Starting phenix.real_space_refine on Wed Feb 12 12:44:44 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7szi_25567/02_2025/7szi_25567.cif Found real_map, /net/cci-nas-00/data/ceres_data/7szi_25567/02_2025/7szi_25567.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7szi_25567/02_2025/7szi_25567.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7szi_25567/02_2025/7szi_25567.map" model { file = "/net/cci-nas-00/data/ceres_data/7szi_25567/02_2025/7szi_25567.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7szi_25567/02_2025/7szi_25567.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 8 5.16 5 C 5058 2.51 5 N 1361 2.21 5 O 1662 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8089 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2669 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 338} Chain breaks: 1 Chain: "B" Number of atoms: 2695 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2695 Classifications: {'peptide': 345} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 341} Chain: "C" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2665 Classifications: {'peptide': 342} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 338} Chain breaks: 1 Chain: "D" Number of atoms: 60 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 60 Classifications: {'peptide': 9} Link IDs: {'TRANS': 8} Time building chain proxies: 5.47, per 1000 atoms: 0.68 Number of scatterers: 8089 At special positions: 0 Unit cell: (74.52, 95.04, 96.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 8 16.00 O 1662 8.00 N 1361 7.00 C 5058 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS D 0 " - pdb=" SG CYS D 8 " distance=2.94 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: 1.73 Conformation dependent library (CDL) restraints added in 1.1 seconds 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1810 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 3 sheets defined 7.3% alpha, 48.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 98 through 103 Processing helix chain 'A' and resid 104 through 106 No H-bonds generated for 'chain 'A' and resid 104 through 106' Processing helix chain 'A' and resid 202 through 206 Processing helix chain 'A' and resid 322 through 329 Processing helix chain 'B' and resid 98 through 103 Processing helix chain 'B' and resid 104 through 106 No H-bonds generated for 'chain 'B' and resid 104 through 106' Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'B' and resid 202 through 206 Processing helix chain 'B' and resid 246 through 248 No H-bonds generated for 'chain 'B' and resid 246 through 248' Processing helix chain 'B' and resid 322 through 329 Processing helix chain 'C' and resid 98 through 103 Processing helix chain 'C' and resid 168 through 172 removed outlier: 3.583A pdb=" N GLN C 172 " --> pdb=" O TRP C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 206 Processing helix chain 'C' and resid 322 through 329 Processing sheet with id=AA1, first strand: chain 'A' and resid 1 through 6 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 1 through 6 current: chain 'A' and resid 51 through 61 removed outlier: 6.331A pdb=" N ASN A 59 " --> pdb=" O THR A 74 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N THR A 74 " --> pdb=" O ASN A 59 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N GLN A 61 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N ALA A 72 " --> pdb=" O GLN A 61 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N SER A 88 " --> pdb=" O TYR A 132 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N TYR A 132 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ASP A 90 " --> pdb=" O ALA A 130 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N ALA A 130 " --> pdb=" O ASP A 90 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N GLY A 92 " --> pdb=" O GLY A 128 " (cutoff:3.500A) removed outlier: 11.343A pdb=" N ASN A 215 " --> pdb=" O ALA A 242 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N ALA A 242 " --> pdb=" O ASN A 215 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N ASN A 252 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR A 243 " --> pdb=" O PHE A 250 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE A 250 " --> pdb=" O THR A 243 " (cutoff:3.500A) removed outlier: 9.358A pdb=" N ALA A 251 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 7.620A pdb=" N LEU A 283 " --> pdb=" O ALA A 251 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ARG A 270 " --> pdb=" O ALA A 300 " (cutoff:3.500A) removed outlier: 4.725A pdb=" N ALA A 300 " --> pdb=" O ARG A 270 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N SER A 272 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N