Starting phenix.real_space_refine on Sat Aug 23 14:11:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6e0g_8947/08_2025/6e0g_8947.cif Found real_map, /net/cci-nas-00/data/ceres_data/6e0g_8947/08_2025/6e0g_8947.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6e0g_8947/08_2025/6e0g_8947.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6e0g_8947/08_2025/6e0g_8947.map" model { file = "/net/cci-nas-00/data/ceres_data/6e0g_8947/08_2025/6e0g_8947.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6e0g_8947/08_2025/6e0g_8947.cif" } resolution = 2.9 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= 0.029 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 60 5.16 5 C 8240 2.51 5 N 2190 2.21 5 O 2420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12910 Number of models: 1 Model: "" Number of chains: 1 Chain: "J" Number of atoms: 1291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1291 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 6, 'TRANS': 158} Restraints were copied for chains: A, B, C, D, E, F, G, H, I Time building chain proxies: 1.72, per 1000 atoms: 0.13 Number of scatterers: 12910 At special positions: 0 Unit cell: (137.256, 142.416, 65.016, 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 60 16.00 O 2420 8.00 N 2190 7.00 C 8240 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: 0.85 Conformation dependent library (CDL) restraints added in 575.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3060 Finding SS restraints... Secondary structure from input PDB file: 70 helices and 35 sheets defined 35.8% alpha, 18.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'J' and resid 61 through 64 removed outlier: 3.519A pdb=" N LYS J 64 " --> pdb=" O ASN J 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 61 through 64' Processing helix chain 'J' and resid 82 through 90 Processing helix chain 'J' and resid 92 through 97 Processing helix chain 'J' and resid 109 through 118 Processing helix chain 'J' and resid 120 through 124 Processing helix chain 'J' and resid 139 through 145 Processing helix chain 'J' and resid 181 through 198 removed outlier: 3.531A pdb=" N ALA J 185 " --> pdb=" O ASN J 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 64 removed outlier: 3.519A pdb=" N LYS A 64 " --> pdb=" O ASN A 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 61 through 64' Processing helix chain 'A' and resid 82 through 90 Processing helix chain 'A' and resid 92 through 97 Processing helix chain 'A' and resid 109 through 118 Processing helix chain 'A' and resid 120 through 124 Processing helix chain 'A' and resid 139 through 145 Processing helix chain 'A' and resid 181 through 198 removed outlier: 3.532A pdb=" N ALA A 185 " --> pdb=" O ASN A 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 64 removed outlier: 3.519A pdb=" N LYS B 64 " --> pdb=" O ASN B 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 61 through 64' Processing helix chain 'B' and resid 82 through 90 Processing helix chain 'B' and resid 92 through 97 Processing helix chain 'B' and resid 109 through 118 Processing helix chain 'B' and resid 120 through 124 Processing helix chain 'B' and resid 139 through 145 Processing helix chain 'B' and resid 181 through 198 removed outlier: 3.532A pdb=" N ALA B 185 " --> pdb=" O ASN B 181 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 64 removed outlier: 3.519A pdb=" N LYS C 64 " --> pdb=" O ASN C 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 61 through 64' Processing helix chain 'C' and resid 82 through 90 Processing helix chain 'C' and resid 92 through 97 Processing helix chain 'C' and resid 109 through 118 Processing helix chain 'C' and resid 120 through 124 Processing helix chain 'C' and resid 139 through 145 Processing helix chain 'C' and resid 181 through 198 removed outlier: 3.531A pdb=" N ALA C 185 " --> pdb=" O ASN C 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 64 removed outlier: 3.519A pdb=" N LYS D 64 " --> pdb=" O ASN D 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 61 through 64' Processing helix chain 'D' and resid 82 through 90 Processing helix chain 'D' and resid 92 through 97 Processing helix chain 'D' and resid 109 through 118 Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 139 through 145 Processing helix chain 'D' and resid 181 through 198 removed outlier: 3.531A pdb=" N ALA D 185 " --> pdb=" O ASN D 181 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 64 removed outlier: 3.519A pdb=" N LYS E 64 " --> pdb=" O ASN E 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 61 through 64' Processing helix chain 'E' and resid 82 through 90 Processing helix chain 'E' and resid 92 through 97 Processing helix chain 'E' and resid 109 through 118 Processing helix chain 'E' and resid 120 through 124 Processing helix chain 'E' and resid 139 through 145 Processing helix chain 'E' and resid 181 through 198 removed outlier: 3.531A pdb=" N ALA E 185 " --> pdb=" O ASN E 181 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 64 removed outlier: 