Starting phenix.real_space_refine on Thu Jul 2 05:33:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7paf_13268/07_2026/7paf_13268.cif Found real_map, /net/cci-nas-00/data/ceres_data/7paf_13268/07_2026/7paf_13268.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7paf_13268/07_2026/7paf_13268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7paf_13268/07_2026/7paf_13268.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7paf_13268/07_2026/7paf_13268.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7paf_13268/07_2026/7paf_13268.cif" model { file = "/net/cci-nas-00/data/ceres_data/7paf_13268/07_2026/7paf_13268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7paf_13268/07_2026/7paf_13268.cif" } resolution = 3.75 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= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 892 atoms to isotropic. 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 24 5.16 5 C 3992 2.51 5 N 926 2.21 5 O 1062 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6005 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 2 Chain: "A" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2116 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 6, 'TRANS': 271} Chain breaks: 1 Chain: "C" Number of atoms: 869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 869 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 2, 'TRANS': 109} Chain breaks: 2 Chain: "D" Number of atoms: 2116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2116 Classifications: {'peptide': 278} Link IDs: {'PTRANS': 6, 'TRANS': 271} Chain breaks: 1 Chain: "D" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'PGT': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Time building chain proxies: 1.61, per 1000 atoms: 0.27 Number of scatterers: 6005 At special positions: 0 Unit cell: (102.726, 78.142, 93.946, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 1 15.00 O 1062 8.00 N 926 7.00 C 3992 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 26 " - pdb=" SG CYS B 100 " distance=2.03 Simple disulfide: pdb=" SG CYS C 26 " - pdb=" SG CYS C 100 " distance=2.03 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: 0.52 Conformation dependent library (CDL) restraints added in 233.5 milliseconds 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1424 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 6 sheets defined 63.5% alpha, 16.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'B' and resid 91 through 95 removed outlier: 3.680A pdb=" N THR B 95 " --> pdb=" O PRO B 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 7 through 31 removed outlier: 4.048A pdb=" N LEU A 11 " --> pdb=" O VAL A 7 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR A 26 " --> pdb=" O THR A 22 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 59 removed outlier: 4.149A pdb=" N PHE A 49 " --> pdb=" O PHE A 45 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N ILE A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 83 Processing helix chain 'A' and resid 83 through 98 Processing helix chain 'A' and resid 100 through 109 Processing helix chain 'A' and resid 109 through 120 removed outlier: 4.056A pdb=" N SER A 113 " --> pdb=" O TYR A 109 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N PHE A 118 " --> pdb=" O VAL A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 144 removed outlier: 4.429A pdb=" N PHE A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLY A 132 " --> pdb=" O ASN A 128 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N THR A 144 " --> pdb=" O ILE A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 153 through 178 removed outlier: 3.516A pdb=" N ALA A 166 " --> pdb=" O VAL A 162 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N SER A 171 " --> pdb=" O TRP A 167 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N VAL A 172 " --> pdb=" O GLY A 168 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N MET A 178 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 207 removed outlier: 3.531A pdb=" N LEU A 188 " --> pdb=" O GLU A 184 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ARG A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 214 Processing helix chain 'A' and resid 215 through 253 Proline residue: A 245 - end of helix removed outlier: 3.582A pdb=" N ALA A 248 " --> pdb=" O GLN A 244 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THR A 249 " --> pdb=" O PRO A 245 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N GLY A 250 " --> pdb=" O ALA A 246 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ASN A 252 " --> pdb=" O ALA A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.603A pdb=" N TRP A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 289 removed outlier: 3.524A pdb=" N ILE A 276 " --> pdb=" O ASP A 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 95 removed outlier: 3.674A pdb=" N THR C 95 " --> pdb=" O