Starting phenix.real_space_refine on Fri Jul 25 12:33:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zpi_60345/07_2025/8zpi_60345_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zpi_60345/07_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8zpi_60345/07_2025/8zpi_60345.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zpi_60345/07_2025/8zpi_60345.map" model { file = "/net/cci-nas-00/data/ceres_data/8zpi_60345/07_2025/8zpi_60345_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zpi_60345/07_2025/8zpi_60345_trim.cif" } resolution = 3.12 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 6.61, per 1000 atoms: 0.86 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: 1.97 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.81 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: 2.10 Time building geometry restraints manager: 2.34 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: 4.030 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: 0.360 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 22.990 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.710 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.011 0.001 TRP A 267 HIS 0.002 0.000 HIS B 269 PHE 0.009 0.001 PHE B 237 TYR 0.009 0.001 TYR B 165 ARG 0.009 0.000 ARG B 76 Details of bonding type rmsd hydrogen bonds : bond 0.11936 ( 368) hydrogen bonds : angle 5.72786 ( 1032) covalent geometry : bond 0.00281 ( 7800) covalent geometry : angle 0.42051 (10565) *********************** 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 : 0.778 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: 0.2418 time to fit residues: 45.8814 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 : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 40 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 38 optimal weight: 0.7980 chunk 75 optimal weight: 0.5980 chunk 29 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 56 optimal weight: 4.9990 chunk 87 optimal weight: 3.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 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 = 0.3914 r_free = 0.3914 target = 0.171417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.141719 restraints weight = 8685.598| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.88 r_work: 0.3437 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7800 Z= 0.131 Angle : 0.518 8.201 10565 Z= 0.273 Chirality : 0.041 0.214 1194 Planarity : 0.004 0.056 1362 Dihedral : 4.188 39.740 1032 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 3.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 0.70 % Allowed : 5.75 % Favored : 93.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.27), residues: 958 helix: 1.98 (0.25), residues: 446 sheet: 0.37 (0.43), residues: 110 loop : -0.27 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 267 HIS 0.002 0.001 HIS A 164 PHE 0.013 0.002 PHE B 136 TYR 0.010 0.001 TYR B 369 ARG 0.011 0.001 ARG B 130 Details of bonding type rmsd hydrogen bonds : bond 0.04161 ( 368) hydrogen bonds : angle 4.59623 ( 1032) covalent geometry : bond 0.00277 ( 7800) covalent geometry : angle 0.51802 (10565) *********************** 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 116 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 110 time to evaluate : 0.829 Fit side-chains REVERT: A 30 MET cc_start: 0.7836 (mmp) cc_final: 0.7019 (ptt) REVERT: A 31 ASP cc_start: 0.7472 (t0) cc_final: 0.6368 (m-30) REVERT: B 1 MET cc_start: 0.4826 (OUTLIER) cc_final: 0.4166 (ttt) REVERT: B 30 MET cc_start: 0.7570 (mmt) cc_final: 0.6436 (ptm) REVERT: B 31 ASP cc_start: 0.7441 (t0) cc_final: 0.6455 (m-30) REVERT: B 35 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7033 (mt-10) REVERT: B 343 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7734 (mt-10) REVERT: B 464 LYS cc_start: 0.7294 (mttt) cc_final: 0.6801 (ttpp) outliers start: 6 outliers final: 2 residues processed: 115 average time/residue: 0.2050 time to fit residues: 32.2175 Evaluate side-chains 96 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 93 time to evaluate : 0.908 ------------------------------------------------------------------------------- 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 310 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 18 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 2 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 91 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3957 r_free = 0.3957 target = 0.171277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.140253 restraints weight = 8617.631| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 2.00 r_work: 0.3484 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3343 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3475 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= 0.124 Angle : 0.465 5.797 10565 Z= 0.244 Chirality : 0.039 0.169 1194 Planarity : 0.004 0.046 1362 Dihedral : 4.131 39.044 1032 Min Nonbonded Distance : 2.634 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.12 % Allowed : 9.62 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.27), residues: 