Starting phenix.real_space_refine on Wed Jun 3 17:00:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zpi_60345/06_2026/8zpi_60345_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zpi_60345/06_2026/8zpi_60345.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8zpi_60345/06_2026/8zpi_60345_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zpi_60345/06_2026/8zpi_60345_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zpi_60345/06_2026/8zpi_60345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zpi_60345/06_2026/8zpi_60345.map" } resolution = 3.12 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 38 5.16 5 C 4868 2.51 5 N 1286 2.21 5 O 1456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7649 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3810 Classifications: {'peptide': 481} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 458} Chain: "B" Number of atoms: 3810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3810 Classifications: {'peptide': 481} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 21, 'TRANS': 458} Chain: "A" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'PLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'PLP': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'PLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 1.85, per 1000 atoms: 0.24 Number of scatterers: 7649 At special positions: 0 Unit cell: (116.167, 69.6999, 83.8666, 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 38 16.00 P 1 15.00 O 1456 8.00 N 1286 7.00 C 4868 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: 0.63 Conformation dependent library (CDL) restraints added in 466.6 milliseconds 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1812 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 6 sheets defined 51.4% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 18 through 39 removed outlier: 3.864A pdb=" N SER A 39 " --> pdb=" O GLU A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.608A pdb=" N ILE A 67 " --> pdb=" O PRO A 63 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 109 Processing helix chain 'A' and resid 120 through 137 Processing helix chain 'A' and resid 149 through 167 removed outlier: 3.656A pdb=" N ALA A 153 " --> pdb=" O GLY A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 190 through 199 removed outlier: 3.741A pdb=" N LYS A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 204 No H-bonds generated for 'chain 'A' and resid 202 through 204' Processing helix chain 'A' and resid 218 through 232 Processing helix chain 'A' and resid 253 through 265 Processing helix chain 'A' and resid 274 through 281 removed outlier: 3.762A pdb=" N ALA A 277 " --> pdb=" O TYR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 290 through 294 Processing helix chain 'A' and resid 300 through 305 removed outlier: 4.471A pdb=" N TRP A 304 " --> pdb=" O ASN A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 326 removed outlier: 4.028A pdb=" N LEU A 322 " --> pdb=" O ASN A 318 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N PHE A 326 " --> pdb=" O LEU A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 365 removed outlier: 3.853A pdb=" N LEU A 357 " --> pdb=" O ASP A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 388 Processing helix chain 'A' and resid 414 through 434 Processing helix chain 'A' and resid 458 through 476 removed outlier: 3.608A pdb=" N ILE A 462 " --> pdb=" O PRO A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 removed outlier: 4.172A pdb=" N ASN A 480 " --> pdb=" O HIS A 476 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER A 481 " --> pdb=" O HIS A 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 476 through 481' Processing helix chain 'B' and resid 18 through 39 removed outlier: 3.829A pdb=" N SER B 39 " --> pdb=" O GLU B 35 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 77 removed outlier: 3.596A pdb=" N ILE B 67 " --> pdb=" O PRO B 63 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ASN B 77 " --> pdb=" O GLU B 73 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 109 Processing helix chain 'B' and resid 120 through 137 Processing helix chain 'B' and resid 149 through 167 removed outlier: 3.654A pdb=" N ALA B 153 " --> pdb=" O GLY B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 190 through 199 removed outlier: 3.743A pdb=" N LYS B 194 " --> pdb=" O THR B 190 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 204 No H-bonds generated for 'chain 'B' and resid 202 through 204' Processing helix chain 'B' and resid 218 through 232 Processing helix chain 'B' and resid 253 through 265 Processing helix chain 'B' and resid 274 through 281 removed outlier: 3.762A pdb=" N ALA B 277 " --> pdb=" O TYR