3.519A pdb=" N LYS F 64 " --> pdb=" O ASN F 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 61 through 64' Processing helix chain 'F' and resid 82 through 90 Processing helix chain 'F' and resid 92 through 97 Processing helix chain 'F' and resid 109 through 118 Processing helix chain 'F' and resid 120 through 124 Processing helix chain 'F' and resid 139 through 145 Processing helix chain 'F' and resid 181 through 198 removed outlier: 3.532A pdb=" N ALA F 185 " --> pdb=" O ASN F 181 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 64 removed outlier: 3.518A pdb=" N LYS G 64 " --> pdb=" O ASN G 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 61 through 64' Processing helix chain 'G' and resid 82 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 109 through 118 Processing helix chain 'G' and resid 120 through 124 Processing helix chain 'G' and resid 139 through 145 Processing helix chain 'G' and resid 181 through 198 removed outlier: 3.532A pdb=" N ALA G 185 " --> pdb=" O ASN G 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 64 removed outlier: 3.518A pdb=" N LYS H 64 " --> pdb=" O ASN H 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 61 through 64' Processing helix chain 'H' and resid 82 through 90 Processing helix chain 'H' and resid 92 through 97 Processing helix chain 'H' and resid 109 through 118 Processing helix chain 'H' and resid 120 through 124 Processing helix chain 'H' and resid 139 through 145 Processing helix chain 'H' and resid 181 through 198 removed outlier: 3.531A pdb=" N ALA H 185 " --> pdb=" O ASN H 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 64 removed outlier: 3.519A pdb=" N LYS I 64 " --> pdb=" O ASN I 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 61 through 64' Processing helix chain 'I' and resid 82 through 90 Processing helix chain 'I' and resid 92 through 97 Processing helix chain 'I' and resid 109 through 118 Processing helix chain 'I' and resid 120 through 124 Processing helix chain 'I' and resid 139 through 145 Processing helix chain 'I' and resid 181 through 198 removed outlier: 3.531A pdb=" N ALA I 185 " --> pdb=" O ASN I 181 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'J' and resid 46 through 47 Processing sheet with id=AA2, first strand: chain 'J' and resid 50 through 51 Processing sheet with id=AA3, first strand: chain 'J' and resid 133 through 135 removed outlier: 7.446A pdb=" N LEU J 134 " --> pdb=" O VAL J 102 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA J 104 " --> pdb=" O LEU J 134 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LEU A 134 " --> pdb=" O VAL A 102 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA A 104 " --> pdb=" O LEU A 134 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'J' and resid 148 through 149 removed outlier: 3.501A pdb=" N ILE J 154 " --> pdb=" O ILE J 149 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 46 through 47 Processing sheet with id=AA6, first strand: chain 'A' and resid 50 through 51 Processing sheet with id=AA7, first strand: chain 'A' and resid 148 through 149 removed outlier: 3.501A pdb=" N ILE A 154 " --> pdb=" O ILE A 149 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 47 Processing sheet with id=AA9, first strand: chain 'B' and resid 50 through 51 Processing sheet with id=AB1, first strand: chain 'B' and resid 133 through 135 removed outlier: 7.446A pdb=" N LEU B 134 " --> pdb=" O VAL B 102 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA B 104 " --> pdb=" O LEU B 134 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU F 134 " --> pdb=" O VAL F 102 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA F 104 " --> pdb=" O LEU F 134 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 148 through 149 removed outlier: 3.501A pdb=" N ILE B 154 " --> pdb=" O ILE B 149 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 46 through 47 Processing sheet with id=AB4, first strand: chain 'C' and resid 50 through 51 Processing sheet with id=AB5, first strand: chain 'C' and resid 133 through 135 removed outlier: 7.446A pdb=" N LEU C 134 " --> pdb=" O VAL C 102 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA C 104 " --> pdb=" O LEU C 134 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU G 134 " --> pdb=" O VAL G 102 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA G 104 " --> pdb=" O LEU G 134 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 148 through 149 removed outlier: 3.501A pdb=" N ILE C 154 " --> pdb=" O ILE C 149 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 46 through 47 Processing sheet with id=AB8, first strand: chain 'D' and resid 50 through 51 Processing sheet with id=AB9, first strand: chain 'D' and resid 133 through 135 removed outlier: 7.446A pdb=" N LEU D 134 " --> pdb=" O VAL D 102 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ALA D 104 " --> pdb=" O LEU D 134 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N LEU H 134 " --> pdb=" O VAL H 102 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA H 104 " --> pdb=" O