958 helix: 2.01 (0.25), residues: 444 sheet: 0.46 (0.43), residues: 110 loop : -0.40 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 267 HIS 0.003 0.001 HIS B 269 PHE 0.025 0.001 PHE B 428 TYR 0.015 0.001 TYR B 369 ARG 0.008 0.001 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.04534 ( 368) hydrogen bonds : angle 4.57230 ( 1032) covalent geometry : bond 0.00283 ( 7800) covalent geometry : angle 0.46451 (10565) *********************** 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 110 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 0.807 Fit side-chains REVERT: A 30 MET cc_start: 0.8112 (mmp) cc_final: 0.7145 (ptp) REVERT: A 31 ASP cc_start: 0.7494 (t0) cc_final: 0.6728 (m-30) REVERT: A 35 GLU cc_start: 0.7507 (mm-30) cc_final: 0.7145 (mt-10) REVERT: A 223 GLU cc_start: 0.7355 (tt0) cc_final: 0.7091 (tt0) REVERT: B 31 ASP cc_start: 0.7534 (t0) cc_final: 0.6625 (m-30) REVERT: B 223 GLU cc_start: 0.7411 (tt0) cc_final: 0.7174 (tt0) REVERT: B 464 LYS cc_start: 0.7541 (mttt) cc_final: 0.7049 (ttpp) outliers start: 1 outliers final: 1 residues processed: 110 average time/residue: 0.2097 time to fit residues: 31.0987 Evaluate side-chains 101 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 100 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 69 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 12 optimal weight: 3.9990 chunk 13 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 29 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 54 optimal weight: 0.5980 chunk 19 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.171304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.140110 restraints weight = 8641.606| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.04 r_work: 0.3476 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3333 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3867 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 4.896 10565 Z= 0.228 Chirality : 0.038 0.135 1194 Planarity : 0.004 0.040 1362 Dihedral : 4.025 40.450 1032 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.29 % Allowed : 10.09 % Favored : 88.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.27), residues: 958 helix: 1.95 (0.25), residues: 446 sheet: 0.45 (0.42), residues: 110 loop : -0.42 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 267 HIS 0.002 0.000 HIS B 269 PHE 0.034 0.001 PHE A 428 TYR 0.009 0.001 TYR A 358 ARG 0.005 0.000 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.03646 ( 368) hydrogen bonds : angle 4.40806 ( 1032) covalent geometry : bond 0.00214 ( 7800) covalent geometry : angle 0.43446 (10565) *********************** 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 114 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.867 Fit side-chains REVERT: A 30 MET cc_start: 0.8006 (mmp) cc_final: 0.7094 (ptp) REVERT: A 31 ASP cc_start: 0.7429 (t0) cc_final: 0.6693 (m-30) REVERT: A 35 GLU cc_start: 0.7585 (mm-30) cc_final: 0.7064 (mt-10) REVERT: A 223 GLU cc_start: 0.7489 (tt0) cc_final: 0.7226 (tt0) REVERT: B 31 ASP cc_start: 0.7441 (t0) cc_final: 0.6672 (m-30) REVERT: B 35 GLU cc_start: 0.7897 (tp30) cc_final: 0.7387 (mt-10) REVERT: B 76 ARG cc_start: 0.7486 (ttp80) cc_final: 0.7189 (ttp80) REVERT: B 223 GLU cc_start: 0.7493 (tt0) cc_final: 0.7235 (tt0) REVERT: B 433 GLU cc_start: 0.7550 (OUTLIER) cc_final: 0.6864 (mp0) REVERT: B 464 LYS cc_start: 0.7612 (mttt) cc_final: 0.7137 (ttpp) outliers start: 11 outliers final: 7 residues processed: 109 average time/residue: 0.2212 time to fit residues: 32.3087 Evaluate side-chains 104 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 96 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 247 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 106 THR Chi-restraints excluded: chain B residue 433 GLU 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 54 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 44 optimal weight: 0.0370 chunk 86 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 13 optimal weight: 0.9980 chunk 66 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.2064 ------------------------------------------------------------------------------- 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 = 0.166935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.135741 restraints weight = 8587.183| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.02 r_work: 0.3413 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3279 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.4396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7800 Z= 0.137 Angle : 0.491 7.494 10565 Z= 0.253 Chirality : 0.039 0.142 1194 Planarity : 0.004 0.037 1362 Dihedral : 4.187 37.130 1032 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.64 % Allowed : 10.45 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.27), residues: 958 helix: 1.75 (0.25), residues: 446 sheet: 0.28 (0.43), residues: 110 loop : -0.58 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 267 HIS 0.003 0.001 HIS B 269 PHE 0.019 0.002 PHE A 428 TYR 0.015 0.001 TYR B 369 ARG 0.006 0.001 