Starting phenix.real_space_refine on Sat Jun 7 20:39:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ixx_60980/06_2025/9ixx_60980_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ixx_60980/06_2025/9ixx_60980.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ixx_60980/06_2025/9ixx_60980.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ixx_60980/06_2025/9ixx_60980.map" model { file = "/net/cci-nas-00/data/ceres_data/9ixx_60980/06_2025/9ixx_60980_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ixx_60980/06_2025/9ixx_60980_neut_trim.cif" } resolution = 3.15 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= 0.000 sd= 0.003 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 57 5.16 5 C 5765 2.51 5 N 1545 2.21 5 O 1669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9036 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1908 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Chain: "B" Number of atoms: 2597 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2597 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "E" Number of atoms: 1768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1768 Classifications: {'peptide': 230} Link IDs: {'PTRANS': 10, 'TRANS': 219} Chain breaks: 2 Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 407 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 3, 'TRANS': 50} Chain: "R" Number of atoms: 2322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2322 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "R" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 34 Unusual residues: {'LTD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.20, per 1000 atoms: 0.58 Number of scatterers: 9036 At special positions: 0 Unit cell: (121.128, 88.168, 125.248, 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 57 16.00 O 1669 8.00 N 1545 7.00 C 5765 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 111 " - pdb=" SG CYS R 187 " 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.16 Conformation dependent library (CDL) restraints added in 975.9 milliseconds 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2140 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 14 sheets defined 37.9% alpha, 22.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.39 Creating SS restraints... Processing helix chain 'A' and resid 6 through 33 removed outlier: 3.850A pdb=" N VAL A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 212 through 216 Processing helix chain 'A' and resid 232 through 245 Processing helix chain 'A' and resid 248 through 252 removed outlier: 4.470A pdb=" N THR A 251 " --> pdb=" O TRP A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 271 Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 279 through 285 removed outlier: 3.839A pdb=" N TYR A 285 " --> pdb=" O PHE A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 318 Processing helix chain 'A' and resid 338 through 358 removed outlier: 3.621A pdb=" N ILE A 342 " --> pdb=" O ASN A 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 30 Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.937A pdb=" N ILE B 38 " --> pdb=" O THR B 34 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 55 Processing helix chain 'E' and resid 86 through 90 removed outlier: 3.563A pdb=" N THR E 90 " --> pdb=" O SER E 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 23 Processing helix chain 'G' and resid 28 through 43 removed outlier: 3.732A pdb=" N ALA G 32 " --> pdb=" O LYS G 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 64 removed outlier: 3.771A pdb=" N GLU R 39 " --> pdb=" O ASN R 35 " (cutoff:3.500A) Proline residue: R 42 - end of helix removed outlier: 4.201A pdb=" N LEU R 58 " --> pdb=" O LEU R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 71 through 90 Processing helix chain 'R' and resid 90 through 100 removed outlier: 4.168A pdb=" N ARG R 94 " --> pdb=" O THR R 90 " (cutoff:3.500A) Processing helix chain 'R' and resid 107 through 142 removed outlier: 3.773A pdb=" N TYR R 119 " --> pdb=" O SER R 115 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N MET R 140 " --> pdb=" O ARG R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 152 through 171 removed outlier: 4.168A pdb=" N TRP R 156 " --> pdb=" O ILE R 152 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 176 Processing helix chain 'R' and resid 191 through 193 No H-bonds generated for 'chain 'R' and resid 191 through 193' Processing helix chain 'R' and resid 194 through 209 removed outlier: 3.650A pdb=" N LEU R 198 " --> pdb=" O LYS R 194 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N THR R 200 " --> pdb=" O ALA R 196 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N TYR R 203 " --> pdb=" O GLN R 199 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE R 204 " --> pdb=" O THR R 200 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA R 205 " --> pdb=" O MET R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 210 through 229 Processing helix chain 'R' and resid 240 through 258 removed outlier: 4.051A pdb=" N LYS R 244 " --> pdb=" O VAL R 240 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE R 250 " --> pdb=" O LEU R 246 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE R 251 " --> pdb=" O THR R 247 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N THR R 252 " --> pdb=" O