LEU H 134 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 148 through 149 removed outlier: 3.501A pdb=" N ILE D 154 " --> pdb=" O ILE D 149 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 46 through 47 Processing sheet with id=AC3, first strand: chain 'E' and resid 50 through 51 Processing sheet with id=AC4, first strand: chain 'E' and resid 133 through 135 removed outlier: 7.446A pdb=" N LEU E 134 " --> pdb=" O VAL E 102 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA E 104 " --> pdb=" O LEU E 134 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LEU I 134 " --> pdb=" O VAL I 102 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N ALA I 104 " --> pdb=" O LEU I 134 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 148 through 149 removed outlier: 3.501A pdb=" N ILE E 154 " --> pdb=" O ILE E 149 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 46 through 47 Processing sheet with id=AC7, first strand: chain 'F' and resid 50 through 51 Processing sheet with id=AC8, first strand: chain 'F' and resid 148 through 149 removed outlier: 3.502A pdb=" N ILE F 154 " --> pdb=" O ILE F 149 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'G' and resid 46 through 47 Processing sheet with id=AD1, first strand: chain 'G' and resid 50 through 51 Processing sheet with id=AD2, first strand: chain 'G' and resid 148 through 149 removed outlier: 3.501A pdb=" N ILE G 154 " --> pdb=" O ILE G 149 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 46 through 47 Processing sheet with id=AD4, first strand: chain 'H' and resid 50 through 51 Processing sheet with id=AD5, first strand: chain 'H' and resid 148 through 149 removed outlier: 3.501A pdb=" N ILE H 154 " --> pdb=" O ILE H 149 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 46 through 47 Processing sheet with id=AD7, first strand: chain 'I' and resid 50 through 51 Processing sheet with id=AD8, first strand: chain 'I' and resid 148 through 149 removed outlier: 3.501A pdb=" N ILE I 154 " --> pdb=" O ILE I 149 " (cutoff:3.500A) 550 hydrogen bonds defined for protein. 1500 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: 1.96 Time building geometry restraints manager: 1.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3620 1.33 - 1.45: 2287 1.45 - 1.57: 7163 1.57 - 1.69: 0 1.69 - 1.81: 100 Bond restraints: 13170 Sorted by residual: bond pdb=" CA LEU F 189 " pdb=" C LEU F 189 " ideal model delta sigma weight residual 1.524 1.485 0.040 1.24e-02 6.50e+03 1.02e+01 bond pdb=" CA LEU E 189 " pdb=" C LEU E 189 " ideal model delta sigma weight residual 1.524 1.485 0.040 1.24e-02 6.50e+03 1.02e+01 bond pdb=" CA LEU C 189 " pdb=" C LEU C 189 " ideal model delta sigma weight residual 1.524 1.485 0.040 1.24e-02 6.50e+03 1.02e+01 bond pdb=" CA LEU B 189 " pdb=" C LEU B 189 " ideal model delta sigma weight residual 1.524 1.485 0.039 1.24e-02 6.50e+03 1.00e+01 bond pdb=" CA LEU G 189 " pdb=" C LEU G 189 " ideal model delta sigma weight residual 1.524 1.485 0.039 1.24e-02 6.50e+03 9.99e+00 ... (remaining 13165 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 16729 2.02 - 4.03: 962 4.03 - 6.05: 109 6.05 - 8.06: 20 8.06 - 10.08: 10 Bond angle restraints: 17830 Sorted by residual: angle pdb=" N PHE E 192 " pdb=" CA PHE E 192 " pdb=" C PHE E 192 " ideal model delta sigma weight residual 111.82 105.56 6.26 1.16e+00 7.43e-01 2.91e+01 angle pdb=" N PHE G 192 " pdb=" CA PHE G 192 " pdb=" C PHE G 192 " ideal model delta sigma weight residual 111.82 105.56 6.26 1.16e+00 7.43e-01 2.91e+01 angle pdb=" N PHE H 192 " pdb=" CA PHE H 192 " pdb=" C PHE H 192 " ideal model delta sigma weight residual 111.82 105.57 6.25 1.16e+00 7.43e-01 2.91e+01 angle pdb=" N PHE C 192 " pdb=" CA PHE C 192 " pdb=" C PHE C 192 " ideal model delta sigma weight residual 111.82 105.58 6.24 1.16e+00 7.43e-01 2.89e+01 angle pdb=" N PHE B 192 " pdb=" CA PHE B 192 " pdb=" C PHE B 192 " ideal model delta sigma weight residual 111.82 105.59 6.23 1.16e+00 7.43e-01 2.89e+01 ... (remaining 17825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.69: 7430 15.69 - 31.37: 350 31.37 - 47.06: 60 47.06 - 62.75: 10 62.75 - 78.44: 10 Dihedral angle restraints: 7860 sinusoidal: 3100 harmonic: 4760 Sorted by residual: dihedral pdb=" CA TRP I 116 " pdb=" C TRP I 116 " pdb=" N VAL I 117 " pdb=" CA VAL I 117 " ideal model delta harmonic sigma weight residual 180.00 156.55 23.45 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA TRP F 116 " pdb=" C TRP F 116 " pdb=" N VAL F 117 " pdb=" CA VAL F 117 " ideal model delta harmonic sigma weight residual 180.00 156.56 23.44 0 5.00e+00 4.00e-02 2.20e+01 dihedral pdb=" CA TRP J 116 " pdb=" C TRP J 116 " pdb=" N VAL J 117 " pdb=" CA VAL J 117 " ideal model delta harmonic sigma weight residual 180.00 156.57 23.43 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 7857 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1014 0.039 - 0.077: 599 0.077 - 0.116: 205 0.116 - 0.155: 136 0.155 - 0.194: 46 Chirality restraints: 2000 Sorted by residual: chirality pdb=" CB VAL C 110 " pdb=" CA