Starting phenix.real_space_refine on Tue Mar 3 16:15:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7paf_13268/03_2026/7paf_13268.cif Found real_map, /net/cci-nas-00/data/ceres_data/7paf_13268/03_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_13268/03_2026/7paf_13268.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7paf_13268/03_2026/7paf_13268.map" model { file = "/net/cci-nas-00/data/ceres_data/7paf_13268/03_2026/7paf_13268.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7paf_13268/03_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-5986/lib/python3.9/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: 1.26, per 1000 atoms: 0.21 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: 0.67 Conformation dependent library (CDL) restraints added in 226.4 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: 0.21 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: 0.87 Time building geometry restraints manager: 0.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 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: 3203 17.31 - 34.61: 253 34.61 - 51.92: 33 51.92 - 69.23: 9 69.23 - 86.53: 4 Dihedral angle restraints: 3502 sinusoidal: 1266 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 3499 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: 4.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 6.790 Find NCS groups from input model: 0.070 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:1.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7538 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 : 13.225 86.535 2072 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 covalent geometry : bond 0.00415 ( 6142) covalent geometry : angle 0.68136 ( 8354) SS BOND : bond 0.00057 ( 2) SS BOND : angle 1.35446 ( 4) hydrogen bonds : bond 0.13430 ( 396) hydrogen bonds : angle 5.89402 ( 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 : 0.200 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: 0.0647 time to fit residues: 14.8162 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 : 0.222 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4494 r_free = 0.4494 target = 0.191211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.157746 restraints weight = 8559.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.158367 restraints weight = 7539.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.158547 restraints weight = 7045.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.158785 restraints weight = 6813.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.158875 restraints weight = 6711.176| |-----------------------------------------------------------------------------| r_work (final): 0.4120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.2001 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= 0.160 Angle : 0.656 8.400 8358 Z= 0.339 Chirality : 0.041 0.135 1000 Planarity : 0.005 0.062 1002 Dihedral : 6.747 58.838 860 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.26 % Allowed : 3.68 % Favored : 96.05 % Rotamer: Outliers : 2.37 % Allowed : 18.35 % Favored : 79.27 % 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: -0.25 (0.24), residues: 456 sheet: 0.21 (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 0.016 0.001 PHE A 196 TRP 0.013 0.001 TRP C 107 HIS 0.005 0.001 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 6142) covalent geometry : angle 0.65574 ( 8354) SS BOND : bond 0.00035 ( 2) SS BOND : angle 0.39569 ( 4) hydrogen bonds : bond 0.03972 ( 396) hydrogen bonds : angle 4.60988 ( 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 : 0.180 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 REVERT: B 63 TYR cc_start: 0.8010 (m-80) cc_final: 0.7639 (m-80) outliers start: 15 outliers final: 12 residues processed: 138 average time/residue: 0.0514 time to fit residues: 10.2465 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 : 0.202 ------------------------------------------------------------------------------- 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: 0.7980 chunk 3 optimal weight: 3.9990 chunk 50 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 44 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 18 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 63 optimal weight: 7.9990 chunk 33 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN A 90 ASN D 88 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.190751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.154980 restraints weight = 8835.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.155392 restraints weight = 7828.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 15)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.155391 restraints weight = 7318.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.155391 restraints weight = 7318.