Starting phenix.real_space_refine on Wed Aug 5 18:59:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nzr_49957/08_2026/9nzr_49957.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nzr_49957/08_2026/9nzr_49957.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.26 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9nzr_49957/08_2026/9nzr_49957.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nzr_49957/08_2026/9nzr_49957.map" model { file = "/net/cci-nas-00/data/ceres_data/9nzr_49957/08_2026/9nzr_49957.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nzr_49957/08_2026/9nzr_49957.cif" } resolution = 3.26 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= 0.028 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 184 5.49 5 S 24 5.16 5 C 6288 2.51 5 N 2038 2.21 5 O 2526 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11060 Number of models: 1 Model: "" Number of chains: 5 Chain: "D" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 668 Classifications: {'DNA': 33} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 32} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 471 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "A" Number of atoms: 3611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 448, 3611 Classifications: {'peptide': 448} Incomplete info: {'truncation_to_alanine': 19} Link IDs: {'PTRANS': 13, 'TRANS': 434} Chain breaks: 2 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 67 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2, 'ARG:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 3543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 441, 3543 Classifications: {'peptide': 441} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 28} Link IDs: {'PTRANS': 12, 'TRANS': 428} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 115 Unresolved non-hydrogen angles: 137 Unresolved non-hydrogen dihedrals: 95 Planarities with less than four sites: {'GLU:plan': 8, 'GLN:plan1': 4, 'ARG:plan': 2, 'ASP:plan': 4, 'ASN:plan1': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 80 Chain: "C" Number of atoms: 2767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 2767 Classifications: {'RNA': 129} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 4, 'rna3p_pur': 63, 'rna3p_pyr': 50} Link IDs: {'rna2p': 16, 'rna3p': 112} Chain breaks: 2 Time building chain proxies: 2.46, per 1000 atoms: 0.22 Number of scatterers: 11060 At special positions: 0 Unit cell: (121.29, 127.821, 110.094, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 184 15.00 O 2526 8.00 N 2038 7.00 C 6288 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.82 Conformation dependent library (CDL) restraints added in 222.8 milliseconds 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1672 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 9 sheets defined 50.6% alpha, 16.0% beta 73 base pairs and 119 stacking pairs defined. Time for finding SS restraints: 1.19 Creating SS restraints... Processing helix chain 'A' and resid 24 through 41 Processing helix chain 'A' and resid 42 through 68 removed outlier: 3.699A pdb=" N GLU A 61 " --> pdb=" O ASN A 57 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 80 removed outlier: 3.755A pdb=" N GLN A 72 " --> pdb=" O SER A 68 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU A 73 " --> pdb=" O PRO A 69 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N TYR A 80 " --> pdb=" O LYS A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 85 removed outlier: 3.588A pdb=" N ASN A 84 " --> pdb=" O TYR A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 114 Processing helix chain 'A' and resid 125 through 137 removed outlier: 3.638A pdb=" N TYR A 129 " --> pdb=" O GLN A 125 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL A 131 " --> pdb=" O SER A 127 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU A 137 " --> pdb=" O SER A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 158 removed outlier: 3.963A pdb=" N ASN A 158 " --> pdb=" O SER A 154 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 165 Processing helix chain 'A' and resid 219 through 229 Processing helix chain 'A' and resid 300 through 306 Processing helix chain 'A' and resid 308 through 314 removed outlier: 3.862A pdb=" N ARG A 314 " --> pdb=" O ARG A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 320 removed outlier: 4.047A pdb=" N THR A 320 " --> pdb=" O LEU A 316 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 330 Processing helix chain 'A' and resid 331 through 335 removed outlier: 3.571A pdb=" N ARG A 335 " --> pdb=" O ALA A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 337 No H-bonds generated for 'chain 'A' and resid 336 through 337' Processing helix chain 'A' and resid 338 through 362 removed outlier: 3.855A pdb=" N ASN A 342 " --> pdb=" O GLY A 338 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TRP A 343 " --> pdb=" O LYS A 339 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 411 Processing helix chain 'A' and resid 468 through 478 Processing helix chain 'B' and resid 24 through 68 removed outlier: 4.942A pdb=" N TYR B 44 " --> pdb=" O ASN B 40 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LYS B 45 " --> pdb=" O ASP B 41 " (cutoff:3.500A) removed outlier: 6.008A pdb=" N GLU B 61 " --> pdb=" O ASN B 57 " (cutoff:3.500A) removed outlier: 5.775A pdb=" N TYR B 62 " --> pdb=" O ASP B 58 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG B 63 " --> pdb=" O ALA B 59 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 80 removed outlier: 3.672A pdb=" N TYR B 80 " --> pdb=" O LYS B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 114 removed outlier: 4.274A pdb=" N ARG B 114 " --> pdb=" O HIS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 137 removed outlier: 3.839A pdb=" N VAL B 131 " --> pdb=" O SER B 127 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLU B 135 " --> pdb=" O VAL B 131 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU B 137 " --> pdb=" O SER B 133 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 166 removed outlier: 3.685A pdb=" N ASN B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LEU B 161 " --> pdb=" O LYS B 157 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ASP B 162 " --> pdb=" O ASN B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 206 No H-bonds generated for 'chain 'B' and resid 204 through 206' Processing helix chain 'B' and resid 220 through 229 removed outlier: 4.207A pdb=" N ARG B 226 " --> pdb=" O GLU B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 318 removed outlier: 3.589A pdb=" N PHE B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 328 through 362 removed outlier: 3.532A pdb=" N ASN B 362 " --> pdb=" O TYR B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 410 removed outlier: 4.116A pdb=" N LEU B 399 " --> pdb=" O SER B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 468 through 478 Processing sheet with id=AA1, first strand: chain 'A' and resid 179 through 181 removed outlier: 3.818A pdb=" N SER A 237 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 238 " --> pdb=" O LEU A 250 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N ARG A 247 " --> pdb=" O VAL A 14 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 251 " --> pdb=" O ARG A 10 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU A 13 " --> pdb=" O SER A 212 " (cutoff:3.500A) removed outlier: 5.571A pdb=" N ILE A 199 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 179 through 181 removed outlier: 3.818A pdb=" N SER A 237 " --> pdb=" O PHE A 181 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER A 238 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 184 through 185 Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 291 removed outlier: 6.176A pdb=" N ALA A 366 " --> pdb=" O PRO A 264 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ARG A 266 " --> pdb=" O ALA A 366 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N GLN A 368 " --> pdb=" O ARG A 266 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N VAL A 268 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N GLU A 370 " --> pdb=" O VAL A 268 " (cutoff:3.500A) removed outlier: 8.344A pdb=" N VAL A 270 " --> pdb=" O GLU A 370 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N GLY A 365 " --> pdb=" O GLU A 413 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ARG A 415 " --> pdb=" O GLY A 365 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ILE A 367 " --> pdb=" O ARG A 415 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N VAL A 417 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N MET A 369 " --> pdb=" O VAL A 417 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 442 through 443 Processing sheet with id=AA6, first strand: chain 'B' and resid 179 through 180 removed outlier: 5.000A pdb=" N ARG B 247 " --> pdb=" O VAL B 14 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N ILE B 199 " --> pdb=" O LEU B 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 179 through 180 Processing sheet with id=AA8, first strand: chain 'B' and resid 290 through 292 removed outlier: 3.622A pdb=" N LEU B 278 " --> pdb=" O ILE B 292 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR B 279 " --> pdb=" O ASP B 271 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N GLY B 365 " --> pdb=" O PRO B 264 " (cutoff:3.500A) removed outlier: 7.658A pdb=" N ARG B 266 " --> pdb=" O GLY B 365 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ILE B 367 " --> pdb=" O ARG B 266 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N VAL B 268 " --> pdb=" O ILE B 367 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N MET B 369 " --> pdb=" O VAL B 268 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL B 270 " --> pdb=" O MET B 369 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N GLY B 365 " --> pdb=" O GLU B 413 " (cutoff:3.500A) removed outlier: 7.960A pdb=" N ARG B 415 " --> pdb=" O GLY B 365 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE B 367 " --> pdb=" O ARG B 415 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 442 through 443 384 hydrogen bonds defined for protein. 