Starting phenix.real_space_refine on Tue Mar 3 15:08:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6tar_10425/03_2026/6tar_10425.cif Found real_map, /net/cci-nas-00/data/ceres_data/6tar_10425/03_2026/6tar_10425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6tar_10425/03_2026/6tar_10425.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6tar_10425/03_2026/6tar_10425.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6tar_10425/03_2026/6tar_10425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6tar_10425/03_2026/6tar_10425.map" } resolution = 2.8 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= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 4270 2.51 5 N 1170 2.21 5 O 1260 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 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: 6715 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1343 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 4, 'TRANS': 159} Restraints were copied for chains: B, C, D, E Time building chain proxies: 1.06, per 1000 atoms: 0.16 Number of scatterers: 6715 At special positions: 0 Unit cell: (117.467, 112.623, 60.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 1260 8.00 N 1170 7.00 C 4270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 366.8 milliseconds 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1530 Finding SS restraints... Secondary structure from input PDB file: 55 helices and 0 sheets defined 68.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 57 through 76 removed outlier: 3.618A pdb=" N VAL A 61 " --> pdb=" O ASP A 57 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY A 76 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 85 removed outlier: 3.835A pdb=" N LYS A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 89 removed outlier: 3.540A pdb=" N LEU A 89 " --> pdb=" O ILE A 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 86 through 89' Processing helix chain 'A' and resid 92 through 102 removed outlier: 4.114A pdb=" N THR A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP A 97 " --> pdb=" O MET A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 105 No H-bonds generated for 'chain 'A' and resid 103 through 105' Processing helix chain 'A' and resid 108 through 119 Processing helix chain 'A' and resid 124 through 135 removed outlier: 4.032A pdb=" N ILE A 128 " --> pdb=" O PRO A 124 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN A 135 " --> pdb=" O GLU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 154 removed outlier: 3.903A pdb=" N PHE A 146 " --> pdb=" O PRO A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 163 through 172 removed outlier: 3.560A pdb=" N GLU A 167 " --> pdb=" O ASP A 163 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 181 Processing helix chain 'A' and resid 190 through 205 removed outlier: 3.550A pdb=" N LEU A 194 " --> pdb=" O THR A 190 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN A 205 " --> pdb=" O ILE A 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 76 removed outlier: 3.618A pdb=" N VAL B 61 " --> pdb=" O ASP B 57 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY B 76 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 85 removed outlier: 3.836A pdb=" N LYS B 84 " --> pdb=" O GLU B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 86 through 89 removed outlier: 3.540A pdb=" N LEU B 89 " --> pdb=" O ILE B 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 86 through 89' Processing helix chain 'B' and resid 92 through 102 removed outlier: 4.112A pdb=" N THR B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP B 97 " --> pdb=" O MET B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 105 No H-bonds generated for 'chain 'B' and resid 103 through 105' Processing helix chain 'B' and resid 108 through 119 Processing helix chain 'B' and resid 124 through 135 removed outlier: 4.032A pdb=" N ILE B 128 " --> pdb=" O PRO B 124 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ASN B 135 " --> pdb=" O GLU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 154 removed outlier: 3.903A pdb=" N PHE B 146 " --> pdb=" O PRO B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 172 removed outlier: 3.559A pdb=" N GLU B 167 " --> pdb=" O ASP B 163 " (cutoff:3.500A) Processing helix chain 'B' and resid 176 through 181 Processing helix chain 'B' and resid 190 through 205 removed outlier: 3.550A pdb=" N LEU B 194 " --> pdb=" O THR B 190 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ASN B 205 " --> pdb=" O ILE B 201 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 76 removed outlier: 3.618A pdb=" N VAL C 61 " --> pdb=" O ASP C 57 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY C 76 " --> pdb=" O LYS C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 85 removed outlier: 3.835A pdb=" N LYS C 84 " --> pdb=" O GLU C 80 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 89 removed outlier: 3.540A pdb=" N LEU C 89 " --> pdb=" O ILE C 