Starting phenix.real_space_refine on Thu Jul 2 10:52:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zyu_60579/07_2026/8zyu_60579.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zyu_60579/07_2026/8zyu_60579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zyu_60579/07_2026/8zyu_60579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zyu_60579/07_2026/8zyu_60579.map" model { file = "/net/cci-nas-00/data/ceres_data/8zyu_60579/07_2026/8zyu_60579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zyu_60579/07_2026/8zyu_60579.cif" } resolution = 2.65 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= 0.072 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: 6 Type Number sf(0) Gaussians P 7 5.49 5 S 36 5.16 5 C 5402 2.51 5 N 1424 2.21 5 O 1577 1.98 5 F 1 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 8447 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 2734 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2734 Classifications: {'peptide': 362} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 28, 'TRANS': 333} Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 160 Unresolved non-hydrogen dihedrals: 102 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLU:plan': 11, 'ASP:plan': 4, 'ARG:plan': 5, 'ASN:plan1': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 89 Chain: "D" Number of atoms: 1639 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1639 Classifications: {'peptide': 221} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 209} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 57 Classifications: {'peptide': 6} Link IDs: {'PTRANS': 1, 'TRANS': 4} Chain: "Q" Number of atoms: 1535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1535 Classifications: {'peptide': 216} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 30} Link IDs: {'PTRANS': 11, 'TRANS': 204} Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 144 Unresolved non-hydrogen dihedrals: 95 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 2, 'ASP:plan': 3, 'GLN:plan1': 4, 'GLU:plan': 5, 'ASN:plan1': 2, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 68 Chain: "R" Number of atoms: 2409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2409 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 24} Link IDs: {'PTRANS': 10, 'TRANS': 302} Chain breaks: 3 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 123 Unresolved non-hydrogen dihedrals: 83 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'ASP:plan': 4, 'TYR:plan': 1, 'ARG:plan': 1, 'GLN:plan1': 2, 'HIS:plan': 2, 'GLU:plan': 1, 'TRP:plan': 1, 'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 56 Chain: "R" Number of atoms: 73 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 73 Unusual residues: {'PIO': 1, 'SRW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Time building chain proxies: 1.98, per 1000 atoms: 0.23 Number of scatterers: 8447 At special positions: 0 Unit cell: (74.16, 100.528, 170.568, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 7 15.00 F 1 9.00 O 1577 8.00 N 1424 7.00 C 5402 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS D 45 " - pdb=" SG CYS D 119 " distance=2.03 Simple disulfide: pdb=" SG CYS D 170 " - pdb=" SG CYS D 226 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 44 " - pdb=" SG CYS Q 109 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 155 " - pdb=" SG CYS Q 215 " distance=2.03 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " 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: 0.73 Conformation dependent library (CDL) restraints added in 449.3 milliseconds 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2110 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 17 sheets defined 26.9% alpha, 34.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'B' and resid 43 through 48 removed outlier: 4.003A pdb=" N LYS B 48 " --> pdb=" O PRO B 44 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 108 Processing helix chain 'D' and resid 110 through 114 Processing helix chain 'D' and resid 186 through 188 No H-bonds generated for 'chain 'D' and resid 186 through 188' Processing helix chain 'D' and resid 217 through 219 No H-bonds generated for 'chain 'D' and resid 217 through 219' Processing helix chain 'Q' and resid 100 through 104 removed outlier: 3.883A pdb=" N PHE Q 104 " --> pdb=" O PRO Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 142 through 149 Processing helix chain 'Q' and resid 170 through 174 Processing helix chain 'Q' and resid 204 through 210 removed outlier: 3.654A pdb=" N GLU Q 208 " --> pdb=" O LYS Q 204 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 90 Processing helix chain 'R' and resid 100 through 127 removed outlier: 3.625A pdb=" N HIS R 104 " --> pdb=" O THR R 100 " (cutoff:3.500A) Proline residue: R 121 - end of helix removed outlier: 3.857A pdb=" N TYR R 125 " --> pdb=" O PRO R 121 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASN R 126 " --> pdb=" O VAL R 122 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 172 removed outlier: 3.558A pdb=" N CYS R 141 " --> pdb=" O GLY R 137 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR R 145 " --> pdb=" O CYS R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 180 removed outlier: 4.060A