B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 289 Processing helix chain 'B' and resid 290 through 294 Processing helix chain 'B' and resid 300 through 305 removed outlier: 4.451A pdb=" N TRP B 304 " --> pdb=" O ASN B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 326 removed outlier: 4.002A pdb=" N LEU B 322 " --> pdb=" O ASN B 318 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE B 326 " --> pdb=" O LEU B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 365 removed outlier: 3.849A pdb=" N LEU B 357 " --> pdb=" O ASP B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 388 Processing helix chain 'B' and resid 414 through 434 Processing helix chain 'B' and resid 458 through 476 removed outlier: 3.536A pdb=" N ILE B 462 " --> pdb=" O PRO B 458 " (cutoff:3.500A) Processing helix chain 'B' and resid 476 through 481 removed outlier: 4.126A pdb=" N ASN B 480 " --> pdb=" O HIS B 476 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER B 481 " --> pdb=" O HIS B 477 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 476 through 481' Processing sheet with id=AA1, first strand: chain 'A' and resid 143 through 147 removed outlier: 3.885A pdb=" N ALA A 312 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N SER A 296 " --> pdb=" O LEU A 268 " (cutoff:3.500A) removed outlier: 9.925A pdb=" N TRP A 267 " --> pdb=" O GLN A 235 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N PHE A 237 " --> pdb=" O TRP A 267 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N HIS A 269 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL A 239 " --> pdb=" O HIS A 269 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N ASP A 271 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N ALA A 241 " --> pdb=" O ASP A 271 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N VAL A 181 " --> pdb=" O PHE A 237 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N VAL A 239 " --> pdb=" O VAL A 181 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU A 183 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ALA A 241 " --> pdb=" O LEU A 183 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N SER A 185 " --> pdb=" O ALA A 241 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 393 through 395 Processing sheet with id=AA3, first strand: chain 'A' and resid 441 through 442 Processing sheet with id=AA4, first strand: chain 'B' and resid 143 through 147 removed outlier: 3.922A pdb=" N ALA B 312 " --> pdb=" O VAL B 147 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER B 296 " --> pdb=" O LEU B 268 " (cutoff:3.500A) removed outlier: 9.928A pdb=" N TRP B 267 " --> pdb=" O GLN B 235 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N PHE B 237 " --> pdb=" O TRP B 267 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N HIS B 269 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N VAL B 239 " --> pdb=" O HIS B 269 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N ASP B 271 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ALA B 241 " --> pdb=" O ASP B 271 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N VAL B 181 " --> pdb=" O PHE B 237 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N VAL B 239 " --> pdb=" O VAL B 181 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N LEU B 183 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ALA B 241 " --> pdb=" O LEU B 183 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N SER B 185 " --> pdb=" O ALA B 241 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 393 through 395 Processing sheet with id=AA6, first strand: chain 'B' and resid 441 through 442 368 hydrogen bonds defined for protein. 1032 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.03 Time building geometry restraints manager: 0.84 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: 2504 1.34 - 1.46: 1485 1.46 - 1.57: 3743 1.57 - 1.69: 2 1.69 - 1.81: 66 Bond restraints: 7800 Sorted by residual: bond pdb=" O4P PLP A 501 " pdb=" P PLP A 501 " ideal model delta sigma weight residual 1.687 1.611 0.076 2.00e-02 2.50e+03 1.45e+01 bond pdb=" C2 PLP A 501 " pdb=" N1 PLP A 501 " ideal model delta sigma weight residual 1.325 1.380 -0.055 2.00e-02 2.50e+03 7.47e+00 bond pdb=" C2 PLP B 501 " pdb=" N1 PLP B 501 " ideal model delta sigma weight residual 1.325 1.378 -0.053 2.00e-02 2.50e+03 6.93e+00 bond pdb=" CB PRO B 391 " pdb=" CG PRO B 391 " ideal model delta sigma weight residual 1.492 1.616 -0.124 5.00e-02 4.00e+02 6.20e+00 bond pdb=" C4 PLP B 501 " pdb=" C4A PLP B 501 " ideal model delta sigma weight residual 1.462 1.500 -0.038 2.00e-02 2.50e+03 3.65e+00 ... (remaining 7795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.71: 10443 1.71 - 3.43: 110 3.43 - 5.14: 8 5.14 - 6.85: 2 6.85 - 8.57: 2 Bond angle