1101 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 181 hydrogen bonds 338 hydrogen bond angles 0 basepair planarities 73 basepair parallelities 119 stacking parallelities Total time for adding SS restraints: 1.67 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2524 1.33 - 1.46: 3616 1.46 - 1.58: 5124 1.58 - 1.70: 364 1.70 - 1.82: 36 Bond restraints: 11664 Sorted by residual: bond pdb=" C3' DT D 1 " pdb=" O3' DT D 1 " ideal model delta sigma weight residual 1.435 1.487 -0.052 1.30e-02 5.92e+03 1.59e+01 bond pdb=" C3' DC D 16 " pdb=" O3' DC D 16 " ideal model delta sigma weight residual 1.435 1.485 -0.050 1.30e-02 5.92e+03 1.47e+01 bond pdb=" N9 A C 59 " pdb=" C4 A C 59 " ideal model delta sigma weight residual 1.374 1.397 -0.023 6.00e-03 2.78e+04 1.44e+01 bond pdb=" C1' DT D 12 " pdb=" N1 DT D 12 " ideal model delta sigma weight residual 1.468 1.514 -0.046 1.40e-02 5.10e+03 1.10e+01 bond pdb=" C3' DG D 5 " pdb=" C2' DG D 5 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.84e+00 ... (remaining 11659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.83: 16320 2.83 - 5.67: 242 5.67 - 8.50: 42 8.50 - 11.33: 3 11.33 - 14.17: 1 Bond angle restraints: 16608 Sorted by residual: angle pdb=" C1' C C 62 " pdb=" N1 C C 62 " pdb=" C2 C C 62 " ideal model delta sigma weight residual 118.80 127.58 -8.78 1.10e+00 8.26e-01 6.37e+01 angle pdb=" O4' A C 60 " pdb=" C1' A C 60 " pdb=" N9 A C 60 " ideal model delta sigma weight residual 108.20 114.20 -6.00 8.00e-01 1.56e+00 5.62e+01 angle pdb=" C3' U C 39 " pdb=" O3' U C 39 " pdb=" P U C 40 " ideal model delta sigma weight residual 119.70 127.47 -7.77 1.20e+00 6.94e-01 4.19e+01 angle pdb=" C1' C C 62 " pdb=" N1 C C 62 " pdb=" C6 C C 62 " ideal model delta sigma weight residual 120.80 113.58 7.22 1.20e+00 6.94e-01 3.62e+01 angle pdb=" N1 C C 62 " pdb=" C2 C C 62 " pdb=" O2 C C 62 " ideal model delta sigma weight residual 118.90 122.37 -3.47 6.00e-01 2.78e+00 3.35e+01 ... (remaining 16603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.93: 6371 34.93 - 69.87: 572 69.87 - 104.80: 45 104.80 - 139.74: 3 139.74 - 174.67: 3 Dihedral angle restraints: 6994 sinusoidal: 4400 harmonic: 2594 Sorted by residual: dihedral pdb=" CA THR A 320 " pdb=" C THR A 320 " pdb=" N ASN A 321 " pdb=" CA ASN A 321 " ideal model delta harmonic sigma weight residual 180.00 154.41 25.59 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA ILE B 276 " pdb=" C ILE B 276 " pdb=" N PRO B 277 " pdb=" CA PRO B 277 " ideal model delta harmonic sigma weight residual -180.00 -159.20 -20.80 0 5.00e+00 4.00e-02 1.73e+01 dihedral pdb=" C4' U C 39 " pdb=" C3' U C 39 " pdb=" O3' U C 39 " pdb=" P U C 40 " ideal model delta sinusoidal sigma weight residual -110.00 64.67 -174.67 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 6991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 1589 0.076 - 0.152: 305 0.152 - 0.229: 13 0.229 - 0.305: 5 0.305 - 0.381: 1 Chirality restraints: 1913 Sorted by residual: chirality pdb=" C1' A C 60 " pdb=" O4' A C 60 " pdb=" C2' A C 60 " pdb=" N9 A C 60 " both_signs ideal model delta sigma weight residual False 2.44 2.05 0.38 2.00e-01 2.50e+01 3.63e+00 chirality pdb=" C3' G C 136 " pdb=" C4' G C 136 " pdb=" O3' G C 136 " pdb=" C2' G C 136 " both_signs ideal model delta sigma weight residual False -2.48 -2.19 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CB ILE B 356 " pdb=" CA ILE B 356 " pdb=" CG1 ILE B 356 " pdb=" CG2 ILE B 356 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1910 not shown) Planarity restraints: 1471 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 418 " 0.057 5.00e-02 4.00e+02 8.65e-02 1.20e+01 pdb=" N PRO A 419 " -0.150 5.00e-02 4.00e+02 pdb=" CA PRO A 419 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 419 " 0.047 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 470 " -0.024 2.00e-02 2.50e+03 2.05e-02 1.05e+01 pdb=" CG TRP A 470 " 0.056 2.00e-02 2.50e+03 pdb=" CD1 TRP A 470 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 470 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 470 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 470 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 470 " -0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 470 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 470 " -0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 470 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 335 " 0.231 9.50e-02 1.11e+02 1.04e-01 7.77e+00 pdb=" NE ARG A 335 " -0.020 2.00e-02 2.50e+03 pdb=" CZ ARG A 335 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG A 335 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 335 " 0.002 2.00e-02 2.50e+03 ... (remaining 1468 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 2213 2.78 - 3.31: 9554 3.31 - 3.84: 20814 3.84 - 4.37: 23477 4.37 - 4.90: 35592 Nonbonded interactions: 91650 Sorted by model distance: nonbonded pdb=" O ASN A 315 " pdb=" OG SER A 319 " model vdw 2.254 3.040 nonbonded pdb=" OE2 GLU A 404 " pdb=" OH TYR A 416 " model vdw 2.262 3.040 nonbonded pdb=" OH TYR B 129 " pdb=" OG SER B 142 " model vdw 2.300 3.040 nonbonded pdb=" OH TYR A 279 " pdb=" CD1 TRP A 470 " model vdw 2.326 3.260 nonbonded pdb=" NH2 ARG A 317 " pdb=" OE2 GLU B 357 " model vdw 2.332 3.120 ... (remaining 91645 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 6 through 26 or (resid 27 and (name N or name CA or name C \ or name O or name CB )) or resid 28 through 33 or (resid 34 and (name N or name \ CA or name C or name O or name CB )) or resid 35 through 60 or (resid 61 and (n \ ame N or name CA or name C or name O or name CB )) or resid 62 through 78 or (re \ sid 79 and (name N or name CA or name C or name O or name CB )) or resid 80 thro \ ugh 88 or (resid 89 through 90 and (name N or name CA or name C or name O or nam \ e CB )) or resid 91 through 114 or (resid 125 and (name N or name CA or name C o \ r name O or name CB )) or resid 126 through 137 or (resid 138 and (name N or nam \ e CA or name C or name O or name CB )) or resid 139 through 191 or (resid 192 an \ d (name N or name CA or name C or name O or name CB )) or resid 193 through 195 \ or (resid 196 and (name N or name CA or name C or name O or name CB )) or