THR R 248 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU R 258 " --> pdb=" O ILE R 254 " (cutoff:3.500A) Processing helix chain 'R' and resid 260 through 272 Processing helix chain 'R' and resid 282 through 296 Processing helix chain 'R' and resid 296 through 306 Proline residue: R 302 - end of helix Processing helix chain 'R' and resid 309 through 321 Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.560A pdb=" N ALA A 220 " --> pdb=" O ARG A 35 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N TYR A 327 " --> pdb=" O VAL A 254 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 56 removed outlier: 6.936A pdb=" N ILE B 343 " --> pdb=" O ARG B 53 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N THR B 55 " --> pdb=" O LEU B 341 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU B 341 " --> pdb=" O THR B 55 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 63 through 68 removed outlier: 6.487A pdb=" N ALA B 78 " --> pdb=" O TYR B 64 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N MET B 66 " --> pdb=" O VAL B 76 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL B 76 " --> pdb=" O MET B 66 " (cutoff:3.500A) removed outlier: 5.777A pdb=" N TRP B 68 " --> pdb=" O LEU B 74 " (cutoff:3.500A) removed outlier: 8.570A pdb=" N LEU B 74 " --> pdb=" O TRP B 68 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS B 83 " --> pdb=" O SER B 79 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ASP B 88 " --> pdb=" O LYS B 94 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LYS B 94 " --> pdb=" O ASP B 88 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 105 through 110 removed outlier: 6.889A pdb=" N GLY B 120 " --> pdb=" O MET B 106 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N CYS B 108 " --> pdb=" O ALA B 118 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA B 118 " --> pdb=" O CYS B 108 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N TYR B 110 " --> pdb=" O TYR B 116 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N TYR B 116 " --> pdb=" O TYR B 110 " (cutoff:3.500A) removed outlier: 5.007A pdb=" N GLY B 121 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 5.004A pdb=" N ILE B 125 " --> pdb=" O GLY B 121 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ASN B 130 " --> pdb=" O VAL B 140 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N VAL B 140 " --> pdb=" O ASN B 130 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 151 through 156 removed outlier: 7.019A pdb=" N SER B 165 " --> pdb=" O SER B 152 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N CYS B 154 " --> pdb=" O VAL B 163 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL B 163 " --> pdb=" O CYS B 154 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N PHE B 156 " --> pdb=" O GLN B 161 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N GLN B 161 " --> pdb=" O PHE B 156 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N ASP B 175 " --> pdb=" O GLN B 181 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N GLN B 181 " --> pdb=" O ASP B 175 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 192 through 197 removed outlier: 7.408A pdb=" N GLY B 207 " --> pdb=" O MET B 193 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LEU B 195 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N VAL B 205 " --> pdb=" O LEU B 195 " (cutoff:3.500A) removed outlier: 5.623A pdb=" N LEU B 197 " --> pdb=" O LEU B 203 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N LEU B 203 " --> pdb=" O LEU B 197 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLN B 225 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N ASP B 217 " --> pdb=" O CYS B 223 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N CYS B 223 " --> pdb=" O ASP B 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 234 through 239 removed outlier: 3.986A pdb=" N SER B 250 " --> pdb=" O THR B 254 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N THR B 254 " --> pdb=" O SER B 250 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N CYS B 255 " --> pdb=" O THR B 268 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR B 268 " --> pdb=" O CYS B 255 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N LEU B 257 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 264 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 278 through 283 removed outlier: 3.725A pdb=" N SER B 280 " --> pdb=" O GLY B 293 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN B 298 " --> pdb=" O TYR B 294 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASP B 303 " --> pdb=" O ARG B 309 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ARG B 309 " --> pdb=" O ASP B 303 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 2 through 6 Processing sheet with id=AB1, first strand: chain 'E' and resid 9 through 11 removed outlier: 5.999A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N MET E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N TYR E 49 " --> pdb=" O MET E 33 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP E 35 " --> pdb=" O VAL E 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 9 through 11 removed outlier: 5.999A pdb=" N GLY E 9 " --> pdb=" O THR E 117 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG E 97 " --> pdb=" O PHE E 109 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N PHE E 109 " --> pdb=" O ARG E 97 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'E' and resid 146 through 148 removed outlier: 4.297A pdb=" N GLU E 246 " --> pdb=" O VAL E 147 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N TRP E 176 " --> pdb=" O LEU E 188 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'R' and resid 180 through 181 445 hydrogen bonds defined for protein. 