PRO C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 31 removed outlier: 4.077A pdb=" N LEU D 11 " --> pdb=" O VAL D 7 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR D 26 " --> pdb=" O THR D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 59 removed outlier: 4.148A pdb=" N PHE D 49 " --> pdb=" O PHE D 45 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ILE D 50 " --> pdb=" O LEU D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 83 Processing helix chain 'D' and resid 83 through 98 Processing helix chain 'D' and resid 100 through 109 Processing helix chain 'D' and resid 109 through 120 removed outlier: 4.050A pdb=" N SER D 113 " --> pdb=" O TYR D 109 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N PHE D 118 " --> pdb=" O VAL D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 144 removed outlier: 4.424A pdb=" N PHE D 131 " --> pdb=" O LYS D 127 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N GLY D 132 " --> pdb=" O ASN D 128 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N THR D 144 " --> pdb=" O ILE D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 153 through 178 removed outlier: 3.516A pdb=" N ALA D 166 " --> pdb=" O VAL D 162 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N SER D 171 " --> pdb=" O TRP D 167 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N VAL D 172 " --> pdb=" O GLY D 168 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N MET D 178 " --> pdb=" O SER D 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 207 removed outlier: 3.543A pdb=" N LEU D 188 " --> pdb=" O GLU D 184 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 214 removed outlier: 3.518A pdb=" N VAL D 213 " --> pdb=" O PHE D 210 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 244 Processing helix chain 'D' and resid 247 through 253 removed outlier: 3.697A pdb=" N ASN D 252 " --> pdb=" O ALA D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 266 removed outlier: 3.603A pdb=" N TRP D 258 " --> pdb=" O SER D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 289 removed outlier: 3.526A pdb=" N ILE D 276 " --> pdb=" O ASP D 272 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 6 through 11 Processing sheet with id=AA2, first strand: chain 'B' and resid 14 through 17 removed outlier: 6.381A pdb=" N GLY B 14 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N SER B 128 " --> pdb=" O GLY B 14 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL B 16 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ALA B 101 " --> pdb=" O GLY B 39 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N TYR B 37 " --> pdb=" O ALA B 103 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 14 through 17 removed outlier: 6.381A pdb=" N GLY B 14 " --> pdb=" O THR B 126 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N SER B 128 " --> pdb=" O GLY B 14 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL B 16 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N TYR B 118 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 6 through 11 Processing sheet with id=AA5, first strand: chain 'C' and resid 14 through 17 removed outlier: 6.382A pdb=" N GLY C 14 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N SER C 128 " --> pdb=" O GLY C 14 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL C 16 " --> pdb=" O SER C 128 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA C 101 " --> pdb=" O GLY C 39 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N TYR C 37 " --> pdb=" O ALA C 103 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 14 through 17 removed outlier: 6.382A pdb=" N GLY C 14 " --> pdb=" O THR C 126 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N SER C 128 " --> pdb=" O GLY C 14 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N VAL C 16 " --> pdb=" O SER C 128 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N TYR C 118 " --> pdb=" O ALA C 102 " (cutoff:3.500A) 404 hydrogen bonds defined for protein. 1170 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: 0.98 Time building geometry restraints manager: 0.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 900 1.32 - 1.44: 1772 1.44 - 1.56: 3428 1.56 - 1.68: 2 1.68 - 1.81: 40 Bond restraints: 6142 Sorted by residual: bond pdb=" C11 PGT D 301 " pdb=" O3 PGT D 301 " ideal model delta sigma weight residual 1.327 1.454 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" C31 PGT D 301 " pdb=" O2 PGT D 301 " ideal model delta sigma weight residual 1.331 1.456 -0.125 2.00e-02 2.50e+03 3.91e+01 bond pdb=" C LYS D 247 " pdb=" O LYS D 247 " ideal model delta sigma weight residual 1.232 1.197 0.035 1.38e-02 5.25e+03 6.50e+00 bond pdb=" C LYS A 247 " pdb=" O LYS A 247 " ideal model delta sigma weight residual 1.232 1.198 0.035 1.38e-02 5.25e+03 6.35e+00 bond pdb=" CA PRO A 245 " pdb=" CB PRO A 245 " ideal model delta sigma weight residual 1.533 1.505 0.028 1.42e-02 