resid \ 197 through 221 or (resid 222 and (name N or name CA or name C or name O or name \ CB )) or resid 223 through 230 or (resid 231 and (name N or name CA or name C o \ r name O or name CB )) or resid 232 through 235 or (resid 236 and (name N or nam \ e CA or name C or name O or name CB )) or resid 237 through 287 or (resid 288 an \ d (name N or name CA or name C )) or resid 289 through 295 or (resid 296 and (na \ me N or name CA or name C or name O or name CB )) or resid 297 through 305 or (r \ esid 306 through 307 and (name N or name CA or name C or name O or name CB )) or \ resid 308 through 317 or (resid 318 and (name N or name CA or name C or name O \ or name CB )) or resid 327 through 368 or (resid 369 through 370 and (name N or \ name CA or name C or name O or name CB )) or resid 371 through 436 or (resid 437 \ and (name N or name CA or name C or name O or name CB )) or resid 438 through 4 \ 48 or (resid 449 and (name N or name CA or name C or name O or name CB )) or res \ id 450 through 478)) selection = (chain 'B' and (resid 6 through 81 or (resid 82 and (name N or name CA or name C \ or name O or name CB )) or resid 83 through 89 or (resid 90 and (name N or name \ CA or name C or name O or name CB )) or resid 91 through 242 or (resid 243 and \ (name N or name CA or name C or name O or name CB )) or resid 244 through 300 or \ (resid 301 and (name N or name CA or name C or name O or name CB )) or resid 30 \ 2 through 308 or (resid 309 and (name N or name CA or name C or name O or name C \ B )) or resid 310 or (resid 311 and (name N or name CA or name C or name O or na \ me CB )) or resid 312 through 336 or (resid 337 and (name N or name CA or name C \ or name O or name CB )) or resid 338 through 371 or (resid 392 and (name N or n \ ame CA or name C or name O or name CB )) or resid 393 through 435 or (resid 436 \ through 437 and (name N or name CA or name C or name O or name CB )) or resid 43 \ 8 through 455 or (resid 456 and (name N or name CA or name C or name O or name C \ B )) or resid 465 through 478)) } 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: 2.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.060 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.020 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:1.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 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 : 0.005 0.052 11664 Z= 0.351 Angle : 0.948 14.168 16608 Z= 0.720 Chirality : 0.059 0.381 1913 Planarity : 0.007 0.104 1471 Dihedral : 21.625 174.672 5322 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.13 % Allowed : 12.05 % Favored : 87.82 % 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: -0.63 (0.27), residues: 875 helix: -0.04 (0.23), residues: 427 sheet: -0.04 (0.49), residues: 127 loop : -0.92 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 314 TYR 0.020 0.002 TYR A 129 PHE 0.020 0.002 PHE B 71 TRP 0.056 0.003 TRP A 470 HIS 0.011 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.35 (11664) covalent geometry : angle 0.94779 / 0.72 (16608) hydrogen bonds : bond 0.12645 / 14.01 ( 553) hydrogen bonds : angle 5.24774 / 7.06 ( 1439) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.247 Fit side-chains REVERT: A 174 LYS cc_start: 0.8259 (mtmt) cc_final: 0.7996 (mmtm) REVERT: A 362 ASN cc_start: 0.8372 (m-40) cc_final: 0.8146 (m-40) REVERT: B 11 LYS cc_start: 0.8406 (tttt) cc_final: 0.8072 (ttmt) REVERT: B 392 ARG cc_start: 0.6600 (ttp-110) cc_final: 0.6015 (tpm170) outliers start: 1 outliers final: 1 residues processed: 114 average time/residue: 0.0976 time to fit residues: 15.4800 Evaluate side-chains 84 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 49 optimal weight: 0.5980 chunk 97 optimal weight: 50.0000 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 4.9990 chunk 100 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 231 GLN A 300 ASN A 424 GLN B 42 ASN B 331 GLN B 368 GLN B 471 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.193513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.143907 restraints weight = 15438.751| |-----------------------------------------------------------------------------| r_work (start): 0.3774 rms_B_bonded: 1.96 r_work: 0.3497 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.1169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11664 Z= 0.164 Angle : 0.617 8.452 16608 Z= 0.357 Chirality : 0.044 0.338 1913 Planarity : 0.005 0.053 1471 Dihedral : 22.959 170.453 3574 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.01 % Allowed : 12.99 % Favored : 85.01 % 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: 0.16 (0.28), residues: 875 helix: 1.07 (0.25), residues: 428 sheet: -0.31 (0.46), residues: 130 loop : -0.98 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 314 TYR 0.049 0.002 TYR A 405 PHE 0.012 0.001 PHE B 203 TRP 0.032 0.002 TRP A 470 HIS 0.005 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.16 (11664) covalent geometry : angle 0.61679 / 0.36 (16608) hydrogen bonds : bond 0.05857 / 6.45 ( 553) hydrogen bonds : angle 4.12272 / 5.39 ( 1439) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.253 Fit side-chains REVERT: A 157 LYS cc_start: 0.7670 (tttt) cc_final: 0.7343 (ttmt) REVERT: A 174 LYS cc_start: 0.8423 (mtmt) cc_final: 0.8189 (mmtm) REVERT: A 476 ILE cc_start: 0.8579 (tp) cc_final: 0.8334 (tp) REVERT: B 11 LYS cc_start: 0.8507 (tttt) cc_final: 0.8182 (ttmt) REVERT: B 315 ASN