Starting phenix.real_space_refine on Fri Aug 22 20:14:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zpi_60345/08_2025/8zpi_60345_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zpi_60345/08_2025/8zpi_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_60345/08_2025/8zpi_60345_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zpi_60345/08_2025/8zpi_60345_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zpi_60345/08_2025/8zpi_60345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zpi_60345/08_2025/8zpi_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/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: 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: 3 Time building chain proxies: 1.82, 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: 0.60 Conformation dependent library (CDL) restraints added in 433.7 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.21 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: 0.94 Time building geometry restraints manager: 0.83 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=" 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=" CB PRO A 391 " pdb=" CG PRO A 391 " ideal model delta sigma weight residual 1.492 1.568 -0.076 5.00e-02 4.00e+02 2.30e+00 bond pdb=" N PRO B 391 " pdb=" CA PRO B 391 " ideal model delta sigma weight residual 1.472 1.458 0.013 1.34e-02 5.57e+03 9.77e-01 bond pdb=" CG1 ILE B 465 " pdb=" CD1 ILE B 465 " ideal model delta sigma weight residual 1.513 1.479 0.034 3.90e-02 6.57e+02 7.51e-01 bond pdb=" CA GLY B 144 " pdb=" C GLY B 144 " ideal model delta sigma weight residual 1.519 1.511 0.008 8.90e-03 1.26e+04 7.27e-01 ... (remaining 7795 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 10412 1.42 - 2.84: 130 2.84 - 4.26: 19 4.26 - 5.68: 1 5.68 - 7.10: 3 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=" 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 angle pdb=" N GLY A 66 " pdb=" CA GLY A 66 " pdb=" C GLY A 66 " ideal model delta sigma weight residual 115.33 109.59 5.74 2.74e+00 1.33e-01 4.39e+00 ... (remaining 10560 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 4169 16.16 - 32.32: 435 32.32 - 48.47: 99 48.47 - 64.63: 16 64.63 - 80.79: 1 Dihedral angle restraints: 4720 sinusoidal: 1918 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 4717 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=" 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=" C ARG A 390 " -0.069 5.00e-02 4.00e+02 1.02e-01 1.68e+01 pdb=" N PRO A 391 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO A 391 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 391 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 76 " -0.089 9.50e-02 1.11e+02 4.03e-02 1.26e+00 pdb=" NE ARG B 76 " 0.008 2.00e-02 2.50e+03 pdb=" CZ ARG B 76 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG B 76 " 0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG B 76 " -0.000 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: 3.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 7.630 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.290 ------------------------------------------------------------------------------- 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= 0.112 Angle : 0.421 7.102 10565 Z= 0.238 Chirality : 0.037 0.145 1194 Planarity : 0.005 0.116 1362 Dihedral : 13.378 80.788 2908 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 aren 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 covalent geometry : bond 0.00281 ( 7800) covalent geometry : angle 0.42051 (10565) hydrogen bonds : bond 0.11936 ( 368) hydrogen bonds : angle 5.72786 ( 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 : 0.255 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: 0.0927 time to fit residues: 17.7239 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 : 0.176 ------------------------------------------------------------------------------- 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... 