VAL C 110 " pdb=" CG1 VAL C 110 " pdb=" CG2 VAL C 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.38e-01 chirality pdb=" CB VAL F 110 " pdb=" CA VAL F 110 " pdb=" CG1 VAL F 110 " pdb=" CG2 VAL F 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.28e-01 chirality pdb=" CB VAL H 110 " pdb=" CA VAL H 110 " pdb=" CG1 VAL H 110 " pdb=" CG2 VAL H 110 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.26e-01 ... (remaining 1997 not shown) Planarity restraints: 2320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP I 116 " 0.028 2.00e-02 2.50e+03 2.50e-02 1.56e+01 pdb=" CG TRP I 116 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP I 116 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP I 116 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP I 116 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP I 116 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP I 116 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 116 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 116 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP I 116 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 116 " 0.028 2.00e-02 2.50e+03 2.49e-02 1.55e+01 pdb=" CG TRP A 116 " -0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP A 116 " 0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP A 116 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 116 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 116 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP A 116 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 116 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 116 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 116 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 116 " -0.028 2.00e-02 2.50e+03 2.48e-02 1.54e+01 pdb=" CG TRP B 116 " 0.066 2.00e-02 2.50e+03 pdb=" CD1 TRP B 116 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TRP B 116 " -0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP B 116 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 116 " 0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP B 116 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 116 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 116 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP B 116 " -0.006 2.00e-02 2.50e+03 ... (remaining 2317 not shown) Histogram of nonbonded interaction distances: 2.03 - 2.60: 179 2.60 - 3.18: 10776 3.18 - 3.75: 20200 3.75 - 4.33: 31088 4.33 - 4.90: 49695 Nonbonded interactions: 111938 Sorted by model distance: nonbonded pdb=" O GLU E 190 " pdb=" N GLN E 193 " model vdw 2.030 3.120 nonbonded pdb=" O GLU C 190 " pdb=" N GLN C 193 " model vdw 2.030 3.120 nonbonded pdb=" O GLU A 190 " pdb=" N GLN A 193 " model vdw 2.031 3.120 nonbonded pdb=" O GLU G 190 " pdb=" N GLN G 193 " model vdw 2.031 3.120 nonbonded pdb=" O GLU J 190 " pdb=" N GLN J 193 " model vdw 2.031 3.120 ... (remaining 111933 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: 0.05 Found NCS groups: ncs_group { reference = chain 'J' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 0.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 10.490 Find NCS groups from input model: 0.110 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:6.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 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 : 0.010 0.061 13170 Z= 0.431 Angle : 1.035 10.077 17830 Z= 0.595 Chirality : 0.064 0.194 2000 Planarity : 0.008 0.052 2320 Dihedral : 10.035 78.437 4800 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.61 % Allowed : 6.75 % Favored : 92.64 % Rotamer: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % 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 aren not related in a simple way. whole: -3.72 (0.18), residues: 1630 helix: -4.10 (0.10), residues: 550 sheet: -2.55 (0.28), residues: 270 loop : -1.00 (0.22), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 180 TYR 0.037 0.005 TYR C 145 PHE 0.044 0.006 PHE C 88 TRP 0.066 0.015 TRP I 116 HIS 0.011 0.003 HIS H 113 Details of bonding type rmsd covalent geometry : bond 0.01015 (13170) covalent geometry : angle 1.03473 (17830) hydrogen bonds : bond 0.19296 ( 550) hydrogen bonds : angle 9.42623 ( 1500) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 345 time to evaluate : 0.496 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: symmetry clash REVERT: J 165 LYS cc_start: 0.6588 (mttt) cc_final: 0.6295 (mmmt) REVERT: A 123 LYS cc_start: 0.7811 (mttt) cc_final: 0.7592 (mmtp) REVERT: B 57 ASP cc_start: 0.7173 (t0) cc_final: 0.6915 (t0) REVERT: B 165 LYS cc_start: 0.6391 (mttt) cc_final: 0.6090 (mmmt) REVERT: C 165 LYS cc_start: 0.6560 (mttt) cc_final: 0.6337 (mmmt) REVERT: E 165 LYS cc_start: 0.6449 (mttt) cc_final: 0.6181 (mmmt) REVERT: F 165 LYS cc_start: 0.6495 (mttt) cc_final: 0.6265 (mmmt) REVERT: F 190 GLU cc_start: 0.6766 (tt0) cc_final: 0.6236 (mt-10) REVERT: G 40 GLU cc_start: 0.6853 (mt-10) cc_final: 0.6590 (pt0) REVERT: H 165 LYS cc_start: 0.6552 (mttt) cc_final: 0.6227 (mmmt) REVERT: I 165 