1245 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: 2.58 Time building geometry restraints manager: 2.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1448 1.31 - 1.44: 2564 1.44 - 1.56: 5121 1.56 - 1.69: 4 1.69 - 1.81: 83 Bond restraints: 9220 Sorted by residual: bond pdb=" C SER R 241 " pdb=" O SER R 241 " ideal model delta sigma weight residual 1.236 1.302 -0.066 1.19e-02 7.06e+03 3.06e+01 bond pdb=" C10 LTD R 401 " pdb=" C11 LTD R 401 " ideal model delta sigma weight residual 1.447 1.537 -0.090 2.00e-02 2.50e+03 2.03e+01 bond pdb=" C22 LTD R 401 " pdb=" N3 LTD R 401 " ideal model delta sigma weight residual 1.332 1.421 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C21 LTD R 401 " pdb=" CA3 LTD R 401 " ideal model delta sigma weight residual 1.543 1.454 0.089 2.00e-02 2.50e+03 1.99e+01 bond pdb=" N SER R 241 " pdb=" CA SER R 241 " ideal model delta sigma weight residual 1.459 1.512 -0.054 1.24e-02 6.50e+03 1.87e+01 ... (remaining 9215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.94: 12432 3.94 - 7.88: 31 7.88 - 11.83: 9 11.83 - 15.77: 3 15.77 - 19.71: 1 Bond angle restraints: 12476 Sorted by residual: angle pdb=" O VAL R 240 " pdb=" C VAL R 240 " pdb=" N SER R 241 " ideal model delta sigma weight residual 121.87 113.34 8.53 1.01e+00 9.80e-01 7.14e+01 angle pdb=" N ILE R 249 " pdb=" CA ILE R 249 " pdb=" C ILE R 249 " ideal model delta sigma weight residual 110.72 118.54 -7.82 1.01e+00 9.80e-01 5.99e+01 angle pdb=" C ASN R 301 " pdb=" CA ASN R 301 " pdb=" CB ASN R 301 " ideal model delta sigma weight residual 112.76 100.22 12.54 1.86e+00 2.89e-01 4.55e+01 angle pdb=" C3 LTD R 401 " pdb=" C4 LTD R 401 " pdb=" C5 LTD R 401 " ideal model delta sigma weight residual 113.85 133.56 -19.71 3.00e+00 1.11e-01 4.32e+01 angle pdb=" CA VAL R 240 " pdb=" C VAL R 240 " pdb=" N SER R 241 " ideal model delta sigma weight residual 117.53 124.81 -7.28 1.19e+00 7.06e-01 3.74e+01 ... (remaining 12471 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.98: 5399 22.98 - 45.96: 69 45.96 - 68.95: 13 68.95 - 91.93: 5 91.93 - 114.91: 2 Dihedral angle restraints: 5488 sinusoidal: 2171 harmonic: 3317 Sorted by residual: dihedral pdb=" CB2 LTD R 401 " pdb=" C22 LTD R 401 " pdb=" CA2 LTD R 401 " pdb=" N3 LTD R 401 " ideal model delta sinusoidal sigma weight residual 87.84 -157.25 -114.91 1 3.00e+01 1.11e-03 1.52e+01 dihedral pdb=" N2 LTD R 401 " pdb=" C22 LTD R 401 " pdb=" CA2 LTD R 401 " pdb=" N3 LTD R 401 " ideal model delta sinusoidal sigma weight residual -150.23 -44.78 -105.45 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" C PHE R 307 " pdb=" N PHE R 307 " pdb=" CA PHE R 307 " pdb=" CB PHE R 307 " ideal model delta harmonic sigma weight residual -122.60 -130.72 8.12 0 2.50e+00 1.60e-01 1.05e+01 ... (remaining 5485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 1314 0.079 - 0.158: 96 0.158 - 0.237: 4 0.237 - 0.316: 1 0.316 - 0.395: 2 Chirality restraints: 1417 Sorted by residual: chirality pdb=" C6 LTD R 401 " pdb=" SG2 LTD R 401 " pdb=" C5 LTD R 401 " pdb=" C7 LTD R 401 " both_signs ideal model delta sigma weight residual False -3.17 -2.77 -0.40 2.00e-01 2.50e+01 3.90e+00 chirality pdb=" CA PHE R 307 " pdb=" N PHE R 307 " pdb=" C PHE R 307 " pdb=" CB PHE R 307 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.70e+00 chirality pdb=" CA TYR R 305 " pdb=" N TYR R 305 " pdb=" C TYR R 305 " pdb=" CB TYR R 305 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1414 not shown) Planarity restraints: 1574 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL R 240 " -0.017 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C VAL R 240 " 0.055 2.00e-02 2.50e+03 pdb=" O VAL R 240 " -0.019 2.00e-02 2.50e+03 pdb=" N SER R 241 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO R 302 " 0.016 2.00e-02 2.50e+03 3.16e-02 9.99e+00 pdb=" C PRO R 302 " -0.055 2.00e-02 2.50e+03 pdb=" O PRO R 302 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU R 303 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C HIS R 142 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.63e+00 pdb=" N PRO R 143 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO R 143 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO R 143 " 0.023 5.00e-02 4.00e+02 ... (remaining 1571 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 82 2.56 - 3.15: 7783 3.15 - 3.73: 13864 3.73 - 4.32: 19901 4.32 - 4.90: 33288 Nonbonded interactions: 74918 Sorted by model distance: nonbonded pdb=" O ILE B 128 " pdb=" OG SER B 141 " model vdw 1.977 3.040 nonbonded pdb=" NH1 ARG A 323 " pdb=" CE1 HIS A 324 " model vdw 2.077 3.340 nonbonded pdb=" OG SER B 79 " pdb=" OD1 ASP B 81 " model vdw 2.129 3.040 nonbonded pdb=" O ALA A 41 " pdb=" OG SER A 44 " model vdw 2.151 3.040 nonbonded pdb=" OG1 THR B 226 " pdb=" OE2 GLU G 21 " model vdw 2.170 3.040 ... (remaining 74913 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: 1.540 