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 86 through 89' Processing helix chain 'C' and resid 92 through 102 removed outlier: 4.113A pdb=" N THR C 96 " --> pdb=" O GLY C 92 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N TRP C 97 " --> pdb=" O MET C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 105 No H-bonds generated for 'chain 'C' and resid 103 through 105' Processing helix chain 'C' and resid 108 through 119 Processing helix chain 'C' and resid 124 through 135 removed outlier: 4.033A pdb=" N ILE C 128 " --> pdb=" O PRO C 124 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN C 135 " --> pdb=" O GLU C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 154 removed outlier: 3.903A pdb=" N PHE C 146 " --> pdb=" O PRO C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 172 removed outlier: 3.559A pdb=" N GLU C 167 " --> pdb=" O ASP C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 181 Processing helix chain 'C' and resid 190 through 205 removed outlier: 3.551A pdb=" N LEU C 194 " --> pdb=" O THR C 190 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN C 205 " --> pdb=" O ILE C 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 76 removed outlier: 3.617A pdb=" N VAL D 61 " --> pdb=" O ASP D 57 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLY D 76 " --> pdb=" O LYS D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 80 through 85 removed outlier: 3.836A pdb=" N LYS D 84 " --> pdb=" O GLU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 89 removed outlier: 3.540A pdb=" N LEU D 89 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 86 through 89' Processing helix chain 'D' and resid 92 through 102 removed outlier: 4.114A pdb=" N THR D 96 " --> pdb=" O GLY D 92 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TRP D 97 " --> pdb=" O MET D 93 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 105 No H-bonds generated for 'chain 'D' and resid 103 through 105' Processing helix chain 'D' and resid 108 through 119 Processing helix chain 'D' and resid 124 through 135 removed outlier: 4.032A pdb=" N ILE D 128 " --> pdb=" O PRO D 124 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN D 135 " --> pdb=" O GLU D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 142 through 154 removed outlier: 3.903A pdb=" N PHE D 146 " --> pdb=" O PRO D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 172 removed outlier: 3.559A pdb=" N GLU D 167 " --> pdb=" O ASP D 163 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 181 Processing helix chain 'D' and resid 190 through 205 removed outlier: 3.551A pdb=" N LEU D 194 " --> pdb=" O THR D 190 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ASN D 205 " --> pdb=" O ILE D 201 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 76 removed outlier: 3.617A pdb=" N VAL E 61 " --> pdb=" O ASP E 57 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY E 76 " --> pdb=" O LYS E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 80 through 85 removed outlier: 3.834A pdb=" N LYS E 84 " --> pdb=" O GLU E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 89 removed outlier: 3.540A pdb=" N LEU E 89 " --> pdb=" O ILE E 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 86 through 89' Processing helix chain 'E' and resid 92 through 102 removed outlier: 4.113A pdb=" N THR E 96 " --> pdb=" O GLY E 92 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N TRP E 97 " --> pdb=" O MET E 93 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 105 No H-bonds generated for 'chain 'E' and resid 103 through 105' Processing helix chain 'E' and resid 108 through 119 Processing helix chain 'E' and resid 124 through 135 removed outlier: 4.031A pdb=" N ILE E 128 " --> pdb=" O PRO E 124 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN E 135 " --> pdb=" O GLU E 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 154 removed outlier: 3.903A pdb=" N PHE E 146 " --> pdb=" O PRO E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 163 through 172 removed outlier: 3.560A pdb=" N GLU E 167 " --> pdb=" O ASP E 163 " (cutoff:3.500A) Processing helix chain 'E' and resid 176 through 181 Processing helix chain 'E' and resid 190 through 205 removed outlier: 3.549A pdb=" N LEU E 194 " --> pdb=" O THR E 190 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN E 205 " --> pdb=" O ILE E 201 " (cutoff:3.500A) 295 hydrogen bonds defined for protein. 