pdb=" N THR R 178 " --> pdb=" O PHE R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 201 Processing helix chain 'R' and resid 201 through 206 removed outlier: 3.850A pdb=" N PHE R 205 " --> pdb=" O VAL R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 229 through 267 removed outlier: 3.751A pdb=" N VAL R 235 " --> pdb=" O ALA R 231 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLN R 238 " --> pdb=" O LYS R 234 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N PHE R 247 " --> pdb=" O MET R 243 " (cutoff:3.500A) Proline residue: R 248 - end of helix Processing helix chain 'R' and resid 300 through 326 removed outlier: 4.173A pdb=" N VAL R 309 " --> pdb=" O LEU R 305 " (cutoff:3.500A) Proline residue: R 318 - end of helix Processing helix chain 'R' and resid 335 through 368 removed outlier: 4.208A pdb=" N MET R 347 " --> pdb=" O HIS R 343 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N SER R 356 " --> pdb=" O LEU R 352 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER R 357 " --> pdb=" O PHE R 353 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N THR R 358 " --> pdb=" O TYR R 354 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASN R 360 " --> pdb=" O SER R 356 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 368 through 382 Processing sheet with id=AA1, first strand: chain 'B' and resid 111 through 116 Processing sheet with id=AA2, first strand: chain 'B' and resid 25 through 27 removed outlier: 3.622A pdb=" N TYR B 143 " --> pdb=" O ILE B 167 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LYS B 169 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 9.680A pdb=" N VAL B 141 " --> pdb=" O LYS B 169 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 51 through 64 current: chain 'B' and resid 287 through 289 Processing sheet with id=AA3, first strand: chain 'B' and resid 73 through 84 removed outlier: 6.389A pdb=" N CYS B 58 " --> pdb=" O LEU B 78 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL B 80 " --> pdb=" O LEU B 56 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N LEU B 56 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N ASN B 82 " --> pdb=" O VAL B 54 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N VAL B 54 " --> pdb=" O ASN B 82 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N GLN B 84 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL B 52 " --> pdb=" O GLN B 84 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 140 through 150 current: chain 'R' and resid 288 through 291 Processing sheet with id=AA4, first strand: chain 'B' and resid 182 through 187 Processing sheet with id=AA5, first strand: chain 'B' and resid 206 through 207 removed outlier: 4.143A pdb=" N TYR B 320 " --> pdb=" O PHE B 348 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N LEU B 350 " --> pdb=" O VAL B 318 " (cutoff:3.500A) removed outlier: 9.240A pdb=" N VAL B 318 " --> pdb=" O LEU B 350 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LYS B 229 " --> pdb=" O VAL B 327 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER B 329 " --> pdb=" O VAL B 227 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL B 227 " --> pdb=" O SER B 329 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE B 230 " --> pdb=" O GLU B 256 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N GLU B 256 " --> pdb=" O ILE B 230 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ILE B 232 " --> pdb=" O MET B 254 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N MET B 254 " --> pdb=" O ILE B 232 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N VAL B 234 " --> pdb=" O VAL B 252 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 26 through 30 Processing sheet with id=AA7, first strand: chain 'D' and resid 34 through 35 removed outlier: 6.774A pdb=" N ILE D 57 " --> pdb=" O SER D 73 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N SER D 73 " --> pdb=" O ILE D 57 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N TRP D 59 " --> pdb=" O VAL D 71 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 34 through 35 removed outlier: 3.798A pdb=" N TYR D 132 " --> pdb=" O ARG D 121 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 150 through 154 removed outlier: 3.502A pdb=" N LYS D 173 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY D 169 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N TYR D 206 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 150 through 154 removed outlier: 3.502A pdb=" N LYS D 173 " --> pdb=" O SER D 150 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLY D 169 " --> pdb=" O LEU D 154 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N TYR D 206 " --> pdb=" O ASP D 174 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 181 through 184 removed outlier: 4.695A pdb=" N TYR D 224 " --> pdb=" O VAL D 241 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS D 239 " --> pdb=" O CYS D 226 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Q' and resid 25 through 27 Processing sheet with id=AB4, first strand: chain 'Q' and resid 31 through 33 removed outlier: 6.561A pdb=" N LEU Q 32 " --> pdb=" O GLU Q 126 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N VAL Q 54 " --> pdb=" O TYR Q 70 