4.96e+03 3.98e+00 ... (remaining 6137 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 8184 1.94 - 3.89: 138 3.89 - 5.83: 17 5.83 - 7.77: 12 7.77 - 9.72: 3 Bond angle restraints: 8354 Sorted by residual: angle pdb=" N ALA A 246 " pdb=" CA ALA A 246 " pdb=" C ALA A 246 " ideal model delta sigma weight residual 111.28 117.52 -6.24 1.09e+00 8.42e-01 3.28e+01 angle pdb=" N ALA D 246 " pdb=" CA ALA D 246 " pdb=" C ALA D 246 " ideal model delta sigma weight residual 111.36 117.49 -6.13 1.09e+00 8.42e-01 3.16e+01 angle pdb=" C PRO A 245 " pdb=" N ALA A 246 " pdb=" CA ALA A 246 " ideal model delta sigma weight residual 120.28 126.45 -6.17 1.34e+00 5.57e-01 2.12e+01 angle pdb=" C GLN A 244 " pdb=" N PRO A 245 " pdb=" CA PRO A 245 " ideal model delta sigma weight residual 119.84 115.64 4.20 1.25e+00 6.40e-01 1.13e+01 angle pdb=" N GLN D 244 " pdb=" CA GLN D 244 " pdb=" C GLN D 244 " ideal model delta sigma weight residual 109.81 117.23 -7.42 2.21e+00 2.05e-01 1.13e+01 ... (remaining 8349 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.31: 3198 17.31 - 34.61: 246 34.61 - 51.92: 33 51.92 - 69.23: 6 69.23 - 86.53: 4 Dihedral angle restraints: 3487 sinusoidal: 1251 harmonic: 2236 Sorted by residual: dihedral pdb=" CA ILE D 125 " pdb=" C ILE D 125 " pdb=" N SER D 126 " pdb=" CA SER D 126 " ideal model delta harmonic sigma weight residual -180.00 -161.19 -18.81 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA ILE A 125 " pdb=" C ILE A 125 " pdb=" N SER A 126 " pdb=" CA SER A 126 " ideal model delta harmonic sigma weight residual 180.00 -161.22 -18.78 0 5.00e+00 4.00e-02 1.41e+01 dihedral pdb=" CB GLU A 179 " pdb=" CG GLU A 179 " pdb=" CD GLU A 179 " pdb=" OE1 GLU A 179 " ideal model delta sinusoidal sigma weight residual 0.00 83.63 -83.63 1 3.00e+01 1.11e-03 9.48e+00 ... (remaining 3484 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 856 0.056 - 0.111: 129 0.111 - 0.167: 11 0.167 - 0.223: 0 0.223 - 0.278: 4 Chirality restraints: 1000 Sorted by residual: chirality pdb=" CA GLN A 244 " pdb=" N GLN A 244 " pdb=" C GLN A 244 " pdb=" CB GLN A 244 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.94e+00 chirality pdb=" CA GLN D 244 " pdb=" N GLN D 244 " pdb=" C GLN D 244 " pdb=" CB GLN D 244 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.91e+00 chirality pdb=" C5 PGT D 301 " pdb=" C4 PGT D 301 " pdb=" C6 PGT D 301 " pdb=" O5 PGT D 301 " both_signs ideal model delta sigma weight residual False -2.30 -2.56 0.26 2.00e-01 2.50e+01 1.72e+00 ... (remaining 997 not shown) Planarity restraints: 1002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN A 244 " -0.047 5.00e-02 4.00e+02 7.21e-02 8.31e+00 pdb=" N PRO A 245 " 0.125 5.00e-02 4.00e+02 pdb=" CA PRO A 245 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 245 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN D 244 " 0.019 5.00e-02 4.00e+02 2.92e-02 1.36e+00 pdb=" N PRO D 245 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO D 245 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 245 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP D 258 " 0.005 2.00e-02 2.50e+03 1.08e-02 1.16e+00 pdb=" C TRP D 258 " -0.019 2.00e-02 2.50e+03 pdb=" O TRP D 258 " 0.007 2.00e-02 2.50e+03 pdb=" N THR D 259 " 0.006 2.00e-02 2.50e+03 ... (remaining 999 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1324 2.78 - 3.31: 6020 3.31 - 3.84: 9833 3.84 - 4.37: 11009 4.37 - 4.90: 19546 Nonbonded interactions: 47732 Sorted by model distance: nonbonded pdb=" OD2 ASP C 104 " pdb=" OH TYR C 118 " model vdw 2.247 3.040 nonbonded pdb=" OD2 ASP B 104 " pdb=" OH TYR B 118 " model vdw 2.252 3.040 nonbonded pdb=" OD1 ASN D 128 " pdb=" N THR D 129 " model vdw 2.342 3.120 nonbonded pdb=" OD1 ASN A 128 " pdb=" N THR A 129 " model vdw 2.342 3.120 nonbonded pdb=" OG SER D 13 " pdb=" OD1 ASN D 252 " model vdw 2.388 3.040 ... (remaining 47727 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' selection = (chain 'D' and resid 6 through 290) } ncs_group { reference = chain 'B' selection = chain 'C' } 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 group one per residue 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: 4.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 7.610 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 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 : 0.004 0.127 6144 Z= 0.206 Angle : 0.682 9.715 8358 Z= 0.373 Chirality : 0.043 0.278 1000 Planarity : 0.003 0.072 1002 Dihedral : 12.963 86.535 2057 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.82 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.26), residues: 760 helix: -1.55 (0.21), residues: 450 sheet: -0.63 (0.45), residues: 114 loop : -2.66 (0.38), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 191 TYR 0.012 0.001 TYR A 255 PHE 0.009 0.001 PHE D 225 TRP 0.005 0.001 TRP A 17 HIS 0.005 0.001 HIS A 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.21 ( 6142) covalent geometry : angle 0.68136 / 0.37 ( 8354) SS BOND : bond 0.00057 / 0.03 ( 2) SS BOND : angle 1.35446 / 0.79 ( 4) hydrogen bonds : bond 0.13430 / 8.82 ( 396) hydrogen bonds : angle 5.89402 / 3.86 ( 1170) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 8 LEU cc_start: 0.6788 (mt) cc_final: 0.6427 (mm) REVERT: D 184 GLU cc_start: 0.7670 (pm20) cc_final: 0.7376 (pm20) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.0634 time to fit residues: 14.6592 Evaluate side-chains 120 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.7980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 38 optimal weight: 10.0000 chunk 61 optimal weight: 0.0870 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 192 GLN D 192 GLN D 244 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.191155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 118)---------------| | r_work = 0.4109 r_free = 0.4109 target = 0.158308 restraints weight = 8563.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.158843 restraints weight = 7472.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.159177 restraints weight = 6961.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.159199 restraints weight = 6484.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.159237 restraints weight = 6599.752| |-----------------------------------------------------------------------------| r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6144 Z= 0.159 Angle : 0.656 8.512 8358 Z= 0.339 Chirality : 0.041 0.135 1000 Planarity : 0.005 0.061 1002 Dihedral : 5.716 47.361 845 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.82 % Favored : 95.92 % Rotamer: Outliers : 2.37 % Allowed : 18.20 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.13 (0.30), residues: 760 helix: -0.24 (0.24), residues: 456 sheet: 0.18 (0.48), residues: 114 loop : -2.31 (0.41), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG D 63 TYR 0.014 0.001 TYR D 109 PHE 0.017 0.001 PHE A 196 TRP 0.011 0.001 TRP C 107 HIS 0.005 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00371 / 0.16 ( 6142) covalent geometry : angle 0.65637 / 0.34 ( 8354) SS BOND : bond 0.00034 / 0.02 ( 2) SS BOND : angle 0.37697 / 0.22 ( 4) hydrogen bonds : bond 0.03976 / 2.70 ( 396) hydrogen bonds : angle 4.60722 / 3.06 ( 1170) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 12 residues processed: 138 average time/residue: 0.0612 time to fit residues: 11.9317 Evaluate side-chains 122 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 172 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 17 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 63 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 88 GLN A 90 ASN D 88 GLN D 90 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.186401 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.156687 restraints weight = 8512.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.155878 restraints weight = 13188.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.156715 restraints weight = 11448.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.156593 restraints weight = 8737.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.156956 restraints weight = 8477.996| |-----------------------------------------------------------------------------| r_work (final): 0.4124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 6144 Z= 0.221 Angle : 0.691 7.050 8358 Z= 0.361 Chirality : 0.043 0.133 1000 Planarity : 0.004 0.047 1002 Dihedral : 6.214 58.330 845 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 15.09 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.74 % Favored : 95.13 % Rotamer: Outliers : 3.96 % Allowed : 23.58 % Favored : 72.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.30), residues: 760 helix: -0.06 (0.24), residues: 454 sheet: 0.17 (0.49), residues: 114 loop : -2.23 (0.42), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 191 TYR 0.016 0.002 TYR A 109 PHE 0.021 0.002 PHE A 225 TRP 0.014 0.002 TRP C 40 HIS 0.012 0.002 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00534 / 0.22 ( 6142) covalent geometry : angle 0.69116 / 0.36 ( 8354) SS BOND : bond 0.00067 / 0.04 ( 2) SS BOND : angle 0.35162 / 0.20 ( 4) hydrogen bonds : bond 0.04068 / 2.76 ( 396) hydrogen bonds : angle 4.65437 / 3.10 ( 1170) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 0.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 TYR cc_start: 0.7883 (m-80) cc_final: 0.7585 (m-80) outliers start: 25 outliers final: 16 residues processed: 141 average time/residue: 0.0611 time to fit residues: 12.0787 Evaluate side-chains 131 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 115 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 184 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 57 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 48 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 71 optimal weight: 0.0980 chunk 39 optimal weight: 20.0000 chunk 62 optimal weight: 0.0870 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.189887 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.161769 restraints weight = 8680.