885 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: 0.93 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2186 1.34 - 1.46: 1085 1.46 - 1.57: 3584 1.57 - 1.69: 0 1.69 - 1.80: 25 Bond restraints: 6880 Sorted by residual: bond pdb=" N PHE E 133 " pdb=" CA PHE E 133 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.31e-02 5.83e+03 5.94e+00 bond pdb=" N PHE C 133 " pdb=" CA PHE C 133 " ideal model delta sigma weight residual 1.456 1.488 -0.032 1.31e-02 5.83e+03 5.87e+00 bond pdb=" N PHE A 133 " pdb=" CA PHE A 133 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.31e-02 5.83e+03 5.70e+00 bond pdb=" N PHE B 133 " pdb=" CA PHE B 133 " ideal model delta sigma weight residual 1.456 1.488 -0.031 1.31e-02 5.83e+03 5.66e+00 bond pdb=" N PHE D 133 " pdb=" CA PHE D 133 " ideal model delta sigma weight residual 1.456 1.487 -0.031 1.31e-02 5.83e+03 5.50e+00 ... (remaining 6875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 8763 1.80 - 3.59: 437 3.59 - 5.39: 65 5.39 - 7.19: 10 7.19 - 8.98: 10 Bond angle restraints: 9285 Sorted by residual: angle pdb=" C HIS E 118 " pdb=" N PHE E 119 " pdb=" CA PHE E 119 " ideal model delta sigma weight residual 122.60 116.50 6.10 1.56e+00 4.11e-01 1.53e+01 angle pdb=" C HIS C 118 " pdb=" N PHE C 119 " pdb=" CA PHE C 119 " ideal model delta sigma weight residual 122.60 116.51 6.09 1.56e+00 4.11e-01 1.52e+01 angle pdb=" CA THR A 122 " pdb=" CB THR A 122 " pdb=" CG2 THR A 122 " ideal model delta sigma weight residual 110.50 117.13 -6.63 1.70e+00 3.46e-01 1.52e+01 angle pdb=" C PRO C 121 " pdb=" N THR C 122 " pdb=" CA THR C 122 " ideal model delta sigma weight residual 121.54 128.99 -7.45 1.91e+00 2.74e-01 1.52e+01 angle pdb=" CA THR D 122 " pdb=" CB THR D 122 " pdb=" CG2 THR D 122 " ideal model delta sigma weight residual 110.50 117.13 -6.63 1.70e+00 3.46e-01 1.52e+01 ... (remaining 9280 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.14: 3375 14.14 - 28.29: 480 28.29 - 42.43: 150 42.43 - 56.58: 35 56.58 - 70.72: 5 Dihedral angle restraints: 4045 sinusoidal: 1675 harmonic: 2370 Sorted by residual: dihedral pdb=" CA ASN E 44 " pdb=" CB ASN E 44 " pdb=" CG ASN E 44 " pdb=" OD1 ASN E 44 " ideal model delta sinusoidal sigma weight residual -90.00 -160.72 70.72 2 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ASN B 44 " pdb=" CB ASN B 44 " pdb=" CG ASN B 44 " pdb=" OD1 ASN B 44 " ideal model delta sinusoidal sigma weight residual -90.00 -160.67 70.67 2 2.00e+01 2.50e-03 1.07e+01 dihedral pdb=" CA ASN C 44 " pdb=" CB ASN C 44 " pdb=" CG ASN C 44 " pdb=" OD1 ASN C 44 " ideal model delta sinusoidal sigma weight residual -90.00 -160.67 70.67 2 2.00e+01 2.50e-03 1.07e+01 ... (remaining 4042 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 785 0.062 - 0.123: 136 0.123 - 0.185: 44 0.185 - 0.246: 5 0.246 - 0.308: 10 Chirality restraints: 980 Sorted by residual: chirality pdb=" CB ILE C 183 " pdb=" CA ILE C 183 " pdb=" CG1 ILE C 183 " pdb=" CG2 ILE C 183 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.37e+00 chirality pdb=" CB ILE A 183 " pdb=" CA ILE A 183 " pdb=" CG1 ILE A 183 " pdb=" CG2 ILE A 183 " both_signs ideal model delta sigma weight residual False 2.64 2.34 0.31 2.00e-01 2.50e+01 2.36e+00 chirality pdb=" CB ILE E 183 " pdb=" CA ILE E 183 " pdb=" CG1 ILE E 183 " pdb=" CG2 ILE E 183 " both_signs ideal model delta sigma weight residual False 2.64 2.35 0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 977 not shown) Planarity restraints: 1205 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 112 " -0.010 2.00e-02 2.50e+03 2.01e-02 4.06e+00 pdb=" C ILE B 112 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE B 112 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA B 113 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE E 112 " 0.010 2.00e-02 2.50e+03 1.99e-02 3.98e+00 pdb=" C ILE E 112 " -0.034 2.00e-02 2.50e+03 pdb=" O ILE E 112 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA E 113 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 112 " -0.010 2.00e-02 2.50e+03 1.98e-02 3.94e+00 pdb=" C ILE A 112 " 0.034 2.00e-02 2.50e+03 pdb=" O ILE A 112 " -0.013 2.00e-02 2.50e+03 pdb=" N ALA A 113 " -0.012 2.00e-02 2.50e+03 ... (remaining 1202 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2092 2.84 - 3.35: 5496 3.35 - 3.87: 9302 3.87 - 4.38: 9425 4.38 - 4.90: 17315 Nonbonded interactions: 43630 Sorted by model distance: nonbonded pdb=" O SER A 78 " pdb=" OG SER A 78 " model vdw 2.319 3.040 nonbonded pdb=" O SER D 78 " pdb=" OG SER D 78 " model vdw 2.319 3.040 nonbonded pdb=" O SER B 78 " pdb=" OG SER B 78 " model vdw 2.320 3.040 nonbonded pdb=" O SER C 78 " pdb=" OG SER C 78 " model vdw 2.320 3.040 nonbonded pdb=" O SER E 78 " pdb=" OG SER E 78 " model vdw 2.321 3.040 ... (remaining 43625 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 6.810 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7667 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 : 0.005 0.038 6880 Z= 0.298 Angle : 0.915 8.983 9285 Z= 0.574 Chirality : 0.060 0.308 980 Planarity : 0.006 0.041 1205 Dihedral : 14.526 70.721 2515 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 0.69 % Allowed : 10.14 % Favored : 89.17 % 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: -3.91 (0.23), residues: 810 helix: -1.87 (0.20), residues: 440 sheet: None (None), residues: 0 loop : -3.56 (0.23), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 185 TYR 0.016 0.002 TYR A 126 PHE 0.012 0.002 PHE D 45 TRP 0.013 0.002 TRP C 108 HIS 0.004 0.001 HIS C 203 Details of bonding type rmsd covalent geometry : bond 0.00520 ( 6880) covalent geometry : angle 0.91471 ( 9285) hydrogen bonds : bond 0.15119 ( 295) hydrogen bonds : angle 4.72658 ( 885) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 123 time to evaluate : 0.244 Fit side-chains REVERT: A 45 PHE cc_start: 0.8601 (OUTLIER) cc_final: 0.8010 (t80) REVERT: A 141 ASP cc_start: 0.7559 (m-30) cc_final: 0.7261 (m-30) REVERT: B 103 LYS cc_start: 0.8453 (mttt) cc_final: 0.8200 (mtmm) REVERT: C 45 PHE cc_start: 0.9016 (OUTLIER) cc_final: 0.8695 (t80) REVERT: D 45 PHE cc_start: 0.8733 (OUTLIER) cc_final: 0.8216 (t80) REVERT: D 73 ASP cc_start: 0.8168 (t0) cc_final: 0.7944 (t0) REVERT: E 45 PHE cc_start: 0.8819 (OUTLIER) cc_final: 0.7568 (t80) outliers start: 5 outliers final: 0 residues processed: 128 average time/residue: 0.4381 time to fit residues: 59.3016 Evaluate side-chains 95 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 91 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 PHE Chi-restraints excluded: chain C residue 45 PHE Chi-restraints excluded: chain D residue 45 PHE Chi-restraints excluded: chain E residue 45 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 0.0970 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 74 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN A 162 HIS A 203 HIS B 44 ASN B 58 HIS B 162 HIS B 182 HIS C 44 ASN C 162 HIS C 203 HIS D 44 ASN D 149 GLN D 162 HIS D 203 HIS E 44 ASN E 58 HIS E 162 HIS E 203 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3810 r_free = 0.3810 target = 0.126906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.113405 restraints weight = 11579.606| |-----------------------------------------------------------------------------| r_work (start): 0.3678 rms_B_bonded: 3.02 r_work: 0.3556 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.2102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 6880 Z= 0.108 Angle : 0.486 5.614 9285 Z= 0.267 Chirality : 0.040 0.223 980 Planarity : 0.003 0.024 1205 Dihedral : 5.729 51.165 888 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 1.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 2.78 % Allowed : 15.00 % Favored : 82.22 % 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: -1.68 (0.28), residues: 810 helix: 0.14 (0.24), residues: 450 sheet: None (None), residues: 0 loop : -2.87 (0.27), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 102 TYR 0.009 0.001 TYR A 126 PHE 0.006 0.001 PHE D 132 TRP 0.012 0.001 TRP A 108 HIS 0.004 0.000 HIS B 182 Details of bonding type rmsd covalent geometry : bond 0.00215 ( 6880) covalent geometry : angle 0.48564 ( 9285) hydrogen bonds : bond 0.03302 ( 295) hydrogen bonds : angle 3.56653 ( 885) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.239 Fit side-chains REVERT: A 73 ASP cc_start: 0.8609 (t0) cc_final: 0.8335 (t0) REVERT: A 141 ASP cc_start: 0.8154 (m-30) cc_final: 0.7866 (m-30) REVERT: B 73 ASP cc_start: 0.8105 (t0) cc_final: 0.7884 (t0) REVERT: C 73 ASP cc_start: 0.8308 (t0) cc_final: 0.8078 (t0) REVERT: C 137 GLN cc_start: 0.8794 (tt0) cc_final: 0.8575 (tm-30) REVERT: D 137 GLN cc_start: 0.8591 (tt0) cc_final: 0.8054 (tm-30) REVERT: E 101 VAL cc_start: 0.8912 (t) cc_final: 0.8700 (p) outliers start: 20 outliers final: 3 residues processed: 130 average time/residue: 0.3291 time to fit residues: 46.1279 Evaluate side-chains 102 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 99 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 203 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 10.0000 chunk 3 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 78 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 5 optimal weight: 0.3980 chunk 72 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 chunk 62 optimal weight: 10.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 182 HIS C 182 HIS E 182 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.124890 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.111560 restraints weight = 11657.696| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.98 r_work: 0.3545 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 6880 Z= 0.100 Angle : 0.483 5.694 9285 Z= 0.259 Chirality : 0.040 0.243 980 Planarity : 0.003 0.023 1205 Dihedral : 3.672 13.217 880 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 2.36 % Allowed : 19.31 % Favored : 78.33 % 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: -0.62 (0.31), residues: 810 helix: 1.01 (0.26), residues: 460 sheet: None (None), residues: 0 loop : -2.49 (0.30), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 102 TYR 0.011 0.001 TYR C 179 PHE 0.009 0.001 PHE B 52 TRP 0.010 0.001 TRP A 108 HIS 0.004 0.001 HIS B 182 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 6880) covalent geometry : angle 0.48256 ( 9285) hydrogen bonds : bond 0.03085 ( 295) hydrogen bonds : angle 3.31311 ( 885) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 103 time to evaluate : 0.191 Fit side-chains REVERT: A 73 ASP cc_start: 0.8680 (t0) cc_final: 