Starting phenix.real_space_refine on Thu Jul 2 14:40:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xyd_38769/07_2026/8xyd_38769.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xyd_38769/07_2026/8xyd_38769.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xyd_38769/07_2026/8xyd_38769.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xyd_38769/07_2026/8xyd_38769.map" model { file = "/net/cci-nas-00/data/ceres_data/8xyd_38769/07_2026/8xyd_38769.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xyd_38769/07_2026/8xyd_38769.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.002 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 63 5.16 5 C 5774 2.51 5 N 1528 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 55 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9035 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2464 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 2464 Classifications: {'peptide': 303} Link IDs: {'PTRANS': 11, 'TRANS': 291} Chain: "B" Number of atoms: 2584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2584 Classifications: {'peptide': 336} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "C" Number of atoms: 418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 418 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 4, 'TRANS': 49} Chain: "D" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1753 Classifications: {'peptide': 217} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 214} Chain breaks: 2 Chain: "E" Number of atoms: 1781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1781 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'PFS': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.10, per 1000 atoms: 0.23 Number of scatterers: 9035 At special positions: 0 Unit cell: (87.344, 123.6, 127.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 63 16.00 P 1 15.00 O 1669 8.00 N 1528 7.00 C 5774 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 90 " - pdb=" SG CYS A 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 159 " - pdb=" SG CYS E 229 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 485.3 milliseconds 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2142 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 37.8% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 12 through 44 removed outlier: 4.111A pdb=" N THR A 16 " --> pdb=" O GLU A 12 " (cutoff:3.500A) Proline residue: A 19 - end of helix removed outlier: 3.523A pdb=" N TYR A 44 " --> pdb=" O PHE A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.714A pdb=" N PHE A 49 " --> pdb=" O CYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 79 Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 86 through 121 removed outlier: 3.708A pdb=" N CYS A 90 " --> pdb=" O PRO A 86 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ASN A 91 " --> pdb=" O LYS A 87 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N PHE A 98 " --> pdb=" O GLY A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 127 Processing helix chain 'A' and resid 130 through 155 removed outlier: 4.000A pdb=" N TYR A 151 " --> pdb=" O GLY A 147 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N PHE A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 214 Processing helix chain 'A' and resid 223 through 260 Proline residue: A 247 - end of helix removed outlier: 4.015A pdb=" N LEU A 253 " --> pdb=" O HIS A 249 " (cutoff:3.500A) Proline residue: A 254 - end of helix Processing helix chain 'A' and resid 267 through 294 removed outlier: 3.718A pdb=" N VAL A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR A 278 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Proline residue: A 290 - end of helix Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'B' and resid 6 through 25 removed outlier: 3.624A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 10 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'D' and resid 8 through 31 removed outlier: 3.863A pdb=" N ALA D 12 " --> pdb=" O GLU D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 53 removed outlier: 3.627A pdb=" N LYS D 46 " --> pdb=" O GLY D 42 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N THR D 48 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ILE D 49 " --> pdb=" O GLY D 45 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 218 removed outlier: 4.547A pdb=" N ILE D 212 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N HIS D 213 " --> pdb=" O LYS D 210 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N CYS D 214 " --> pdb=" O TRP D 211 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N GLY D 217 " --> pdb=" O CYS D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 242 through 255 Processing helix chain 'D' and resid 270 through 278 Processing helix chain 'D' and resid 282 through 286 Processing helix chain 'D' and resid 295 through 309 removed outlier: 4.215A pdb=" N ALA D 301 " --> pdb=" O GLU D 297 " (cutoff:3.500A) Processing