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.155391 restraints weight = 7318.260| |-----------------------------------------------------------------------------| r_work (final): 0.4070 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 6144 Z= 0.195 Angle : 0.660 7.062 8358 Z= 0.344 Chirality : 0.042 0.133 1000 Planarity : 0.004 0.046 1002 Dihedral : 6.896 58.725 860 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 14.18 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.87 % Favored : 95.00 % Rotamer: Outliers : 3.80 % Allowed : 23.10 % Favored : 73.10 % 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: -0.77 (0.30), residues: 760 helix: 0.02 (0.24), residues: 458 sheet: 0.29 (0.49), residues: 114 loop : -2.12 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 63 TYR 0.015 0.002 TYR A 109 PHE 0.017 0.002 PHE D 225 TRP 0.013 0.002 TRP C 40 HIS 0.010 0.002 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00469 ( 6142) covalent geometry : angle 0.66034 ( 8354) SS BOND : bond 0.00069 ( 2) SS BOND : angle 0.33616 ( 4) hydrogen bonds : bond 0.03901 ( 396) hydrogen bonds : angle 4.54776 ( 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 153 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 TYR cc_start: 0.8057 (m-80) cc_final: 0.7703 (m-80) outliers start: 24 outliers final: 16 residues processed: 142 average time/residue: 0.0559 time to fit residues: 11.0523 Evaluate side-chains 132 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 116 time to evaluate : 0.160 ------------------------------------------------------------------------------- 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 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 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: 0.8980 chunk 61 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 39 optimal weight: 20.0000 chunk 62 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.187418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.157661 restraints weight = 8702.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 70)----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.152607 restraints weight = 9122.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.153461 restraints weight = 7841.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.154190 restraints weight = 7131.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.155139 restraints weight = 6663.761| |-----------------------------------------------------------------------------| r_work (final): 0.4087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6144 Z= 0.195 Angle : 0.674 7.281 8358 Z= 0.352 Chirality : 0.042 0.136 1000 Planarity : 0.004 0.040 1002 Dihedral : 7.009 59.426 860 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 13.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 5.54 % Allowed : 22.94 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.60 (0.31), residues: 760 helix: 0.19 (0.25), residues: 458 sheet: 0.17 (0.48), residues: 114 loop : -2.02 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 63 TYR 0.015 0.002 TYR A 109 PHE 0.016 0.002 PHE D 225 TRP 0.016 0.002 TRP B 40 HIS 0.007 0.001 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00473 ( 6142) covalent geometry : angle 0.67447 ( 8354) SS BOND : bond 0.00079 ( 2) SS BOND : angle 0.17676 ( 4) hydrogen bonds : bond 0.03848 ( 396) hydrogen bonds : angle 4.49665 ( 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 149 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 114 time to evaluate : 0.170 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: B 63 TYR cc_start: 0.8036 (m-80) cc_final: 0.7749 (m-80) REVERT: A 43 HIS cc_start: 0.7980 (OUTLIER) cc_final: 0.7692 (t-170) REVERT: A 222 MET cc_start: 0.7563 (mmm) cc_final: 0.7325 (mmm) REVERT: D 43 HIS cc_start: 0.7994 (OUTLIER) cc_final: 0.7725 (t-170) REVERT: D 222 MET cc_start: 0.7513 (mmm) cc_final: 0.7264 (mmm) outliers start: 35 outliers final: 19 residues processed: 136 average time/residue: 0.0605 time to fit residues: 11.6107 Evaluate side-chains 133 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.263 ------------------------------------------------------------------------------- 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 51 LEU 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 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: 3.9990 chunk 2 optimal weight: 9.9990 chunk 42 optimal weight: 0.0970 chunk 72 optimal weight: 0.6980 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 8.9990 chunk 60 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 overall best weight: 1.0780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 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 = 0.4441 r_free = 0.4441 target = 0.185683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.156756 restraints weight = 8734.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.155238 restraints weight = 11591.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.155914 restraints weight = 10442.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.155848 restraints weight = 9190.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.156051 restraints weight = 8543.213| |-----------------------------------------------------------------------------| r_work (final): 0.4100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6144 Z= 0.220 Angle : 0.707 7.604 8358 Z= 0.365 Chirality : 0.043 0.133 1000 Planarity : 0.004 0.036 1002 Dihedral : 7.259 60.441 860 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 4.75 % Allowed : 24.21 % Favored : 71.04 % 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: -0.58 (0.31), residues: 760 helix: 0.17 (0.25), residues: 458 sheet: 0.30 (0.48), residues: 114 loop : -1.96 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 191 TYR 0.015 0.002 TYR A 109 PHE 0.018 0.002 PHE D 225 TRP 0.010 0.002 TRP C 40 HIS 0.008 0.002 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00537 ( 6142) covalent geometry : angle 0.70674 ( 8354) SS BOND : bond 0.00049 ( 2) SS BOND : angle 0.17514 ( 4) hydrogen bonds : bond 