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.04901 ( 368) hydrogen bonds : angle 4.61762 ( 1032) covalent geometry : bond 0.00326 ( 7800) covalent geometry : angle 0.49149 (10565) *********************** 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 106 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 92 time to evaluate : 0.893 Fit side-chains REVERT: A 1 MET cc_start: 0.4546 (ppp) cc_final: 0.3989 (mmt) REVERT: A 30 MET cc_start: 0.8003 (mmp) cc_final: 0.7014 (ptp) REVERT: A 31 ASP cc_start: 0.7534 (t0) cc_final: 0.6826 (m-30) REVERT: A 35 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7261 (mt-10) REVERT: B 31 ASP cc_start: 0.7496 (t0) cc_final: 0.6747 (m-30) REVERT: B 35 GLU cc_start: 0.8054 (tp30) cc_final: 0.7523 (mt-10) REVERT: B 76 ARG cc_start: 0.7626 (ttp80) cc_final: 0.7343 (ttp80) REVERT: B 464 LYS cc_start: 0.7757 (mttt) cc_final: 0.7226 (ttpp) outliers start: 14 outliers final: 10 residues processed: 101 average time/residue: 0.2134 time to fit residues: 29.2318 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 : 0.808 ------------------------------------------------------------------------------- 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 69 LEU Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 349 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 52 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 69 optimal weight: 0.0670 chunk 81 optimal weight: 5.9990 chunk 44 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 0.0870 chunk 88 optimal weight: 4.9990 chunk 67 optimal weight: 0.0670 overall best weight: 0.6438 ------------------------------------------------------------------------------- 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 = 0.173134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.141200 restraints weight = 8505.669| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 2.14 r_work: 0.3456 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3315 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4520 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= 0.096 Angle : 0.435 7.677 10565 Z= 0.226 Chirality : 0.038 0.132 1194 Planarity : 0.004 0.038 1362 Dihedral : 4.043 40.139 1032 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 1.29 % Allowed : 10.92 % Favored : 87.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.27), residues: 958 helix: 1.91 (0.25), residues: 446 sheet: 0.36 (0.42), residues: 110 loop : -0.49 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 267 HIS 0.002 0.000 HIS B 269 PHE 0.021 0.001 PHE A 428 TYR 0.016 0.001 TYR A 392 ARG 0.007 0.000 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.03764 ( 368) hydrogen bonds : angle 4.42221 ( 1032) covalent geometry : bond 0.00214 ( 7800) covalent geometry : angle 0.43490 (10565) *********************** 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 108 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 97 time to evaluate : 0.902 Fit side-chains REVERT: A 1 MET cc_start: 0.4464 (ppp) cc_final: 0.3931 (mmt) REVERT: A 30 MET cc_start: 0.7890 (mmp) cc_final: 0.6855 (ptp) REVERT: A 31 ASP cc_start: 0.7424 (t0) cc_final: 0.6742 (m-30) REVERT: A 35 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7110 (mt-10) REVERT: B 31 ASP cc_start: 0.7421 (t0) cc_final: 0.6647 (m-30) REVERT: B 35 GLU cc_start: 0.7975 (tp30) cc_final: 0.7325 (mt-10) REVERT: B 76 ARG cc_start: 0.7526 (ttp80) cc_final: 0.7235 (ttp80) REVERT: B 464 LYS cc_start: 0.7671 (mttt) cc_final: 0.7149 (ttpp) outliers start: 11 outliers final: 10 residues processed: 103 average time/residue: 0.2055 time to fit residues: 28.6125 Evaluate side-chains 101 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.784 ------------------------------------------------------------------------------- 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 69 LEU Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 439 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 24 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 84 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 46 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 78 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN B 80 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.171904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.138955 restraints weight = 8591.133| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 2.22 r_work: 0.3434 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4645 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 : 0.445 7.192 10565 Z= 0.230 Chirality : 0.038 0.136 1194 Planarity : 0.004 0.038 1362 Dihedral : 4.037 39.269 1032 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.70 % Favored : 95.30 % Rotamer: Outliers : 1.88 % Allowed : 10.80 % Favored : 87.