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: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 22.850 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: 0.000 Load rotamer database and sin/cos tables:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5364 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 : 0.008 0.661 9222 Z= 0.725 Angle : 0.651 19.711 12478 Z= 0.368 Chirality : 0.042 0.395 1417 Planarity : 0.003 0.041 1574 Dihedral : 9.060 114.909 3345 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.30 % Allowed : 3.05 % Favored : 96.65 % 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: -1.89 (0.23), residues: 1123 helix: -0.21 (0.25), residues: 383 sheet: -1.45 (0.30), residues: 250 loop : -1.93 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 87 HIS 0.002 0.000 HIS B 230 PHE 0.010 0.001 PHE R 300 TYR 0.023 0.001 TYR R 306 ARG 0.005 0.000 ARG R 243 Details of bonding type rmsd hydrogen bonds : bond 0.12717 ( 441) hydrogen bonds : angle 5.60993 ( 1245) SS BOND : bond 0.00424 ( 1) SS BOND : angle 2.47896 ( 2) covalent geometry : bond 0.00374 ( 9220) covalent geometry : angle 0.65070 (12476) Misc. bond : bond 0.66143 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 197 time to evaluate : 0.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 81 ASP cc_start: 0.6610 (p0) cc_final: 0.5897 (t0) REVERT: B 144 LEU cc_start: 0.6111 (pp) cc_final: 0.5420 (mt) REVERT: B 227 PHE cc_start: 0.6149 (m-80) cc_final: 0.5934 (m-80) REVERT: B 282 SER cc_start: 0.5861 (t) cc_final: 0.5593 (p) REVERT: R 170 SER cc_start: 0.5590 (p) cc_final: 0.5316 (p) REVERT: R 243 ARG cc_start: 0.7254 (ttm-80) cc_final: 0.6819 (ttp-170) outliers start: 3 outliers final: 2 residues processed: 200 average time/residue: 0.2414 time to fit residues: 63.6121 Evaluate side-chains 133 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain R residue 306 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 1.9990 chunk 84 optimal weight: 6.9990 chunk 47 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 57 optimal weight: 20.0000 chunk 45 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 53 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 101 optimal weight: 6.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 197 HIS A 216 ASN A 234 GLN A 354 ASN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 HIS B 273 ASN B 300 ASN B 345 ASN E 34 HIS R 148 HIS R 242 HIS ** R 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4661 r_free = 0.4661 target = 0.253412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.220419 restraints weight = 8669.455| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 1.59 r_work: 0.4163 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.4025 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.4025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9222 Z= 0.158 Angle : 0.616 8.681 12478 Z= 0.322 Chirality : 0.044 0.193 1417 Planarity : 0.005 0.039 1574 Dihedral : 7.746 84.609 1279 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.44 % Allowed : 8.83 % Favored : 88.73 % 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: -0.68 (0.24), residues: 1123 helix: 1.10 (0.26), residues: 384 sheet: -1.12 (0.29), residues: 276 loop : -1.27 (0.28), residues: 463 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 46 HIS 0.007 0.001 HIS G 43 PHE 0.023 0.002 PHE B 283 TYR 0.024 0.002 TYR R 116 ARG 0.005 0.001 ARG R 315 Details of bonding type rmsd hydrogen bonds : bond 0.03739 ( 441) hydrogen bonds : angle 4.58029 ( 1245) SS BOND : bond 0.00197 ( 1) SS BOND : angle 0.43578 ( 2) covalent geometry : bond 0.00356 ( 9220) covalent geometry : angle 0.61592 (12476) Misc. bond : bond 0.00231 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 159 time to evaluate : 0.969 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 243 ILE cc_start: 0.7282 (mt) cc_final: 0.6986 (mt) REVERT: B 64 TYR cc_start: 0.7922 (OUTLIER) cc_final: 0.7534 (m-80) REVERT: B 144 LEU cc_start: 0.7749 (pp) cc_final: 0.6841 (mt) outliers start: 24 outliers final: 12 residues processed: 174 average time/residue: 0.2529 time to fit residues: 58.1498 Evaluate side-chains 135 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 122 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 ASN Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 326 THR Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 148 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 66 optimal weight: 0.0270 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.4042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS B 345 ASN E 194 ASN R 148 HIS ** R 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.237766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.204954 restraints weight = 8736.030| |-----------------------------------------------------------------------------| r_work (start): 0.4234 rms_B_bonded: 1.47 r_work: 0.3979 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work (final): 0.3979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.5372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9222 Z= 0.155 Angle : 0.587 8.970 12478 Z= 0.306 Chirality : 0.043 0.163 1417 Planarity : 0.004 0.043 1574 Dihedral : 7.160 84.715 1275 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.84 % Allowed : 11.57 % Favored : 85.58 % 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: -0.30 (0.24), residues: 1123 helix: 1.51 (0.26), residues: 384 sheet: -0.84 (0.30), residues: 257 loop : -1.20 (0.27), residues: 482 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 248 HIS 0.038 0.003 HIS R 148 PHE 0.014 0.001 PHE B 156 TYR 0.013 0.002 TYR A 358 ARG 0.003 0.000 ARG A 35 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 441) hydrogen bonds : angle 4.47099 ( 1245) SS BOND : bond 0.00055 ( 1) SS BOND : angle 0.41352 ( 2) covalent geometry : bond 0.00361 ( 9220) covalent geometry : angle 0.58723 (12476) Misc. bond : bond 0.00228 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 133 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 ILE cc_start: 0.7784 (mt) cc_final: 0.7386 (mt) REVERT: B 279 THR cc_start: 0.8440 (m) cc_final: 0.8098 (p) REVERT: E 140 MET cc_start: 0.7307 (mtp) cc_final: 0.6679 (mmm) REVERT: G 47 ASP cc_start: 0.7002 (t0) cc_final: 0.6776 (t0) REVERT: R 104 TRP cc_start: 0.7232 (t-100) cc_final: 0.6917 (t-100) REVERT: R 167 MET cc_start: 0.6759 (mtp) cc_final: 0.6366 (mtp) outliers start: 28 outliers final: 16 residues processed: 150 average time/residue: 0.2321 time to fit residues: 47.8226 Evaluate side-chains 133 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 117 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain E residue 62 THR Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 135 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 83 optimal weight: 4.9990 chunk 76 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 5 optimal weight: 7.9990 chunk 63 optimal weight: 0.2980 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 0.0070 chunk 48 optimal weight: 0.9980 chunk 14 optimal weight: 6.9990 chunk 65 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 overall best weight: 0.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 HIS B 230 HIS ** B 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 ASN ** 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 = 0.4530 r_free = 0.4530 target = 0.238120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.206216 restraints weight = 8678.866| |-----------------------------------------------------------------------------| r_work (start): 0.4236 rms_B_bonded: 1.43 r_work: 0.3997 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3853 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3853 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.5689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9222 Z= 0.111 Angle : 0.516 6.409 12478 Z= 0.269 Chirality : 0.040 0.165 1417 Planarity : 0.003 0.037 1574 Dihedral : 6.983 82.780 1275 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.34 % Allowed : 14.01 % Favored : 83.65 % 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 (0.25), residues: 1123 helix: 1.73 (0.26), residues: 389 sheet: -0.65 (0.30), residues: 272 loop : -1.11 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 87 HIS 0.007 0.001 HIS B 230 PHE 0.009 0.001 PHE R 93 TYR 0.013 0.001 TYR E 59 ARG 0.003 0.000 ARG E 37 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 441) hydrogen bonds : angle 4.25572 ( 1245) SS BOND : bond 0.00027 ( 1) SS BOND : angle 0.58003 ( 2) covalent geometry : bond 0.00247 ( 9220) covalent geometry : angle 0.51631 (12476) Misc. bond : bond 0.00012 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 243 ILE cc_start: 0.7999 (mt) cc_final: 0.7779 (mt) REVERT: E 140 MET cc_start: 0.7470 (mtp) cc_final: 0.6609 (mmm) REVERT: E 234 GLU cc_start: 0.7280 (mt-10) cc_final: 0.6871 (mt-10) REVERT: R 104 TRP cc_start: 0.7288 (t-100) cc_final: 0.6946 (t-100) REVERT: R 291 LEU cc_start: 0.7994 (tp) cc_final: 0.7778 (tt) outliers start: 23 outliers final: 17 residues processed: 140 average time/residue: 0.2249 time to fit residues: 43.5471 Evaluate side-chains 136 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 64 TYR Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 204 SER Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 165 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 97 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 104 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 45 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 75 optimal weight: 9.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 204 GLN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS ** R 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 ASN ** 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 = 0.4511 r_free = 0.4511 target = 0.236145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4236 r_free = 0.4236 target = 0.204910 restraints weight = 8657.998| |-----------------------------------------------------------------------------| r_work (start): 0.4229 rms_B_bonded: 1.42 r_work: 0.3989 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3846 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.6048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9222 Z= 0.112 Angle : 0.520 6.437 12478 Z= 0.269 Chirality : 0.040 0.165 1417 Planarity : 0.003 0.037 1574 Dihedral : 6.762 84.390 1275 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.44 % Allowed : 14.92 % Favored : 82.64 % 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: 0.09 (0.25), residues: 1123 helix: 1.76 (0.26), residues: 391 sheet: -0.48 (0.30), residues: 