VAL A 298 " --> pdb=" O SER A 272 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ALA A 274 " --> pdb=" O VAL A 296 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N VAL A 296 " --> pdb=" O ALA A 274 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU A 276 " --> pdb=" O LYS A 294 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N LYS A 294 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N SER A 278 " --> pdb=" O ILE A 292 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP A 282 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLY A 288 " --> pdb=" O ASP A 282 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 15 " --> pdb=" O PHE A 344 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 1 through 6 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 1 through 6 current: chain 'B' and resid 50 through 61 removed outlier: 6.339A pdb=" N ASN B 59 " --> pdb=" O THR B 74 " (cutoff:3.500A) removed outlier: 5.461A pdb=" N THR B 74 " --> pdb=" O ASN B 59 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N GLN B 61 " --> pdb=" O ALA B 72 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ALA B 72 " --> pdb=" O GLN B 61 " (cutoff:3.500A) removed outlier: 12.668A pdb=" N ARG B 75 " --> pdb=" O TYR B 95 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N TYR B 95 " --> pdb=" O ARG B 75 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER B 88 " --> pdb=" O TYR B 132 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR B 132 " --> pdb=" O SER B 88 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ASP B 90 " --> pdb=" O ALA B 130 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ALA B 130 " --> pdb=" O ASP B 90 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N GLY B 92 " --> pdb=" O GLY B 128 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA B 147 " --> pdb=" O SER B 180 " (cutoff:3.500A) removed outlier: 11.207A pdb=" N ASN B 215 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N ALA B 242 " --> pdb=" O ASN B 215 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N ASN B 252 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR B 243 " --> pdb=" O PHE B 250 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N PHE B 250 " --> pdb=" O THR B 243 " (cutoff:3.500A) removed outlier: 9.298A pdb=" N ALA B 251 " --> pdb=" O LEU B 283 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N LEU B 283 " --> pdb=" O ALA B 251 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N GLY B 280 " --> pdb=" O ASP B 291 " (cutoff:3.500A) removed outlier: 5.391A pdb=" N ASP B 291 " --> pdb=" O GLY B 280 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ASP B 282 " --> pdb=" O ASP B 289 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASP B 289 " --> pdb=" O ASP B 282 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 1 through 6 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 1 through 6 current: chain 'C' and resid 50 through 61 removed outlier: 6.530A pdb=" N THR C 51 " --> pdb=" O LEU C 81 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N LEU C 81 " --> pdb=" O THR C 51 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N TYR C 53 " --> pdb=" O ALA C 79 " (cutoff:3.500A) removed outlier: 4.610A pdb=" N ALA C 79 " --> pdb=" O TYR C 53 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N GLN C 55 " --> pdb=" O ALA C 77 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA C 77 " --> pdb=" O GLN C 55 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLU C 57 " --> pdb=" O ARG C 75 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N SER C 88 " --> pdb=" O TYR C 132 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N TYR C 132 " --> pdb=" O SER C 88 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ASP C 90 " --> pdb=" O ALA C 130 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N ALA C 130 " --> pdb=" O ASP C 90 " (cutoff:3.500A) removed outlier: 5.994A pdb=" N GLY C 92 " --> pdb=" O GLY C 128 " (cutoff:3.500A) removed outlier: 11.341A pdb=" N ASN C 215 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA C 242 " --> pdb=" O ASN C 215 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N TYR C 231 " --> pdb=" O TYR C 263 " (cutoff:3.500A) removed outlier: 5.357A pdb=" N TYR C 263 " --> pdb=" O TYR C 231 " (cutoff:3.500A) removed outlier: 7.579A pdb=" N ALA C 233 " --> pdb=" O ALA C 261 " (cutoff:3.500A) removed outlier: 5.332A pdb=" N ALA C 261 " --> pdb=" O ALA C 233 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N GLN C 235 " --> pdb=" O VAL C 259 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N VAL C 259 " --> pdb=" O GLN C 235 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N