restraints: 10565 Sorted by residual: angle pdb=" CA PRO B 391 " pdb=" N PRO B 391 " pdb=" CD PRO B 391 " ideal model delta sigma weight residual 112.00 104.90 7.10 1.40e+00 5.10e-01 2.57e+01 angle pdb=" N PRO B 391 " pdb=" CD PRO B 391 " pdb=" CG PRO B 391 " ideal model delta sigma weight residual 103.20 98.67 4.53 1.50e+00 4.44e-01 9.13e+00 angle pdb=" O2P PLP A 501 " pdb=" P PLP A 501 " pdb=" O4P PLP A 501 " ideal model delta sigma weight residual 101.47 110.04 -8.57 3.00e+00 1.11e-01 8.15e+00 angle pdb=" CA PRO A 391 " pdb=" N PRO A 391 " pdb=" CD PRO A 391 " ideal model delta sigma weight residual 112.00 108.47 3.53 1.40e+00 5.10e-01 6.35e+00 angle pdb=" C GLY A 143 " pdb=" N GLY A 144 " pdb=" CA GLY A 144 " ideal model delta sigma weight residual 121.82 119.98 1.84 8.40e-01 1.42e+00 4.81e+00 ... (remaining 10560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 4171 16.16 - 32.32: 435 32.32 - 48.47: 102 48.47 - 64.63: 15 64.63 - 80.79: 1 Dihedral angle restraints: 4724 sinusoidal: 1922 harmonic: 2802 Sorted by residual: dihedral pdb=" CA GLN A 141 " pdb=" CB GLN A 141 " pdb=" CG GLN A 141 " pdb=" CD GLN A 141 " ideal model delta sinusoidal sigma weight residual 60.00 114.69 -54.69 3 1.50e+01 4.44e-03 9.30e+00 dihedral pdb=" CA GLN B 141 " pdb=" CB GLN B 141 " pdb=" CG GLN B 141 " pdb=" CD GLN B 141 " ideal model delta sinusoidal sigma weight residual 60.00 114.63 -54.63 3 1.50e+01 4.44e-03 9.30e+00 dihedral pdb=" CB MET B 30 " pdb=" CG MET B 30 " pdb=" SD MET B 30 " pdb=" CE MET B 30 " ideal model delta sinusoidal sigma weight residual 180.00 127.25 52.75 3 1.50e+01 4.44e-03 9.14e+00 ... (remaining 4721 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 783 0.029 - 0.058: 290 0.058 - 0.087: 71 0.087 - 0.116: 39 0.116 - 0.145: 11 Chirality restraints: 1194 Sorted by residual: chirality pdb=" CA ILE A 182 " pdb=" N ILE A 182 " pdb=" C ILE A 182 " pdb=" CB ILE A 182 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.25e-01 chirality pdb=" CA ILE B 182 " pdb=" N ILE B 182 " pdb=" C ILE B 182 " pdb=" CB ILE B 182 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA ILE B 62 " pdb=" N ILE B 62 " pdb=" C ILE B 62 " pdb=" CB ILE B 62 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 1191 not shown) Planarity restraints: 1362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 PLP B 501 " -0.014 2.00e-02 2.50e+03 9.05e-02 2.05e+02 pdb=" C2A PLP B 501 " -0.044 2.00e-02 2.50e+03 pdb=" C3 PLP B 501 " 0.060 2.00e-02 2.50e+03 pdb=" C4 PLP B 501 " 0.089 2.00e-02 2.50e+03 pdb=" C4A PLP B 501 " -0.215 2.00e-02 2.50e+03 pdb=" C5 PLP B 501 " 0.040 2.00e-02 2.50e+03 pdb=" C5A PLP B 501 " 0.070 2.00e-02 2.50e+03 pdb=" C6 PLP B 501 " -0.032 2.00e-02 2.50e+03 pdb=" N1 PLP B 501 " -0.060 2.00e-02 2.50e+03 pdb=" O3 PLP B 501 " 0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG B 390 " 0.079 5.00e-02 4.00e+02 1.16e-01 2.16e+01 pdb=" N PRO B 391 " -0.201 5.00e-02 4.00e+02 pdb=" CA PRO B 391 " 0.059 5.00e-02 4.00e+02 pdb=" CD PRO B 391 " 0.062 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C2 PLP A 501 " 0.005 2.00e-02 2.50e+03 2.86e-02 2.04e+01 pdb=" C2A PLP A 501 " 0.014 2.00e-02 2.50e+03 pdb=" C3 PLP A 501 " -0.018 2.00e-02 2.50e+03 pdb=" C4 PLP A 501 " -0.030 2.00e-02 2.50e+03 pdb=" C4A PLP A 501 " 0.068 2.00e-02 2.50e+03 pdb=" C5 PLP A 501 " -0.013 2.00e-02 2.50e+03 pdb=" C5A PLP A 501 " -0.022 2.00e-02 2.50e+03 pdb=" C6 PLP A 501 " 0.009 2.00e-02 2.50e+03 pdb=" N1 PLP A 501 " 0.019 2.00e-02 2.50e+03 pdb=" O3 PLP A 501 " -0.033 2.00e-02 2.50e+03 ... (remaining 1359 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 32 2.56 - 3.15: 6284 3.15 - 3.73: 11549 3.73 - 4.32: 16335 4.32 - 4.90: 28468 Nonbonded interactions: 62668 Sorted by model distance: nonbonded pdb=" OH TYR A 392 " pdb=" OD1 ASP A 470 " model vdw 1.977 3.040 nonbonded pdb=" OH TYR B 392 " pdb=" OD1 ASP B 470 " model vdw 1.989 3.040 nonbonded pdb=" O ASN A 111 " pdb=" OG SER A 118 " model vdw 2.148 3.040 nonbonded pdb=" OH TYR A 358 " pdb=" OE1 GLN B 70 " model vdw 2.160 3.040 nonbonded pdb=" O ASN B 111 " pdb=" OG SER B 118 " model vdw 2.182 3.040 ... (remaining 62663 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 1 through 481 or (resid 501 and (name C2 or name C2A or na \ me C3 or name C4 or name C4A or name C5 or name C5A or name C6 or name N1 or nam \ e O1P or name O2P or name O3 or name O3P or name O4P)))) selection = chain 'B' } 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: 6.700 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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 8.580 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7446 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 : 0.003 0.124 7800 Z= 0.140 Angle : 0.446 8.566 10565 Z= 