cc_start: 0.6715 (p0) cc_final: 0.6295 (p0) REVERT: B 328 GLN cc_start: 0.7746 (pm20) cc_final: 0.7005 (mp10) REVERT: B 337 GLU cc_start: 0.8439 (mt-10) cc_final: 0.7799 (pt0) REVERT: B 373 THR cc_start: 0.5366 (OUTLIER) cc_final: 0.5146 (m) REVERT: B 392 ARG cc_start: 0.6595 (ttp-110) cc_final: 0.6143 (tpm170) REVERT: B 405 TYR cc_start: 0.8439 (t80) cc_final: 0.8126 (t80) outliers start: 15 outliers final: 10 residues processed: 107 average time/residue: 0.0982 time to fit residues: 15.0857 Evaluate side-chains 94 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 0.200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 373 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 48 optimal weight: 10.0000 chunk 26 optimal weight: 2.9990 chunk 68 optimal weight: 4.9990 chunk 47 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 58 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 69 optimal weight: 0.0970 chunk 95 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 15 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 345 HIS ** B 471 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.193404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.142842 restraints weight = 15635.765| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.02 r_work: 0.3484 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 11664 Z= 0.138 Angle : 0.565 7.279 16608 Z= 0.330 Chirality : 0.042 0.342 1913 Planarity : 0.004 0.043 1471 Dihedral : 22.894 170.072 3573 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.87 % Allowed : 14.06 % Favored : 84.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.52 (0.28), residues: 875 helix: 1.51 (0.25), residues: 433 sheet: -0.51 (0.44), residues: 137 loop : -0.87 (0.33), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 314 TYR 0.024 0.001 TYR A 405 PHE 0.011 0.001 PHE A 56 TRP 0.023 0.001 TRP A 470 HIS 0.007 0.001 HIS B 345 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.14 (11664) covalent geometry : angle 0.56483 / 0.33 (16608) hydrogen bonds : bond 0.05379 / 5.81 ( 553) hydrogen bonds : angle 3.84060 / 5.04 ( 1439) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.330 Fit side-chains REVERT: A 157 LYS cc_start: 0.7703 (tttt) cc_final: 0.7371 (ttmt) REVERT: A 174 LYS cc_start: 0.8443 (mtmt) cc_final: 0.8179 (mmtm) REVERT: B 11 LYS cc_start: 0.8504 (tttt) cc_final: 0.8185 (ttmt) REVERT: B 66 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.8209 (mm) REVERT: B 110 HIS cc_start: 0.7561 (t70) cc_final: 0.7184 (t70) REVERT: B 328 GLN cc_start: 0.7885 (pm20) cc_final: 0.7461 (pm20) REVERT: B 337 GLU cc_start: 0.8445 (mt-10) cc_final: 0.7827 (pt0) REVERT: B 392 ARG cc_start: 0.6649 (ttp-110) cc_final: 0.6220 (tpm170) REVERT: B 405 TYR cc_start: 0.8537 (t80) cc_final: 0.8183 (t80) outliers start: 14 outliers final: 11 residues processed: 102 average time/residue: 0.1051 time to fit residues: 15.3002 Evaluate side-chains 91 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 267 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 90 optimal weight: 9.9990 chunk 88 optimal weight: 0.8980 chunk 99 optimal weight: 50.0000 chunk 96 optimal weight: 20.0000 chunk 17 optimal weight: 0.0470 chunk 27 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 7 optimal weight: 0.9980 chunk 33 optimal weight: 0.0570 chunk 45 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 overall best weight: 0.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.193119 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.143078 restraints weight = 15588.411| |-----------------------------------------------------------------------------| r_work (start): 0.3763 rms_B_bonded: 1.97 r_work: 0.3487 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11664 Z= 0.129 Angle : 0.543 7.257 16608 Z= 0.315 Chirality : 0.041 0.343 1913 Planarity : 0.004 0.051 1471 Dihedral : 22.862 170.628 3573 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.14 % Allowed : 15.26 % Favored : 82.60 % 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: 0.86 (0.28), residues: 875 helix: 1.92 (0.25), residues: 425 sheet: -0.47 (0.44), residues: 135 loop : -0.80 (0.33), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 314 TYR 0.025 0.001 TYR A 405 PHE 0.013 0.001 PHE B 203 TRP 0.020 0.001 TRP A 470 HIS 0.005 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.13 (11664) covalent geometry : angle 0.54278 / 0.32 (16608) hydrogen bonds : bond 0.05055 / 5.49 ( 553) hydrogen bonds : angle 3.70494 / 4.79 ( 1439) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.301 Fit side-chains REVERT: A 157 LYS cc_start: 0.7769 (tttt) cc_final: 0.7435 (ttmt) REVERT: A 161 LEU cc_start: 0.8808 (OUTLIER) cc_final: 0.8607 (tp) REVERT: A 174 LYS cc_start: 0.8447 (mtmt) cc_final: 0.8191 (mmtm) REVERT: A 290 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7003 (tmm) REVERT: B 11 LYS cc_start: 0.8505 (tttt) cc_final: 0.8206 (ttmt) REVERT: B 66 ILE cc_start: 0.8544 (OUTLIER) cc_final: 0.8228 (mm) REVERT: B 315 ASN cc_start: 0.6370 (p0) cc_final: 0.6143 (p0) REVERT: B 328 GLN cc_start: 0.7951 (pm20) cc_final: 0.7410 (pm20) REVERT: B 392 ARG cc_start: 0.6681 (ttp-110) cc_final: 0.6251 (tpm170) REVERT: B 405 TYR cc_start: 0.8541 (t80) cc_final: 0.8161 (t80) outliers start: 16 outliers final: 11 residues processed: 94 average time/residue: 0.1099 time to fit residues: 14.6606 Evaluate side-chains 91 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 139 