helix chain 'D' and resid 330 through 351 Processing helix chain 'E' and resid 28 through 32 Processing helix chain 'E' and resid 53 through 56 removed outlier: 3.677A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing sheet with id=AA1, first strand: chain 'A' and resid 159 through 161 removed outlier: 3.525A pdb=" N ASN A 159 " --> pdb=" O ARG A 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 52 removed outlier: 3.596A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.897A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.641A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.033A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.208A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.986A 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 153 removed outlier: 7.022A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.411A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 4.163A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.410A 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 278 removed outlier: 3.712A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N ASN B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 185 through 191 Processing sheet with id=AB1, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.730A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (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 194 through 195 removed outlier: 3.559A pdb=" N ASN E 194 " --> pdb=" O TYR E 190 " (cutoff:3.500A) removed outlier: 5.685A pdb=" N LEU E 187 " --> pdb=" O LEU E 178 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N LEU E 178 " --> pdb=" O LEU E 187 " (cutoff:3.500A) 457 hydrogen bonds defined for protein. 1284 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: 1.42 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.62: 9137 1.62 - 2.06: 91 2.06 - 2.49: 0 2.49 - 2.93: 0 2.93 - 3.37: 1 Bond restraints: 9229 Sorted by residual: bond pdb=" OXT PFS A 401 " pdb=" C2 PFS A 401 " ideal model delta sigma weight residual 1.436 3.365 -1.929 2.00e-02 2.50e+03 9.31e+03 bond pdb=" C PFS A 401 " pdb=" O2 PFS A 401 " ideal model delta sigma weight residual 1.205 1.400 -0.195 2.00e-02 2.50e+03 9.49e+01 bond pdb=" C PFS A 401 " pdb=" OXT PFS A 401 " ideal model delta sigma weight residual 1.331 1.184 0.147 2.00e-02 2.50e+03 5.38e+01 bond pdb=" C SER A 283 " pdb=" O SER A 283 " ideal model delta sigma weight residual 1.237 1.295 -0.058 1.17e-02 7.31e+03 2.48e+01 bond pdb=" C VAL A 251 " pdb=" O VAL A 251 " ideal model delta sigma weight residual 1.237 1.188 0.049 1.17e-02 7.31e+03 1.74e+01 ... (remaining 9224 not shown) Histogram of bond angle deviations from ideal: 0.00 - 18.18: 12493 18.18 - 36.36: 2 36.36 - 54.54: 0 54.54 - 72.72: 0 72.72 - 90.90: 1 Bond angle restraints: 12496 Sorted by residual: angle pdb=" C PFS A 401 " pdb=" OXT PFS A 401 " pdb=" C2 PFS A 401 " ideal model delta sigma weight residual 119.46 28.56 90.90 3.00e+00 1.11e-01 9.18e+02 angle pdb=" OXT PFS A 401 " pdb=" C2 PFS A 401 " pdb=" C3 PFS A 401 " ideal model delta sigma weight residual 103.92 132.69 -28.77 3.00e+00 1.11e-01 9.20e+01 angle pdb=" C21 PFS A 401 " pdb=" C22 PFS A 401 " pdb=" C23 PFS A 401 " ideal model delta sigma weight residual 113.40 94.46 18.94 3.00e+00 1.11e-01 3.99e+01 angle pdb=" N VAL A 250 " pdb=" CA VAL A 250 " pdb=" C VAL A 250 " ideal model delta sigma weight residual 110.74 105.63 5.11 9.10e-01 1.21e+00 3.15e+01 angle pdb=" C GLN A 216 " pdb=" N PRO A 217 " pdb=" CA PRO A 217 " ideal model delta sigma weight residual 119.78 114.13 5.65 1.03e+00 9.43e-01 3.01e+01 ... (remaining 12491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5281 17.99 - 35.98: 132 35.98 - 53.98: 54 53.98 - 71.97: 11 71.97 - 89.96: 3 Dihedral angle restraints: 5481 sinusoidal: 2164 harmonic: 3317 Sorted by residual: dihedral pdb=" N PHE D 354 " pdb=" C PHE D 354 " pdb=" CA PHE D 354 " pdb=" CB PHE D 354 " ideal model delta harmonic sigma weight residual 122.80 132.33 -9.53 0 2.50e+00 1.60e-01 1.45e+01 dihedral pdb=" C PHE D 354 " pdb=" N PHE D 354 " pdb=" CA PHE D 354 " pdb=" CB PHE D 354 " ideal model delta harmonic sigma weight residual -122.60 -132.05 9.45 0 2.50e+00 1.60e-01 1.43e+01 dihedral pdb=" C LEU E 247 " pdb=" N LEU E 247 " pdb=" CA LEU E 247 " pdb=" CB LEU E 247 " ideal model delta harmonic sigma weight residual -122.60 -131.77 9.17 0 2.50e+00 1.60e-01 1.35e+01 ... (remaining 5478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.340: 1402 0.340 - 0.679: 2 0.679 - 1.019: 0 1.019 - 1.358: 1 1.358 - 1.698: 6 Chirality restraints: 1411 Sorted by residual: chirality pdb=" CG LEU A 231 " pdb=" CB LEU A 231 " pdb=" CD1 LEU A 231 " pdb=" CD2 LEU A 231 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.21e+01 chirality pdb=" CG LEU A 28 " pdb=" CB LEU A 28 " pdb=" CD1 LEU A 28 " pdb=" CD2 LEU A 28 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.15e+01 chirality pdb=" CG LEU A 89 " pdb=" CB LEU A 89 " pdb=" CD1 LEU A 89 " pdb=" CD2 LEU A 89 " both_signs ideal model delta sigma weight residual False -2.59 -0.90 -1.69 2.00e-01 2.50e+01 7.13e+01 ... (remaining 1408 not shown) Planarity restraints: 1575 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 253 " 0.054 5.00e-02 4.00e+02 8.16e-02 1.07e+01 pdb=" N PRO A 254 " -0.141 5.00e-02 4.00e+02 pdb=" CA PRO A 254 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO A 254 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 251 " 0.013 2.00e-02 2.50e+03 2.54e-02 6.44e+00 pdb=" C VAL A 251 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL A 251 " 0.016 2.00e-02 2.50e+03 pdb=" N GLN A 252 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 274 " -0.011 2.00e-02 2.50e+03 2.21e-02 4.90e+00 pdb=" C ALA A 274 " 0.038 2.00e-02 2.50e+03 pdb=" O ALA A 274 " -0.015 2.00e-02 2.50e+03 pdb=" N HIS A 275 " -0.013 2.00e-02 2.50e+03 ... (remaining 1572 not shown) Histogram of nonbonded interaction distances: 1.40 - 2.10: 1 2.10 - 2.80: 2318 2.80 - 3.50: 12436 3.50 - 4.20: 21162 4.20 - 4.90: 37807 Nonbonded interactions: 73724 Sorted by model distance: nonbonded pdb=" C2 PFS A 401 " pdb=" O2 PFS A 401 " model vdw 1.399 2.776 nonbonded pdb=" OG SER A 7 " pdb=" OE1 GLU A 259 " model vdw 2.099 3.040 nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.159 3.040 nonbonded pdb=" OG SER D 293 " pdb=" OE1 GLU D 298 " model vdw 2.187 3.040 nonbonded pdb=" OG SER B 281 " pdb=" O HIS C 44 " model vdw 2.191 3.040 ... (remaining 73719 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: 1.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 9.670 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 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:6.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6208 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 : 0.021 1.929 9232 Z= 1.034 Angle : 1.109 90.903 12502 Z= 0.471 Chirality : 0.125 1.698 1411 Planarity : 0.003 0.082 1575 Dihedral : 10.033 89.959 3330 Min Nonbonded Distance : 1.399 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.41 % Allowed : 4.87 % Favored : 94.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.60 (0.23), residues: 1126 helix: 0.31 (0.25), residues: 382 sheet: -0.86 (0.27), residues: 273 loop : -2.34 (0.25), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 46 TYR 0.011 0.001 TYR A 102 PHE 0.018 0.001 PHE A 97 TRP 0.013 0.001 TRP A 255 HIS 0.003 0.000 HIS A 249 Details of bonding type rmsd/Z covalent geometry : bond 0.02050 / 1.03 ( 9229) covalent geometry : angle 1.10950 / 0.47 (12496) SS BOND : bond 0.00192 / 0.09 ( 3) SS BOND : angle 0.61840 / 0.31 ( 6) hydrogen bonds : bond 0.13069 / 8.19 ( 457) hydrogen bonds : angle 5.75044 / 4.21 ( 1284) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 219 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 ASP cc_start: 0.7707 (m-30) cc_final: 0.7411 (m-30) outliers start: 4 outliers final: 1 residues processed: 222 average time/residue: 0.6205 time to fit residues: 146.2051 Evaluate side-chains 95 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 184 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 20.0000 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 chunk 53 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 3.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 117 GLN A 188 HIS ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 62 HIS B 75 GLN B 156 GLN ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 237 ASN D 333 GLN ** E 179 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 183 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.056543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.044922 restraints weight = 44895.538| |-----------------------------------------------------------------------------| r_work (start): 0.3250 rms_B_bonded: 4.47 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.3698 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 9232 Z= 0.205 Angle : 0.747 10.510 12502 Z= 0.378 Chirality : 0.045 0.189 1411 Planarity : 0.005 0.090 1575 Dihedral : 6.911 58.110 1271 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 3.25 % Allowed : 12.88 % Favored : 83.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.25), residues: 1126 helix: 1.23 (0.26), residues: 395 sheet: -0.58 (0.28), residues: 291 loop : -1.76 (0.28), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 256 TYR 0.024 0.002 TYR E 235 PHE 0.025 0.002 PHE E 239 TRP 0.024 0.002 TRP B 332 HIS 0.005 0.001 HIS A 188 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 ( 9229) covalent geometry : angle 0.74734 / 0.38 (12496) SS BOND : bond 0.00213 / 0.11 ( 3) SS BOND : angle 0.65437 / 0.32 ( 6) hydrogen bonds : bond 0.04160 / 2.78 ( 457) hydrogen bonds : angle 4.60822 / 3.35 ( 1284) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.6562 (mmm) cc_final: 0.6158 (mtp) REVERT: A 273 ASP cc_start: 0.8998 (m-30) cc_final: 0.8634 (m-30) REVERT: B 9 GLN cc_start: 0.9014 (mp10) cc_final: 0.8802 (mp10) REVERT: B 105 TYR cc_start: 0.7649 (OUTLIER) cc_final: 0.7135 (t80) REVERT: B 225 HIS cc_start: 0.7589 (OUTLIER) cc_final: 0.7094 (t-90) REVERT: B 266 HIS cc_start: 0.8464 (OUTLIER) cc_final: 0.8013 (t-170) REVERT: C 28 ILE cc_start: 0.9096 (tt) cc_final: 0.8886 (pp) REVERT: D 333 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.8024 (tp-100) REVERT: E 34 MET cc_start: 0.8229 (mmm) cc_final: 0.8014 (mmm) REVERT: E 75 PRO cc_start: 0.8993 (Cg_exo) cc_final: 0.8781 (Cg_endo) outliers start: 32 outliers final: 13 residues processed: 135 average time/residue: 0.6320 time to fit residues: 90.6747 Evaluate side-chains 105 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 88 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 285 ASN Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 161 SER Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 333 GLN Chi-restraints excluded: chain E residue 141 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 75 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 2 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 101 optimal weight: 10.0000 chunk 84 optimal weight: 1.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 186 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.052973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.041076 restraints weight = 45094.427| |-----------------------------------------------------------------------------| r_work (start): 0.3127 rms_B_bonded: 4.39 r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9232 Z= 0.174 Angle : 0.646 7.630 12502 Z= 0.334 Chirality : 0.044 0.189 1411 Planarity : 0.005 0.089 1575 Dihedral : 5.988 55.302 1269 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 3.45 % Allowed : 12.88 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.25), residues: 1126 helix: 1.57 (0.27), residues: 394 sheet: -0.27 (0.28), residues: 291 loop : -1.44 (0.29), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 205 TYR 0.019 0.002 TYR A 102 PHE 0.015 0.002 PHE A 195 TRP 0.012 0.001 TRP B 211 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.17 ( 9229) covalent geometry : angle 0.64569 / 0.33 (12496) SS BOND : bond 0.00283 / 0.14 ( 3) SS BOND : angle 0.53614 / 0.29 ( 6) hydrogen bonds : bond 0.03981 / 2.65 ( 457) hydrogen bonds : angle 4.42358 / 3.19 ( 1284) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 99 time to evaluate : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 ASP cc_start: 0.9122 (m-30) cc_final: 0.8750 (m-30) REVERT: B 101 MET cc_start: 0.8726 (ttm) cc_final: 0.8475 (mtp) REVERT: B 154 ASP cc_start: 0.8242 (m-30) cc_final: 0.7579 (t0) REVERT: B 280 LYS cc_start: 0.8837 (mtpp) cc_final: 0.8560 (mtpm) REVERT: C 38 MET cc_start: 0.8933 (ttm) cc_final: 0.8651 (ttm) REVERT: D 276 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8813 (mm-30) REVERT: D 333 GLN cc_start: 0.8883 (OUTLIER) cc_final: 0.8269 (tp-100) REVERT: E 34 MET cc_start: 0.8308 (mmm) cc_final: 0.8080 (mmm) REVERT: E 94 TYR cc_start: 0.8453 (m-10) cc_final: 0.8139 (m-80) REVERT: E 219 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8211 (tm) outliers start: 34 outliers final: 14 residues processed: 122 average time/residue: 0.6737 time to fit residues: 87.2641 Evaluate side-chains 103 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 333 GLN Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 219 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 14 optimal weight: 6.9990 chunk 90 optimal weight: 0.0470 chunk 57 optimal weight: 4.9990 chunk 65 optimal weight: 0.3980 chunk 3 optimal weight: 8.9990 chunk 87 optimal weight: 9.9990 chunk 1 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 50 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 overall best weight: 2.2884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.050730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.038714 restraints weight = 46004.667| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 4.40 r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 9232 Z= 0.171 Angle : 0.654 9.982 12502 Z= 0.339 Chirality : 0.044 0.188 1411 Planarity : 0.004 0.086 1575 Dihedral : 5.652 56.171 1269 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 3.04 % Allowed : 13.89 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.18 (0.25), residues: 1126 helix: 1.77 (0.27), residues: 394 sheet: -0.03 (0.29), residues: 292 loop : -1.31 (0.29), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 27 TYR 0.021 0.001 TYR E 235 PHE 0.013 0.001 PHE A 195 TRP 0.011 0.001 TRP B 211 HIS 0.005 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 9229) covalent geometry : angle 0.65386 / 0.34 (12496) SS BOND : bond 0.00370 / 0.18 ( 3) SS BOND : angle 0.65244 / 0.33 ( 6) hydrogen bonds : bond 0.03770 / 2.52 ( 457) hydrogen bonds : angle 4.34443 / 3.12 ( 1284) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 94 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 ASP cc_start: 0.9171 (m-30) cc_final: 0.8815 (m-30) REVERT: B 198 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7341 (pp) REVERT: B 266 HIS cc_start: 0.8929 (OUTLIER) cc_final: 0.8452 (t-170) REVERT: C 38 MET cc_start: 0.9032 (ttm) cc_final: 0.8796 (ttm) REVERT: D 276 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8863 (mm-30) REVERT: D 333 GLN cc_start: 0.8818 (OUTLIER) cc_final: 0.8431 (tp-100) REVERT: E 42 GLU cc_start: 0.8829 (tp30) cc_final: 0.8537 (tp30) REVERT: E 83 MET cc_start: 0.8069 (mtm) cc_final: 0.7563 (mpp) REVERT: E 89 GLU cc_start: 0.9265 (tp30) cc_final: 0.8833 (tm-30) outliers start: 30 outliers final: 17 residues processed: 120 average time/residue: 0.6375 time to fit residues: 81.1922 Evaluate side-chains 102 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 time to evaluate : 0.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 HIS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 176 HIS Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain D residue 315 ASP Chi-restraints excluded: chain D residue 333 GLN Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 189 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 37 optimal weight: 7.9990 chunk 65 optimal weight: 0.9990 chunk 63 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 69 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 269 GLN D 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.050755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.038799 restraints weight = 45247.540| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 4.35 r_work: 0.2917 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.5944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9232 Z= 0.132 Angle : 0.651 13.075 12502 Z= 0.329 Chirality : 0.043 0.183 1411 Planarity : 0.004 0.082 1575 Dihedral : 5.435 56.452 1269 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.74 % Allowed : 15.82 % Favored : 81.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.25), residues: 1126 helix: 1.84 (0.27), residues: 394 sheet: 0.08 (0.29), residues: 300 loop : -1.17 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 72 TYR 0.017 0.001 TYR E 235 PHE 0.015 0.001 PHE E 29 TRP 0.008 0.001 TRP E 176 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 ( 9229) covalent geometry : angle 0.65148 / 0.33 (12496) SS BOND : bond 0.00359 / 0.17 ( 3) SS BOND : angle 0.56677 / 0.30 ( 6) hydrogen bonds : bond 0.03510 / 2.35 ( 457) hydrogen bonds : angle 4.26204 / 3.06 ( 1284) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 95 time to evaluate : 0.382 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 273 ASP cc_start: 0.9188 (m-30) cc_final: 0.8839 (m-30) REVERT: B 9 GLN cc_start: 0.8912 (mp10) cc_final: 0.8630 (mp10) REVERT: B 32 GLN cc_start: 0.9274 (mp10) cc_final: 0.8961 (mp10) REVERT: B 47 THR cc_start: 0.9195 (OUTLIER) cc_final: 0.8939 (m) REVERT: B 198 LEU cc_start: 0.7626 (OUTLIER) cc_final: 0.7375 (pp) REVERT: B 266 HIS cc_start: 0.9055 (OUTLIER) cc_final: 0.8641 (t-170) REVERT: D 276 GLU cc_start: 0.9247 (mm-30) cc_final: 0.9046 (mm-30) REVERT: E 42 GLU cc_start: 0.9145 (tp30) cc_final: 0.8788 (tp30) REVERT: E 83 MET cc_start: 0.8357 (mtm) cc_final: 0.7712 (mpp) REVERT: E 89 GLU cc_start: 0.9314 (tp30) cc_final: 0.8914 (tm-30) REVERT: E 163 LYS cc_start: 0.8893 (OUTLIER) cc_final: 0.8504 (ptmm) outliers start: 27 outliers final: 12 residues processed: 115 average time/residue: 0.7071 time to fit residues: 86.1983 Evaluate side-chains 99 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 29 LYS Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain E residue 189 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 63 optimal weight: 7.9990 chunk 22 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 67 optimal weight: 0.7980 chunk 100 optimal weight: 9.9990 chunk 94 optimal weight: 0.0570 chunk 96 optimal weight: 0.9980 chunk 8 optimal weight: 0.3980 chunk 24 optimal weight: 3.9990 overall best weight: 0.8500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 268 HIS D 244 HIS D 304 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.050867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.039067 restraints weight = 45175.544| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 4.29 r_work: 0.2927 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.6142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9232 Z= 0.126 Angle : 0.667 13.665 12502 Z= 0.335 Chirality : 0.042 0.194 1411 Planarity : 0.004 0.089 1575 Dihedral : 5.371 55.621 1269 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.94 % Allowed : 16.53 % Favored : 80.