THR C 237 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 5.324A pdb=" N PHE C 257 " --> pdb=" O THR C 237 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N THR C 239 " --> pdb=" O GLN C 255 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N GLN C 255 " --> pdb=" O THR C 239 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ASN C 241 " --> pdb=" O LYS C 253 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N LYS C 253 " --> pdb=" O ASN C 241 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N THR C 243 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 9.410A pdb=" N ALA C 251 " --> pdb=" O LEU C 283 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N LEU C 283 " --> pdb=" O ALA C 251 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY C 280 " --> pdb=" O ASP C 291 " (cutoff:3.500A) removed outlier: 5.480A pdb=" N ASP C 291 " --> pdb=" O GLY C 280 " (cutoff:3.500A) removed outlier: 7.342A pdb=" N ASP C 282 " --> pdb=" O ASP C 289 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ASP C 289 " --> pdb=" O ASP C 282 " (cutoff:3.500A) 366 hydrogen bonds defined for protein. 1020 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.37 Time building geometry restraints manager: 2.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2729 1.34 - 1.46: 2197 1.46 - 1.58: 3323 1.58 - 1.69: 0 1.69 - 1.81: 14 Bond restraints: 8263 Sorted by residual: bond pdb=" CA GLY A 117 " pdb=" C GLY A 117 " ideal model delta sigma weight residual 1.522 1.513 0.009 1.06e-02 8.90e+03 7.19e-01 bond pdb=" C TYR A 116 " pdb=" N GLY A 117 " ideal model delta sigma weight residual 1.336 1.328 0.008 1.01e-02 9.80e+03 6.36e-01 bond pdb=" CA GLY B 117 " pdb=" C GLY B 117 " ideal model delta sigma weight residual 1.522 1.513 0.009 1.29e-02 6.01e+03 4.90e-01 bond pdb=" CA PHE A 83 " pdb=" CB PHE A 83 " ideal model delta sigma weight residual 1.524 1.533 -0.009 1.30e-02 5.92e+03 4.31e-01 bond pdb=" N GLY A 221 " pdb=" CA GLY A 221 " ideal model delta sigma weight residual 1.454 1.448 0.006 9.90e-03 1.02e+04 3.81e-01 ... (remaining 8258 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.88: 10571 0.88 - 1.76: 520 1.76 - 2.64: 66 2.64 - 3.53: 19 3.53 - 4.41: 9 Bond angle restraints: 11185 Sorted by residual: angle pdb=" C TYR A 116 " pdb=" N GLY A 117 " pdb=" CA GLY A 117 " ideal model delta sigma weight residual 122.47 120.21 2.26 8.90e-01 1.26e+00 6.47e+00 angle pdb=" C GLY D 3 " pdb=" N GLN D 4 " pdb=" CA GLN D 4 " ideal model delta sigma weight residual 121.54 125.95 -4.41 1.91e+00 2.74e-01 5.32e+00 angle pdb=" CA GLY A 221 " pdb=" C GLY A 221 " pdb=" N GLY A 222 " ideal model delta sigma weight residual 115.49 117.81 -2.32 1.03e+00 9.43e-01 5.09e+00 angle pdb=" CA TYR B 58 " pdb=" CB TYR B 58 " pdb=" CG TYR B 58 " ideal model delta sigma weight residual 113.90 117.79 -3.89 1.80e+00 3.09e-01 4.67e+00 angle pdb=" C TYR B 116 " pdb=" N GLY B 117 " pdb=" CA GLY B 117 " ideal model delta sigma weight residual 122.69 120.38 2.31 1.08e+00 8.57e-01 4.58e+00 ... (remaining 11180 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.35: 4222 15.35 - 30.70: 352 30.70 - 46.06: 75 46.06 - 61.41: 37 61.41 - 76.76: 5 Dihedral angle restraints: 4691 sinusoidal: 1765 harmonic: 2926 Sorted by residual: dihedral pdb=" CB CYS D 0 " pdb=" SG CYS D 0 " pdb=" SG CYS D 8 " pdb=" CB CYS D 8 " ideal model delta sinusoidal sigma weight residual 93.00 152.84 -59.84 1 1.00e+01 1.00e-02 4.78e+01 dihedral pdb=" CB LYS C 153 " pdb=" CG LYS C 153 " pdb=" CD LYS C 153 " pdb=" CE LYS C 153 " ideal model delta sinusoidal sigma weight residual 60.00 111.18 -51.18 3 1.50e+01 4.44e-03 8.98e+00 dihedral pdb=" CG LYS A 171 " pdb=" CD LYS A 171 " pdb=" CE LYS A 171 " pdb=" NZ LYS A 171 " ideal model delta sinusoidal sigma weight residual -60.00 -110.97 50.97 3 1.50e+01 4.44e-03 8.96e+00 ... (remaining 4688 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 626 0.026 - 0.052: 343 0.052 - 0.078: 98 0.078 - 0.105: 40 0.105 - 0.131: 26 Chirality restraints: 1133 Sorted by residual: chirality pdb=" CA VAL B 273 " pdb=" N VAL B 273 " pdb=" C VAL B 273 " pdb=" CB VAL B 273 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.27e-01 chirality pdb=" CA VAL A 273 " pdb=" N VAL A 273 " pdb=" C VAL A 273 " pdb=" CB VAL A 273 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.08e-01 chirality pdb=" CA VAL C 273 " pdb=" N VAL C 273 " pdb=" C VAL C 273 " pdb=" CB VAL C 273 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 1130 not shown) Planarity restraints: 1505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 58 " -0.018 2.00e-02 2.50e+03 1.11e-02 2.47e+00 pdb=" CG TYR B 58 