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TYR Q 70 " --> pdb=" O VAL Q 54 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N TRP Q 56 " --> pdb=" O LEU Q 68 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'Q' and resid 31 through 33 removed outlier: 6.561A pdb=" N LEU Q 32 " --> pdb=" O GLU Q 126 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR Q 118 " --> pdb=" O GLN Q 111 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'Q' and resid 136 through 139 removed outlier: 3.719A pdb=" N VAL Q 154 " --> pdb=" O PHE Q 139 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS Q 155 " --> pdb=" O SER Q 198 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER Q 198 " --> pdb=" O CYS Q 155 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ASN Q 159 " --> pdb=" O TYR Q 194 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N TYR Q 194 " --> pdb=" O ASN Q 159 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'Q' and resid 167 through 168 removed outlier: 3.707A pdb=" N VAL Q 226 " --> pdb=" O VAL Q 217 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'R' and resid 207 through 210 439 hydrogen bonds defined for protein. 1206 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: 1.44 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1305 1.30 - 1.43: 2317 1.43 - 1.56: 4954 1.56 - 1.69: 22 1.69 - 1.82: 51 Bond restraints: 8649 Sorted by residual: bond pdb=" C23 SRW R 500 " pdb=" O2 SRW R 500 " ideal model delta sigma weight residual 1.429 1.189 0.240 2.00e-02 2.50e+03 1.45e+02 bond pdb=" C13 SRW R 500 " pdb=" N1 SRW R 500 " ideal model delta sigma weight residual 1.357 1.491 -0.134 2.00e-02 2.50e+03 4.47e+01 bond pdb=" C3 SRW R 500 " pdb=" C8 SRW R 500 " ideal model delta sigma weight residual 1.519 1.632 -0.113 2.00e-02 2.50e+03 3.22e+01 bond pdb=" OG1 TPO R 407 " pdb=" P TPO R 407 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C10 SRW R 500 " pdb=" N1 SRW R 500 " ideal model delta sigma weight residual 1.456 1.556 -0.100 2.00e-02 2.50e+03 2.52e+01 ... (remaining 8644 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 11684 2.77 - 5.54: 103 5.54 - 8.31: 21 8.31 - 11.08: 6 11.08 - 13.85: 4 Bond angle restraints: 11818 Sorted by residual: angle pdb=" C TYR R 167 " pdb=" CA TYR R 167 " pdb=" CB TYR R 167 " ideal model delta sigma weight residual 110.88 119.83 -8.95 1.57e+00 4.06e-01 3.25e+01 angle pdb=" C14 SRW R 500 " pdb=" C24 SRW R 500 " pdb=" C26 SRW R 500 " ideal model delta sigma weight residual 122.08 135.93 -13.85 3.00e+00 1.11e-01 2.13e+01 angle pdb=" N PHE R 312 " pdb=" CA PHE R 312 " pdb=" C PHE R 312 " ideal model delta sigma weight residual 111.36 106.46 4.90 1.09e+00 8.42e-01 2.02e+01 angle pdb=" O1 PIO R 501 " pdb=" P1 PIO R 501 " pdb=" O13 PIO R 501 " ideal model delta sigma weight residual 97.64 110.17 -12.53 3.00e+00 1.11e-01 1.74e+01 angle pdb=" CA PHE R 312 " pdb=" CB PHE R 312 " pdb=" CG PHE R 312 " ideal model delta sigma weight residual 113.80 109.72 4.08 1.00e+00 1.00e+00 1.67e+01 ... (remaining 11813 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.49: 4905 30.49 - 60.99: 205 60.99 - 91.48: 19 91.48 - 121.98: 5 121.98 - 152.47: 4 Dihedral angle restraints: 5138 sinusoidal: 1866 harmonic: 3272 Sorted by residual: dihedral pdb=" CB CYS Q 155 " pdb=" SG CYS Q 155 " pdb=" SG CYS Q 215 " pdb=" CB CYS Q 215 " ideal model delta sinusoidal sigma weight residual 93.00 54.10 38.90 1 1.00e+01 1.00e-02 2.13e+01 dihedral pdb=" C25 SRW R 500 " pdb=" C24 SRW R 500 " pdb=" C26 SRW R 500 " pdb=" F1 SRW R 500 " ideal model delta sinusoidal sigma weight residual 106.02 -101.51 -152.47 1 3.00e+01 1.11e-03 2.01e+01 dihedral pdb=" C14 SRW R 500 " pdb=" C24 SRW R 500 " pdb=" C26 SRW R 500 " pdb=" C25 SRW R 500 " ideal model delta sinusoidal sigma weight residual 110.71 -107.83 -141.46 1 3.00e+01 1.11e-03 1.90e+01 ... (remaining 5135 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 1320 0.098 - 0.197: 64 0.197 - 0.295: 1 0.295 - 0.394: 0 0.394 - 0.492: 1 Chirality restraints: 1386 Sorted by residual: chirality pdb=" C24 SRW R 500 " pdb=" C14 SRW R 500 " pdb=" C25 SRW R 500 " pdb=" F1 SRW R 500 " both_signs ideal model delta sigma weight residual True 1.45 1.94 -0.49 2.00e-01 2.50e+01 6.05e+00 chirality pdb=" CA GLU R 165 " pdb=" N GLU R 165 " pdb=" C GLU R 165 " pdb=" CB GLU R 165 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C1 PIO R 501 " pdb=" C2 PIO R 501 " pdb=" C6 PIO R 501 " pdb=" O1 PIO R 501 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.45e-01 ... (remaining 1383 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL R 201 " 0.066 5.00e-02 4.00e+02 9.93e-02 1.58e+01 pdb=" N PRO R 202 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO R 202 " 0.051 5.00e-02 4.00e+02 pdb=" CD PRO R 202 " 0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS R 132 " 0.040 5.00e-02 4.00e+02 6.10e-02 5.95e+00 pdb=" N PRO R 133 " -0.105 5.00e-02 4.00e+02 pdb=" CA PRO R 133 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 133 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE R 312 " 0.020 2.00e-02 2.50e+03 1.35e-02 3.19e+00 pdb=" CG PHE R 312 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE R 312 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE R 312 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 