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 = 0.164799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.133689 restraints weight = 8758.430| |-----------------------------------------------------------------------------| r_work (start): 0.3522 rms_B_bonded: 2.02 r_work: 0.3400 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 7800 Z= 0.259 Angle : 0.644 7.224 10565 Z= 0.337 Chirality : 0.047 0.186 1194 Planarity : 0.005 0.067 1362 Dihedral : 4.613 33.025 1032 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % 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 aren not related in a simple way. whole: 0.66 (0.26), residues: 958 helix: 1.61 (0.24), residues: 444 sheet: 0.04 (0.43), residues: 110 loop : -0.74 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 76 TYR 0.029 0.002 TYR B 369 PHE 0.017 0.002 PHE A 237 TRP 0.021 0.003 TRP B 267 HIS 0.006 0.002 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00638 ( 7800) covalent geometry : angle 0.64406 (10565) hydrogen bonds : bond 0.07204 ( 368) hydrogen bonds : angle 5.26823 ( 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 107 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 0.295 Fit side-chains REVERT: A 27 LYS cc_start: 0.7608 (tttm) cc_final: 0.6927 (tppt) REVERT: A 31 ASP cc_start: 0.7608 (t0) cc_final: 0.6616 (m-30) REVERT: B 31 ASP cc_start: 0.7541 (t0) cc_final: 0.6614 (m-30) REVERT: B 464 LYS cc_start: 0.7632 (mttt) cc_final: 0.7123 (ttpp) outliers start: 10 outliers final: 8 residues processed: 104 average time/residue: 0.0945 time to fit residues: 13.3677 Evaluate side-chains 91 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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: 0.6980 chunk 61 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 chunk 48 optimal weight: 6.9990 chunk 80 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 57 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 70 GLN A 189 HIS A 300 ASN B 70 GLN B 189 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.167666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.136423 restraints weight = 8653.937| |-----------------------------------------------------------------------------| r_work (start): 0.3551 rms_B_bonded: 2.03 r_work: 0.3430 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3290 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3290 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7800 Z= 0.123 Angle : 0.475 5.194 10565 Z= 0.253 Chirality : 0.040 0.140 1194 Planarity : 0.004 0.054 1362 Dihedral : 4.358 39.366 1032 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 0.70 % Allowed : 10.80 % Favored : 88.50 % 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 aren not related in a simple way. whole: 0.77 (0.26), residues: 958 helix: 1.65 (0.24), residues: 444 sheet: 0.16 (0.44), residues: 110 loop : -0.65 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 76 TYR 0.011 0.001 TYR B 165 PHE 0.011 0.001 PHE B 338 TRP 0.012 0.002 TRP B 267 HIS 0.003 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 7800) covalent geometry : angle 0.47470 (10565) hydrogen bonds : bond 0.04768 ( 368) hydrogen bonds : angle 4.83786 ( 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 102 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 96 time to evaluate : 0.324 Fit side-chains REVERT: A 30 MET cc_start: 0.7761 (mmm) cc_final: 0.6963 (ptp) REVERT: A 31 ASP cc_start: 0.7534 (t0) cc_final: 0.6827 (m-30) REVERT: A 35 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7162 (mt-10) REVERT: A 73 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7494 (tm-30) REVERT: A 76 ARG cc_start: 0.7544 (mtm110) cc_final: 0.7337 (ttp80) REVERT: B 31 ASP cc_start: 0.7517 (t0) cc_final: 0.6755 (m-30) REVERT: B 35 GLU cc_start: 0.7635 (mm-30) cc_final: 0.7211 (mt-10) REVERT: B 223 GLU cc_start: 0.7618 (tt0) cc_final: 0.7372 (tt0) REVERT: B 343 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8202 (mt-10) REVERT: B 464 LYS cc_start: 0.7609 (mttt) cc_final: 0.7101 (ttpp) outliers start: 6 outliers final: 5 residues processed: 98 average time/residue: 0.1035 time to fit residues: 13.6154 Evaluate side-chains 97 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 15 SER Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 439 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 59 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 90 optimal weight: 5.9990 chunk 73 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3852 r_free = 0.3852 target = 0.162108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.130698 restraints weight = 8907.446| |-----------------------------------------------------------------------------| r_work (start): 0.3489 rms_B_bonded: 2.07 r_work: 0.3362 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 7800 Z= 0.201 Angle : 0.544 5.381 10565 Z= 