LYS cc_start: 0.6283 (mttt) cc_final: 0.6052 (mmmt) outliers start: 0 outliers final: 0 residues processed: 345 average time/residue: 0.5688 time to fit residues: 212.8658 Evaluate side-chains 292 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 292 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 91 optimal weight: 0.7980 chunk 149 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 101 GLN C 101 GLN F 44 GLN F 99 ASN F 101 GLN I 101 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.213509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.188521 restraints weight = 13900.129| |-----------------------------------------------------------------------------| r_work (start): 0.4020 rms_B_bonded: 1.70 r_work: 0.3879 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13170 Z= 0.142 Angle : 0.614 6.200 17830 Z= 0.334 Chirality : 0.047 0.146 2000 Planarity : 0.006 0.053 2320 Dihedral : 5.442 24.071 1780 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 3.12 % Allowed : 11.23 % Favored : 85.65 % 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 aren not related in a simple way. whole: -2.60 (0.19), residues: 1630 helix: -2.80 (0.14), residues: 550 sheet: -1.89 (0.30), residues: 270 loop : -0.64 (0.23), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 39 TYR 0.017 0.002 TYR B 145 PHE 0.029 0.003 PHE H 71 TRP 0.027 0.005 TRP J 116 HIS 0.004 0.001 HIS I 113 Details of bonding type rmsd covalent geometry : bond 0.00320 (13170) covalent geometry : angle 0.61379 (17830) hydrogen bonds : bond 0.04069 ( 550) hydrogen bonds : angle 6.11860 ( 1500) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 364 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 321 time to evaluate : 0.504 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 37 THR cc_start: 0.7911 (OUTLIER) cc_final: 0.7710 (m) REVERT: J 165 LYS cc_start: 0.6379 (mttt) cc_final: 0.5769 (mmmt) REVERT: A 123 LYS cc_start: 0.8006 (mttt) cc_final: 0.7693 (mmtp) REVERT: C 40 GLU cc_start: 0.6659 (mt-10) cc_final: 0.6365 (mp0) REVERT: C 138 SER cc_start: 0.8623 (p) cc_final: 0.8017 (p) REVERT: C 165 LYS cc_start: 0.6335 (mttt) cc_final: 0.5923 (mmmt) REVERT: D 140 GLU cc_start: 0.7499 (pt0) cc_final: 0.7159 (mt-10) REVERT: D 165 LYS cc_start: 0.6390 (mtmm) cc_final: 0.5464 (mmmt) REVERT: E 140 GLU cc_start: 0.7367 (pt0) cc_final: 0.7145 (mt-10) REVERT: E 165 LYS cc_start: 0.6342 (mttt) cc_final: 0.5790 (mmmt) REVERT: F 40 GLU cc_start: 0.6715 (mt-10) cc_final: 0.6396 (mp0) REVERT: F 75 MET cc_start: 0.7822 (OUTLIER) cc_final: 0.7618 (ptt) REVERT: F 111 TYR cc_start: 0.7469 (m-80) cc_final: 0.7163 (m-80) REVERT: G 40 GLU cc_start: 0.6967 (mt-10) cc_final: 0.6494 (pt0) REVERT: G 116 TRP cc_start: 0.6744 (OUTLIER) cc_final: 0.5774 (p-90) REVERT: H 91 ARG cc_start: 0.7297 (mmm-85) cc_final: 0.7004 (mtp-110) REVERT: H 165 LYS cc_start: 0.6341 (mttt) cc_final: 0.5918 (mmmt) REVERT: I 40 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6713 (pt0) REVERT: I 62 ASP cc_start: 0.6515 (m-30) cc_final: 0.6201 (t0) REVERT: I 91 ARG cc_start: 0.7273 (mmm-85) cc_final: 0.6999 (mtp-110) outliers start: 43 outliers final: 21 residues processed: 352 average time/residue: 0.5231 time to fit residues: 201.1000 Evaluate side-chains 292 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 268 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain J residue 116 TRP Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 116 TRP Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 116 TRP Chi-restraints excluded: chain C residue 116 TRP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 116 TRP Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 116 TRP Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 116 TRP Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 116 TRP Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 116 TRP Chi-restraints excluded: chain I residue 138 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 85 optimal weight: 0.1980 chunk 118 optimal weight: 0.0980 chunk 101 optimal weight: 7.9990 chunk 126 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 122 optimal weight: 8.9990 chunk 83 optimal weight: 4.9990 chunk 154 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 GLN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 GLN ** I 113 HIS ** 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 = 0.4260 r_free = 0.4260 target = 0.211697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.189080 restraints weight = 14223.967| |-----------------------------------------------------------------------------| r_work (start): 0.4016 rms_B_bonded: 1.58 r_work: 0.3872 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 13170 Z= 0.146 Angle : 0.591 6.091 17830 Z= 0.315 Chirality : 0.047 0.144 2000 Planarity : 0.005 0.051 2320 Dihedral : 5.058 22.482 1780 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.78 % Allowed : 13.19 % Favored : 82.03 % 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 aren not related in a simple way. whole: -1.63 (0.21), residues: 