0.03993 ( 396) hydrogen bonds : angle 4.52591 ( 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 151 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 121 time to evaluate : 0.165 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: B 63 TYR cc_start: 0.7910 (m-80) cc_final: 0.7697 (m-80) REVERT: B 108 MET cc_start: 0.4074 (ptm) cc_final: 0.3856 (ptm) REVERT: A 43 HIS cc_start: 0.7957 (OUTLIER) cc_final: 0.7709 (t-170) REVERT: A 46 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8211 (mp) REVERT: C 108 MET cc_start: 0.4244 (ptm) cc_final: 0.3975 (ptm) REVERT: D 43 HIS cc_start: 0.8015 (OUTLIER) cc_final: 0.7675 (t-170) outliers start: 30 outliers final: 19 residues processed: 141 average time/residue: 0.0614 time to fit residues: 12.1596 Evaluate side-chains 136 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 43 HIS Chi-restraints excluded: chain D residue 48 ILE Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 62 VAL 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 289 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 61 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 70 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 35 optimal weight: 0.2980 chunk 40 optimal weight: 0.0470 chunk 68 optimal weight: 0.6980 chunk 65 optimal weight: 0.6980 chunk 55 optimal weight: 0.4980 overall best weight: 0.4078 ------------------------------------------------------------------------------- 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 = 0.4504 r_free = 0.4504 target = 0.191832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4194 r_free = 0.4194 target = 0.163687 restraints weight = 8562.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.162467 restraints weight = 11360.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.163029 restraints weight = 10222.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4182 r_free = 0.4182 target = 0.163348 restraints weight = 8402.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.163559 restraints weight = 7650.575| |-----------------------------------------------------------------------------| r_work (final): 0.4188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6144 Z= 0.141 Angle : 0.659 7.553 8358 Z= 0.335 Chirality : 0.040 0.134 1000 Planarity : 0.003 0.034 1002 Dihedral : 7.124 59.568 860 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 14.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 3.64 % Allowed : 24.68 % Favored : 71.68 % 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: -0.11 (0.31), residues: 760 helix: 0.53 (0.25), residues: 458 sheet: 0.67 (0.49), residues: 114 loop : -1.91 (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 D 287 PHE 0.014 0.001 PHE C 72 TRP 0.012 0.001 TRP A 17 HIS 0.003 0.001 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00334 ( 6142) covalent geometry : angle 0.65940 ( 8354) SS BOND : bond 0.00042 ( 2) SS BOND : angle 0.12920 ( 4) hydrogen bonds : bond 0.03654 ( 396) hydrogen bonds : angle 4.33383 ( 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 147 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.220 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: 0.4090 (ptm) cc_final: 0.3869 (ptm) REVERT: A 37 PHE cc_start: 0.6694 (m-80) cc_final: 0.6482 (m-80) REVERT: C 108 MET cc_start: 0.4080 (ptm) cc_final: 0.3814 (ptm) REVERT: D 37 PHE cc_start: 0.6737 (m-80) cc_final: 0.6527 (m-80) REVERT: D 230 MET cc_start: 0.7895 (tpp) cc_final: 0.7690 (mmp) REVERT: D 277 MET cc_start: 0.7286 (mmt) cc_final: 0.7078 (mmm) outliers start: 23 outliers final: 16 residues processed: 137 average time/residue: 0.0588 time to fit residues: 11.1803 Evaluate side-chains 128 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 112 time to evaluate : 0.140 ------------------------------------------------------------------------------- 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 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 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 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 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: 1.9990 chunk 3 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 34 optimal weight: 0.0020 chunk 50 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 30 optimal weight: 0.0370 chunk 60 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.7668 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN C 86 GLN ** 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 = 0.4477 r_free = 0.4477 target = 0.190702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.163388 restraints weight = 8814.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.162768 restraints weight = 12708.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.163264 restraints weight = 11437.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.163203 restraints weight = 10149.