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.25), residues: 1126 helix: 1.90 (0.27), residues: 394 sheet: 0.17 (0.29), residues: 300 loop : -1.16 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 72 TYR 0.015 0.001 TYR E 235 PHE 0.012 0.001 PHE E 29 TRP 0.008 0.001 TRP B 82 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.13 ( 9229) covalent geometry : angle 0.66733 / 0.34 (12496) SS BOND : bond 0.00348 / 0.17 ( 3) SS BOND : angle 0.58368 / 0.32 ( 6) hydrogen bonds : bond 0.03354 / 2.26 ( 457) hydrogen bonds : angle 4.24217 / 3.05 ( 1284) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 96 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.8771 (OUTLIER) cc_final: 0.8166 (mpp) REVERT: A 273 ASP cc_start: 0.9174 (m-30) cc_final: 0.8801 (m-30) REVERT: B 9 GLN cc_start: 0.8811 (mp10) cc_final: 0.8588 (mp-120) REVERT: B 27 ASP cc_start: 0.9545 (t0) cc_final: 0.9165 (m-30) REVERT: B 32 GLN cc_start: 0.9328 (mp10) cc_final: 0.9048 (mp10) REVERT: B 45 MET cc_start: 0.8623 (OUTLIER) cc_final: 0.8274 (mpm) REVERT: B 47 THR cc_start: 0.9227 (OUTLIER) cc_final: 0.9009 (m) REVERT: B 198 LEU cc_start: 0.7640 (OUTLIER) cc_final: 0.7397 (pp) REVERT: B 262 MET cc_start: 0.7215 (tmm) cc_final: 0.6900 (tmm) REVERT: B 266 HIS cc_start: 0.9042 (OUTLIER) cc_final: 0.8654 (t-170) REVERT: D 272 ASP cc_start: 0.9220 (OUTLIER) cc_final: 0.8770 (p0) REVERT: D 276 GLU cc_start: 0.9270 (mm-30) cc_final: 0.9056 (mm-30) REVERT: D 306 GLN cc_start: 0.9407 (mm-40) cc_final: 0.8960 (mp10) REVERT: E 42 GLU cc_start: 0.9226 (tp30) cc_final: 0.8644 (pp20) REVERT: E 43 LYS cc_start: 0.9245 (mmmm) cc_final: 0.8710 (mmmm) REVERT: E 46 GLU cc_start: 0.8731 (OUTLIER) cc_final: 0.8514 (pm20) REVERT: E 76 LYS cc_start: 0.9531 (mmmm) cc_final: 0.9322 (mppt) REVERT: E 163 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8557 (ptmm) outliers start: 29 outliers final: 12 residues processed: 118 average time/residue: 0.6557 time to fit residues: 82.3426 Evaluate side-chains 106 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 86 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 45 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain E residue 189 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 38 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 87 optimal weight: 0.9990 chunk 7 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 340 ASN D 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.049746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.037860 restraints weight = 45569.730| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 4.31 r_work: 0.2882 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.6444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9232 Z= 0.149 Angle : 0.673 13.866 12502 Z= 0.338 Chirality : 0.043 0.179 1411 Planarity : 0.004 0.090 1575 Dihedral : 5.332 53.353 1269 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.64 % Allowed : 17.75 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.25), residues: 1126 helix: 1.88 (0.27), residues: 394 sheet: 0.22 (0.29), residues: 303 loop : -1.15 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 205 TYR 0.019 0.001 TYR B 264 PHE 0.012 0.001 PHE E 29 TRP 0.009 0.001 TRP B 211 HIS 0.005 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.15 ( 9229) covalent geometry : angle 0.67317 / 0.34 (12496) SS BOND : bond 0.00347 / 0.17 ( 3) SS BOND : angle 0.59120 / 0.32 ( 6) hydrogen bonds : bond 0.03490 / 2.33 ( 457) hydrogen bonds : angle 4.25137 / 3.06 ( 1284) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 89 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8380 (mpp) REVERT: A 273 ASP cc_start: 0.9236 (m-30) cc_final: 0.8885 (m-30) REVERT: B 27 ASP cc_start: 0.9481 (t0) cc_final: 0.9260 (m-30) REVERT: B 32 GLN cc_start: 0.9388 (mp10) cc_final: 0.9126 (mp10) REVERT: B 47 THR cc_start: 0.9208 (OUTLIER) cc_final: 0.8964 (m) REVERT: B 198 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7543 (pp) REVERT: B 266 HIS cc_start: 0.9072 (OUTLIER) cc_final: 0.8676 (t-170) REVERT: C 47 GLU cc_start: 0.8967 (mp0) cc_final: 0.8673 (tp30) REVERT: D 272 ASP cc_start: 0.9240 (OUTLIER) cc_final: 0.8763 (p0) REVERT: D 276 GLU cc_start: 0.9267 (mm-30) cc_final: 0.9027 (mm-30) REVERT: E 42 GLU cc_start: 0.9280 (tp30) cc_final: 0.8802 (pp20) REVERT: E 43 LYS cc_start: 0.9303 (mmmm) cc_final: 0.9024 (mmmm) REVERT: E 46 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8202 (pm20) REVERT: E 163 LYS cc_start: 0.8937 (OUTLIER) cc_final: 0.8639 (ptmm) REVERT: E 183 GLN cc_start: 0.8552 (OUTLIER) cc_final: 0.7786 (pp30) outliers start: 26 outliers final: 14 residues processed: 109 average time/residue: 0.6817 time to fit residues: 78.8323 Evaluate side-chains 104 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 164 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain D residue 272 ASP Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain E residue 183 GLN Chi-restraints excluded: chain E residue 189 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 107 optimal weight: 0.0000 chunk 75 optimal weight: 9.9990 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 46 optimal weight: 9.9990 chunk 59 optimal weight: 8.9990 chunk 61 optimal weight: 0.0970 chunk 63 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 269 GLN B 13 GLN C 11 GLN D 