0.284 Chirality : 0.042 0.148 1194 Planarity : 0.005 0.048 1362 Dihedral : 4.480 35.931 1032 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer: Outliers : 2.00 % Allowed : 11.15 % 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 aren not related in a simple way. whole: 0.47 (0.26), residues: 958 helix: 1.43 (0.24), residues: 444 sheet: -0.01 (0.42), residues: 110 loop : -0.83 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 76 TYR 0.016 0.002 TYR B 369 PHE 0.013 0.002 PHE A 237 TRP 0.017 0.003 TRP A 421 HIS 0.004 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00501 ( 7800) covalent geometry : angle 0.54387 (10565) hydrogen bonds : bond 0.05881 ( 368) hydrogen bonds : angle 5.02975 ( 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: 17 poor density : 83 time to evaluate : 0.314 Fit side-chains REVERT: A 1 MET cc_start: 0.4933 (ppp) cc_final: 0.4086 (mtp) REVERT: A 27 LYS cc_start: 0.7702 (tttm) cc_final: 0.7086 (tppt) REVERT: A 31 ASP cc_start: 0.7503 (t0) cc_final: 0.6860 (m-30) REVERT: A 35 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7230 (mt-10) REVERT: B 31 ASP cc_start: 0.7478 (t0) cc_final: 0.6739 (m-30) REVERT: B 35 GLU cc_start: 0.7661 (mm-30) cc_final: 0.7272 (mt-10) REVERT: B 464 LYS cc_start: 0.7737 (mttt) cc_final: 0.7221 (ttpp) outliers start: 17 outliers final: 12 residues processed: 97 average time/residue: 0.1074 time to fit residues: 13.8522 Evaluate side-chains 93 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 THR Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 439 LEU 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 139 ASP Chi-restraints excluded: chain B residue 229 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 80 optimal weight: 3.9990 chunk 17 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 91 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 61 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.3898 r_free = 0.3898 target = 0.166200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.134998 restraints weight = 8762.193| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.03 r_work: 0.3392 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3250 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3250 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.4652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7800 Z= 0.135 Angle : 0.481 5.737 10565 Z= 0.253 Chirality : 0.040 0.138 1194 Planarity : 0.004 0.043 1362 Dihedral : 4.348 38.431 1032 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 1.29 % Allowed : 11.97 % Favored : 86.74 % 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 aren not related in a simple way. whole: 0.61 (0.26), residues: 958 helix: 1.55 (0.24), residues: 444 sheet: 0.03 (0.43), residues: 110 loop : -0.75 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 76 TYR 0.014 0.001 TYR B 392 PHE 0.010 0.001 PHE B 466 TRP 0.019 0.002 TRP B 421 HIS 0.003 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 7800) covalent geometry : angle 0.48087 (10565) hydrogen bonds : bond 0.04792 ( 368) hydrogen bonds : angle 4.81765 ( 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 95 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 84 time to evaluate : 0.323 Fit side-chains REVERT: A 1 MET cc_start: 0.4970 (OUTLIER) cc_final: 0.4103 (mtp) REVERT: A 27 LYS cc_start: 0.7732 (tttm) cc_final: 0.7188 (tppt) REVERT: A 31 ASP cc_start: 0.7516 (t0) cc_final: 0.6881 (m-30) REVERT: A 35 GLU cc_start: 0.7641 (mm-30) cc_final: 0.7143 (mt-10) REVERT: B 31 ASP cc_start: 0.7522 (t0) cc_final: 0.6871 (m-30) REVERT: B 35 GLU cc_start: 0.7625 (mm-30) cc_final: 0.7221 (mt-10) REVERT: B 464 LYS cc_start: 0.7742 (mttt) cc_final: 0.7293 (ttpp) outliers start: 11 outliers final: 9 residues processed: 91 average time/residue: 0.1140 time to fit residues: 13.7587 Evaluate side-chains 91 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 229 THR 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 15 SER Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 439 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.9980 chunk 3 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 31 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 87 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 89 optimal weight: 5.