0.243 Chirality : 0.037 0.145 1194 Planarity : 0.006 0.116 1362 Dihedral : 13.393 80.788 2912 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.81 (0.28), residues: 958 helix: 2.80 (0.26), residues: 436 sheet: 0.42 (0.44), residues: 110 loop : -0.36 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 76 TYR 0.009 0.001 TYR B 165 PHE 0.009 0.001 PHE B 237 TRP 0.011 0.001 TRP A 267 HIS 0.002 0.000 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 ( 7800) covalent geometry : angle 0.44605 / 0.24 (10565) hydrogen bonds : bond 0.11936 / 6.92 ( 368) hydrogen bonds : angle 5.72786 / 4.00 ( 1032) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 148 time to evaluate : 0.343 Fit side-chains REVERT: A 30 MET cc_start: 0.7644 (mmp) cc_final: 0.6825 (ptp) REVERT: B 464 LYS cc_start: 0.6743 (mttt) cc_final: 0.6443 (ttpp) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1252 time to fit residues: 23.6951 Evaluate side-chains 99 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 9.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 74 optimal weight: 4.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3902 r_free = 0.3902 target = 0.166427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.134597 restraints weight = 8730.918| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 2.17 r_work: 0.3375 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 7800 Z= 0.264 Angle : 0.664 6.700 10565 Z= 0.350 Chirality : 0.048 0.165 1194 Planarity : 0.005 0.066 1362 Dihedral : 4.605 20.947 1036 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 1.17 % Allowed : 7.04 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.56 (0.26), residues: 958 helix: 1.51 (0.24), residues: 446 sheet: -0.04 (0.42), residues: 110 loop : -0.77 (0.29), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 350 TYR 0.030 0.002 TYR B 369 PHE 0.017 0.002 PHE B 466 TRP 0.019 0.002 TRP A 267 HIS 0.005 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00640 / 0.26 ( 7800) covalent geometry : angle 0.66421 / 0.35 (10565) hydrogen bonds : bond 0.07057 / 4.66 ( 368) hydrogen bonds : angle 5.22670 / 3.69 ( 1032) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 100 time to evaluate : 0.231 Fit side-chains REVERT: A 27 LYS cc_start: 0.7613 (tttm) cc_final: 0.6907 (tppt) REVERT: A 31 ASP cc_start: 0.7549 (t0) cc_final: 0.6564 (m-30) REVERT: A 224 LYS cc_start: 0.8298 (mptt) cc_final: 0.8094 (mmtp) REVERT: B 31 ASP cc_start: 0.7513 (t0) cc_final: 0.6557 (m-30) REVERT: B 464 LYS cc_start: 0.7646 (mttt) cc_final: 0.7117 (ttpp) outliers start: 10 outliers final: 8 residues processed: 107 average time/residue: 0.1043 time to fit residues: 14.9296 Evaluate side-chains 99 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 91 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 349 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 43 optimal weight: 5.9990 chunk 61 optimal weight: 0.4980 chunk 28 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 80 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 300 ASN B 70 GLN B 189 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.170621 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.138760 restraints weight = 8614.732| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.17 r_work: 0.3435 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.4099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7800 Z= 0.113 Angle : 0.460 5.379 10565 Z= 0.247 Chirality : 0.039 0.146 1194 Planarity : 0.004 0.050 1362 Dihedral : 3.983 13.237 1036 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 0.47 % Allowed : 10.68 % Favored : 88.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.80 (0.26), residues: 958 helix: 1.69 (0.24), residues: 444 sheet: 0.15 (0.43), residues: 110 loop : -0.64 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 76 TYR 0.010 0.001 TYR A 358 PHE 0.010 0.001 PHE B 338 TRP 0.011 0.001 TRP A 267 HIS 0.002 0.000 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.11 ( 7800) covalent geometry : angle 0.46029 / 0.25 (10565) hydrogen bonds : bond 0.04498 / 3.00 ( 368) hydrogen bonds : angle 4.78506 / 3.37 ( 1032) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 95 time to evaluate : 0.370 Fit side-chains REVERT: A 30 MET cc_start: 0.7728 (mmm) cc_final: 0.6882 (ptp) REVERT: A 31 ASP cc_start: 0.7437 (t0) cc_final: 0.6705 (m-30) REVERT: A 35 GLU cc_start: 0.7542 (mm-30) cc_final: 0.7049 (mt-10) REVERT: A 76 ARG cc_start: 0.7444 (mtm110) cc_final: 0.7232 (ttp80) REVERT: A 224 LYS cc_start: 0.8208 (mptt) cc_final: 0.7959 (mmtp) REVERT: B 31 ASP cc_start: 0.7399 (t0) cc_final: 0.6647 (m-30) REVERT: B 35 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7113 (mt-10) REVERT: B 223 GLU cc_start: 0.7554 (tt0) cc_final: 0.7290 (tt0) REVERT: B 464 LYS cc_start: 0.7576 (mttt) cc_final: 0.7042 (ttpp) outliers start: 4 outliers final: 3 residues processed: 97 average time/residue: 0.1070 time to fit residues: 13.9124 Evaluate side-chains 93 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 90 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 15 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 59 optimal weight: 0.0040 chunk 2 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- 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 = 0.3882 r_free = 0.3882 target = 0.164992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.133623 restraints weight = 8843.156| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.07 r_work: 0.3405 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 7800 Z= 0.137 Angle : 0.475 5.127 10565 Z= 0.251 Chirality : 0.040 0.143 1194 Planarity : 0.004 0.043 1362 Dihedral : 3.935 13.569 1036 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.17 % Allowed : 11.85 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.73 (0.26), residues: 958 helix: 1.68 (0.24), residues: 444 sheet: 0.07 (0.42), residues: 110 loop : -0.73 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 76 TYR 0.012 0.001 TYR B 369 PHE 0.011 0.001 PHE B 466 TRP 0.019 0.002 TRP A 421 HIS 0.003 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 7800) covalent geometry : angle 0.47463 / 0.25 (10565) hydrogen bonds : bond 0.04837 / 3.21 ( 368) hydrogen bonds : angle 4.76908 / 3.35 ( 1032) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.319 Fit side-chains REVERT: A 1 MET cc_start: 0.4511 (ppp) cc_final: 0.3715 (mtp) REVERT: A 27 LYS cc_start: 0.7690 (tttm) cc_final: 0.7057 (tppt) REVERT: A 31 ASP cc_start: 0.7466 (t0) cc_final: 0.6830 (m-30) REVERT: A 35 GLU cc_start: 0.7595 (mm-30) cc_final: 0.7120 (mt-10) REVERT: A 76 ARG cc_start: 0.7507 (mtm110) cc_final: 0.7291 (ttp80) REVERT: A 224 LYS cc_start: 0.8263 (mptt) cc_final: 0.7969 (mmtp) REVERT: B 31 ASP cc_start: 0.7443 (t0) cc_final: 0.6734 (m-30) REVERT: B 35 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7142 (mt-10) REVERT: B 76 ARG cc_start: 0.7725 (mtm110) cc_final: 0.7475 (ttp80) REVERT: B 464 LYS cc_start: 0.7682 (mttt) cc_final: 0.7178 (ttpp) outliers start: 10 outliers final: 6 residues processed: 97 average time/residue: 0.1029 time to fit residues: 13.2971 Evaluate side-chains 95 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 439 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 80 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 91 optimal weight: 0.8980 chunk 9 optimal weight: 0.1980 chunk 61 optimal weight: 0.7980 chunk 59 optimal weight: 0.0050 chunk 36 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 1 optimal weight: 0.0670 chunk 93 optimal weight: 0.2980 overall best weight: 0.2732 ------------------------------------------------------------------------------- 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 = 0.3977 r_free = 0.3977 target = 0.173994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.143757 restraints weight = 8589.388| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.07 r_work: 0.3491 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3350 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 7800 Z= 0.083 Angle : 0.409 5.327 10565 Z= 0.218 Chirality : 0.037 0.126 1194 Planarity : 0.004 0.039 1362 Dihedral : 3.584 12.646 1036 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 0.94 % Allowed : 11.62 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.16 (0.27), residues: 958 helix: 2.00 (0.25), residues: 444 sheet: 0.43 (0.44), residues: 110 loop : -0.52 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 76 TYR 0.014 0.001 TYR B 392 PHE 0.009 0.001 PHE B 428 TRP 0.019 0.002 TRP B 421 HIS 0.002 0.000 HIS B 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00171 / 0.08 ( 7800) covalent geometry : angle 0.40928 / 0.22 (10565) hydrogen bonds : bond 0.03195 / 2.13 ( 368) hydrogen bonds : angle 4.38488 / 3.07 ( 1032) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 100 time to evaluate : 0.320 Fit side-chains REVERT: A 1 MET cc_start: 0.4404 (ppp) cc_final: 0.3564 (mtp) REVERT: A 30 MET cc_start: 0.7488 (mmm) cc_final: 0.6915 (ptt) REVERT: A 31 ASP cc_start: 0.7400 (t0) cc_final: 0.6702 (m-30) REVERT: A 35 GLU cc_start: 0.7527 (mm-30) cc_final: 0.6934 (mt-10) REVERT: A 76 ARG cc_start: 0.7406 (mtm110) cc_final: 0.7116 (ttp80) REVERT: A 224 LYS cc_start: 0.8214 (mptt) cc_final: 0.7958 (mmtp) REVERT: B 31 ASP cc_start: 0.7405 (t0) cc_final: 0.6649 (m-30) REVERT: B 35 GLU cc_start: 0.7492 (mm-30) cc_final: 0.6948 (mt-10) REVERT: B 343 GLU cc_start: 0.8439 (mm-30) cc_final: 0.8089 (mt-10) REVERT: B 464 LYS