.6695 (OUTLIER) cc_final: 0.5684 (tt) REVERT: S 90 ASP cc_start: 0.7724 (m-30) cc_final: 0.7375 (m-30) REVERT: S 151 LYS cc_start: 0.6966 (mmtm) cc_final: 0.5757 (pttt) outliers start: 23 outliers final: 14 residues processed: 116 average time/residue: 0.2250 time to fit residues: 35.3665 Evaluate side-chains 117 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 99 time to evaluate : 0.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain R residue 116 GLN Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 103 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 85 optimal weight: 9.9990 chunk 94 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 91 HIS ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.178177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.142878 restraints weight = 12328.333| |-----------------------------------------------------------------------------| r_work (start): 0.3773 rms_B_bonded: 2.37 r_work: 0.3549 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.2848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8568 Z= 0.184 Angle : 0.520 9.576 11605 Z= 0.269 Chirality : 0.041 0.195 1347 Planarity : 0.003 0.050 1447 Dihedral : 4.131 23.235 1186 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 2.37 % Allowed : 17.59 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.27), residues: 1057 helix: 1.62 (0.28), residues: 379 sheet: -0.42 (0.32), residues: 274 loop : -1.30 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 36 HIS 0.010 0.001 HIS R 154 PHE 0.018 0.001 PHE B 199 TYR 0.009 0.001 TYR R 296 ARG 0.007 0.000 ARG A 313 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 99 time to evaluate : 0.824 Fit side-chains REVERT: B 17 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8237 (tm-30) REVERT: B 23 LYS cc_start: 0.8427 (mtpp) cc_final: 0.8219 (mtpp) REVERT: B 270 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8155 (mm) REVERT: B 283 ARG cc_start: 0.8321 (tpt-90) cc_final: 0.7633 (mmm160) REVERT: C 18 GLN cc_start: 0.8539 (tp-100) cc_final: 0.8164 (tp-100) REVERT: C 21 MET cc_start: 0.8852 (tpp) cc_final: 0.8081 (ttt) REVERT: R 116 GLN cc_start: 0.6072 (OUTLIER) cc_final: 0.5469 (mp10) REVERT: R 353 ILE cc_start: 0.7931 (tp) cc_final: 0.7650 (tp) REVERT: S 34 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.6663 (ttt) REVERT: S 70 ILE cc_start: 0.6819 (OUTLIER) cc_final: 0.5684 (tt) REVERT: S 90 ASP cc_start: 0.7762 (m-30) cc_final: 0.7364 (m-30) REVERT: S 151 LYS cc_start: 0.6950 (mmtm) cc_final: 0.5895 (pttt) outliers start: 21 outliers final: 15 residues processed: 113 average time/residue: 0.2187 time to fit residues: 33.4831 Evaluate side-chains 117 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 324 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 14 LEU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain R residue 116 GLN Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 40 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 7 optimal weight: 0.3980 chunk 65 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 0.1980 chunk 9 optimal weight: 6.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 91 HIS ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.176955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.141232 restraints weight = 12177.131| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.31 r_work: 0.3533 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8568 Z= 0.223 Angle : 0.550 9.447 11605 Z= 0.284 Chirality : 0.042 0.213 1347 Planarity : 0.003 0.048 1447 Dihedral : 4.306 24.346 1186 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 2.14 % Allowed : 17.93 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.26), residues: 1057 helix: 1.56 (0.28), residues: 379 sheet: -0.42 (0.31), residues: 270 loop : -1.35 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP S 36 HIS 0.011 0.001 HIS S 220 PHE 0.021 0.001 PHE B 199 TYR 0.015 0.001 TYR S 59 ARG 0.007 0.000 ARG A 313 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 98 time to evaluate : 0.985 Fit side-chains REVERT: B 17 GLN cc_start: 0.8592 (tm-30) cc_final: 0.8174 (tm-30) REVERT: B 270 ILE cc_start: 0.8360 (OUTLIER) cc_final: 0.8131 (mm) REVERT: B 283 ARG cc_start: 0.8343 (tpt-90) cc_final: 0.7654 (mmm160) REVERT: B 289 TYR cc_start: 0.8238 (m-80) cc_final: 0.7954 (m-80) REVERT: C 18 GLN cc_start: 0.8502 (tp-100) cc_final: 0.7915 (tp-100) REVERT: C 21 MET cc_start: 0.8873 (tpp) cc_final: 0.8097 (ttt) REVERT: R 116 GLN cc_start: 0.6039 (OUTLIER) cc_final: 0.5414 (mp10) REVERT: R 353 ILE cc_start: 0.7984 (tp) cc_final: 0.7695 (tp) REVERT: S 34 MET cc_start: 0.7023 (OUTLIER) cc_final: 0.6675 (ttt) REVERT: S 70 ILE cc_start: 0.6927 (OUTLIER) cc_final: 0.5719 (tt) REVERT: S 90 ASP cc_start: 0.7747 (m-30) cc_final: 0.7388 (m-30) REVERT: S 151 LYS cc_start: 0.7263 (mmtm) cc_final: 0.6125 (pttt) outliers start: 19 outliers final: 15 residues processed: 110 average time/residue: 0.2352 time to fit residues: 35.7646 Evaluate side-chains 116 residues out of total 938 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 97 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 270 ILE Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain R residue 116 GLN Chi-restraints excluded: chain R residue 123 SER Chi-restraints excluded: chain R residue 249 VAL Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 97 VAL Chi-restraints excluded: chain S residue 201 THR Chi-restraints excluded: chain S residue 218 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 0 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 46 optimal weight: 5.9990 chunk 35 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 89 optimal weight: 0.4980 chunk 24 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 chunk 106 optimal weight: 0.4980 chunk 76 optimal weight: 0.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS B 91 HIS ** R 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4168 r_free = 0.4168 target = 0.177898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.142934 restraints weight = 12369.745| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 2.39 r_work: 0.3543 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.3422 rms_B_bonded: 4.78 restraints_weight: 0.2500 r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8568 Z= 0.187 Angle : 0.524 9.422 11605 Z= 0.271 Chirality : 0.041 0.199 1347 Planarity : 0.003 0.049 1447 Dihedral : 4.185 23.998 1186 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.37 % Allowed : 17.59 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.27), residues: 1057 helix: 1.62 (0.28), residues: 379 sheet: -0.34 (0.32), residues: 268 loop : -1.26 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP S 36 HIS 0.010 0.001 HIS R 154 PHE 0.017 0.001 PHE B 199 TYR 0.011 0.001 TYR S 59 ARG 0.007 0.000 ARG A 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4996.05 seconds wall clock time: 86 minutes 51.23 seconds (5211.23 seconds total)