VAL Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 267 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 51 optimal weight: 2.9990 chunk 65 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 55.7863 > 50:) chunk 57 optimal weight: 0.6980 chunk 96 optimal weight: 20.0000 chunk 37 optimal weight: 4.9990 chunk 36 optimal weight: 0.6980 chunk 70 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 48 optimal weight: 20.0000 chunk 3 optimal weight: 20.0000 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 149 ASN A 318 GLN B 67 HIS B 363 ASN B 368 GLN B 431 HIS B 475 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.180483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.126385 restraints weight = 15108.041| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 2.20 r_work: 0.3200 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.072 11664 Z= 0.267 Angle : 0.695 8.973 16608 Z= 0.384 Chirality : 0.049 0.417 1913 Planarity : 0.005 0.045 1471 Dihedral : 22.910 170.517 3573 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.61 % Allowed : 14.73 % Favored : 81.66 % 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: 0.57 (0.28), residues: 875 helix: 1.52 (0.25), residues: 431 sheet: -0.65 (0.44), residues: 131 loop : -0.69 (0.34), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 314 TYR 0.025 0.002 TYR B 173 PHE 0.018 0.002 PHE A 56 TRP 0.016 0.002 TRP A 470 HIS 0.004 0.002 HIS B 67 Details of bonding type rmsd/Z covalent geometry : bond 0.00597 / 0.27 (11664) covalent geometry : angle 0.69527 / 0.38 (16608) hydrogen bonds : bond 0.06002 / 6.62 ( 553) hydrogen bonds : angle 4.00219 / 5.22 ( 1439) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 85 time to evaluate : 0.325 Fit side-chains REVERT: A 157 LYS cc_start: 0.7743 (tttt) cc_final: 0.7326 (ttmt) REVERT: A 165 ARG cc_start: 0.7911 (mtt180) cc_final: 0.7600 (mtt90) REVERT: A 174 LYS cc_start: 0.8792 (mtmt) cc_final: 0.8311 (mmtm) REVERT: A 290 MET cc_start: 0.8120 (OUTLIER) cc_final: 0.6487 (tmm) REVERT: B 66 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8254 (mm) REVERT: B 183 ILE cc_start: 0.8415 (tp) cc_final: 0.8208 (tt) REVERT: B 315 ASN cc_start: 0.6363 (p0) cc_final: 0.6088 (p0) REVERT: B 337 GLU cc_start: 0.8603 (mt-10) cc_final: 0.8031 (pt0) outliers start: 27 outliers final: 19 residues processed: 106 average time/residue: 0.0966 time to fit residues: 14.5966 Evaluate side-chains 102 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 81 time to evaluate : 0.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 233 ASP Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 431 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 60 optimal weight: 0.9980 chunk 103 optimal weight: 8.9990 chunk 4 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 94 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 80 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 52 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 67 HIS B 475 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.185277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.135229 restraints weight = 15026.670| |-----------------------------------------------------------------------------| r_work (start): 0.3616 rms_B_bonded: 2.28 r_work: 0.3276 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3276 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.2601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 11664 Z= 0.142 Angle : 0.566 7.346 16608 Z= 0.327 Chirality : 0.042 0.360 1913 Planarity : 0.004 0.048 1471 Dihedral : 22.836 171.667 3573 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.14 % Allowed : 16.33 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.29), residues: 875 helix: 1.89 (0.25), residues: 426 sheet: -0.70 (0.43), residues: 131 loop : -0.62 (0.34), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 314 TYR 0.017 0.001 TYR B 156 PHE 0.011 0.001 PHE A 56 TRP 0.033 0.002 TRP A 470 HIS 0.010 0.001 HIS B 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 (11664) covalent geometry : angle 0.56576 / 0.33 (16608) hydrogen bonds : bond 0.05232 / 5.74 ( 553) hydrogen bonds : angle 3.77460 / 4.92 ( 1439) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 82 time to evaluate : 0.310 Fit side-chains REVERT: A 157 LYS cc_start: 0.7850 (tttt) cc_final: 0.7442 (ttmt) REVERT: A 174 LYS cc_start: 0.8669 (mtmt) cc_final: 0.8403 (mmtm) REVERT: A 290 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7066 (tmm) REVERT: A 318 GLN cc_start: 0.7747 (OUTLIER) cc_final: 0.7360 (tp-100) REVERT: B 66 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8362 (mm) REVERT: B 183 ILE cc_start: 0.8415 (tp) cc_final: 0.8183 (tt) REVERT: B 249 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7469 (tt) REVERT: B 315 ASN cc_start: 0.6257 (p0) cc_final: 0.5916 (p0) REVERT: B 337 GLU cc_start: 0.8568 (mt-10) cc_final: 0.8059 (pt0) REVERT: B 405 TYR cc_start: 0.8770 (t80) cc_final: 0.8354 (t80) outliers start: 16 outliers final: 9 residues processed: 94 average time/residue: 0.0949 time to fit residues: 12.8464 Evaluate side-chains 89 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 169 THR Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 318 GLN Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 189 LEU Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 431 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 51 optimal weight: 5.9990 chunk 21 optimal weight: 