1630 helix: -1.41 (0.18), residues: 550 sheet: -1.53 (0.33), residues: 270 loop : -0.48 (0.24), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 180 TYR 0.017 0.002 TYR A 73 PHE 0.020 0.003 PHE E 71 TRP 0.024 0.005 TRP J 116 HIS 0.003 0.001 HIS H 113 Details of bonding type rmsd covalent geometry : bond 0.00341 (13170) covalent geometry : angle 0.59056 (17830) hydrogen bonds : bond 0.03760 ( 550) hydrogen bonds : angle 5.67280 ( 1500) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 278 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: J 116 TRP cc_start: 0.6944 (OUTLIER) cc_final: 0.6323 (t60) REVERT: J 165 LYS cc_start: 0.6274 (mttt) cc_final: 0.5843 (mmmt) REVERT: A 98 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7163 (tt) REVERT: A 123 LYS cc_start: 0.8021 (mttt) cc_final: 0.7727 (mmtp) REVERT: A 129 MET cc_start: 0.6825 (tpp) cc_final: 0.6608 (tpt) REVERT: B 98 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7262 (tt) REVERT: C 165 LYS cc_start: 0.6172 (mttt) cc_final: 0.5848 (mmmt) REVERT: D 116 TRP cc_start: 0.6944 (OUTLIER) cc_final: 0.6480 (t60) REVERT: D 140 GLU cc_start: 0.7601 (pt0) cc_final: 0.7204 (mt-10) REVERT: D 165 LYS cc_start: 0.5998 (mtmm) cc_final: 0.5293 (mmmt) REVERT: E 91 ARG cc_start: 0.7297 (mmm-85) cc_final: 0.6931 (mtp-110) REVERT: E 165 LYS cc_start: 0.6269 (mttt) cc_final: 0.5799 (mmmt) REVERT: F 40 GLU cc_start: 0.6623 (mt-10) cc_final: 0.6372 (mp0) REVERT: F 116 TRP cc_start: 0.6846 (OUTLIER) cc_final: 0.6413 (t60) REVERT: F 165 LYS cc_start: 0.6328 (mttt) cc_final: 0.5939 (mmmt) REVERT: G 116 TRP cc_start: 0.6657 (OUTLIER) cc_final: 0.6425 (t60) REVERT: H 40 GLU cc_start: 0.7089 (OUTLIER) cc_final: 0.5660 (mp0) REVERT: H 98 LEU cc_start: 0.7410 (OUTLIER) cc_final: 0.7161 (tt) REVERT: H 165 LYS cc_start: 0.6251 (mttt) cc_final: 0.5787 (mmmt) REVERT: I 62 ASP cc_start: 0.6542 (m-30) cc_final: 0.6242 (t0) REVERT: I 91 ARG cc_start: 0.7337 (mmm-85) cc_final: 0.6660 (mtp-110) REVERT: I 165 LYS cc_start: 0.6222 (mttt) cc_final: 0.5691 (mmmt) outliers start: 66 outliers final: 26 residues processed: 313 average time/residue: 0.5697 time to fit residues: 194.5966 Evaluate side-chains 276 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 242 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 85 ILE Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 116 TRP Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 98 LEU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 116 TRP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 116 TRP Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 116 TRP Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain I residue 116 TRP Chi-restraints excluded: chain I residue 138 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 133 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 148 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 140 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 122 optimal weight: 8.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 GLN I 99 ASN ** I 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.206572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.182824 restraints weight = 14343.780| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 1.63 r_work: 0.3814 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.3058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 13170 Z= 0.195 Angle : 0.624 6.556 17830 Z= 0.329 Chirality : 0.048 0.144 2000 Planarity : 0.006 0.051 2320 Dihedral : 5.168 21.577 1780 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 5.29 % Allowed : 12.83 % Favored : 81.88 % 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 aren not related in a simple way. whole: -1.28 (0.21), residues: 1630 helix: -0.93 (0.20), residues: 550 sheet: -1.41 (0.35), residues: 270 loop : -0.40 (0.24), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 157 TYR 0.019 0.002 TYR J 145 PHE 0.018 0.003 PHE J 88 TRP 0.026 0.005 TRP J 116 HIS 0.004 0.001 HIS H 113 Details of bonding type rmsd covalent geometry : bond 0.00461 (13170) covalent geometry : angle 0.62375 (17830) hydrogen bonds : bond 0.03987 ( 550) hydrogen bonds : angle 5.90538 ( 1500) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 259 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 165 LYS cc_start: 0.6377 (mttt) cc_final: 0.5901 (mmmt) REVERT: A 40 GLU cc_start: 0.7059 (OUTLIER) cc_final: 0.5995 (mp0) REVERT: A 165 LYS cc_start: 0.5960 (mtmm) cc_final: 0.5302 (mmmt) REVERT: B 98 LEU cc_start: 0.7431 (OUTLIER) cc_final: 0.7220 (tt) REVERT: B 165 LYS cc_start: 0.6421 (mttt) cc_final: 0.5777 (mmmt) REVERT: C 165 LYS cc_start: 0.6295 (mttt) cc_final: 0.5918 (mmmt) REVERT: D 85 ILE cc_start: 0.7583 (OUTLIER) cc_final: 0.7382 (mt) REVERT: D 140 GLU cc_start: 0.7693 (pt0) cc_final: 0.7221 (mp0) REVERT: D 165 LYS cc_start: 0.5987 (mtmm) cc_final: 0.5338 (mmmt) REVERT: E 91 ARG cc_start: 0.7318 (mmm-85) cc_final: 0.6895 (mtp-110) REVERT: E 129 MET cc_start: 0.6666 (tpt) cc_final: 0.6426 (tpt) REVERT: E 165 LYS cc_start: 0.6329 (mttt) cc_final: 0.5813 (mmmt) REVERT: F 98 LEU cc_start: 0.7337 (OUTLIER) cc_final: 0.6875 (tt) REVERT: F 116 TRP cc_start: 0.6839 (OUTLIER) cc_final: 0.6366 (t60) REVERT: F 165 LYS cc_start: 0.6409 (mttt) cc_final: 0.5926 (mmmt) REVERT: G 91 ARG cc_start: 0.7343 (mmm-85) cc_final: 0.6994 (mtp-110) REVERT: H 40 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.5567 (mp0) REVERT: H 129 MET cc_start: 0.7099 (tpp) cc_final: 0.6644 (tpt) REVERT: H 165 LYS cc_start: 0.6299 (mttt) cc_final: 0.5808 (mmmt) REVERT: I 62 ASP cc_start: 0.6591 (m-30) cc_final: 0.6203 (t0) REVERT: I 91 ARG cc_start: 0.7362 (mmm-85) cc_final: 0.6629 (mtp-110) REVERT: I 165 LYS cc_start: 0.6331 (mttt) cc_final: 0.5788 (mmmt) outliers start: 73 outliers final: 40 residues processed: 290 average time/residue: 0.5021 time to fit residues: 159.1199 Evaluate side-chains 294 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 248 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 116 TRP Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain C residue 40 GLU Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain C residue 116 TRP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 116 TRP Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 116 TRP Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain I residue 116 TRP Chi-restraints excluded: chain I residue 138 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 121 optimal weight: 8.9990 chunk 123 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 147 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 71 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 141 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 149 optimal weight: 7.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN E 99 ASN F 99 ASN ** F 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 193 GLN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 GLN I 99 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.206206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.182607 restraints weight = 14328.160| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 1.63 r_work: 0.3814 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.3234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13170 Z= 0.184 Angle : 0.625 11.434 17830 Z= 0.325 Chirality : 0.048 0.142 2000 Planarity : 0.005 0.051 2320 Dihedral : 5.049 21.416 1780 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 13.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 4.86 % Allowed : 13.48 % Favored : 81.67 % 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 aren not related in a simple way. whole: -1.08 (0.22), residues: 1630 helix: -0.65 (0.20), residues: 550 sheet: -1.36 (0.35), residues: 270 loop : -0.35 (0.24), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 180 TYR 0.017 0.002 TYR D 145 PHE 0.016 0.003 PHE E 71 TRP 0.025 0.005 TRP J 116 HIS 0.003 0.001 HIS H 113 Details of bonding type rmsd covalent geometry : bond 0.00437 (13170) covalent geometry : angle 0.62533 (17830) hydrogen bonds : bond 0.03807 ( 550) hydrogen bonds : angle 5.82372 ( 1500) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 254 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 165 LYS cc_start: 0.6308 (mttt) cc_final: 0.5822 (mmmt) REVERT: A 40 GLU cc_start: 0.7037 (OUTLIER) cc_final: 0.5929 (mp0) REVERT: A 91 ARG cc_start: 0.7344 (mmm-85) cc_final: 0.7003 (mtp-110) REVERT: B 165 LYS cc_start: 0.6418 (mttt) cc_final: 0.5788 (mmmt) REVERT: C 91 ARG cc_start: 0.7238 (mmm-85) cc_final: 0.7013 (mtp-110) REVERT: C 165 LYS cc_start: 0.6277 (mttt) cc_final: 0.5898 (mmmt) REVERT: D 85 ILE cc_start: 0.7521 (OUTLIER) cc_final: 0.7294 (mt) REVERT: D 165 LYS cc_start: 0.5877 (mtmm) cc_final: 0.5435 (mmmt) REVERT: E 91 ARG cc_start: 0.7260 (mmm-85) cc_final: 0.6859 (mtp-110) REVERT: E 129 MET cc_start: 0.6719 (tpt) cc_final: 0.6180 (tpt) REVERT: E 165 LYS cc_start: 0.6339 (mttt) cc_final: 0.5814 (mmmt) REVERT: F 98 LEU cc_start: 0.7380 (OUTLIER) cc_final: 0.6782 (tt) REVERT: F 165 LYS cc_start: 0.6330 (mttt) cc_final: 0.5861 (mmmt) REVERT: G 91 ARG cc_start: 0.7393 (mmm-85) cc_final: 0.7085 (mtp-110) REVERT: G 116 TRP cc_start: 0.6874 (OUTLIER) cc_final: 0.6368 (t60) REVERT: H 129 MET cc_start: 0.7085 (tpp) cc_final: 0.6667 (tpt) REVERT: H 165 LYS cc_start: 0.6280 (mttt) cc_final: 0.5802 (mmmt) REVERT: I 91 ARG cc_start: 0.7201 (mmm-85) cc_final: 0.6678 (mtp-110) REVERT: I 165 LYS cc_start: 0.6301 (mttt) cc_final: 0.5826 (mmmt) outliers start: 67 outliers final: 39 residues processed: 289 average time/residue: 0.5300 time to fit residues: 167.8621 Evaluate side-chains 284 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 241 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 116 TRP Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 193 GLN Chi-restraints excluded: chain C residue 68 ILE Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain C residue 85 ILE Chi-restraints excluded: chain C residue 116 TRP Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain E residue 138 