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.160276 restraints weight = 13590.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4162 r_free = 0.4162 target = 0.161049 restraints weight = 11399.462| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.161182 restraints weight = 9042.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.161380 restraints weight = 8299.260| |-----------------------------------------------------------------------------| r_work (final): 0.4171 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6144 Z= 0.155 Angle : 0.648 7.313 8358 Z= 0.335 Chirality : 0.040 0.135 1000 Planarity : 0.004 0.040 1002 Dihedral : 6.125 59.079 845 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 4.27 % Allowed : 23.58 % Favored : 72.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.41 (0.31), residues: 760 helix: 0.37 (0.25), residues: 458 sheet: 0.23 (0.48), residues: 114 loop : -2.00 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 63 TYR 0.017 0.001 TYR A 287 PHE 0.009 0.001 PHE D 225 TRP 0.012 0.002 TRP B 40 HIS 0.004 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 6142) covalent geometry : angle 0.64775 / 0.33 ( 8354) SS BOND : bond 0.00075 / 0.04 ( 2) SS BOND : angle 0.15718 / 0.09 ( 4) hydrogen bonds : bond 0.03705 / 2.54 ( 396) hydrogen bonds : angle 4.40704 / 2.93 ( 1170) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 HIS cc_start: 0.7957 (OUTLIER) cc_final: 0.7664 (t-170) REVERT: D 43 HIS cc_start: 0.7989 (OUTLIER) cc_final: 0.7649 (t-170) outliers start: 27 outliers final: 17 residues processed: 137 average time/residue: 0.0678 time to fit residues: 12.9017 Evaluate side-chains 132 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 113 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 184 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 25 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 59 optimal weight: 0.6980 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 4 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 124 GLN ** 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 = 0.4496 r_free = 0.4496 target = 0.190893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.162136 restraints weight = 8676.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.161000 restraints weight = 12862.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.161657 restraints weight = 10871.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.161886 restraints weight = 8855.686| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.162078 restraints weight = 8131.106| |-----------------------------------------------------------------------------| r_work (final): 0.4165 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6144 Z= 0.156 Angle : 0.641 7.884 8358 Z= 0.328 Chirality : 0.040 0.134 1000 Planarity : 0.003 0.038 1002 Dihedral : 6.096 55.024 845 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 13.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 5.54 % Allowed : 23.10 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.31), residues: 760 helix: 0.49 (0.25), residues: 458 sheet: 0.56 (0.49), residues: 114 loop : -1.87 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 63 TYR 0.014 0.002 TYR A 287 PHE 0.011 0.001 PHE D 225 TRP 0.010 0.001 TRP A 17 HIS 0.005 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.16 ( 6142) covalent geometry : angle 0.64077 / 0.33 ( 8354) SS BOND : bond 0.00064 / 0.03 ( 2) SS BOND : angle 0.17135 / 0.10 ( 4) hydrogen bonds : bond 0.03676 / 2.52 ( 396) hydrogen bonds : angle 4.36241 / 2.88 ( 1170) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 123 time to evaluate : 0.230 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 MET cc_start: 0.3987 (ptm) cc_final: 0.3689 (ptm) REVERT: A 43 HIS cc_start: 0.7974 (OUTLIER) cc_final: 0.7686 (t-170) REVERT: A 222 MET cc_start: 0.7685 (mmm) cc_final: 0.7389 (mmm) REVERT: C 108 MET cc_start: 0.4057 (ptm) cc_final: 0.3776 (ptm) REVERT: D 43 HIS cc_start: 0.7998 (OUTLIER) cc_final: 0.7697 (t-170) outliers start: 35 outliers final: 21 residues processed: 144 average time/residue: 0.0615 time to fit residues: 12.2432 Evaluate side-chains 137 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain B residue 125 VAL Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain C residue 125 VAL Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 184 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.5980 chunk 18 optimal weight: 0.2980 chunk 70 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 68 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.193669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.160931 restraints weight = 8936.