0.8442 (t0) REVERT: A 141 ASP cc_start: 0.8338 (m-30) cc_final: 0.8075 (m-30) REVERT: B 134 GLN cc_start: 0.8108 (tp-100) cc_final: 0.7686 (tm-30) REVERT: B 154 LEU cc_start: 0.8753 (OUTLIER) cc_final: 0.8499 (tt) REVERT: B 182 HIS cc_start: 0.7781 (OUTLIER) cc_final: 0.7558 (m170) REVERT: C 73 ASP cc_start: 0.8395 (t0) cc_final: 0.8179 (t0) REVERT: D 73 ASP cc_start: 0.8444 (t0) cc_final: 0.8129 (t0) REVERT: D 174 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7819 (mt) REVERT: E 79 ASP cc_start: 0.8736 (t0) cc_final: 0.8496 (t0) REVERT: E 154 LEU cc_start: 0.8465 (tp) cc_final: 0.8003 (tp) outliers start: 17 outliers final: 8 residues processed: 109 average time/residue: 0.3159 time to fit residues: 37.3918 Evaluate side-chains 106 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 182 HIS Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain E residue 159 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 61 optimal weight: 6.9990 chunk 70 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 38 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 69 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 156 GLN E 58 HIS E 182 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.118067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.104863 restraints weight = 11878.592| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.00 r_work: 0.3444 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 6880 Z= 0.131 Angle : 0.502 5.196 9285 Z= 0.273 Chirality : 0.042 0.254 980 Planarity : 0.003 0.024 1205 Dihedral : 3.968 12.861 880 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 4.44 % Allowed : 20.42 % Favored : 75.14 % 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: -0.22 (0.31), residues: 810 helix: 1.43 (0.27), residues: 455 sheet: None (None), residues: 0 loop : -2.40 (0.30), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 185 TYR 0.017 0.002 TYR C 179 PHE 0.010 0.001 PHE B 133 TRP 0.010 0.001 TRP A 108 HIS 0.017 0.001 HIS B 182 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 6880) covalent geometry : angle 0.50224 ( 9285) hydrogen bonds : bond 0.04373 ( 295) hydrogen bonds : angle 3.36860 ( 885) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 109 time to evaluate : 0.252 Fit side-chains REVERT: A 141 ASP cc_start: 0.8404 (m-30) cc_final: 0.8145 (m-30) REVERT: A 154 LEU cc_start: 0.8040 (mt) cc_final: 0.7823 (tp) REVERT: B 154 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8140 (tp) REVERT: C 73 ASP cc_start: 0.8596 (t0) cc_final: 0.8316 (t0) REVERT: D 73 ASP cc_start: 0.8588 (t0) cc_final: 0.8254 (t0) REVERT: D 137 GLN cc_start: 0.8627 (tt0) cc_final: 0.8291 (tm-30) REVERT: D 174 LEU cc_start: 0.8033 (OUTLIER) cc_final: 0.7808 (mt) REVERT: E 154 LEU cc_start: 0.8446 (tp) cc_final: 0.7990 (tp) outliers start: 32 outliers final: 18 residues processed: 133 average time/residue: 0.3115 time to fit residues: 44.7873 Evaluate side-chains 118 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 98 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain E residue 159 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 53 optimal weight: 5.9990 chunk 47 optimal weight: 0.9990 chunk 13 optimal weight: 6.9990 chunk 45 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 26 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 4 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 156 GLN D 156 GLN E 156 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.108099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.095788 restraints weight = 12397.371| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.92 r_work: 0.3308 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 6880 Z= 0.251 Angle : 0.665 7.855 9285 Z= 0.363 Chirality : 0.049 0.298 980 Planarity : 0.004 0.031 1205 Dihedral : 4.781 13.954 880 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % Rotamer: Outliers : 5.97 % Allowed : 22.08 % Favored : 71.94 % 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: -0.94 (0.30), residues: 810 helix: 0.92 (0.25), residues: 475 sheet: None (None), residues: 0 loop : -3.09 (0.29), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 TYR 0.020 0.003 TYR D 179 PHE 0.015 0.002 PHE A 132 TRP 0.014 0.002 TRP A 108 HIS 0.004 0.001 HIS C 118 Details of bonding type rmsd covalent geometry : bond 0.00595 ( 6880) covalent geometry : angle 0.66530 ( 9285) hydrogen bonds : bond 0.07158 ( 295) hydrogen bonds : angle 3.93018 ( 885) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 118 time to evaluate : 0.243 Fit side-chains REVERT: A 86 ILE cc_start: 0.8524 (OUTLIER) cc_final: 0.7978 (mm) REVERT: A 101 VAL cc_start: 0.8697 (t) cc_final: 0.8412 (t) REVERT: A 141 ASP cc_start: 0.8128 (m-30) cc_final: 0.7861 (m-30) REVERT: A 205 ASN cc_start: 0.6803 (t0) cc_final: 0.5705 (m-40) REVERT: B 154 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8329 (tp) REVERT: B 179 TYR cc_start: 0.7263 (OUTLIER) cc_final: 0.6165 (m-10) REVERT: B 183 ILE