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR B 58 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR B 58 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 58 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 58 " -0.002 2.00e-02 2.50e+03 pdb=" CZ TYR B 58 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 58 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 58 " 0.014 2.00e-02 2.50e+03 8.94e-03 1.60e+00 pdb=" CG TYR C 58 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TYR C 58 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 58 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 58 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 58 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR C 58 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 58 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL C 207 " 0.017 5.00e-02 4.00e+02 2.61e-02 1.09e+00 pdb=" N PRO C 208 " -0.045 5.00e-02 4.00e+02 pdb=" CA PRO C 208 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO C 208 " 0.015 5.00e-02 4.00e+02 ... (remaining 1502 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2113 2.79 - 3.32: 6730 3.32 - 3.85: 13116 3.85 - 4.37: 16407 4.37 - 4.90: 29830 Nonbonded interactions: 68196 Sorted by model distance: nonbonded pdb=" OH TYR B 22 " pdb=" OE2 GLU B 110 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR A 22 " pdb=" OE2 GLU A 110 " model vdw 2.303 3.040 nonbonded pdb=" NH1 ARG B 93 " pdb=" OD1 ASN B 127 " model vdw 2.309 3.120 nonbonded pdb=" OG1 THR C 105 " pdb=" OE2 GLU C 258 " model vdw 2.317 3.040 nonbonded pdb=" ND2 ASN A 252 " pdb=" OE2 GLU A 284 " model vdw 2.328 3.120 ... (remaining 68191 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 0 through 184 or resid 189 through 344)) selection = (chain 'B' and (resid 0 through 184 or resid 189 through 344)) selection = (chain 'C' and (resid 0 through 184 or resid 189 through 344)) } 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: 1.090 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 21.550 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 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 : 0.002 0.027 8263 Z= 0.161 Angle : 0.441 4.406 11185 Z= 0.258 Chirality : 0.038 0.131 1133 Planarity : 0.002 0.026 1505 Dihedral : 13.000 76.760 2878 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.51 % Favored : 96.39 % Rotamer: Outliers : 0.12 % Allowed : 0.00 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.26), residues: 1026 helix: -0.12 (0.84), residues: 37 sheet: 1.39 (0.22), residues: 510 loop : -1.07 (0.28), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 186 HIS 0.002 0.001 HIS B 197 PHE 0.013 0.001 PHE A 137 TYR 0.026 0.001 TYR B 58 ARG 0.002 0.000 ARG C 125 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 58 time to evaluate : 0.856 Fit side-chains REVERT: A 160 GLU cc_start: 0.8425 (tp30) cc_final: 0.8151 (tm-30) REVERT: A 235 GLN cc_start: 0.8972 (OUTLIER) cc_final: 0.8566 (pp30) outliers start: 1 outliers final: 0 residues processed: 58 average time/residue: 1.7084 time to fit residues: 104.1966 Evaluate side-chains 52 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 51 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 235 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 42 optimal weight: 0.0030 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 59 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 overall best weight: 1.0992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 151 GLN B 151 GLN B 154 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.071917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2643 r_free = 0.2643 target = 0.059891 restraints weight = 15176.168| |-----------------------------------------------------------------------------| r_work (start): 0.2639 rms_B_bonded: 2.49 r_work: 0.2537 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2420 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.0975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8263 Z= 0.225 Angle : 0.511 6.562 11185 Z= 0.290 Chirality : 0.041 0.173 1133 Planarity : 0.003 0.029 1505 Dihedral : 4.392 45.095 1158 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.61 % Favored : 96.30 % Rotamer: Outliers : 0.60 % Allowed : 4.46 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.26), residues: 1026 helix: 0.72 (0.93), residues: 37 sheet: 1.30 (0.22), residues: 532 loop : -0.95 (0.29), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 56 HIS 0.003 0.001 HIS B 197 PHE 0.015 0.001 PHE A 137 TYR 0.023 0.001 TYR B 58 ARG 0.003 0.000 ARG C 285 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.830 Fit side-chains REVERT: C 285 ARG cc_start: 