PHE R 312 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE R 312 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE R 312 " 0.005 2.00e-02 2.50e+03 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 128 2.67 - 3.23: 7583 3.23 - 3.79: 13107 3.79 - 4.34: 17966 4.34 - 4.90: 29833 Nonbonded interactions: 68617 Sorted by model distance: nonbonded pdb=" OD1 ASP B 203 " pdb=" OH TYR B 207 " model vdw 2.114 3.040 nonbonded pdb=" N GLU B 109 " pdb=" OE1 GLU B 109 " model vdw 2.211 3.120 nonbonded pdb=" N GLU B 151 " pdb=" OE1 GLU B 151 " model vdw 2.234 3.120 nonbonded pdb=" O PRO B 251 " pdb=" NZ LYS B 283 " model vdw 2.252 3.120 nonbonded pdb=" OG1 THR B 55 " pdb=" OD1 ASN B 82 " model vdw 2.277 3.040 ... (remaining 68612 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: 3.940 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: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.250 Find NCS groups from input model: 0.040 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:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 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 : 0.006 0.240 8654 Z= 0.291 Angle : 0.715 13.850 11828 Z= 0.340 Chirality : 0.044 0.492 1386 Planarity : 0.005 0.099 1478 Dihedral : 16.866 152.470 3013 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 0.23 % Allowed : 19.06 % Favored : 80.71 % 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 (0.26), residues: 1095 helix: 1.18 (0.33), residues: 258 sheet: 0.95 (0.28), residues: 331 loop : -0.60 (0.29), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG Q 45 TYR 0.012 0.001 TYR R 354 PHE 0.022 0.001 PHE R 312 TRP 0.007 0.001 TRP R 316 HIS 0.002 0.001 HIS D 58 Details of bonding type rmsd/Z covalent geometry : bond 0.00578 / 0.29 ( 8649) covalent geometry : angle 0.71485 / 0.34 (11818) SS BOND : bond 0.00218 / 0.12 ( 5) SS BOND : angle 0.55995 / 0.30 ( 10) hydrogen bonds : bond 0.17494 / 12.00 ( 407) hydrogen bonds : angle 7.62063 / 5.46 ( 1206) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 107 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: B 187 ARG cc_start: 0.7851 (tpt90) cc_final: 0.7594 (tpt90) REVERT: R 266 MET cc_start: 0.6418 (ppp) cc_final: 0.6093 (ptt) outliers start: 2 outliers final: 2 residues processed: 108 average time/residue: 0.5057 time to fit residues: 58.5227 Evaluate side-chains 98 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 96 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 161 TYR Chi-restraints excluded: chain R residue 167 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.6980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 106 optimal weight: 4.9990 overall best weight: 0.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 247 GLN D 26 GLN D 135 GLN R 158 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4251 r_free = 0.4251 target = 0.205905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 117)---------------| | r_work = 0.3538 r_free = 0.3538 target = 0.140679 restraints weight = 8497.481| |-----------------------------------------------------------------------------| r_work (start): 0.3492 rms_B_bonded: 2.00 r_work: 0.3265 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.3126 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.0984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8654 Z= 0.155 Angle : 0.597 9.509 11828 Z= 0.306 Chirality : 0.044 0.205 1386 Planarity : 0.005 0.063 1478 Dihedral : 13.233 147.706 1260 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 3.08 % Allowed : 16.32 % Favored : 80.59 % 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: 0.47 (0.26), residues: 1095 helix: 1.17 (0.32), residues: 263 sheet: 0.96 (0.28), residues: 336 loop : -0.59 (0.29), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 166 TYR 0.016 0.001 TYR R 339 PHE 0.024 0.002 PHE D 125 TRP 0.008 0.001 TRP D 133 HIS 0.003 0.001 HIS R 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.16 ( 8649) covalent geometry : angle 0.59618 / 0.31 (11818) SS BOND : bond 0.00470 / 0.26 ( 5) SS BOND : angle 1.10457 / 0.61 ( 10) hydrogen bonds : bond 0.03822 / 2.52 ( 407) hydrogen bonds : angle 5.36947 / 3.84 ( 1206) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 103 time to evaluate : 0.221 Fit side-chains REVERT: B 211 GLU cc_start: 0.8634 (tt0) cc_final: 0.8431 (tt0) REVERT: D 135 GLN cc_start: 0.8450 (OUTLIER) cc_final: 0.7786 (mp-120) REVERT: Q 45 ARG cc_start: 0.7960 (tpp-160) cc_final: 0.7728 (tpm170) REVERT: R 286 PHE cc_start: 0.7294 (OUTLIER) cc_final: 0.6584 (t80) outliers start: 27 outliers final: 11 residues processed: 118 average time/residue: 0.4209 time to fit residues: 53.3129 Evaluate side-chains 110 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 97 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain D residue 34 LEU Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain L residue 11 TYR Chi-restraints excluded: chain Q residue 127 ILE Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 286 PHE Chi-restraints excluded: chain R residue 359 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 106 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 66 optimal weight: 0.5980 chunk 102 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 