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.159582 restraints weight = 9514.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.160329 restraints weight = 9100.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.160562 restraints weight = 7458.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.160718 restraints weight = 6811.272| |-----------------------------------------------------------------------------| r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6144 Z= 0.155 Angle : 0.649 7.266 8358 Z= 0.334 Chirality : 0.041 0.131 1000 Planarity : 0.003 0.035 1002 Dihedral : 6.161 57.550 845 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 3.64 % Allowed : 24.37 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.04 (0.31), residues: 760 helix: 0.54 (0.25), residues: 458 sheet: 0.82 (0.50), residues: 114 loop : -1.83 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 191 TYR 0.017 0.002 TYR D 287 PHE 0.011 0.001 PHE D 54 TRP 0.010 0.001 TRP A 17 HIS 0.005 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.15 ( 6142) covalent geometry : angle 0.64905 / 0.33 ( 8354) SS BOND : bond 0.00081 / 0.04 ( 2) SS BOND : angle 0.11021 / 0.06 ( 4) hydrogen bonds : bond 0.03676 / 2.52 ( 396) hydrogen bonds : angle 4.30018 / 2.85 ( 1170) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 108 MET cc_start: 0.4032 (ptm) cc_final: 0.3736 (ptm) REVERT: A 43 HIS cc_start: 0.7990 (OUTLIER) cc_final: 0.7673 (t-170) REVERT: A 46 LEU cc_start: 0.8261 (OUTLIER) cc_final: 0.8040 (mt) REVERT: C 108 MET cc_start: 0.4146 (ptm) cc_final: 0.3853 (ptm) REVERT: D 43 HIS cc_start: 0.7969 (OUTLIER) cc_final: 0.7609 (t-170) outliers start: 23 outliers final: 17 residues processed: 144 average time/residue: 0.0603 time to fit residues: 12.1265 Evaluate side-chains 135 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 184 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 38 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 0.0050 chunk 50 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 86 GLN C 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.193348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 76)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.157864 restraints weight = 8897.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.158683 restraints weight = 7948.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.158750 restraints weight = 7293.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.158885 restraints weight = 6970.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.158891 restraints weight = 6838.870| |-----------------------------------------------------------------------------| r_work (final): 0.4118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6144 Z= 0.164 Angle : 0.685 7.356 8358 Z= 0.352 Chirality : 0.042 0.159 1000 Planarity : 0.003 0.033 1002 Dihedral : 6.157 56.244 845 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.75 % Allowed : 25.79 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.31), residues: 760 helix: 0.41 (0.25), residues: 470 sheet: 0.85 (0.50), residues: 114 loop : -2.12 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 71 TYR 0.018 0.002 TYR D 287 PHE 0.047 0.002 PHE B 72 TRP 0.010 0.001 TRP A 17 HIS 0.005 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00395 / 0.16 ( 6142) covalent geometry : angle 0.68492 / 0.35 ( 8354) SS BOND : bond 0.00055 / 0.03 ( 2) SS BOND : angle 0.15296 / 0.09 ( 4) hydrogen bonds : bond 0.03801 / 2.58 ( 396) hydrogen bonds : angle 4.38024 / 2.92 ( 1170) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 116 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 HIS cc_start: 0.8008 (OUTLIER) cc_final: 0.7628 (t-170) REVERT: A 222 MET cc_start: 0.7641 (mmm) cc_final: 0.7281 (mmm) REVERT: D 43 HIS cc_start: 0.8045 (OUTLIER) cc_final: 0.7647 (t-170) REVERT: D 210 PHE cc_start: 0.6932 (OUTLIER) cc_final: 0.5830 (m-80) REVERT: D 230 MET cc_start: 0.7785 (mmp) cc_final: 0.7562 (mmp) outliers start: 30 outliers final: 20 residues processed: 134 average time/residue: 0.0620 time to fit residues: 11.4450 Evaluate side-chains 137 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 114 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 210 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 4 optimal weight: 0.0470 chunk 57 optimal weight: 0.8980 chunk 47 optimal weight: 0.9990 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 61 optimal weight: 0.6980 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.191278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.162006 restraints weight = 8564.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.161010 restraints weight = 12747.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.161946 restraints weight = 12001.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.161522 restraints weight = 8892.