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.07 (0.27), residues: 958 helix: 1.88 (0.25), residues: 446 sheet: 0.39 (0.43), residues: 110 loop : -0.50 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 267 HIS 0.002 0.000 HIS B 269 PHE 0.020 0.001 PHE A 428 TYR 0.018 0.001 TYR B 392 ARG 0.008 0.000 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.03977 ( 368) hydrogen bonds : angle 4.42919 ( 1032) covalent geometry : bond 0.00246 ( 7800) covalent geometry : angle 0.44528 (10565) *********************** 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 110 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 94 time to evaluate : 0.925 Fit side-chains REVERT: A 1 MET cc_start: 0.4459 (ppp) cc_final: 0.3810 (mmt) REVERT: A 30 MET cc_start: 0.7910 (mmp) cc_final: 0.6832 (ptp) REVERT: A 31 ASP cc_start: 0.7473 (t0) cc_final: 0.6614 (m-30) REVERT: A 35 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7102 (mt-10) REVERT: B 31 ASP cc_start: 0.7489 (t0) cc_final: 0.6740 (m-30) REVERT: B 35 GLU cc_start: 0.8076 (tp30) cc_final: 0.7416 (mt-10) REVERT: B 76 ARG cc_start: 0.7590 (ttp80) cc_final: 0.7312 (ttp80) REVERT: B 464 LYS cc_start: 0.7724 (mttt) cc_final: 0.7221 (ttpp) outliers start: 16 outliers final: 13 residues processed: 105 average time/residue: 0.2508 time to fit residues: 35.2754 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 : 0.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 146 MET 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 69 LEU Chi-restraints excluded: chain B residue 80 ASN Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 336 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 38 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 42 optimal weight: 6.9990 chunk 87 optimal weight: 4.9990 chunk 51 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 63 optimal weight: 1.9990 chunk 75 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.170991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.138599 restraints weight = 8671.407| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.18 r_work: 0.3431 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.4777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7800 Z= 0.126 Angle : 0.464 6.530 10565 Z= 0.240 Chirality : 0.038 0.137 1194 Planarity : 0.004 0.043 1362 Dihedral : 4.090 38.735 1032 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 3.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.76 % Allowed : 11.03 % Favored : 87.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.27), residues: 958 helix: 1.81 (0.25), residues: 446 sheet: 0.27 (0.42), residues: 110 loop : -0.57 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 267 HIS 0.003 0.001 HIS B 269 PHE 0.019 0.001 PHE A 428 TYR 0.023 0.001 TYR B 392 ARG 0.008 0.000 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.04295 ( 368) hydrogen bonds : angle 4.51202 ( 1032) covalent geometry : bond 0.00301 ( 7800) covalent geometry : angle 0.46446 (10565) *********************** 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 102 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.802 Fit side-chains REVERT: A 1 MET cc_start: 0.4471 (ppp) cc_final: 0.3904 (mmt) REVERT: A 30 MET cc_start: 0.7873 (mmp) cc_final: 0.6778 (ptp) REVERT: A 31 ASP cc_start: 0.7418 (t0) cc_final: 0.6573 (m-30) REVERT: A 35 GLU cc_start: 0.7634 (mm-30) cc_final: 0.7077 (mt-10) REVERT: B 31 ASP cc_start: 0.7441 (t0) cc_final: 0.6693 (m-30) REVERT: B 35 GLU cc_start: 0.8079 (tp30) cc_final: 0.7418 (mt-10) REVERT: B 76 ARG cc_start: 0.7556 (ttp80) cc_final: 0.7268 (ttp80) REVERT: B 464 LYS cc_start: 0.7742 (mttt) cc_final: 0.7245 (ttpp) outliers start: 15 outliers final: 12 residues processed: 97 average time/residue: 0.2057 time to fit residues: 27.1950 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 : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 146 MET 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 69 LEU Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 336 THR Chi-restraints excluded: chain B residue 439 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 71 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 40 optimal weight: 0.0040 chunk 92 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 overall best weight: 0.6996 ------------------------------------------------------------------------------- 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 = 0.3916 r_free = 0.3916 target = 0.168566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.138269 restraints weight = 8665.431| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 1.95 r_work: 0.3462 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3326 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 7800 Z= 0.099 Angle : 0.440 6.523 10565 Z= 0.228 Chirality : 0.037 0.132 1194 Planarity : 0.005 0.074 1362 Dihedral : 4.054 39.718 1032 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.53 % Allowed : 11.38 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.27), residues: 958 helix: 1.89 (0.25), residues: 446 sheet: 0.37 (0.43), residues: 110 loop : -0.48 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 267 HIS 0.002 0.000 HIS B 269 PHE 0.018 0.001 PHE A 428 TYR 0.027 0.001 TYR A 392 ARG 0.008 0.000 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.03810 ( 368) hydrogen bonds : angle 4.41027 ( 1032) covalent geometry : bond 0.00224 ( 7800) covalent geometry : angle 0.43995 (10565) *********************** 