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.3909 r_free = 0.3909 target = 0.167641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.136352 restraints weight = 8647.790| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 2.05 r_work: 0.3427 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4753 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 : 0.438 5.604 10565 Z= 0.230 Chirality : 0.038 0.132 1194 Planarity : 0.004 0.041 1362 Dihedral : 4.146 40.017 1032 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.22 % Favored : 94.78 % Rotamer: Outliers : 1.53 % Allowed : 12.79 % Favored : 85.68 % 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 aren not related in a simple way. whole: 0.86 (0.27), residues: 958 helix: 1.78 (0.25), residues: 444 sheet: 0.12 (0.42), residues: 110 loop : -0.66 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 76 TYR 0.015 0.001 TYR B 392 PHE 0.010 0.001 PHE B 428 TRP 0.021 0.002 TRP A 421 HIS 0.002 0.000 HIS B 351 Details of bonding type rmsd covalent geometry : bond 0.00223 ( 7800) covalent geometry : angle 0.43789 (10565) hydrogen bonds : bond 0.03892 ( 368) hydrogen bonds : angle 4.57072 ( 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 106 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.313 Fit side-chains REVERT: A 1 MET cc_start: 0.4902 (OUTLIER) cc_final: 0.4059 (mtp) REVERT: A 27 LYS cc_start: 0.7714 (tttm) cc_final: 0.7160 (ttmt) REVERT: A 30 MET cc_start: 0.7679 (mmm) cc_final: 0.6978 (ptt) REVERT: A 31 ASP cc_start: 0.7477 (t0) cc_final: 0.6849 (m-30) REVERT: A 35 GLU cc_start: 0.7576 (mm-30) cc_final: 0.7042 (mt-10) REVERT: B 31 ASP cc_start: 0.7431 (t0) cc_final: 0.6732 (m-30) REVERT: B 35 GLU cc_start: 0.7573 (mm-30) cc_final: 0.7122 (mt-10) REVERT: B 76 ARG cc_start: 0.7615 (mtm110) cc_final: 0.7385 (ttp80) REVERT: B 343 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8242 (mt-10) REVERT: B 464 LYS cc_start: 0.7751 (mttt) cc_final: 0.7240 (ttpp) outliers start: 13 outliers final: 6 residues processed: 104 average time/residue: 0.1152 time to fit residues: 15.8266 Evaluate side-chains 93 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 380 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 90 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 14 optimal weight: 0.1980 chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 0.2980 chunk 28 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 91 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.3939 r_free = 0.3939 target = 0.169933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.138538 restraints weight = 8640.695| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.04 r_work: 0.3472 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.4837 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= 0.097 Angle : 0.434 7.307 10565 Z= 0.227 Chirality : 0.038 0.133 1194 Planarity : 0.004 0.039 1362 Dihedral : 4.077 39.999 1032 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.82 % Allowed : 14.08 % Favored : 85.09 % 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 aren not related in a simple way. whole: 0.99 (0.27), residues: 958 helix: 1.90 (0.25), residues: 444 sheet: 0.19 (0.42), residues: 110 loop : -0.60 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 76 TYR 0.022 0.001 TYR B 392 PHE 0.022 0.001 PHE B 428 TRP 0.022 0.002 TRP A 421 HIS 0.002 0.000 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00216 ( 7800) covalent geometry : angle 0.43399 (10565) hydrogen bonds : bond 0.03795 ( 368) hydrogen bonds : angle 4.49516 ( 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 93 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 0.318 Fit side-chains REVERT: A 1 MET cc_start: 0.4880 (OUTLIER) cc_final: 0.4033 (mtp) REVERT: A 27 LYS cc_start: 0.7682 (tttm) cc_final: 0.7162 (ttmt) REVERT: A 30 MET cc_start: 0.7617 (mmm) cc_final: 0.6856 (ptt) REVERT: A 31 ASP cc_start: 0.7454 (t0) cc_final: 0.6812 (m-30) REVERT: A 35 GLU cc_start: 0.7545 (mm-30) cc_final: 0.6991 (mt-10) REVERT: B 30 MET cc_start: 0.7629 (mmt) cc_final: 0.6442 (ptt) REVERT: B 31 ASP cc_start: 0.7449 (t0) cc_final: 0.6755 (m-30) REVERT: B 35 GLU cc_start: 0.7506 (mm-30) cc_final: 0.7042 (mt-10) REVERT: B 76 ARG cc_start: 0.7643 (mtm110) cc_final: 0.7431 (ttp80) REVERT: B 343 GLU cc_start: 0.8421 (mm-30) cc_final: 0.8112 (mt-10) REVERT: B 464 LYS cc_start: 0.7739 (mttt) cc_final: 0.7230 (ttpp) outliers start: 7 outliers final: 6 residues processed: 90 average time/residue: 0.1003 time to fit residues: 12.1712 