0.8973 (mmt-90) cc_final: 0.8497 (mmt-90) outliers start: 5 outliers final: 1 residues processed: 55 average time/residue: 1.7103 time to fit residues: 99.1201 Evaluate side-chains 50 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 49 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 5 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 62 optimal weight: 4.9990 chunk 58 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 100 optimal weight: 0.9980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.070130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2607 r_free = 0.2607 target = 0.058056 restraints weight = 15556.736| |-----------------------------------------------------------------------------| r_work (start): 0.2610 rms_B_bonded: 2.51 r_work: 0.2509 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2391 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 8263 Z= 0.366 Angle : 0.538 5.481 11185 Z= 0.303 Chirality : 0.042 0.176 1133 Planarity : 0.003 0.045 1505 Dihedral : 4.422 29.723 1155 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.19 % Favored : 95.71 % Rotamer: Outliers : 0.96 % Allowed : 5.66 % Favored : 93.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.26), residues: 1026 helix: 0.45 (0.86), residues: 43 sheet: 1.16 (0.21), residues: 544 loop : -1.02 (0.30), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 56 HIS 0.006 0.002 HIS B 197 PHE 0.014 0.002 PHE C 344 TYR 0.026 0.002 TYR B 58 ARG 0.004 0.000 ARG C 167 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.873 Fit side-chains REVERT: C 285 ARG cc_start: 0.9050 (mmt-90) cc_final: 0.8528 (mmt-90) REVERT: C 344 PHE cc_start: 0.8830 (p90) cc_final: 0.8550 (p90) outliers start: 8 outliers final: 6 residues processed: 58 average time/residue: 1.6373 time to fit residues: 100.2986 Evaluate side-chains 56 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 258 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 92 optimal weight: 0.0870 chunk 21 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.070138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.058125 restraints weight = 15396.624| |-----------------------------------------------------------------------------| r_work (start): 0.2607 rms_B_bonded: 2.47 r_work: 0.2504 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2386 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8263 Z= 0.342 Angle : 0.527 5.070 11185 Z= 0.298 Chirality : 0.042 0.175 1133 Planarity : 0.003 0.048 1505 Dihedral : 4.422 31.219 1155 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.29 % Favored : 95.61 % Rotamer: Outliers : 1.33 % Allowed : 8.19 % Favored : 90.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.26), residues: 1026 helix: 0.72 (0.95), residues: 37 sheet: 1.03 (0.21), residues: 551 loop : -1.04 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 56 HIS 0.006 0.002 HIS B 197 PHE 0.019 0.001 PHE A 344 TYR 0.023 0.001 TYR B 58 ARG 0.002 0.000 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.917 Fit side-chains outliers start: 11 outliers final: 5 residues processed: 56 average time/residue: 1.6269 time to fit residues: 96.2661 Evaluate side-chains 54 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain C residue 49 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 15 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 40 optimal weight: 0.3980 chunk 83 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.070585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2584 r_free = 0.2584 target = 0.058425 restraints weight = 14342.545| |-----------------------------------------------------------------------------| r_work (start): 0.2586 rms_B_bonded: 2.38 r_work: 0.2475 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2347 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8263 Z= 0.423 Angle : 0.554 5.162 11185 Z= 0.311 Chirality : 0.043 0.176 1133 Planarity : 0.004 0.054 1505 Dihedral : 4.557 33.275 1155 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 2.13 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.48 % Favored : 95.42 % Rotamer: Outliers : 1.08 % Allowed : 9.52 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1026 helix: 0.66 (0.94), residues: 37 sheet: 0.92 (0.21), residues: 552 loop : -1.16 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 56 HIS 0.008 0.002 HIS A 197 PHE 0.021 0.002 PHE A 344 TYR 0.023 0.002 TYR B 58 ARG 0.002 0.000 ARG A 167 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.974 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 56 average time/residue: 1.6493 time to fit residues: 97.4134 Evaluate side-chains 57 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain C residue 49 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 26 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 55 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.072230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.060067 restraints weight = 14219.622| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 2.40 r_work: 0.2515 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2387 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8263 Z= 0.216 Angle : 0.488 4.846 11185 Z= 0.277 Chirality : 0.040 0.173 1133 Planarity : 0.003 0.049 1505 Dihedral : 4.275 29.358 1155 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.90 % Favored : 96.00 % Rotamer: Outliers : 0.84 % Allowed : 10.00 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.26), residues: 1026 helix: 0.43 (0.88), residues: 43 sheet: 0.94 (0.21), residues: 551 loop : -1.16 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 73 HIS 0.003 0.001 HIS B 197 PHE 0.019 0.001 PHE A 344 TYR 0.016 0.001 TYR B 58 ARG 0.002 0.000 ARG C 285 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.882 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 58 average time/residue: 1.6566 time to fit residues: 101.2477 Evaluate side-chains 54 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 266 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 85 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 chunk 30 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 82 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.072251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2655 r_free = 0.2655 target = 0.060260 restraints weight = 15284.192| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 2.45 r_work: 0.2549 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2430 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8263 Z= 0.176 Angle : 0.466 4.513 11185 Z= 0.265 Chirality : 0.040 0.173 1133 Planarity : 0.003 0.047 1505 Dihedral : 4.071 24.130 1155 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.09 % Favored : 95.81 % Rotamer: Outliers : 0.84 % Allowed : 10.84 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.26), residues: 1026 helix: 0.28 (0.86), residues: 43 sheet: 0.97 (0.21), residues: 551 loop : -1.11 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 56 HIS 0.003 0.001 HIS B 197 PHE 0.019 0.001 PHE A 344 TYR 0.014 0.001 TYR B 58 ARG 0.002 0.000 ARG C 285 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 53 time to evaluate : 0.893 Fit side-chains REVERT: A 57 GLU cc_start: 0.9196 (tt0) cc_final: 0.8978 (tt0) REVERT: B 179 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8928 (t) REVERT: C 285 ARG cc_start: 0.8905 (mmt-90) cc_final: 0.8449 (mmt-90) outliers start: 7 outliers final: 3 residues processed: 58 average time/residue: 1.6220 time to fit residues: 99.2865 Evaluate side-chains 55 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 266 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 3 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 93 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 39 optimal weight: 4.9990 chunk 67 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 30 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.072716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2633 r_free = 0.2633 target = 0.060436 restraints weight = 14453.150| |-----------------------------------------------------------------------------| r_work (start): 0.2631 rms_B_bonded: 2.43 r_work: 0.2518 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2390 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 8263 Z= 0.227 Angle : 0.483 4.653 11185 Z= 0.274 Chirality : 0.040 0.174 1133 Planarity : 0.003 0.047 1505 Dihedral : 4.148 23.962 1155 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.00 % Favored : 95.91 % Rotamer: Outliers : 0.72 % Allowed : 10.96 % Favored : 88.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.26), residues: 1026 helix: 0.28 (0.87), residues: 43 sheet: 0.96 (0.21), residues: 560 loop : -1.10 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 56 HIS 0.004 0.001 HIS B 197 PHE 0.019 0.001 PHE A 344 TYR 0.016 0.001 TYR B 58 ARG 0.002 0.000 ARG C 285 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.935 Fit side-chains REVERT: A 57 GLU cc_start: 0.9197 (tt0) cc_final: 0.8935 (tt0) outliers start: 6 outliers final: 6 residues processed: 54 average time/residue: 1.6404 time to fit residues: 93.5058 Evaluate side-chains 56 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain C residue 49 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 77 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 