0.0670 chunk 26 optimal weight: 2.9990 chunk 72 optimal weight: 0.5980 chunk 95 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 69 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 chunk 32 optimal weight: 0.0670 overall best weight: 0.3656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 67 HIS B 368 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.187716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.137556 restraints weight = 14938.451| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 2.03 r_work: 0.3343 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 11664 Z= 0.117 Angle : 0.526 6.901 16608 Z= 0.306 Chirality : 0.040 0.368 1913 Planarity : 0.004 0.048 1471 Dihedral : 22.738 171.679 3573 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.07 % Allowed : 17.94 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.29), residues: 875 helix: 2.14 (0.26), residues: 427 sheet: -0.65 (0.44), residues: 135 loop : -0.58 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 314 TYR 0.015 0.001 TYR B 156 PHE 0.010 0.001 PHE A 56 TRP 0.037 0.002 TRP A 470 HIS 0.015 0.001 HIS B 431 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.12 (11664) covalent geometry : angle 0.52629 / 0.31 (16608) hydrogen bonds : bond 0.04927 / 5.39 ( 553) hydrogen bonds : angle 3.62705 / 4.73 ( 1439) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.354 Fit side-chains REVERT: A 157 LYS cc_start: 0.7705 (tttt) cc_final: 0.7159 (mtmt) REVERT: A 174 LYS cc_start: 0.8509 (mtmt) cc_final: 0.8304 (mmtm) REVERT: A 290 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.6944 (tmm) REVERT: B 66 ILE cc_start: 0.8575 (OUTLIER) cc_final: 0.8269 (mm) REVERT: B 315 ASN cc_start: 0.6241 (p0) cc_final: 0.5899 (p0) REVERT: B 337 GLU cc_start: 0.8521 (mt-10) cc_final: 0.8043 (pt0) REVERT: B 405 TYR cc_start: 0.8721 (t80) cc_final: 0.8376 (t80) outliers start: 8 outliers final: 5 residues processed: 85 average time/residue: 0.0926 time to fit residues: 11.5300 Evaluate side-chains 83 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 76 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 267 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 82 optimal weight: 1.9990 chunk 91 optimal weight: 3.9990 chunk 102 optimal weight: 30.0000 chunk 18 optimal weight: 0.9980 chunk 71 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 50 optimal weight: 0.0020 chunk 93 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 ASN A 318 GLN B 475 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.181060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.127862 restraints weight = 14889.675| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 2.03 r_work: 0.3241 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11664 Z= 0.183 Angle : 0.583 8.190 16608 Z= 0.330 Chirality : 0.043 0.430 1913 Planarity : 0.004 0.047 1471 Dihedral : 22.726 170.750 3573 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 2.28 % Allowed : 17.54 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.29), residues: 875 helix: 2.02 (0.25), residues: 428 sheet: -0.78 (0.42), residues: 137 loop : -0.51 (0.36), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 314 TYR 0.019 0.002 TYR B 156 PHE 0.013 0.002 PHE A 56 TRP 0.039 0.002 TRP A 470 HIS 0.006 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.18 (11664) covalent geometry : angle 0.58296 / 0.33 (16608) hydrogen bonds : bond 0.05195 / 5.77 ( 553) hydrogen bonds : angle 3.72155 / 4.82 ( 1439) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.281 Fit side-chains REVERT: A 66 ILE cc_start: 0.8739 (mt) cc_final: 0.8480 (mm) REVERT: A 157 LYS cc_start: 0.7550 (tttt) cc_final: 0.7070 (ttmt) REVERT: A 174 LYS cc_start: 0.8677 (mtmt) cc_final: 0.8252 (mmtm) REVERT: A 290 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.6574 (tmm) REVERT: B 66 ILE cc_start: 0.8457 (OUTLIER) cc_final: 0.8215 (mm) REVERT: B 337 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8030 (pt0) REVERT: B 405 TYR cc_start: 0.8768 (t80) cc_final: 0.8381 (t80) outliers start: 17 outliers final: 12 residues processed: 92 average time/residue: 0.0918 time to fit residues: 12.2042 Evaluate side-chains 95 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 81 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 40 ASN Chi-restraints excluded: chain A residue 155 THR Chi-restraints excluded: chain A residue 267 ILE Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 188 GLU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 340 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 70 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 92 optimal weight: 0.5980 chunk 51 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 12 optimal weight: 0.2980 chunk 48 optimal weight: 0.0050 chunk 30 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 318 GLN B 475 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.183968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.130033 restraints weight = 14984.417| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.06 r_work: 0.3279 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 11664 Z= 0.122 Angle : 0.536 8.231 16608 Z= 0.308 Chirality : 0.041 0.394 1913 Planarity : 0.004 0.047 1471 Dihedral : 22.711 171.327 3573 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.61 % Allowed : 18.21 % Favored : 80.