cc_start: 0.7652 (mttt) cc_final: 0.7095 (ttpp) outliers start: 8 outliers final: 4 residues processed: 107 average time/residue: 0.1056 time to fit residues: 14.9862 Evaluate side-chains 96 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 336 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 87 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 89 optimal weight: 0.0040 overall best weight: 0.7392 ------------------------------------------------------------------------------- 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 = 0.3923 r_free = 0.3923 target = 0.168876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.137606 restraints weight = 8642.584| |-----------------------------------------------------------------------------| r_work (start): 0.3571 rms_B_bonded: 2.05 r_work: 0.3449 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.4598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 7800 Z= 0.101 Angle : 0.431 5.778 10565 Z= 0.226 Chirality : 0.038 0.135 1194 Planarity : 0.004 0.037 1362 Dihedral : 3.562 12.600 1036 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.80 % Favored : 95.20 % Rotamer: Outliers : 0.70 % Allowed : 11.74 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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 (0.27), residues: 958 helix: 1.95 (0.25), residues: 446 sheet: 0.39 (0.43), residues: 110 loop : -0.55 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 76 TYR 0.015 0.001 TYR B 392 PHE 0.025 0.001 PHE A 428 TRP 0.015 0.002 TRP B 421 HIS 0.002 0.000 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.10 ( 7800) covalent geometry : angle 0.43056 / 0.23 (10565) hydrogen bonds : bond 0.03785 / 2.51 ( 368) hydrogen bonds : angle 4.43012 / 3.11 ( 1032) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 95 time to evaluate : 0.318 Fit side-chains REVERT: A 1 MET cc_start: 0.4408 (ppp) cc_final: 0.3545 (mtp) REVERT: A 27 LYS cc_start: 0.7718 (tttm) cc_final: 0.7223 (ttmt) REVERT: A 30 MET cc_start: 0.7598 (mmm) cc_final: 0.6997 (ptt) REVERT: A 31 ASP cc_start: 0.7464 (t0) cc_final: 0.6810 (m-30) REVERT: A 35 GLU cc_start: 0.7562 (mm-30) cc_final: 0.7005 (mt-10) REVERT: A 76 ARG cc_start: 0.7493 (mtm110) cc_final: 0.7192 (ttp80) REVERT: A 224 LYS cc_start: 0.8261 (mptt) cc_final: 0.7983 (mmtp) REVERT: B 30 MET cc_start: 0.7769 (mmt) cc_final: 0.6687 (ptt) REVERT: B 31 ASP cc_start: 0.7471 (t0) cc_final: 0.6757 (m-30) REVERT: B 35 GLU cc_start: 0.7558 (mm-30) cc_final: 0.7085 (mt-10) REVERT: B 76 ARG cc_start: 0.7565 (ttp80) cc_final: 0.7298 (ttp80) REVERT: B 343 GLU cc_start: 0.8570 (mm-30) cc_final: 0.8260 (mt-10) REVERT: B 464 LYS cc_start: 0.7714 (mttt) cc_final: 0.7209 (ttpp) outliers start: 6 outliers final: 4 residues processed: 100 average time/residue: 0.1028 time to fit residues: 13.7865 Evaluate side-chains 92 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 88 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 336 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 90 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3904 r_free = 0.3904 target = 0.167090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.135817 restraints weight = 8616.201| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.04 r_work: 0.3429 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3293 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3293 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 7800 Z= 0.115 Angle : 0.448 7.291 10565 Z= 0.234 Chirality : 0.038 0.136 1194 Planarity : 0.004 0.039 1362 Dihedral : 3.664 12.578 1036 Min Nonbonded Distance : 2.631 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.29 % Allowed : 11.74 % Favored : 86.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.01 (0.27), residues: 958 helix: 1.88 (0.25), residues: 446 sheet: 0.26 (0.43), residues: 110 loop : -0.57 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 76 TYR 0.017 0.001 TYR B 392 PHE 0.021 0.001 PHE B 428 TRP 0.012 0.002 TRP A 421 HIS 0.003 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.11 ( 7800) covalent geometry : angle 0.44832 / 0.23 (10565) hydrogen bonds : bond 0.04202 / 2.79 ( 368) hydrogen bonds : angle 4.50982 / 3.17 ( 1032) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 0.263 Fit side-chains REVERT: A 30 MET cc_start: 0.7596 (mmm) cc_final: 0.6940 (ptt) REVERT: A 31 ASP cc_start: 0.7486 (t0) cc_final: 0.6843 (m-30) REVERT: A 35 GLU cc_start: 0.7570 (mm-30) cc_final: 0.7008 (mt-10) REVERT: A 224 LYS cc_start: 0.8268 (mptt) cc_final: 0.7938 (mmtp) REVERT: B 30 MET cc_start: 0.7787 (mmt) cc_final: 0.6599 (ptt) REVERT: B 31 ASP cc_start: 0.7465 (t0) cc_final: 0.6802 (m-30) REVERT: B 35 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7113 (mt-10) REVERT: B 76 ARG cc_start: 0.7618 (ttp80) cc_final: 0.7302 (ttp80) REVERT: B 343 GLU cc_start: 0.8568 (mm-30) cc_final: 0.8258 (mt-10) REVERT: B 464 LYS cc_start: 0.7781 (mttt) cc_final: 0.7266 (ttpp) outliers start: 11 outliers final: 9 residues processed: 97 average time/residue: 0.0956 time to fit residues: 12.7027 Evaluate side-chains 97 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 88 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain A residue 460 SER Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 439 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 24 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 chunk 16 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 44 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 0.0170 chunk 55 optimal weight: 0.0570 chunk 62 optimal weight: 2.9990 chunk 48 optimal weight: 0.0170 overall best weight: 0.3574 ------------------------------------------------------------------------------- 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 = 0.3948 r_free = 0.3948 target = 0.171148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.139724 restraints weight = 8657.762| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 2.06 r_work: 0.3473 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 7800 Z= 0.080 Angle : 0.406 6.750 10565 Z= 0.213 Chirality : 0.037 0.129 1194 Planarity : 0.004 0.038 1362 Dihedral : 3.449 11.978 1036 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 0.82 % Allowed : 12.32 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.27 (0.27), residues: 958 helix: 2.05 (0.25), residues: 446 sheet: 0.49 (0.43), residues: 110 loop : -0.42 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 76 TYR 0.019 0.001 TYR B 392 PHE 0.020 0.001 PHE B 428 TRP 0.014 0.001 TRP B 421 HIS 0.001 0.000 HIS A 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00168 / 0.08 ( 7800) covalent geometry : angle 0.40601 / 0.21 (10565) hydrogen bonds : bond 0.03215 / 2.14 ( 368) hydrogen bonds : angle 4.31043 / 3.02 ( 1032) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.294 Fit side-chains REVERT: A 30 MET cc_start: 0.7555 (mmm) cc_final: 0.6960 (ptt) REVERT: A 31 ASP cc_start: 0.7478 (t0) cc_final: 0.6839 (m-30) REVERT: A 35 GLU cc_start: 0.7487 (mm-30) cc_final: 0.6921 (mt-10) REVERT: A 76 ARG cc_start: 0.7384 (ttp80) cc_final: 0.7136 (ttp80) REVERT: A 224 LYS cc_start: 0.8261 (mptt) cc_final: 0.7962 (mmtp) REVERT: B 31 ASP cc_start: 0.7459 (t0) cc_final: 0.6713 (m-30) REVERT: B 35 GLU cc_start: 0.7514 (mm-30) cc_final: 0.6962 (mt-10) REVERT: B 76 ARG cc_start: 0.7535 (ttp80) cc_final: 0.7244 (ttp80) REVERT: B 343 GLU cc_start: 0.8521 (mm-30) cc_final: 0.8225 (mt-10) REVERT: B 464 LYS cc_start: 0.7738 (mttt) cc_final: 0.7249 (ttpp) outliers start: 7 outliers final: 6 residues processed: 97 average time/residue: 0.0943 time to fit residues: 12.5241 Evaluate side-chains 92 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 336 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 29 optimal weight: 4.9990 chunk 86 optimal weight: 0.0770 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 4 optimal weight: 0.0870 chunk 26 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.7518 ------------------------------------------------------------------------------- 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 = 0.3972 r_free = 0.3972 target = 0.172944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.140984 restraints weight = 8671.805| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.14 r_work: 0.3468 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.4906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 7800 Z= 0.099 Angle : 0.429 7.419 10565 Z= 0.223 Chirality : 0.038 0.134 1194 Planarity : 0.004 0.040 1362 Dihedral : 3.503 12.144 1036 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.82 % Allowed : 12.32 % Favored : 86.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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 (0.27), residues: 958 helix: 2.03 (0.25), residues: 446 sheet: 0.47 (0.43), residues: 110 loop : -0.46 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 76 TYR 0.026 0.001 TYR B 392 PHE 0.020 0.001 PHE B 428 TRP 0.011 0.001 TRP B 421 HIS 0.002 0.000 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00226 / 0.10 ( 7800) covalent geometry : angle 0.42895 / 0.22 (10565) hydrogen bonds : bond 0.03679 / 2.44 ( 368) hydrogen bonds : angle 4.36739 / 3.07 ( 1032) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.349 Fit side-chains REVERT: A 30 MET cc_start: 0.7566 (mmm) cc_final: 0.6826 (ptt) REVERT: A 31 ASP cc_start: 0.7401 (t0) cc_final: 0.6759 (m-30) REVERT: A 35 GLU cc_start: 0.7462 (mm-30) cc_final: 0.6878 (mt-10) REVERT: A 76 ARG cc_start: 0.7443 (ttp80) cc_final: 0.7165 (ttp80) REVERT: A 224 LYS cc_start: 0.8198 (mptt) cc_final: 0.7861 (mmtp) REVERT: B 17 GLN cc_start: 0.8123 (mt0) cc_final: 0.7781 (mt0) REVERT: B 30 MET cc_start: 0.7675 (mmt) cc_final: 0.6412 (ptt) REVERT: B 31 ASP cc_start: 0.7419 (t0) cc_final: 0.6638 (m-30) REVERT: B 35 GLU cc_start: 0.7492 (mm-30) cc_final: 0.6925 (mt-10) REVERT: B 76 ARG cc_start: 0.7519 (ttp80) cc_final: 0.7236 (ttp80) REVERT: B 343 GLU cc_start: 0.8388 (mm-30) cc_final: 0.8039 (mt-10) REVERT: B 464 LYS cc_start: 0.7730 (mttt) cc_final: 0.7216 (ttpp) outliers start: 7 outliers final: 6 residues processed: 92 average time/residue: 0.0944 time to fit residues: 11.9734 Evaluate side-chains 91 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 336 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 79 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 42 optimal weight: 5.9990 chunk 53 optimal weight: 0.3980 chunk 27 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 75 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3991 r_free = 0.3991 target = 0.173728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.142584 restraints weight = 8594.001| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.02 r_work: 0.3532 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.4971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 7800 Z= 0.089 Angle : 0.416 7.243 10565 Z= 0.217 Chirality : 0.037 0.131 1194 Planarity : 0.004 0.041 1362 Dihedral : 3.466 12.009 1036 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 0.82 % Allowed : 12.91 % Favored : 86.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.30 (0.27), residues: 958 helix: 2.09 (0.25), residues: 446 sheet: 0.54 (0.43), residues: 110 loop : -0.42 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 76 TYR 0.026 0.001 TYR B 392 PHE 0.020 0.001 PHE B 428 TRP 0.012 0.001 TRP B 421 HIS 0.002 0.000 HIS A 351 Details of bonding type rmsd/Z covalent geometry : bond 0.00196 / 0.09 ( 7800) covalent geometry : angle 0.41637 / 0.22 (10565) hydrogen bonds : bond 0.03442 / 2.29 ( 368) hydrogen bonds : angle 4.31624 / 3.03 ( 1032) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 88 time to evaluate : 0.319 Fit side-chains REVERT: A 30 MET cc_start: 0.7625 (mmm) cc_final: 0.7054 (ptt) REVERT: A 31 ASP cc_start: 0.7503 (t0) cc_final: 0.6826 (m-30) REVERT: A 35 GLU cc_start: 0.7419 (mm-30) cc_final: 0.6892 (mt-10) REVERT: A 76 ARG cc_start: 0.7465 (ttp80) cc_final: 0.7238 (ttp80) REVERT: A 224 LYS cc_start: 0.8287 (mptt) cc_final: 0.7977 (mmtp) REVERT: B 17 GLN cc_start: 0.8090 (mt0) cc_final: 0.7780 (mt0) REVERT: B 31 ASP cc_start: 0.7531 (t0) cc_final: 0.6788 (m-30) REVERT: B 35 GLU cc_start: 0.7487 (mm-30) cc_final: 0.6978 (mt-10) REVERT: B 76 ARG cc_start: 0.7511 (ttp80) cc_final: 0.7286 (ttp80) REVERT: B 343 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8127 (mt-10) REVERT: B 464 LYS cc_start: 0.7739 (mttt) cc_final: 0.7281 (ttpp) outliers start: 7 outliers final: 6 residues processed: 94 average time/residue: 0.1156 time to fit residues: 14.4765 Evaluate side-chains 92 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 145 VAL Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 336 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 3 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 43 optimal weight: 0.6980 chunk 83 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.172496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.141722 restraints weight = 8662.064| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.97 r_work: 0.3516 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3375 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3375 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8310 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 7800 Z= 0.106 Angle : 0.440 7.149 10565 Z= 0.228 Chirality : 0.038 0.135 1194 Planarity : 0.004 0.058 1362 Dihedral : 3.548 12.162 1036 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.70 % Allowed : 13.38 % Favored : 85.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 1.19 (0.27), residues: 958 helix: 2.01 (0.25), residues: 446 sheet: 0.48 (0.44), residues: 110 loop : -0.50 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 134 TYR 0.026 0.001 TYR B 392 PHE 0.019 0.001 PHE B 428 TRP 0.011 0.001 TRP A 267 HIS 0.002 0.001 HIS B 269 Details of bonding type rmsd/Z covalent geometry : bond 0.00245 / 0.11 ( 7800) covalent geometry : angle 0.43966 / 0.23 (10565) hydrogen bonds : bond 0.03845 / 2.55 ( 368) hydrogen bonds : angle 4.39737 / 3.09 ( 1032) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2161.58 seconds wall clock time: 37 minutes 51.58 seconds (2271.58 seconds total)