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.163364 restraints weight = 9256.887| |-----------------------------------------------------------------------------| r_work (final): 0.4177 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.3347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6144 Z= 0.179 Angle : 0.698 7.567 8358 Z= 0.360 Chirality : 0.042 0.162 1000 Planarity : 0.003 0.036 1002 Dihedral : 7.202 59.996 860 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 4.43 % Allowed : 26.42 % 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: -0.15 (0.31), residues: 760 helix: 0.49 (0.25), residues: 458 sheet: 0.67 (0.50), residues: 114 loop : -1.90 (0.44), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 63 TYR 0.014 0.002 TYR A 109 PHE 0.049 0.002 PHE B 72 TRP 0.008 0.001 TRP B 40 HIS 0.006 0.001 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00435 ( 6142) covalent geometry : angle 0.69801 ( 8354) SS BOND : bond 0.00074 ( 2) SS BOND : angle 0.15309 ( 4) hydrogen bonds : bond 0.03854 ( 396) hydrogen bonds : angle 4.43616 ( 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 144 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 116 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 HIS cc_start: 0.8012 (OUTLIER) cc_final: 0.7650 (t-170) REVERT: A 210 PHE cc_start: 0.6774 (OUTLIER) cc_final: 0.5768 (m-80) REVERT: D 43 HIS cc_start: 0.8002 (OUTLIER) cc_final: 0.7639 (t-170) REVERT: D 210 PHE cc_start: 0.6936 (OUTLIER) cc_final: 0.5905 (m-80) outliers start: 28 outliers final: 18 residues processed: 133 average time/residue: 0.0607 time to fit residues: 11.2372 Evaluate side-chains 136 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 114 time to evaluate : 0.202 ------------------------------------------------------------------------------- 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 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 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: 2.9990 chunk 57 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4464 r_free = 0.4464 target = 0.187243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.159223 restraints weight = 8609.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.157942 restraints weight = 10748.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.159013 restraints weight = 9884.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.158967 restraints weight = 8459.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.158989 restraints weight = 7852.614| |-----------------------------------------------------------------------------| r_work (final): 0.4156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 6144 Z= 0.196 Angle : 0.719 7.529 8358 Z= 0.373 Chirality : 0.043 0.167 1000 Planarity : 0.003 0.032 1002 Dihedral : 7.232 60.488 860 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 3.96 % Allowed : 28.16 % Favored : 67.88 % 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: -0.29 (0.31), residues: 760 helix: 0.44 (0.25), residues: 454 sheet: 0.54 (0.50), residues: 114 loop : -2.03 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 23 TYR 0.015 0.002 TYR A 109 PHE 0.039 0.002 PHE B 72 TRP 0.010 0.002 TRP C 107 HIS 0.007 0.001 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 6142) covalent geometry : angle 0.71869 ( 8354) SS BOND : bond 0.00019 ( 2) SS BOND : angle 0.22853 ( 4) hydrogen bonds : bond 0.03902 ( 396) hydrogen bonds : angle 4.53011 ( 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 141 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 116 time to evaluate : 0.137 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 HIS cc_start: 0.8065 (OUTLIER) cc_final: 0.7682 (t-170) REVERT: A 210 PHE cc_start: 0.6822 (OUTLIER) cc_final: 0.5819 (m-80) REVERT: D 43 HIS cc_start: 0.8078 (OUTLIER) cc_final: 0.7700 (t-170) REVERT: D 210 PHE cc_start: 0.6897 (OUTLIER) cc_final: 0.5850 (m-80) REVERT: D 277 MET cc_start: 0.7248 (mmt) cc_final: 0.7041 (mmm) outliers start: 25 outliers final: 18 residues processed: 129 average time/residue: 0.0670 time to fit residues: 11.8248 Evaluate side-chains 133 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 111 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 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 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: 0.6980 chunk 73 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 56 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 38 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 51 optimal weight: 0.1980 chunk 39 optimal weight: 9.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 86 GLN C 86 GLN ** 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 = 0.4488 r_free = 0.4488 target = 0.190237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.161629 restraints weight = 8625.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.159474 restraints weight = 11060.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.160349 restraints weight = 11779.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.160479 restraints weight = 9256.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.161209 restraints weight = 7925.975| |-----------------------------------------------------------------------------| r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7545 moved from start: 0.3586 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 : 0.721 8.797 8358 Z= 0.368 Chirality : 0.043 0.175 1000 Planarity : 0.003 0.035 1002 Dihedral : 7.132 59.990 860 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 4.11 % Allowed : 28.48 % 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: -0.32 (0.31), residues: 760 helix: 0.41 (0.25), residues: 466 sheet: 0.63 (0.50), residues: 114 loop : -2.27 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 23 TYR 0.021 0.002 TYR B 63 PHE 0.010 0.001 PHE D 54 TRP 0.012 0.001 TRP A 17 HIS 0.005 0.001 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 6142) covalent geometry : angle 0.72108 ( 8354) SS BOND : bond 0.00029 ( 2) SS BOND : angle 0.24828 ( 4) hydrogen bonds : bond 0.03777 ( 396) hydrogen bonds : angle 4.41087 ( 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 148 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 122 time to evaluate : 0.