70 optimal weight: 0.0980 chunk 27 optimal weight: 0.2980 chunk 105 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 ASN B 84 GLN D 26 GLN D 135 GLN Q 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4257 r_free = 0.4257 target = 0.206394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 140)---------------| | r_work = 0.3534 r_free = 0.3534 target = 0.140548 restraints weight = 8423.009| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 2.00 r_work: 0.3251 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8654 Z= 0.142 Angle : 0.575 9.673 11828 Z= 0.295 Chirality : 0.044 0.184 1386 Planarity : 0.005 0.055 1478 Dihedral : 13.192 147.891 1256 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.97 % Allowed : 17.01 % Favored : 80.02 % 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: 0.47 (0.26), residues: 1095 helix: 1.26 (0.32), residues: 266 sheet: 0.99 (0.28), residues: 331 loop : -0.66 (0.29), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG R 166 TYR 0.013 0.001 TYR R 153 PHE 0.023 0.001 PHE D 125 TRP 0.008 0.001 TRP Q 169 HIS 0.003 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 8649) covalent geometry : angle 0.57491 / 0.29 (11818) SS BOND : bond 0.00354 / 0.20 ( 5) SS BOND : angle 0.90812 / 0.51 ( 10) hydrogen bonds : bond 0.03466 / 2.29 ( 407) hydrogen bonds : angle 5.02229 / 3.57 ( 1206) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 99 time to evaluate : 0.190 Fit side-chains REVERT: D 135 GLN cc_start: 0.8433 (OUTLIER) cc_final: 0.7826 (mp-120) REVERT: R 286 PHE cc_start: 0.7291 (OUTLIER) cc_final: 0.6600 (t80) outliers start: 26 outliers final: 9 residues processed: 112 average time/residue: 0.4436 time to fit residues: 53.3529 Evaluate side-chains 103 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 229 LYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain L residue 11 TYR Chi-restraints excluded: chain Q residue 127 ILE Chi-restraints excluded: chain Q residue 161 TYR Chi-restraints excluded: chain R residue 286 PHE Chi-restraints excluded: chain R residue 359 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 70 optimal weight: 0.3980 chunk 49 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 6.9990 chunk 31 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 56 optimal weight: 20.0000 chunk 87 optimal weight: 7.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 ASN B 247 GLN D 26 GLN D 135 GLN Q 27 GLN R 126 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.204596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 140)---------------| | r_work = 0.3536 r_free = 0.3536 target = 0.139238 restraints weight = 8545.339| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 1.68 r_work: 0.3258 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3123 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8654 Z= 0.201 Angle : 0.628 10.347 11828 Z= 0.321 Chirality : 0.046 0.203 1386 Planarity : 0.005 0.050 1478 Dihedral : 13.273 148.033 1256 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.65 % Allowed : 17.58 % Favored : 78.77 % 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: 0.32 (0.26), residues: 1095 helix: 1.19 (0.32), residues: 260 sheet: 0.84 (0.28), residues: 332 loop : -0.72 (0.28), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG R 166 TYR 0.015 0.002 TYR R 153 PHE 0.032 0.002 PHE D 125 TRP 0.009 0.002 TRP D 133 HIS 0.004 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 ( 8649) covalent geometry : angle 0.62763 / 0.32 (11818) SS BOND : bond 0.00504 / 0.28 ( 5) SS BOND : angle 1.11630 / 0.62 ( 10) hydrogen bonds : bond 0.03608 / 2.37 ( 407) hydrogen bonds : angle 5.00790 / 3.56 ( 1206) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 94 time to evaluate : 0.331 Fit side-chains REVERT: R 286 PHE cc_start: 0.7339 (OUTLIER) cc_final: 0.6610 (t80) outliers start: 32 outliers final: 14 residues processed: 112 average time/residue: 0.5119 time to fit residues: 61.4720 Evaluate side-chains 105 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 195 THR Chi-restraints excluded: chain L residue 9 ARG Chi-restraints excluded: chain L residue 11 TYR Chi-restraints excluded: chain Q residue 127 ILE Chi-restraints excluded: chain Q residue 161 TYR Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 266 MET Chi-restraints excluded: chain R residue 286 PHE Chi-restraints excluded: chain R residue 359 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 11 optimal weight: 0.0770 chunk 88 optimal weight: 4.9990 chunk 38 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 79 optimal weight: 20.0000 chunk 44 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 56 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 ASN B 84 GLN D 26 GLN ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.207314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 118)---------------| | r_work = 0.3534 r_free = 0.3534 target = 0.139818 restraints weight = 8526.573| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 1.94 r_work: 0.3299 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3163 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8654 Z= 0.120 Angle : 0.553 9.497 11828 Z= 0.281 Chirality : 0.043 0.175 1386 Planarity : 0.004 0.049 