Evaluate side-chains 91 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 84 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 380 VAL 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 380 VAL 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: 4.9990 chunk 16 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 65 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3954 r_free = 0.3954 target = 0.170924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.140359 restraints weight = 8794.812| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 1.97 r_work: 0.3493 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.4907 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= 0.107 Angle : 0.446 6.842 10565 Z= 0.231 Chirality : 0.038 0.133 1194 Planarity : 0.004 0.039 1362 Dihedral : 4.058 39.333 1032 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.41 % Allowed : 13.62 % Favored : 84.98 % 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 aren not related in a simple way. whole: 0.97 (0.27), residues: 958 helix: 1.90 (0.25), residues: 444 sheet: 0.12 (0.41), residues: 110 loop : -0.61 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 76 TYR 0.026 0.001 TYR B 392 PHE 0.019 0.001 PHE B 428 TRP 0.024 0.002 TRP A 421 HIS 0.002 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 7800) covalent geometry : angle 0.44566 (10565) hydrogen bonds : bond 0.04024 ( 368) hydrogen bonds : angle 4.52021 ( 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 99 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.291 Fit side-chains REVERT: A 1 MET cc_start: 0.4893 (OUTLIER) cc_final: 0.4038 (mtp) REVERT: A 30 MET cc_start: 0.7692 (mmm) cc_final: 0.7073 (ptt) REVERT: A 31 ASP cc_start: 0.7578 (t0) cc_final: 0.6959 (m-30) REVERT: A 35 GLU cc_start: 0.7514 (mm-30) cc_final: 0.7027 (mt-10) REVERT: B 31 ASP cc_start: 0.7573 (t0) cc_final: 0.6827 (m-30) REVERT: B 35 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7070 (mt-10) REVERT: B 327 ARG cc_start: 0.8252 (tpt-90) cc_final: 0.7980 (ttt-90) REVERT: B 464 LYS cc_start: 0.7810 (mttt) cc_final: 0.7315 (ttpp) outliers start: 12 outliers final: 7 residues processed: 96 average time/residue: 0.0843 time to fit residues: 11.3219 Evaluate side-chains 93 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 85 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 1 MET Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 380 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 29 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 4 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 75 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.166577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.137413 restraints weight = 8767.200| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 1.87 r_work: 0.3451 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3312 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7800 Z= 0.172 Angle : 0.515 5.749 10565 Z= 0.266 Chirality : 0.040 0.141 1194 Planarity : 0.004 0.042 1362 Dihedral : 4.273 36.449 1032 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 1.53 % Allowed : 13.38 % Favored : 85.09 % 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 aren not related in a simple way. whole: 0.68 (0.26), residues: 958 helix: 1.67 (0.25), residues: 444 sheet: -0.11 (0.41), residues: 110 loop : -0.75 (0.29), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 76 TYR 0.019 0.001 TYR A 392 PHE 0.020 0.002 PHE B 428 TRP 0.024 0.003 TRP A 421 HIS 0.004 0.001 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 7800) covalent geometry : angle 0.51471 (10565) hydrogen bonds : bond 0.05245 ( 368) hydrogen bonds : angle 4.80931 ( 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 102 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.255 Fit side-chains REVERT: A 27 LYS cc_start: 0.7815 (tttm) cc_final: 0.7420 (ttmt) REVERT: A 30 MET cc_start: 0.7743 (mmm) cc_final: 0.7044 (ptt) REVERT: A 31 ASP cc_start: 0.7600 (t0) cc_final: 0.7001 (m-30) REVERT: A 35 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7143 (mt-10) REVERT: B 30 MET cc_start: 0.7738 (mmt) cc_final: 0.6671 (ptt) REVERT: B 31 ASP cc_start: 0.7597 (t0) cc_final: 0.6883 (m-30) REVERT: B 35 GLU cc_start: 0.7590 (mm-30) cc_final: 0.7165 (mt-10) REVERT: B 327 ARG cc_start: 0.8324 (tpt-90) cc_final: 0.8039 (ttt-90) REVERT: B 464 LYS cc_start: 0.7877 (mttt) cc_final: 