304 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.048364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.036560 restraints weight = 45662.811| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 4.28 r_work: 0.2829 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.6979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 9232 Z= 0.174 Angle : 0.689 11.737 12502 Z= 0.351 Chirality : 0.043 0.183 1411 Planarity : 0.004 0.091 1575 Dihedral : 5.415 54.870 1269 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.84 % Allowed : 18.05 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.25), residues: 1126 helix: 1.70 (0.26), residues: 395 sheet: 0.27 (0.30), residues: 301 loop : -1.08 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 205 TYR 0.017 0.001 TYR E 235 PHE 0.011 0.001 PHE E 29 TRP 0.010 0.001 TRP B 211 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.17 ( 9229) covalent geometry : angle 0.68931 / 0.35 (12496) SS BOND : bond 0.00318 / 0.16 ( 3) SS BOND : angle 0.58731 / 0.31 ( 6) hydrogen bonds : bond 0.03663 / 2.44 ( 457) hydrogen bonds : angle 4.32703 / 3.10 ( 1284) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 86 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.8839 (OUTLIER) cc_final: 0.8451 (mpp) REVERT: A 273 ASP cc_start: 0.9286 (m-30) cc_final: 0.8972 (m-30) REVERT: B 27 ASP cc_start: 0.9478 (t0) cc_final: 0.9237 (m-30) REVERT: B 198 LEU cc_start: 0.7909 (OUTLIER) cc_final: 0.7604 (pp) REVERT: B 266 HIS cc_start: 0.9194 (OUTLIER) cc_final: 0.8876 (t-170) REVERT: E 42 GLU cc_start: 0.9350 (tp30) cc_final: 0.8929 (pp20) REVERT: E 43 LYS cc_start: 0.9324 (mmmm) cc_final: 0.9005 (mmmm) REVERT: E 46 GLU cc_start: 0.8833 (OUTLIER) cc_final: 0.8242 (pm20) REVERT: E 82 GLN cc_start: 0.8823 (mm-40) cc_final: 0.8519 (tp-100) REVERT: E 93 MET cc_start: 0.8857 (tpp) cc_final: 0.8532 (tpt) REVERT: E 163 LYS cc_start: 0.8942 (OUTLIER) cc_final: 0.8659 (ptmm) REVERT: E 183 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7834 (pp30) outliers start: 28 outliers final: 14 residues processed: 108 average time/residue: 0.6875 time to fit residues: 78.7148 Evaluate side-chains 97 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 65 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain E residue 183 GLN Chi-restraints excluded: chain E residue 189 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 69 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 106 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 107 optimal weight: 0.7980 chunk 108 optimal weight: 9.9990 chunk 97 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.048537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.036690 restraints weight = 45583.159| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 4.29 r_work: 0.2840 rms_B_bonded: 4.85 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.7091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9232 Z= 0.148 Angle : 0.725 15.368 12502 Z= 0.360 Chirality : 0.043 0.186 1411 Planarity : 0.004 0.090 1575 Dihedral : 5.418 56.274 1269 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 2.23 % Allowed : 18.97 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.25), residues: 1126 helix: 1.65 (0.26), residues: 395 sheet: 0.32 (0.30), residues: 299 loop : -1.02 (0.30), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 160 TYR 0.019 0.001 TYR D 296 PHE 0.011 0.001 PHE E 29 TRP 0.008 0.001 TRP B 82 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.15 ( 9229) covalent geometry : angle 0.72533 / 0.36 (12496) SS BOND : bond 0.00304 / 0.15 ( 3) SS BOND : angle 0.55768 / 0.29 ( 6) hydrogen bonds : bond 0.03584 / 2.39 ( 457) hydrogen bonds : angle 4.33441 / 3.10 ( 1284) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 83 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 9 MET cc_start: 0.7150 (ttp) cc_final: 0.6723 (ptp) REVERT: A 56 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8438 (mpp) REVERT: A 273 ASP cc_start: 0.9288 (m-30) cc_final: 0.8978 (m-30) REVERT: B 27 ASP cc_start: 0.9490 (t0) cc_final: 0.9241 (m-30) REVERT: B 47 THR cc_start: 0.9184 (OUTLIER) cc_final: 0.8935 (m) REVERT: B 198 LEU cc_start: 0.7901 (OUTLIER) cc_final: 0.7597 (pp) REVERT: B 266 HIS cc_start: 0.9165 (OUTLIER) cc_final: 0.8870 (t-170) REVERT: C 46 LYS cc_start: 0.9490 (mmmt) cc_final: 0.9176 (tppt) REVERT: E 42 GLU cc_start: 0.9352 (tp30) cc_final: 0.8883 (pp20) REVERT: E 43 LYS cc_start: 0.9335 (mmmm) cc_final: 0.8974 (mmmm) REVERT: E 46 GLU cc_start: 0.8863 (OUTLIER) cc_final: 0.8327 (pm20) REVERT: E 82 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8499 (tp-100) REVERT: E 183 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.7901 (pp30) outliers start: 22 outliers final: 9 residues processed: 99 average time/residue: 0.6907 time to fit residues: 72.4933 Evaluate side-chains 94 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 79 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 183 GLN Chi-restraints excluded: chain E residue 189 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 69 optimal weight: 6.9990 chunk 72 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 59 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 106 optimal weight: 5.9990 chunk 93 optimal weight: 10.0000 chunk 55 optimal weight: 0.0870 chunk 49 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 overall best weight: 1.