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 PHE cc_start: 0.6781 (OUTLIER) cc_final: 0.5799 (m-80) REVERT: D 43 HIS cc_start: 0.8007 (OUTLIER) cc_final: 0.7585 (t-170) REVERT: D 210 PHE cc_start: 0.6940 (OUTLIER) cc_final: 0.5934 (m-80) outliers start: 26 outliers final: 19 residues processed: 138 average time/residue: 0.0615 time to fit residues: 11.7688 Evaluate side-chains 138 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.129 ------------------------------------------------------------------------------- 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 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 172 VAL Chi-restraints excluded: chain D residue 184 GLU 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: 0.7980 chunk 16 optimal weight: 4.9990 chunk 61 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 2 optimal weight: 0.3980 chunk 37 optimal weight: 0.0000 chunk 54 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 15 optimal weight: 0.4980 chunk 71 optimal weight: 0.7980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.4501 r_free = 0.4501 target = 0.190908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.157007 restraints weight = 8614.510| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.157425 restraints weight = 7525.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.157448 restraints weight = 7359.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4107 r_free = 0.4107 target = 0.157608 restraints weight = 6980.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.157702 restraints weight = 6926.299| |-----------------------------------------------------------------------------| r_work (final): 0.4138 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.3668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6144 Z= 0.151 Angle : 0.729 9.184 8358 Z= 0.369 Chirality : 0.043 0.188 1000 Planarity : 0.003 0.033 1002 Dihedral : 7.091 59.756 860 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 3.80 % Allowed : 28.80 % 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: -0.23 (0.31), residues: 760 helix: 0.44 (0.25), residues: 466 sheet: 0.81 (0.51), residues: 114 loop : -2.23 (0.43), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 63 TYR 0.017 0.001 TYR B 63 PHE 0.008 0.001 PHE A 54 TRP 0.016 0.001 TRP B 107 HIS 0.004 0.001 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00360 ( 6142) covalent geometry : angle 0.72934 ( 8354) SS BOND : bond 0.00045 ( 2) SS BOND : angle 0.26141 ( 4) hydrogen bonds : bond 0.03765 ( 396) hydrogen bonds : angle 4.44207 ( 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 144 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 120 time to evaluate : 0.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 210 PHE cc_start: 0.6807 (OUTLIER) cc_final: 0.5826 (m-80) REVERT: C 23 ARG cc_start: 0.7266 (mmm160) cc_final: 0.6748 (tpp80) REVERT: D 210 PHE cc_start: 0.6950 (OUTLIER) cc_final: 0.5965 (m-80) outliers start: 24 outliers final: 20 residues processed: 130 average time/residue: 0.0670 time to fit residues: 11.9679 Evaluate side-chains 139 residues out of total 632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 16 VAL 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 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 51 LEU Chi-restraints excluded: chain D residue 62 VAL Chi-restraints excluded: chain D residue 81 LEU 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 39 optimal weight: 10.0000 chunk 12 optimal weight: 0.2980 chunk 21 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 67 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4477 r_free = 0.4477 target = 0.188450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.159229 restraints weight = 8643.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.158581 restraints weight = 12520.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.159395 restraints weight = 11344.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.158873 restraints weight = 9174.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4158 r_free = 0.4158 target = 0.159220 restraints weight = 8403.514| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.3752 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= 0.183 Angle : 0.754 11.899 8358 Z= 0.383 Chirality : 0.044 0.176 1000 Planarity : 0.003 0.033 1002 Dihedral : 7.175 60.030 860 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 15.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 4.27 % Allowed : 28.96 % Favored : 66.77 % 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: -0.30 (0.31), residues: 760 helix: 0.32 (0.24), residues: 466 sheet: 0.87 (0.54), residues: 98 loop : -1.86 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 191 TYR 0.015 0.001 TYR A 109 PHE 0.013 0.001 PHE D 225 TRP 0.020 0.002 TRP B 107 HIS 0.007 0.001 HIS D 43 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 6142) covalent geometry : angle 0.75442 ( 8354) SS BOND : bond 0.00039 ( 2) SS BOND : angle 0.31759 ( 4) hydrogen bonds : bond 0.03829 ( 396) hydrogen bonds : angle 4.48809 ( 1170) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1029.62 seconds wall clock time: 18 minutes 27.57 seconds (1107.57 seconds total)