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4174 r_free = 0.4174 target = 0.162072 restraints weight = 8423.620| |-----------------------------------------------------------------------------| r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6144 Z= 0.160 Angle : 0.682 7.653 8358 Z= 0.352 Chirality : 0.042 0.178 1000 Planarity : 0.003 0.035 1002 Dihedral : 6.108 53.350 845 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.96 % Allowed : 26.90 % Favored : 69.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.18 (0.31), residues: 760 helix: 0.44 (0.25), residues: 470 sheet: 0.84 (0.50), residues: 114 loop : -2.13 (0.44), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 191 TYR 0.020 0.002 TYR D 287 PHE 0.040 0.002 PHE B 72 TRP 0.011 0.001 TRP B 107 HIS 0.005 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 6142) covalent geometry : angle 0.68188 / 0.35 ( 8354) SS BOND : bond 0.00077 / 0.04 ( 2) SS BOND : angle 0.18792 / 0.11 ( 4) hydrogen bonds : bond 0.03730 / 2.54 ( 396) hydrogen bonds : angle 4.39636 / 2.92 ( 1170) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 122 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 HIS cc_start: 0.8018 (OUTLIER) cc_final: 0.7653 (t-170) REVERT: A 210 PHE cc_start: 0.6776 (OUTLIER) cc_final: 0.5733 (m-80) REVERT: A 222 MET cc_start: 0.7628 (mmm) cc_final: 0.7329 (mmm) REVERT: D 43 HIS cc_start: 0.8065 (OUTLIER) cc_final: 0.7613 (t-170) REVERT: D 210 PHE cc_start: 0.6887 (OUTLIER) cc_final: 0.5888 (m-80) outliers start: 25 outliers final: 20 residues processed: 136 average time/residue: 0.0642 time to fit residues: 12.0676 Evaluate side-chains 141 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 86 GLN Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 210 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 13 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 56 optimal weight: 0.0980 chunk 42 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 51 optimal weight: 0.3980 chunk 39 optimal weight: 8.9990 chunk 26 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 86 GLN C 88 ASN ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.190773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.162001 restraints weight = 8614.156| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.160819 restraints weight = 12801.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.161445 restraints weight = 11302.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.161562 restraints weight = 9220.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.161746 restraints weight = 8800.568| |-----------------------------------------------------------------------------| r_work (final): 0.4197 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.3579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6144 Z= 0.155 Angle : 0.703 13.899 8358 Z= 0.359 Chirality : 0.042 0.181 1000 Planarity : 0.003 0.033 1002 Dihedral : 6.081 53.023 845 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.43 % Allowed : 27.85 % Favored : 67.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.31), residues: 760 helix: 0.47 (0.25), residues: 470 sheet: 0.96 (0.51), residues: 114 loop : -2.17 (0.43), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 191 TYR 0.019 0.002 TYR D 287 PHE 0.011 0.001 PHE D 54 TRP 0.011 0.001 TRP C 107 HIS 0.005 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.16 ( 6142) covalent geometry : angle 0.70278 / 0.36 ( 8354) SS BOND : bond 0.00053 / 0.03 ( 2) SS BOND : angle 0.21595 / 0.13 ( 4) hydrogen bonds : bond 0.03730 / 2.53 ( 396) hydrogen bonds : angle 4.41828 / 2.92 ( 1170) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 119 time to evaluate : 0.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 HIS cc_start: 0.8039 (OUTLIER) cc_final: 0.7655 (t-170) REVERT: A 210 PHE cc_start: 0.6767 (OUTLIER) cc_final: 0.5715 (m-80) REVERT: A 222 MET cc_start: 0.7633 (mmm) cc_final: 0.7387 (mmm) REVERT: D 43 HIS cc_start: 0.8085 (OUTLIER) cc_final: 0.7624 (t-170) REVERT: D 210 PHE cc_start: 0.6907 (OUTLIER) cc_final: 0.5908 (m-80) outliers start: 28 outliers final: 21 residues processed: 134 average time/residue: 0.0699 time to fit residues: 12.8968 Evaluate side-chains 138 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 113 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 43 HIS Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 136 ILE Chi-restraints excluded: chain D residue 172 VAL Chi-restraints excluded: chain D residue 184 GLU Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain D residue 210 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 64 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 61 optimal weight: 0.2980 chunk 57 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 37 optimal weight: 0.0980 chunk 54 optimal weight: 0.0370 chunk 27 optimal weight: 0.4980 chunk 15 optimal weight: 0.7980 chunk 71 optimal weight: 1.9990 overall best weight: 0.3258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 86 GLN ** C 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.194484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.167530 restraints weight = 8598.