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 103 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 90 time to evaluate : 0.805 Fit side-chains REVERT: A 1 MET cc_start: 0.4435 (ppp) cc_final: 0.3892 (mmt) REVERT: A 30 MET cc_start: 0.7913 (mmp) cc_final: 0.6896 (ptp) REVERT: A 31 ASP cc_start: 0.7491 (t0) cc_final: 0.6685 (m-30) REVERT: A 35 GLU cc_start: 0.7608 (mm-30) cc_final: 0.7120 (mt-10) REVERT: B 31 ASP cc_start: 0.7532 (t0) cc_final: 0.6819 (m-30) REVERT: B 35 GLU cc_start: 0.8091 (tp30) cc_final: 0.7493 (mt-10) REVERT: B 76 ARG cc_start: 0.7592 (ttp80) cc_final: 0.7349 (ttp80) REVERT: B 464 LYS cc_start: 0.7762 (mttt) cc_final: 0.7286 (ttpp) outliers start: 13 outliers final: 12 residues processed: 98 average time/residue: 0.2058 time to fit residues: 27.3484 Evaluate side-chains 100 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 ASN Chi-restraints excluded: chain A residue 146 MET 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 69 LEU Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 336 THR 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 60 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 81 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 20 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 46 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 22 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 = 0.3976 r_free = 0.3976 target = 0.172399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.142906 restraints weight = 8436.738| |-----------------------------------------------------------------------------| r_work (start): 0.3619 rms_B_bonded: 1.91 r_work: 0.3502 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.4933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 7800 Z= 0.108 Angle : 0.447 7.797 10565 Z= 0.231 Chirality : 0.038 0.134 1194 Planarity : 0.005 0.069 1362 Dihedral : 4.050 39.393 1032 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.41 % Allowed : 11.97 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.27), residues: 958 helix: 1.86 (0.25), residues: 446 sheet: 0.34 (0.42), residues: 110 loop : -0.50 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 267 HIS 0.003 0.001 HIS B 269 PHE 0.018 0.001 PHE A 428 TYR 0.026 0.001 TYR A 392 ARG 0.008 0.000 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 368) hydrogen bonds : angle 4.43935 ( 1032) covalent geometry : bond 0.00251 ( 7800) covalent geometry : angle 0.44700 (10565) ********************** 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 105 residues out of total 852 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 93 time to evaluate : 0.838 Fit side-chains REVERT: A 1 MET cc_start: 0.4373 (ppp) cc_final: 0.3847 (mmt) REVERT: A 30 MET cc_start: 0.7854 (mmp) cc_final: 0.6754 (ptp) REVERT: A 31 ASP cc_start: 0.7435 (t0) cc_final: 0.6598 (m-30) REVERT: A 35 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7075 (mt-10) REVERT: B 17 GLN cc_start: 0.8103 (mt0) cc_final: 0.7767 (mt0) REVERT: B 31 ASP cc_start: 0.7491 (t0) cc_final: 0.6753 (m-30) REVERT: B 35 GLU cc_start: 0.7971 (tp30) cc_final: 0.7411 (mt-10) REVERT: B 76 ARG cc_start: 0.7515 (ttp80) cc_final: 0.7283 (ttp80) REVERT: B 464 LYS cc_start: 0.7718 (mttt) cc_final: 0.7271 (ttpp) outliers start: 12 outliers final: 12 residues processed: 100 average time/residue: 0.2295 time to fit residues: 30.6982 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 : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 146 MET 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 29 PHE Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 247 VAL Chi-restraints excluded: chain B residue 336 THR 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 56 optimal weight: 0.6980 chunk 42 optimal weight: 5.9990 chunk 53 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 43 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3988 r_free = 0.3988 target = 0.173271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.143753 restraints weight = 8486.651| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.91 r_work: 0.3520 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3384 rms_B_bonded: 4.59 restraints_weight: 0.2500 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7800 Z= 0.105 Angle : 0.450 7.722 10565 Z= 0.231 Chirality : 0.038 0.133 1194 Planarity : 0.005 0.091 1362 Dihedral : 4.067 39.628 1032 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 1.41 % Allowed : 11.97 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.27), residues: 958 helix: 1.89 (0.25), residues: 446 sheet: 0.41 (0.43), residues: 110 loop : -0.49 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 267 HIS 0.002 0.000 HIS B 269 PHE 0.018 0.001 PHE A 428 TYR 0.025 0.001 TYR B 392 ARG 0.006 0.000 ARG A 76 Details of bonding type rmsd hydrogen bonds : bond 0.03824 ( 368) hydrogen bonds : angle 4.40951 ( 1032) covalent geometry : bond 0.00242 ( 7800) covalent geometry : angle 0.44999 (10565) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4534.05 seconds wall clock time: 79 minutes 36.15 seconds (4776.15 seconds total)