cc_start: 0.8276 (tt) cc_final: 0.8022 (tp) REVERT: B 200 ILE cc_start: 0.7293 (OUTLIER) cc_final: 0.6821 (mt) REVERT: B 203 HIS cc_start: 0.5868 (OUTLIER) cc_final: 0.5298 (p-80) REVERT: C 118 HIS cc_start: 0.7563 (OUTLIER) cc_final: 0.7303 (OUTLIER) REVERT: D 73 ASP cc_start: 0.8885 (t0) cc_final: 0.8647 (t0) REVERT: D 174 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7884 (mt) outliers start: 43 outliers final: 19 residues processed: 148 average time/residue: 0.2749 time to fit residues: 44.4211 Evaluate side-chains 130 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 105 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 179 TYR Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 200 ILE Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 174 LEU Chi-restraints excluded: chain D residue 203 HIS Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 159 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 76 optimal weight: 0.9990 chunk 29 optimal weight: 0.0870 chunk 57 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 54 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 64 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 HIS B 149 GLN C 99 GLN C 156 GLN D 156 GLN E 156 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.115594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.103298 restraints weight = 12158.509| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 2.90 r_work: 0.3408 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 6880 Z= 0.140 Angle : 0.545 6.275 9285 Z= 0.293 Chirality : 0.043 0.313 980 Planarity : 0.003 0.024 1205 Dihedral : 4.362 14.824 880 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.02 % Favored : 91.98 % Rotamer: Outliers : 5.42 % Allowed : 24.58 % Favored : 70.00 % 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: -0.26 (0.31), residues: 810 helix: 1.45 (0.26), residues: 450 sheet: None (None), residues: 0 loop : -2.44 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 199 TYR 0.016 0.001 TYR D 179 PHE 0.009 0.001 PHE A 132 TRP 0.010 0.001 TRP A 108 HIS 0.005 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 6880) covalent geometry : angle 0.54456 ( 9285) hydrogen bonds : bond 0.04589 ( 295) hydrogen bonds : angle 3.54694 ( 885) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 91 time to evaluate : 0.241 Fit side-chains REVERT: A 141 ASP cc_start: 0.8206 (m-30) cc_final: 0.7920 (m-30) REVERT: A 205 ASN cc_start: 0.6824 (t0) cc_final: 0.5800 (m-40) REVERT: B 154 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8440 (tp) REVERT: C 73 ASP cc_start: 0.8659 (t0) cc_final: 0.8439 (t0) REVERT: D 73 ASP cc_start: 0.8622 (t0) cc_final: 0.8331 (t0) outliers start: 39 outliers final: 26 residues processed: 124 average time/residue: 0.2857 time to fit residues: 38.6352 Evaluate side-chains 110 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 83 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 118 HIS Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 203 HIS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 184 SER Chi-restraints excluded: chain E residue 203 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 68 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 4 optimal weight: 4.9990 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 73 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 55 optimal weight: 6.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 149 GLN B 156 GLN C 99 GLN C 137 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.111827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.099715 restraints weight = 12034.722| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 2.85 r_work: 0.3356 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8067 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.029 6880 Z= 0.196 Angle : 0.601 9.493 9285 Z= 0.322 Chirality : 0.045 0.206 980 Planarity : 0.003 0.028 1205 Dihedral : 4.562 14.877 880 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.52 % Favored : 91.48 % Rotamer: Outliers : 5.14 % Allowed : 24.86 % Favored : 70.00 % 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: -0.64 (0.31), residues: 810 helix: 1.09 (0.25), residues: 480 sheet: None (None), residues: 0 loop : -2.90 (0.30), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 199 TYR 0.018 0.002 TYR D 179 PHE 0.011 0.002 PHE A 132 TRP 0.011 0.001 TRP A 108 HIS 0.005 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00462 ( 6880) covalent geometry : angle 0.60116 ( 9285) hydrogen bonds : bond 0.06099 ( 295) hydrogen bonds : angle 3.70313 ( 885) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 96 time to evaluate : 0.244 Fit side-chains REVERT: A 101 VAL cc_start: 0.8696 (t) cc_final: 0.8439 (t) REVERT: A 205 ASN cc_start: 0.6912 (t0) cc_final: 0.6030 (m-40) REVERT: B 154 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8244 (tp) REVERT: B 183 ILE cc_start: 0.8361 (tt) cc_final: 0.8103 (tp) REVERT: C 73 ASP cc_start: 0.8766 (t0) cc_final: 0.8519 (t0) REVERT: D 73 ASP cc_start: 0.8788 (t0) cc_final: 0.8553 (t0) outliers start: 37 outliers final: 26 residues processed: 127 average time/residue: 0.2859 time to fit residues: 39.6252 Evaluate side-chains 119 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 107 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 203 HIS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 203 HIS Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 203 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 61 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 6 optimal weight: 9.9990 chunk 37 optimal weight: 0.4980 chunk 57 optimal weight: 0.0570 chunk 16 optimal weight: 7.9990 chunk 4 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 overall best weight: 1.5104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 156 GLN B 149 GLN B 156 GLN C 99 GLN C 118 HIS D 149 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.116556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.104257 restraints weight = 12143.725| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 2.89 r_work: 0.3420 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6880 Z= 0.127 Angle : 0.542 11.281 9285 Z= 0.284 Chirality : 0.043 0.318 980 Planarity : 0.003 0.023 1205 Dihedral : 4.190 15.289 880 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 4.86 % Allowed : 25.69 % Favored : 69.44 % 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: -0.00 (0.31), residues: 810 helix: 1.69 (0.26), residues: 450 sheet: None (None), residues: 0 loop : -2.38 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 161 TYR 0.015 0.001 TYR D 179 PHE 0.008 0.001 PHE B 64 TRP 0.010 0.001 TRP B 108 HIS 0.005 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 6880) covalent geometry : angle 0.54168 ( 9285) hydrogen bonds : bond 0.04234 ( 295) hydrogen bonds : angle 3.48488 ( 885) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 85 time to evaluate : 0.228 Fit side-chains REVERT: A 205 ASN cc_start: 0.6756 (t0) cc_final: 0.5803 (m-40) REVERT: B 137 GLN cc_start: 0.8858 (tm-30) cc_final: 0.8528 (tm-30) REVERT: B 154 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8437 (tp) REVERT: C 73 ASP cc_start: 0.8658 (t0) cc_final: 0.8415 (t0) REVERT: D 73 ASP cc_start: 0.8584 (t0) cc_final: 0.8307 (t0) outliers start: 35 outliers final: 24 residues processed: 114 average time/residue: 0.2957 time to fit residues: 36.7310 Evaluate side-chains 108 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 83 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 203 HIS Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 203 HIS Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 203 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 0 optimal weight: 8.9990 chunk 68 optimal weight: 6.9990 chunk 59 optimal weight: 0.0870 chunk 63 optimal weight: 3.9990 chunk 56 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 overall best weight: 1.7964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 HIS B 149 GLN C 99 GLN C 118 HIS C 137 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.115443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.103275 restraints weight = 12136.629| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.88 r_work: 0.3407 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.3407 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8006 moved from start: 0.3943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6880 Z= 0.137 Angle : 0.543 10.602 9285 Z= 0.287 Chirality : 0.042 0.228 980 Planarity : 0.003 0.027 1205 Dihedral : 4.147 15.470 880 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 4.72 % Allowed : 26.11 % Favored : 69.17 % 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: 0.10 (0.31), residues: 810 helix: 1.73 (0.26), residues: 455 sheet: None (None), residues: 0 loop : -2.32 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 161 TYR 0.016 0.002 TYR D 179 PHE 0.008 0.001 PHE B 133 TRP 0.010 0.001 TRP B 108 HIS 0.005 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 6880) covalent geometry : angle 0.54286 ( 9285) hydrogen bonds : bond 0.04647 ( 295) hydrogen bonds : angle 3.44457 ( 885) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 85 time to evaluate : 0.256 Fit side-chains REVERT: A 205 ASN cc_start: 0.7157 (t0) cc_final: 0.5790 (m-40) REVERT: B 137 GLN cc_start: 0.8806 (tm-30) cc_final: 0.8480 (tm-30) REVERT: B 154 LEU cc_start: 0.8658 (OUTLIER) cc_final: 0.8253 (tp) REVERT: C 73 ASP cc_start: 0.8698 (t0) cc_final: 0.8441 (t0) REVERT: C 137 GLN cc_start: 0.8716 (OUTLIER) cc_final: 0.8428 (pp30) REVERT: D 73 ASP cc_start: 0.8643 (t0) cc_final: 0.8394 (t0) outliers start: 34 outliers final: 26 residues processed: 114 average time/residue: 0.2922 time to fit residues: 36.1661 Evaluate side-chains 108 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 80 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 166 THR Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 201 ILE Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 203 HIS Chi-restraints excluded: chain D residue 46 SER Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 93 MET Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 203 HIS Chi-restraints excluded: chain E residue 46 SER Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 203 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 44 optimal weight: 0.2980 chunk 54 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 0.8980 chunk 31 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 74 optimal weight: 7.9990 chunk 27 optimal weight: 0.4980 chunk 72 optimal weight: 0.5980 chunk 23 optimal weight: 6.