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.165701 restraints weight = 10584.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.166332 restraints weight = 10357.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.166804 restraints weight = 8067.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4221 r_free = 0.4221 target = 0.166937 restraints weight = 7183.260| |-----------------------------------------------------------------------------| r_work (final): 0.4225 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6144 Z= 0.137 Angle : 0.694 12.336 8358 Z= 0.351 Chirality : 0.041 0.182 1000 Planarity : 0.003 0.034 1002 Dihedral : 5.923 51.191 845 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 14.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 3.64 % Allowed : 28.96 % Favored : 67.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.32), residues: 760 helix: 0.80 (0.25), residues: 456 sheet: 1.09 (0.57), residues: 98 loop : -1.68 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 191 TYR 0.019 0.001 TYR A 287 PHE 0.008 0.001 PHE D 54 TRP 0.013 0.001 TRP A 17 HIS 0.003 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 6142) covalent geometry : angle 0.69368 / 0.35 ( 8354) SS BOND : bond 0.00068 / 0.03 ( 2) SS BOND : angle 0.35111 / 0.20 ( 4) hydrogen bonds : bond 0.03540 / 2.40 ( 396) hydrogen bonds : angle 4.35779 / 2.88 ( 1170) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 PHE cc_start: 0.6721 (OUTLIER) cc_final: 0.5723 (m-80) REVERT: A 222 MET cc_start: 0.7595 (mmm) cc_final: 0.7343 (mmm) REVERT: D 43 HIS cc_start: 0.8026 (OUTLIER) cc_final: 0.7492 (t-170) outliers start: 23 outliers final: 19 residues processed: 135 average time/residue: 0.0648 time to fit residues: 11.8227 Evaluate side-chains 135 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 114 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 86 GLN Chi-restraints excluded: chain B residue 87 MET Chi-restraints excluded: chain B residue 99 TYR Chi-restraints excluded: chain A residue 7 VAL Chi-restraints excluded: chain A residue 48 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 62 VAL Chi-restraints excluded: chain A residue 81 LEU Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain A residue 210 PHE Chi-restraints excluded: chain C residue 16 VAL Chi-restraints excluded: chain C residue 87 MET Chi-restraints excluded: chain C residue 99 TYR Chi-restraints excluded: chain D residue 7 VAL Chi-restraints excluded: chain D residue 43 HIS Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 189 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 39 optimal weight: 20.0000 chunk 12 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 48 optimal weight: 0.9980 chunk 4 optimal weight: 7.9990 chunk 60 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 0.0470 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 124 GLN ** 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 = 0.4535 r_free = 0.4535 target = 0.197602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 87)----------------| | r_work = 0.4199 r_free = 0.4199 target = 0.164819 restraints weight = 8984.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.163598 restraints weight = 7875.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.163467 restraints weight = 7652.710| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.163616 restraints weight = 8091.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.163781 restraints weight = 7494.448| |-----------------------------------------------------------------------------| r_work (final): 0.4167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.154 6144 Z= 0.246 Angle : 1.144 59.137 8358 Z= 0.642 Chirality : 0.051 0.992 1000 Planarity : 0.003 0.034 1002 Dihedral : 5.936 51.156 845 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.48 % Allowed : 29.43 % Favored : 67.09 % Cbeta Deviations : 0.14 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.32), residues: 760 helix: 0.80 (0.25), residues: 456 sheet: 1.04 (0.57), residues: 98 loop : -1.69 (0.43), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 23 TYR 0.016 0.002 TYR A 287 PHE 0.019 0.001 PHE B 72 TRP 0.012 0.002 TRP A 17 HIS 0.003 0.001 HIS D 43 Details of bonding type rmsd/Z covalent geometry : bond 0.00533 / 0.25 ( 6142) covalent geometry : angle 1.14450 / 0.64 ( 8354) SS BOND : bond 0.00054 / 0.03 ( 2) SS BOND : angle 0.33233 / 0.19 ( 4) hydrogen bonds : bond 0.03507 / 2.37 ( 396) hydrogen bonds : angle 4.36851 / 2.88 ( 1170) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1095.42 seconds wall clock time: 19 minutes 41.46 seconds (1181.46 seconds total)