262 loop : -1.05 (0.29), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 302 HIS 0.011 0.001 HIS B 230 PHE 0.009 0.001 PHE E 26 TYR 0.013 0.001 TYR R 116 ARG 0.005 0.000 ARG B 27 Details of bonding type rmsd hydrogen bonds : bond 0.03413 ( 441) hydrogen bonds : angle 4.20725 ( 1245) SS BOND : bond 0.00017 ( 1) SS BOND : angle 0.55574 ( 2) covalent geometry : bond 0.00249 ( 9220) covalent geometry : angle 0.51952 (12476) Misc. bond : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 119 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 238 ASN cc_start: 0.7209 (m110) cc_final: 0.6942 (m-40) REVERT: A 243 ILE cc_start: 0.8129 (mt) cc_final: 0.7919 (mt) REVERT: B 230 HIS cc_start: 0.6767 (OUTLIER) cc_final: 0.6272 (t70) REVERT: E 140 MET cc_start: 0.7496 (mtp) cc_final: 0.6507 (mmm) REVERT: E 234 GLU cc_start: 0.7320 (mt-10) cc_final: 0.6872 (mt-10) REVERT: G 47 ASP cc_start: 0.7383 (t0) cc_final: 0.7099 (t0) REVERT: R 167 MET cc_start: 0.6764 (mtp) cc_final: 0.6348 (mtp) REVERT: R 291 LEU cc_start: 0.7994 (tp) cc_final: 0.7776 (tt) outliers start: 24 outliers final: 19 residues processed: 134 average time/residue: 0.2160 time to fit residues: 39.9876 Evaluate side-chains 131 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 178 THR Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 172 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 10.0000 chunk 79 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 73 optimal weight: 0.5980 chunk 78 optimal weight: 0.9990 chunk 74 optimal weight: 0.1980 chunk 94 optimal weight: 0.4980 chunk 103 optimal weight: 0.2980 chunk 40 optimal weight: 10.0000 chunk 52 optimal weight: 0.0020 chunk 54 optimal weight: 0.7980 overall best weight: 0.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS ** R 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 ASN ** 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 = 0.4541 r_free = 0.4541 target = 0.239295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.207668 restraints weight = 8672.326| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 1.42 r_work: 0.4038 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3907 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.6123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9222 Z= 0.091 Angle : 0.482 6.534 12478 Z= 0.251 Chirality : 0.039 0.160 1417 Planarity : 0.003 0.035 1574 Dihedral : 6.356 82.484 1275 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.73 % Allowed : 15.94 % Favored : 82.34 % 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 (0.25), residues: 1123 helix: 1.97 (0.26), residues: 390 sheet: -0.25 (0.31), residues: 256 loop : -1.08 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 87 HIS 0.008 0.001 HIS B 230 PHE 0.011 0.001 PHE R 76 TYR 0.012 0.001 TYR R 116 ARG 0.003 0.000 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.03109 ( 441) hydrogen bonds : angle 4.02518 ( 1245) SS BOND : bond 0.00049 ( 1) SS BOND : angle 0.68568 ( 2) covalent geometry : bond 0.00190 ( 9220) covalent geometry : angle 0.48183 (12476) Misc. bond : bond 0.00014 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 1.024 Fit side-chains revert: symmetry clash REVERT: A 238 ASN cc_start: 0.7154 (m110) cc_final: 0.6953 (m-40) REVERT: A 243 ILE cc_start: 0.8160 (mt) cc_final: 0.7934 (mt) REVERT: B 230 HIS cc_start: 0.6152 (OUTLIER) cc_final: 0.5655 (t70) REVERT: E 140 MET cc_start: 0.7577 (mtp) cc_final: 0.6924 (mmm) REVERT: G 47 ASP cc_start: 0.7304 (t0) cc_final: 0.6977 (t0) REVERT: R 167 MET cc_start: 0.6867 (mtp) cc_final: 0.6438 (mtp) REVERT: R 291 LEU cc_start: 0.8023 (tp) cc_final: 0.7789 (tt) outliers start: 17 outliers final: 13 residues processed: 133 average time/residue: 0.2059 time to fit residues: 38.4533 Evaluate side-chains 126 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain B residue 327 ASP Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain R residue 71 THR Chi-restraints excluded: chain R residue 165 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 94 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 chunk 44 optimal weight: 10.0000 chunk 49 optimal weight: 8.9990 chunk 70 optimal weight: 7.9990 chunk 72 optimal weight: 3.9990 chunk 78 optimal weight: 0.9990 chunk 51 optimal weight: 0.5980 chunk 21 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 HIS R 191 ASN ** R 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 ASN ** 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 = 0.4416 r_free = 0.4416 target = 0.224101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.194060 restraints weight = 8861.632| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 1.21 r_work: 0.3900 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3758 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.7038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9222 Z= 0.195 Angle : 0.637 7.256 12478 Z= 0.334 Chirality : 0.045 0.192 1417 Planarity : 0.005 0.050 1574 Dihedral : 6.750 90.005 1275 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 3.25 % Allowed : 14.11 % Favored : 82.64 % 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 (0.25), residues: 1123 helix: 1.51 (0.26), residues: 387 sheet: -0.53 (0.32), residues: 255 loop : -0.91 (0.28), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 302 HIS 0.010 0.002 HIS B 230 