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 HIS B 149 GLN C 99 GLN C 118 HIS C 137 GLN C 149 GLN D 182 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.120533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.108185 restraints weight = 12053.887| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 2.90 r_work: 0.3478 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7922 moved from start: 0.4003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 6880 Z= 0.105 Angle : 0.516 9.582 9285 Z= 0.273 Chirality : 0.041 0.246 980 Planarity : 0.003 0.024 1205 Dihedral : 3.851 15.438 880 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 3.61 % Allowed : 27.36 % Favored : 69.03 % 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: 0.37 (0.32), residues: 810 helix: 1.86 (0.26), residues: 460 sheet: None (None), residues: 0 loop : -2.12 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 102 TYR 0.010 0.001 TYR D 179 PHE 0.010 0.001 PHE B 64 TRP 0.011 0.001 TRP E 98 HIS 0.005 0.001 HIS A 203 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 6880) covalent geometry : angle 0.51622 ( 9285) hydrogen bonds : bond 0.03064 ( 295) hydrogen bonds : angle 3.33530 ( 885) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 86 time to evaluate : 0.173 Fit side-chains REVERT: A 205 ASN cc_start: 0.7026 (t0) cc_final: 0.5645 (m-40) REVERT: B 154 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8193 (tp) REVERT: C 73 ASP cc_start: 0.8508 (t0) cc_final: 0.8263 (t0) REVERT: C 137 GLN cc_start: 0.8690 (OUTLIER) cc_final: 0.8375 (pp30) REVERT: C 179 TYR cc_start: 0.6917 (m-10) cc_final: 0.6684 (m-10) REVERT: D 73 ASP cc_start: 0.8559 (t0) cc_final: 0.8293 (t0) REVERT: E 179 TYR cc_start: 0.6837 (m-10) cc_final: 0.6597 (m-10) outliers start: 26 outliers final: 20 residues processed: 111 average time/residue: 0.2973 time to fit residues: 35.7958 Evaluate side-chains 104 residues out of total 720 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 82 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 68 ILE Chi-restraints excluded: chain A residue 106 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 190 THR Chi-restraints excluded: chain B residue 106 THR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 159 SER Chi-restraints excluded: chain B residue 190 THR Chi-restraints excluded: chain B residue 203 HIS Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 106 THR Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 159 SER Chi-restraints excluded: chain C residue 203 HIS Chi-restraints excluded: chain D residue 68 ILE Chi-restraints excluded: chain D residue 106 THR Chi-restraints excluded: chain D residue 159 SER Chi-restraints excluded: chain D residue 203 HIS Chi-restraints excluded: chain E residue 159 SER Chi-restraints excluded: chain E residue 203 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 27 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 8 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 52 optimal weight: 6.9990 chunk 41 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 182 HIS B 149 GLN C 99 GLN C 118 HIS C 137 GLN D 182 HIS E 182 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.118109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.105820 restraints weight = 11998.275| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 2.89 r_work: 0.3443 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6880 Z= 0.121 Angle : 0.553 15.846 9285 Z= 0.285 Chirality : 0.042 0.267 980 Planarity : 0.003 0.026 1205 Dihedral : 3.840 15.966 880 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 4.44 % Allowed : 27.08 % Favored : 68.47 % 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: 0.53 (0.32), residues: 810 helix: 2.07 (0.26), residues: 455 sheet: None (None), residues: 0 loop : -2.11 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 102 TYR 0.014 0.001 TYR D 179 PHE 0.008 0.001 PHE B 64 TRP 0.009 0.001 TRP E 98 HIS 0.005 0.001 HIS D 182 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 6880) covalent geometry : angle 0.55285 ( 9285) hydrogen bonds : bond 0.03980 ( 295) hydrogen bonds : angle 3.28399 ( 885) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1702.55 seconds wall clock time: 29 minutes 46.68 seconds (1786.68 seconds total)