62 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 5 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.071914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2602 r_free = 0.2602 target = 0.059113 restraints weight = 14568.420| |-----------------------------------------------------------------------------| r_work (start): 0.2602 rms_B_bonded: 2.51 r_work: 0.2486 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2357 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8263 Z= 0.339 Angle : 0.525 4.876 11185 Z= 0.295 Chirality : 0.042 0.171 1133 Planarity : 0.003 0.054 1505 Dihedral : 4.357 26.941 1155 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.58 % Favored : 95.32 % Rotamer: Outliers : 0.72 % Allowed : 11.20 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1026 helix: 0.30 (0.87), residues: 43 sheet: 0.91 (0.21), residues: 557 loop : -1.16 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 56 HIS 0.006 0.002 HIS B 197 PHE 0.021 0.001 PHE A 344 TYR 0.020 0.001 TYR B 58 ARG 0.002 0.000 ARG C 285 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.840 Fit side-chains REVERT: C 285 ARG cc_start: 0.8949 (mmt-90) cc_final: 0.8690 (mmt-90) outliers start: 6 outliers final: 6 residues processed: 53 average time/residue: 1.7811 time to fit residues: 99.4027 Evaluate side-chains 55 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain C residue 49 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 14 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 96 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 overall best weight: 1.3582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.072965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2622 r_free = 0.2622 target = 0.060288 restraints weight = 14211.107| |-----------------------------------------------------------------------------| r_work (start): 0.2617 rms_B_bonded: 2.48 r_work: 0.2505 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2377 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8263 Z= 0.264 Angle : 0.502 4.640 11185 Z= 0.284 Chirality : 0.041 0.174 1133 Planarity : 0.003 0.051 1505 Dihedral : 4.256 25.671 1155 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.00 % Favored : 95.91 % Rotamer: Outliers : 0.84 % Allowed : 11.33 % Favored : 87.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.26), residues: 1026 helix: 0.26 (0.87), residues: 43 sheet: 0.90 (0.21), residues: 553 loop : -1.16 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 56 HIS 0.005 0.001 HIS B 197 PHE 0.021 0.001 PHE A 344 TYR 0.017 0.001 TYR B 58 ARG 0.002 0.000 ARG C 285 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2052 Ramachandran restraints generated. 1026 Oldfield, 0 Emsley, 1026 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.919 Fit side-chains REVERT: C 285 ARG cc_start: 0.8955 (mmt-90) cc_final: 0.8696 (mmt-90) outliers start: 7 outliers final: 7 residues processed: 53 average time/residue: 1.6757 time to fit residues: 93.8204 Evaluate side-chains 55 residues out of total 830 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 148 LEU Chi-restraints excluded: chain B residue 179 THR Chi-restraints excluded: chain B residue 180 SER Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 266 ASP Chi-restraints excluded: chain C residue 49 GLN Chi-restraints excluded: chain C residue 258 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 5.9990 chunk 76 optimal weight: 0.0870 chunk 48 optimal weight: 3.9990 chunk 92 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.073033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.060316 restraints weight = 14427.974| |-----------------------------------------------------------------------------| r_work (start): 0.2619 rms_B_bonded: 2.49 r_work: 0.2506 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2377 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8263 Z= 0.259 Angle : 0.504 4.861 11185 Z= 0.284 Chirality : 0.041 0.186 1133 Planarity : 0.003 0.050 1505 Dihedral : 4.264 25.195 1155 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.29 % Favored : 95.61 % Rotamer: Outliers : 1.08 % Allowed : 11.33 % Favored : 87.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.26), residues: 1026 helix: 0.26 (0.87), residues: 43 sheet: 0.89 (0.21), residues: 557 loop : -1.13 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 56 HIS 0.004 0.001 HIS B 197 PHE 0.025 0.001 PHE A 138 TYR 0.017 0.001 TYR B 58 ARG 0.002 0.000 ARG C 285 =============================================================================== Job complete usr+sys time: 4468.46 seconds wall clock time: 79 minutes 55.68 seconds (4795.68 seconds total)