1478 Dihedral : 13.157 147.893 1256 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.20 % Allowed : 18.95 % Favored : 77.85 % 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: 0.51 (0.26), residues: 1095 helix: 1.40 (0.33), residues: 260 sheet: 1.00 (0.28), residues: 331 loop : -0.68 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 45 TYR 0.013 0.001 TYR R 354 PHE 0.018 0.001 PHE D 125 TRP 0.007 0.001 TRP Q 169 HIS 0.002 0.001 HIS B 110 Details of bonding type rmsd/Z covalent geometry : bond 0.00265 / 0.12 ( 8649) covalent geometry : angle 0.55322 / 0.28 (11818) SS BOND : bond 0.00288 / 0.17 ( 5) SS BOND : angle 0.70248 / 0.39 ( 10) hydrogen bonds : bond 0.03154 / 2.09 ( 407) hydrogen bonds : angle 4.68726 / 3.32 ( 1206) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 100 time to evaluate : 0.282 Fit side-chains REVERT: D 135 GLN cc_start: 0.8443 (OUTLIER) cc_final: 0.7727 (mp10) REVERT: Q 45 ARG cc_start: 0.7985 (ttm170) cc_final: 0.7684 (tpm170) outliers start: 28 outliers final: 11 residues processed: 116 average time/residue: 0.4655 time to fit residues: 58.4134 Evaluate side-chains 107 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 95 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain L residue 9 ARG Chi-restraints excluded: chain L residue 11 TYR Chi-restraints excluded: chain Q residue 127 ILE Chi-restraints excluded: chain Q residue 153 VAL Chi-restraints excluded: chain Q residue 161 TYR Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 178 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 7 optimal weight: 0.2980 chunk 64 optimal weight: 3.9990 chunk 17 optimal weight: 0.0270 chunk 14 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 78 optimal weight: 0.0170 chunk 5 optimal weight: 0.6980 chunk 81 optimal weight: 7.9990 overall best weight: 0.3676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 ASN B 247 GLN D 26 GLN ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.208171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 122)---------------| | r_work = 0.3545 r_free = 0.3545 target = 0.140672 restraints weight = 8457.208| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.88 r_work: 0.3344 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8654 Z= 0.108 Angle : 0.538 9.207 11828 Z= 0.272 Chirality : 0.042 0.164 1386 Planarity : 0.004 0.046 1478 Dihedral : 13.074 147.882 1256 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.51 % Allowed : 19.29 % Favored : 78.20 % 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: 0.69 (0.26), residues: 1095 helix: 1.58 (0.33), residues: 256 sheet: 1.10 (0.28), residues: 332 loop : -0.56 (0.29), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG Q 45 TYR 0.015 0.001 TYR R 153 PHE 0.019 0.001 PHE B 74 TRP 0.007 0.001 TRP R 134 HIS 0.002 0.000 HIS R 320 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.11 ( 8649) covalent geometry : angle 0.53827 / 0.27 (11818) SS BOND : bond 0.00259 / 0.15 ( 5) SS BOND : angle 0.64708 / 0.37 ( 10) hydrogen bonds : bond 0.02952 / 1.97 ( 407) hydrogen bonds : angle 4.44330 / 3.16 ( 1206) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 98 time to evaluate : 0.288 Fit side-chains REVERT: B 187 ARG cc_start: 0.8192 (tpt90) cc_final: 0.7910 (tpt-90) REVERT: D 135 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7671 (mp10) REVERT: Q 45 ARG cc_start: 0.7927 (ttm170) cc_final: 0.7684 (tpm170) outliers start: 22 outliers final: 10 residues processed: 109 average time/residue: 0.5335 time to fit residues: 62.3190 Evaluate side-chains 104 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain L residue 9 ARG Chi-restraints excluded: chain L residue 11 TYR Chi-restraints excluded: chain Q residue 32 LEU Chi-restraints excluded: chain Q residue 153 VAL Chi-restraints excluded: chain Q residue 161 TYR Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 178 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 60 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 73 optimal weight: 30.0000 chunk 101 optimal weight: 5.9990 chunk 29 optimal weight: 0.0980 chunk 26 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 ASN B 84 GLN B 247 GLN D 26 GLN ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.206327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 103)---------------| | r_work = 0.3533 r_free = 0.3533 target = 0.139191 restraints weight = 8560.858| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 1.68 r_work: 0.3304 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8654 Z= 0.131 Angle : 0.564 9.657 11828 Z= 0.285 Chirality : 0.043 0.170 1386 Planarity : 0.004 0.044 1478 Dihedral : 13.096 147.948 1256 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.17 % Allowed : 20.09 % Favored : 77.74 % 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: 0.64 (0.26), residues: 1095 helix: 1.48 (0.33), residues: 260 sheet: 1.13 (0.28), residues: 331 loop : -0.61 (0.28), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 75 TYR 0.017 0.001 TYR R 153 PHE 0.020 0.001 PHE D 125 TRP 0.007 0.001 TRP D 126 HIS 0.003 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 ( 8649) covalent geometry : angle 0.56328 / 0.28 (11818) SS BOND : bond 0.00282 / 0.17 ( 5) SS BOND : angle 0.82954 / 0.46 ( 10) hydrogen bonds : bond 0.03065 / 2.04 ( 407) hydrogen bonds : angle 4.46554 / 3.18 ( 1206) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 92 time to evaluate : 0.324 Fit side-chains REVERT: D 135 GLN cc_start: 0.8449 (OUTLIER) cc_final: 0.7752 (mp10) REVERT: R 288 MET cc_start: 0.8250 (ptp) cc_final: 0.8014 (ptt) outliers start: 19 outliers final: 12 residues processed: 105 average time/residue: 0.5068 time to fit residues: 57.2189 Evaluate side-chains 106 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain L residue 9 ARG Chi-restraints excluded: chain L residue 11 TYR Chi-restraints excluded: chain Q residue 127 ILE Chi-restraints excluded: chain Q residue 153 VAL Chi-restraints excluded: chain Q residue 161 TYR Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 178 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 39 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 85 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 95 optimal weight: 9.9990 chunk 38 optimal weight: 0.9990 chunk 59 optimal weight: 0.2980 chunk 14 optimal weight: 0.4980 chunk 41 optimal weight: 2.9990 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 ASN D 26 GLN ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.207327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 110)---------------| | r_work = 0.3551 r_free = 0.3551 target = 0.141224 restraints weight = 8467.052| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 1.79 r_work: 0.3294 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8654 Z= 0.126 Angle : 0.566 9.717 11828 Z= 0.285 Chirality : 0.043 0.171 1386 Planarity : 0.004 0.043 1478 Dihedral : 13.083 147.975 1256 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.51 % Allowed : 19.86 % Favored : 77.63 % 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: 0.69 (0.26), residues: 1095 helix: 1.55 (0.33), residues: 260 sheet: 1.11 (0.28), residues: 334 loop : -0.58 (0.29), residues: 501 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG Q 45 TYR 0.016 0.001 TYR R 339 PHE 0.019 0.001 PHE D 125 TRP 0.007 0.001 TRP D 133 HIS 0.002 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 8649) covalent geometry : angle 0.56525 / 0.28 (11818) SS BOND : bond 0.00306 / 0.17 ( 5) SS BOND : angle 0.80773 / 0.45 ( 10) hydrogen bonds : bond 0.03033 / 2.02 ( 407) hydrogen bonds : angle 4.42262 / 3.15 ( 1206) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 94 time to evaluate : 0.353 Fit side-chains REVERT: D 135 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.7788 (mp10) REVERT: Q 45 ARG cc_start: 0.8003 (tpp-160) cc_final: 0.7688 (tpm170) REVERT: R 325 MET cc_start: 0.7047 (OUTLIER) cc_final: 0.6724 (pp-130) outliers start: 22 outliers final: 13 residues processed: 108 average time/residue: 0.4915 time to fit residues: 57.1468 Evaluate side-chains 110 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 95 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain L residue 9 ARG Chi-restraints excluded: chain L residue 11 TYR Chi-restraints excluded: chain Q residue 127 ILE Chi-restraints excluded: chain Q residue 153 VAL Chi-restraints excluded: chain Q residue 161 TYR Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain R residue 359 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 84 optimal weight: 0.6980 chunk 3 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 80 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 50 optimal weight: 9.9990 chunk 97 optimal weight: 0.9990 chunk 94 optimal weight: 6.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 ASN B 247 GLN D 26 GLN ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.206469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.156006 restraints weight = 8460.663| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.30 r_work: 0.3366 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8654 Z= 0.141 Angle : 0.581 9.950 11828 Z= 0.294 Chirality : 0.043 0.176 1386 Planarity : 0.004 0.044 1478 Dihedral : 13.110 147.989 1256 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.74 % Allowed : 19.18 % Favored : 78.08 % 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: 0.67 (0.26), residues: 1095 helix: 1.50 (0.33), residues: 260 sheet: 1.09 (0.28), residues: 335 loop : -0.56 (0.29), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 75 TYR 0.017 0.001 TYR R 339 PHE 0.023 0.001 PHE D 125 TRP 0.007 0.001 TRP D 133 HIS 0.003 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 ( 8649) covalent geometry : angle 0.58036 / 0.29 (11818) SS BOND : bond 0.00328 / 0.19 ( 5) SS BOND : angle 0.88226 / 0.49 ( 10) hydrogen bonds : bond 0.03131 / 2.08 ( 407) hydrogen bonds : angle 4.47425 / 3.18 ( 1206) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 96 time to evaluate : 0.354 Fit side-chains REVERT: D 135 GLN cc_start: 0.8431 (OUTLIER) cc_final: 0.7711 (mp10) REVERT: L 9 ARG cc_start: 0.4700 (OUTLIER) cc_final: 0.4036 (mmp-170) REVERT: Q 45 ARG cc_start: 0.7976 (tpp-160) cc_final: 0.7759 (tpm170) REVERT: Q 91 ASP cc_start: 0.8130 (p0) cc_final: 0.7877 (p0) REVERT: R 288 MET cc_start: 0.8231 (ptp) cc_final: 0.8008 (ptt) REVERT: R 325 MET cc_start: 0.7029 (OUTLIER) cc_final: 0.6828 (pp-130) outliers start: 24 outliers final: 11 residues processed: 