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.11 (0.29), residues: 875 helix: 2.14 (0.25), residues: 427 sheet: -0.74 (0.43), residues: 135 loop : -0.50 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 314 TYR 0.015 0.001 TYR B 156 PHE 0.011 0.001 PHE A 56 TRP 0.038 0.002 TRP A 470 HIS 0.007 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.12 (11664) covalent geometry : angle 0.53566 / 0.31 (16608) hydrogen bonds : bond 0.04954 / 5.45 ( 553) hydrogen bonds : angle 3.64112 / 4.75 ( 1439) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.305 Fit side-chains REVERT: A 157 LYS cc_start: 0.7467 (tttt) cc_final: 0.7073 (ttmt) REVERT: A 174 LYS cc_start: 0.8620 (mtmt) cc_final: 0.8193 (mmtm) REVERT: A 290 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.6634 (tmm) REVERT: B 66 ILE cc_start: 0.8426 (OUTLIER) cc_final: 0.8181 (mm) REVERT: B 315 ASN cc_start: 0.6393 (p0) cc_final: 0.5985 (p0) REVERT: B 337 GLU cc_start: 0.8579 (mt-10) cc_final: 0.8027 (pt0) REVERT: B 405 TYR cc_start: 0.8761 (t80) cc_final: 0.8339 (t80) outliers start: 12 outliers final: 8 residues processed: 86 average time/residue: 0.0957 time to fit residues: 11.9884 Evaluate side-chains 87 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 77 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 340 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 101 optimal weight: 9.9990 chunk 65 optimal weight: 0.0670 chunk 75 optimal weight: 0.9990 chunk 47 optimal weight: 0.0970 chunk 68 optimal weight: 0.9980 chunk 84 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 3 optimal weight: 20.0000 chunk 30 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 300 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.183690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.131931 restraints weight = 15001.103| |-----------------------------------------------------------------------------| r_work (start): 0.3582 rms_B_bonded: 2.15 r_work: 0.3281 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 11664 Z= 0.127 Angle : 0.527 8.550 16608 Z= 0.302 Chirality : 0.040 0.414 1913 Planarity : 0.004 0.048 1471 Dihedral : 22.664 170.121 3573 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.61 % Allowed : 18.34 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.22 (0.29), residues: 875 helix: 2.24 (0.25), residues: 428 sheet: -0.75 (0.43), residues: 135 loop : -0.45 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 314 TYR 0.016 0.001 TYR B 156 PHE 0.011 0.001 PHE B 203 TRP 0.043 0.002 TRP A 470 HIS 0.006 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.13 (11664) covalent geometry : angle 0.52717 / 0.30 (16608) hydrogen bonds : bond 0.04871 / 5.35 ( 553) hydrogen bonds : angle 3.56734 / 4.62 ( 1439) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 82 time to evaluate : 0.283 Fit side-chains REVERT: A 16 LEU cc_start: 0.8943 (mt) cc_final: 0.8729 (mt) REVERT: A 157 LYS cc_start: 0.7490 (tttt) cc_final: 0.7116 (ttmt) REVERT: A 174 LYS cc_start: 0.8607 (mtmt) cc_final: 0.8199 (mmtm) REVERT: A 290 MET cc_start: 0.8143 (OUTLIER) cc_final: 0.6515 (tmm) REVERT: B 315 ASN cc_start: 0.6353 (p0) cc_final: 0.5980 (p0) REVERT: B 337 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8196 (pt0) REVERT: B 405 TYR cc_start: 0.8722 (t80) cc_final: 0.8334 (t80) outliers start: 12 outliers final: 11 residues processed: 90 average time/residue: 0.1037 time to fit residues: 13.3088 Evaluate side-chains 88 residues out of total 794 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 111 THR Chi-restraints excluded: chain A residue 128 THR Chi-restraints excluded: chain A residue 271 ASP Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain B residue 7 CYS Chi-restraints excluded: chain B residue 9 THR Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 212 SER Chi-restraints excluded: chain B residue 242 SER Chi-restraints excluded: chain B residue 267 ILE Chi-restraints excluded: chain B residue 340 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 105 random chunks: chunk 79 optimal weight: 8.9990 chunk 74 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 103 optimal weight: 10.0000 chunk 90 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 47 optimal weight: 0.0040 chunk 57 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 92 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 overall best weight: 0.7194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.183382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.123996 restraints weight = 15032.308| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 2.01 r_work: 0.3322 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11664 Z= 0.129 Angle : 0.538 10.426 16608 Z= 0.304 Chirality : 0.040 0.401 1913 Planarity : 0.004 0.053 1471 Dihedral : 22.657 170.402 3573 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.61 % Allowed : 18.88 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.29), residues: 875 helix: 2.25 (0.25), residues: 427 sheet: -0.67 (0.44), residues: 135 loop : -0.46 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 314 TYR 0.014 0.001 TYR B 156 PHE 0.011 0.001 PHE B 203 TRP 0.040 0.002 TRP A 470 HIS 0.006 0.001 HIS A 53 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.13 (11664) covalent geometry : angle 0.53819 / 0.30 (16608) hydrogen bonds : bond 0.04859 / 5.35 ( 553) hydrogen bonds : angle 3.58083 / 4.67 ( 1439) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2280.01 seconds wall clock time: 39 minutes 43.09 seconds (2383.09 seconds total)