PHE 0.017 0.002 PHE B 156 TYR 0.021 0.002 TYR E 190 ARG 0.006 0.001 ARG R 145 Details of bonding type rmsd hydrogen bonds : bond 0.04395 ( 441) hydrogen bonds : angle 4.71789 ( 1245) SS BOND : bond 0.00017 ( 1) SS BOND : angle 0.35373 ( 2) covalent geometry : bond 0.00463 ( 9220) covalent geometry : angle 0.63690 (12476) Misc. bond : bond 0.00060 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 120 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 238 ASN cc_start: 0.6907 (m110) cc_final: 0.6458 (m110) REVERT: A 336 THR cc_start: 0.7051 (OUTLIER) cc_final: 0.6703 (p) REVERT: B 239 PHE cc_start: 0.7832 (OUTLIER) cc_final: 0.6672 (m-80) REVERT: R 104 TRP cc_start: 0.7261 (t-100) cc_final: 0.7059 (t-100) outliers start: 32 outliers final: 24 residues processed: 146 average time/residue: 0.2851 time to fit residues: 57.4403 Evaluate side-chains 132 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 106 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain E residue 193 SER Chi-restraints excluded: chain R residue 44 VAL Chi-restraints excluded: chain R residue 53 VAL Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 144 PHE Chi-restraints excluded: chain R residue 165 LEU Chi-restraints excluded: chain R residue 172 MET Chi-restraints excluded: chain R residue 283 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 22 optimal weight: 0.7980 chunk 108 optimal weight: 0.0370 chunk 96 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 105 optimal weight: 0.7980 chunk 95 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 86 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 overall best weight: 0.7260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN B 230 HIS R 79 ASN ** R 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 ASN ** 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 = 0.4470 r_free = 0.4470 target = 0.230592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.199540 restraints weight = 8889.204| |-----------------------------------------------------------------------------| r_work (start): 0.4180 rms_B_bonded: 1.30 r_work: 0.3948 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3816 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.7056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 9222 Z= 0.108 Angle : 0.527 6.992 12478 Z= 0.272 Chirality : 0.040 0.169 1417 Planarity : 0.003 0.036 1574 Dihedral : 6.325 85.343 1275 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.03 % Allowed : 15.63 % Favored : 82.34 % 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: 0.18 (0.25), residues: 1123 helix: 1.76 (0.26), residues: 387 sheet: -0.30 (0.32), residues: 247 loop : -0.98 (0.28), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 87 HIS 0.010 0.001 HIS B 230 PHE 0.016 0.001 PHE R 76 TYR 0.014 0.001 TYR R 116 ARG 0.003 0.000 ARG A 340 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 441) hydrogen bonds : angle 4.27972 ( 1245) SS BOND : bond 0.00143 ( 1) SS BOND : angle 0.73709 ( 2) covalent geometry : bond 0.00237 ( 9220) covalent geometry : angle 0.52669 (12476) Misc. bond : bond 0.00038 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 111 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7662 (m-30) REVERT: A 336 THR cc_start: 0.7101 (OUTLIER) cc_final: 0.6703 (p) REVERT: B 224 ARG cc_start: 0.7571 (tpp-160) cc_final: 0.6994 (mtt-85) REVERT: B 230 HIS cc_start: 0.6659 (OUTLIER) cc_final: 0.6217 (t70) REVERT: R 291 LEU cc_start: 0.8061 (tp) cc_final: 0.7836 (tt) outliers start: 20 outliers final: 14 residues processed: 128 average time/residue: 0.2111 time to fit residues: 38.1041 Evaluate side-chains 123 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 165 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 34 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 chunk 56 optimal weight: 10.0000 chunk 111 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 7 optimal weight: 0.9980 chunk 70 optimal weight: 6.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN B 230 HIS R 79 ASN ** R 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 ASN ** 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 = 0.4421 r_free = 0.4421 target = 0.224490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.190744 restraints weight = 8762.376| |-----------------------------------------------------------------------------| r_work (start): 0.4106 rms_B_bonded: 1.58 r_work: 0.3831 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.7338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9222 Z= 0.156 Angle : 0.582 7.208 12478 Z= 0.302 Chirality : 0.042 0.193 1417 Planarity : 0.004 0.036 1574 Dihedral : 6.469 85.697 1275 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.44 % Allowed : 15.53 % Favored : 82.03 % 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 (0.25), residues: 1123 helix: 1.61 (0.26), residues: 387 sheet: -0.33 (0.32), residues: 252 loop : -0.99 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 46 HIS 0.005 0.001 HIS E 34 PHE 0.016 0.001 PHE B 156 TYR 0.016 0.002 TYR R 116 ARG 0.005 0.000 ARG A 205 Details of bonding type rmsd hydrogen bonds : bond 0.03939 ( 441) hydrogen bonds : angle 4.45698 ( 1245) SS BOND : bond 0.00112 ( 1) SS BOND : angle 0.52642 ( 2) covalent geometry : bond 0.00366 ( 9220) covalent geometry : angle 0.58246 (12476) Misc. bond : bond 0.00027 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 192 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7587 (m-30) REVERT: A 336 THR cc_start: 0.7420 (OUTLIER) cc_final: 0.7058 (p) REVERT: B 239 PHE cc_start: 0.7722 (OUTLIER) cc_final: 0.6543 (m-80) outliers start: 24 outliers final: 18 residues processed: 125 average time/residue: 0.2477 time to fit residues: 44.1362 Evaluate side-chains 122 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 101 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 152 SER Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 165 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 98 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 102 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 97 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN B 230 HIS R 79 ASN ** R 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 ASN ** 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 = 0.4454 r_free = 0.4454 target = 0.228574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.197369 restraints weight = 8793.786| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 1.45 r_work: 0.3896 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.7382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9222 Z= 0.116 Angle : 0.537 7.164 12478 Z= 0.279 Chirality : 0.041 0.173 1417 Planarity : 0.003 0.036 1574 Dihedral : 6.307 83.080 1275 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.23 % Allowed : 15.53 % Favored : 82.23 % 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: 0.18 (0.25), residues: 1123 helix: 1.75 (0.26), residues: 387 sheet: -0.28 (0.33), residues: 244 loop : -0.98 (0.27), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 87 HIS 0.004 0.001 HIS B 230 PHE 0.016 0.001 PHE R 93 TYR 0.016 0.001 TYR R 263 ARG 0.004 0.000 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 441) hydrogen bonds : angle 4.31167 ( 1245) SS BOND : bond 0.00125 ( 1) SS BOND : angle 0.64047 ( 2) covalent geometry : bond 0.00260 ( 9220) covalent geometry : angle 0.53717 (12476) Misc. bond : bond 0.00038 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2246 Ramachandran restraints generated. 1123 Oldfield, 0 Emsley, 1123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 97 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7515 (m-30) REVERT: A 336 THR cc_start: 0.7469 (OUTLIER) cc_final: 0.7136 (p) REVERT: B 230 HIS cc_start: 0.6286 (OUTLIER) cc_final: 0.5917 (t70) outliers start: 22 outliers final: 18 residues processed: 115 average time/residue: 0.1913 time to fit residues: 32.0289 Evaluate side-chains 117 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 96 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 195 ASN Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 102 SER Chi-restraints excluded: chain B residue 105 VAL Chi-restraints excluded: chain B residue 157 LEU Chi-restraints excluded: chain B residue 230 HIS Chi-restraints excluded: chain B residue 239 PHE Chi-restraints excluded: chain B residue 254 THR Chi-restraints excluded: chain B residue 259 ASP Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain E residue 1 VAL Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 96 VAL Chi-restraints excluded: chain E residue 154 SER Chi-restraints excluded: chain R residue 135 VAL Chi-restraints excluded: chain R residue 141 VAL Chi-restraints excluded: chain R residue 165 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 102 optimal weight: 0.3980 chunk 2 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 61 optimal weight: 0.0670 chunk 18 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 56 optimal weight: 10.0000 overall best weight: 0.8320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 359 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 225 GLN B 230 HIS R 79 ASN ** R 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 301 ASN ** 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 = 0.4477 r_free = 0.4477 target = 0.231954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.197758 restraints weight = 8630.423| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 1.53 r_work: 0.3924 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3778 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.7431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9222 Z= 0.112 Angle : 0.528 7.156 12478 Z= 0.273 Chirality : 0.040 0.170 1417 Planarity : 0.003 0.036 1574 Dihedral : 6.248 81.946 1275 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.54 % Allowed : 15.13 % Favored : 82.34 % 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: 0.24 (0.25), residues: 1123 helix: 1.79 (0.26), residues: 387 sheet: -0.20 (0.32), residues: 243 loop : -0.96 (0.27), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 87 HIS 0.003 0.001 HIS A 324 PHE 0.015 0.001 PHE R 76 TYR 0.015 0.001 TYR R 116 ARG 0.005 0.000 ARG B 224 Details of bonding type rmsd hydrogen bonds : bond 0.03528 ( 441) hydrogen bonds : angle 4.26920 ( 1245) SS BOND : bond 0.00124 ( 1) SS BOND : angle 0.64842 ( 2) covalent geometry : bond 0.00250 ( 9220) covalent geometry : angle 0.52812 (12476) Misc. bond : bond 0.00037 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5605.41 seconds wall clock time: 98 minutes 27.67 seconds (5907.67 seconds total)