111 average time/residue: 0.4699 time to fit residues: 56.1518 Evaluate side-chains 109 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 95 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain L residue 9 ARG Chi-restraints excluded: chain L residue 11 TYR Chi-restraints excluded: chain Q residue 127 ILE Chi-restraints excluded: chain Q residue 153 VAL Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 325 MET Chi-restraints excluded: chain R residue 359 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 51 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 96 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 68 optimal weight: 0.9980 chunk 18 optimal weight: 0.1980 chunk 1 optimal weight: 1.9990 chunk 86 optimal weight: 4.9990 chunk 95 optimal weight: 0.1980 chunk 46 optimal weight: 0.4980 overall best weight: 0.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 ASN B 247 GLN D 26 GLN ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4266 r_free = 0.4266 target = 0.207539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 121)---------------| | r_work = 0.3563 r_free = 0.3563 target = 0.141899 restraints weight = 8416.409| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.76 r_work: 0.3301 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.3164 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8654 Z= 0.122 Angle : 0.565 10.266 11828 Z= 0.284 Chirality : 0.043 0.171 1386 Planarity : 0.004 0.044 1478 Dihedral : 13.075 148.036 1256 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.05 % Allowed : 19.98 % Favored : 77.97 % 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: 0.76 (0.26), residues: 1095 helix: 1.60 (0.33), residues: 256 sheet: 1.13 (0.28), residues: 334 loop : -0.49 (0.29), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 75 TYR 0.016 0.001 TYR R 354 PHE 0.019 0.001 PHE B 74 TRP 0.007 0.001 TRP D 133 HIS 0.002 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 8649) covalent geometry : angle 0.56449 / 0.28 (11818) SS BOND : bond 0.00279 / 0.16 ( 5) SS BOND : angle 0.77812 / 0.43 ( 10) hydrogen bonds : bond 0.03007 / 2.00 ( 407) hydrogen bonds : angle 4.40161 / 3.13 ( 1206) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2190 Ramachandran restraints generated. 1095 Oldfield, 0 Emsley, 1095 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 97 time to evaluate : 0.225 Fit side-chains REVERT: D 135 GLN cc_start: 0.8454 (OUTLIER) cc_final: 0.7789 (mp10) REVERT: L 9 ARG cc_start: 0.4502 (OUTLIER) cc_final: 0.3865 (mmp-170) REVERT: Q 45 ARG cc_start: 0.7957 (tpp-160) cc_final: 0.7612 (tpm170) REVERT: Q 91 ASP cc_start: 0.8135 (p0) cc_final: 0.7861 (p0) REVERT: R 288 MET cc_start: 0.8244 (ptp) cc_final: 0.7989 (ptt) outliers start: 18 outliers final: 12 residues processed: 107 average time/residue: 0.4068 time to fit residues: 46.9736 Evaluate side-chains 110 residues out of total 970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 23 LYS Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 364 VAL Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 51 ASN Chi-restraints excluded: chain D residue 135 GLN Chi-restraints excluded: chain L residue 9 ARG Chi-restraints excluded: chain L residue 11 TYR Chi-restraints excluded: chain Q residue 32 LEU Chi-restraints excluded: chain Q residue 127 ILE Chi-restraints excluded: chain Q residue 153 VAL Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 178 THR Chi-restraints excluded: chain R residue 359 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 106 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 31 optimal weight: 0.3980 chunk 0 optimal weight: 3.9990 chunk 27 optimal weight: 0.0670 chunk 108 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 8 optimal weight: 3.9990 overall best weight: 1.0120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 82 ASN D 26 GLN ** D 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.205756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 113)---------------| | r_work = 0.3544 r_free = 0.3544 target = 0.140403 restraints weight = 8418.208| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 1.80 r_work: 0.3271 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8560 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 8654 Z= 0.162 Angle : 0.614 10.290 11828 Z= 0.309 Chirality : 0.044 0.182 1386 Planarity : 0.005 0.043 1478 Dihedral : 13.137 148.106 1256 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.05 % Allowed : 20.32 % Favored : 77.63 % 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: 0.68 (0.26), residues: 1095 helix: 1.48 (0.33), residues: 257 sheet: 1.07 (0.28), residues: 334 loop : -0.50 (0.29), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 75 TYR 0.016 0.001 TYR R 354 PHE 0.026 0.002 PHE D 125 TRP 0.007 0.001 TRP D 133 HIS 0.003 0.001 HIS B 209 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 8649) covalent geometry : angle 0.61349 / 0.31 (11818) SS BOND : bond 0.00369 / 0.21 ( 5) SS BOND : angle 0.97978 / 0.54 ( 10) hydrogen bonds : bond 0.03258 / 2.16 ( 407) hydrogen bonds : angle 4.51824 / 3.21 ( 1206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3865.45 seconds wall clock time: 66 minutes 28.64 seconds (3988.64 seconds total)