0.7431 (ttpp) outliers start: 13 outliers final: 10 residues processed: 98 average time/residue: 0.0951 time to fit residues: 12.6463 Evaluate side-chains 96 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.307 ------------------------------------------------------------------------------- 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 380 VAL Chi-restraints excluded: chain A residue 439 LEU Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 439 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 79 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 54 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.173009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.143369 restraints weight = 8618.470| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 1.95 r_work: 0.3496 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.5066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7800 Z= 0.097 Angle : 0.445 6.333 10565 Z= 0.234 Chirality : 0.038 0.134 1194 Planarity : 0.004 0.042 1362 Dihedral : 4.093 39.954 1032 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.59 % Allowed : 14.32 % Favored : 85.09 % 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 aren not related in a simple way. whole: 0.92 (0.27), residues: 958 helix: 1.83 (0.25), residues: 444 sheet: -0.06 (0.40), residues: 110 loop : -0.56 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 76 TYR 0.029 0.001 TYR B 392 PHE 0.018 0.001 PHE B 428 TRP 0.026 0.002 TRP A 421 HIS 0.002 0.000 HIS B 269 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 7800) covalent geometry : angle 0.44481 (10565) hydrogen bonds : bond 0.03869 ( 368) hydrogen bonds : angle 4.53967 ( 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: 5 poor density : 90 time to evaluate : 0.314 Fit side-chains REVERT: A 1 MET cc_start: 0.4968 (ppp) cc_final: 0.4080 (mtp) REVERT: A 30 MET cc_start: 0.7670 (mmm) cc_final: 0.6981 (ptt) REVERT: A 31 ASP cc_start: 0.7536 (t0) cc_final: 0.6916 (m-30) REVERT: A 35 GLU cc_start: 0.7500 (mm-30) cc_final: 0.7034 (mt-10) REVERT: B 31 ASP cc_start: 0.7541 (t0) cc_final: 0.6819 (m-30) REVERT: B 35 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7024 (mt-10) REVERT: B 327 ARG cc_start: 0.8251 (tpt-90) cc_final: 0.7978 (ttt-90) REVERT: B 464 LYS cc_start: 0.7821 (mttt) cc_final: 0.7359 (ttpp) outliers start: 5 outliers final: 5 residues processed: 94 average time/residue: 0.0910 time to fit residues: 11.4485 Evaluate side-chains 92 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 87 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 336 THR Chi-restraints excluded: chain A residue 380 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 380 VAL Chi-restraints excluded: chain B residue 439 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 3 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 74 optimal weight: 0.0570 chunk 89 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 83 optimal weight: 2.9990 chunk 91 optimal weight: 0.0670 chunk 88 optimal weight: 4.9990 chunk 10 optimal weight: 0.0050 chunk 9 optimal weight: 0.8980 chunk 84 optimal weight: 0.6980 overall best weight: 0.2450 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.175666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.144745 restraints weight = 8519.631| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 1.99 r_work: 0.3558 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.5114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.084 7800 Z= 0.086 Angle : 0.429 6.371 10565 Z= 0.226 Chirality : 0.038 0.164 1194 Planarity : 0.004 0.042 1362 Dihedral : 3.937 41.668 1032 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 0.35 % Allowed : 15.02 % Favored : 84.62 % 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 aren not related in a simple way. whole: 1.13 (0.27), residues: 958 helix: 2.01 (0.25), residues: 444 sheet: 0.23 (0.41), residues: 110 loop : -0.50 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 76 TYR 0.027 0.001 TYR B 392 PHE 0.017 0.001 PHE B 428 TRP 0.028 0.002 TRP A 421 HIS 0.002 0.000 HIS A 351 Details of bonding type rmsd covalent geometry : bond 0.00191 ( 7800) covalent geometry : angle 0.42888 (10565) hydrogen bonds : bond 0.03128 ( 368) hydrogen bonds : angle 4.36313 ( 1032) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2073.14 seconds wall clock time: 36 minutes 15.44 seconds (2175.44 seconds total)