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 13 GLN D 304 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.048015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.036167 restraints weight = 45941.728| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 4.24 r_work: 0.2819 rms_B_bonded: 4.86 restraints_weight: 0.5000 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.7460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9232 Z= 0.162 Angle : 0.734 15.085 12502 Z= 0.368 Chirality : 0.044 0.181 1411 Planarity : 0.004 0.091 1575 Dihedral : 5.463 58.602 1269 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.72 % Allowed : 19.57 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.26), residues: 1126 helix: 1.53 (0.27), residues: 395 sheet: 0.43 (0.30), residues: 295 loop : -1.03 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 21 TYR 0.027 0.002 TYR D 296 PHE 0.010 0.001 PHE E 68 TRP 0.008 0.001 TRP B 82 HIS 0.004 0.001 HIS B 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.16 ( 9229) covalent geometry : angle 0.73378 / 0.37 (12496) SS BOND : bond 0.00295 / 0.14 ( 3) SS BOND : angle 0.59447 / 0.31 ( 6) hydrogen bonds : bond 0.03660 / 2.45 ( 457) hydrogen bonds : angle 4.38950 / 3.13 ( 1284) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2252 Ramachandran restraints generated. 1126 Oldfield, 0 Emsley, 1126 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8486 (mpp) REVERT: B 47 THR cc_start: 0.9208 (OUTLIER) cc_final: 0.8948 (m) REVERT: B 266 HIS cc_start: 0.9168 (OUTLIER) cc_final: 0.8923 (t-170) REVERT: D 276 GLU cc_start: 0.9253 (mm-30) cc_final: 0.8989 (mm-30) REVERT: E 42 GLU cc_start: 0.9394 (tp30) cc_final: 0.8978 (pp20) REVERT: E 43 LYS cc_start: 0.9374 (mmmm) cc_final: 0.9035 (mmmm) REVERT: E 46 GLU cc_start: 0.8904 (OUTLIER) cc_final: 0.8399 (pm20) REVERT: E 82 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8512 (tp-100) REVERT: E 93 MET cc_start: 0.8919 (tpp) cc_final: 0.8428 (tpt) REVERT: E 163 LYS cc_start: 0.9036 (ttpp) cc_final: 0.8811 (ptmm) REVERT: E 183 GLN cc_start: 0.8813 (OUTLIER) cc_final: 0.7999 (pp30) REVERT: E 244 LYS cc_start: 0.8787 (ptmm) cc_final: 0.8105 (tmtt) outliers start: 17 outliers final: 11 residues processed: 100 average time/residue: 0.7805 time to fit residues: 82.4395 Evaluate side-chains 94 residues out of total 986 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 78 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 MET Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 287 VAL Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 266 HIS Chi-restraints excluded: chain B residue 296 VAL Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain C residue 15 LEU Chi-restraints excluded: chain D residue 269 ASN Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 183 GLN Chi-restraints excluded: chain E residue 189 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 20 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 83 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 75 optimal weight: 20.0000 chunk 28 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 15 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 9 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 304 GLN D 333 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.048378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.036417 restraints weight = 44965.166| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 4.26 r_work: 0.2832 rms_B_bonded: 4.89 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.7580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9232 Z= 0.139 Angle : 0.766 14.842 12502 Z= 0.379 Chirality : 0.043 0.191 1411 Planarity : 0.004 0.094 1575 Dihedral : 5.430 58.877 1269 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 1.72 % Allowed : 19.78 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.26), residues: 1126 helix: 1.52 (0.27), residues: 394 sheet: 0.39 (0.30), residues: 298 loop : -0.95 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 160 TYR 0.027 0.001 TYR D 296 PHE 0.010 0.001 PHE A 195 TRP 0.010 0.001 TRP E 176 HIS 0.005 0.001 HIS A 268 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 ( 9229) covalent geometry : angle 0.76623 / 0.38 (12496) SS BOND : bond 0.00287 / 0.14 ( 3) SS BOND : angle 0.52911 / 0.28 ( 6) hydrogen bonds : bond 0.03555 / 2.37 ( 457) hydrogen bonds : angle 4.39224 / 3.14 ( 1284) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3706.19 seconds wall clock time: 64 minutes 14.41 seconds (3854.41 seconds total)