SER Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 108 ASP Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain F residue 116 TRP Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 116 TRP Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain I residue 116 TRP Chi-restraints excluded: chain I residue 138 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 42 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 60 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 135 optimal weight: 8.9990 chunk 91 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 chunk 82 optimal weight: 9.9990 chunk 148 optimal weight: 6.9990 chunk 107 optimal weight: 0.0870 overall best weight: 1.4962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN E 99 ASN F 99 ASN F 193 GLN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN ** I 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4223 r_free = 0.4223 target = 0.207215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.183684 restraints weight = 14210.187| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 1.65 r_work: 0.3833 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13170 Z= 0.150 Angle : 0.593 8.848 17830 Z= 0.310 Chirality : 0.047 0.140 2000 Planarity : 0.005 0.050 2320 Dihedral : 4.853 21.022 1780 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 4.13 % Allowed : 15.00 % Favored : 80.87 % 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 aren not related in a simple way. whole: -0.86 (0.22), residues: 1630 helix: -0.28 (0.20), residues: 550 sheet: -1.28 (0.35), residues: 270 loop : -0.35 (0.24), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 180 TYR 0.019 0.002 TYR H 67 PHE 0.015 0.002 PHE D 71 TRP 0.023 0.004 TRP D 116 HIS 0.003 0.001 HIS H 113 Details of bonding type rmsd covalent geometry : bond 0.00349 (13170) covalent geometry : angle 0.59306 (17830) hydrogen bonds : bond 0.03582 ( 550) hydrogen bonds : angle 5.62335 ( 1500) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 244 time to evaluate : 0.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 98 LEU cc_start: 0.7599 (OUTLIER) cc_final: 0.7368 (tt) REVERT: J 116 TRP cc_start: 0.6779 (OUTLIER) cc_final: 0.6470 (t60) REVERT: A 40 GLU cc_start: 0.6987 (OUTLIER) cc_final: 0.5838 (mp0) REVERT: A 91 ARG cc_start: 0.7302 (mmm-85) cc_final: 0.6983 (mtp-110) REVERT: D 85 ILE cc_start: 0.7446 (OUTLIER) cc_final: 0.7231 (mt) REVERT: D 116 TRP cc_start: 0.6786 (OUTLIER) cc_final: 0.6532 (t60) REVERT: D 140 GLU cc_start: 0.7648 (pt0) cc_final: 0.7336 (mt-10) REVERT: D 165 LYS cc_start: 0.5596 (mtmm) cc_final: 0.5317 (mmmt) REVERT: E 40 GLU cc_start: 0.6450 (pt0) cc_final: 0.5978 (mp0) REVERT: E 91 ARG cc_start: 0.7227 (mmm-85) cc_final: 0.6814 (mtp-110) REVERT: E 165 LYS cc_start: 0.6317 (mttt) cc_final: 0.5827 (mmmt) REVERT: F 98 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6753 (tt) REVERT: F 165 LYS cc_start: 0.6216 (mttt) cc_final: 0.5806 (mmmt) REVERT: H 40 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.5751 (mp0) REVERT: I 91 ARG cc_start: 0.7231 (mmm-85) cc_final: 0.6728 (mtp-110) REVERT: I 165 LYS cc_start: 0.6229 (mttt) cc_final: 0.5779 (mmmt) outliers start: 57 outliers final: 30 residues processed: 275 average time/residue: 0.5009 time to fit residues: 151.7653 Evaluate side-chains 270 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 233 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 116 TRP Chi-restraints excluded: chain J residue 139 MET Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 75 MET Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 85 ILE Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 116 TRP Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 98 LEU Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 75 MET Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 109 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 115 optimal weight: 7.9990 chunk 9 optimal weight: 0.0370 chunk 80 optimal weight: 10.0000 chunk 156 optimal weight: 0.9990 chunk 118 optimal weight: 3.9990 chunk 145 optimal weight: 0.9990 chunk 126 optimal weight: 0.8980 chunk 79 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 overall best weight: 0.9864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN C 193 GLN D 193 GLN E 99 ASN F 99 ASN F 193 GLN H 99 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.208640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.184550 restraints weight = 14162.524| |-----------------------------------------------------------------------------| r_work (start): 0.3988 rms_B_bonded: 1.71 r_work: 0.3840 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.3641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13170 Z= 0.125 Angle : 0.576 13.777 17830 Z= 0.297 Chirality : 0.046 0.139 2000 Planarity : 0.005 0.054 2320 Dihedral : 4.580 19.577 1780 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 3.33 % Allowed : 16.45 % Favored : 80.22 % 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 aren not related in a simple way. whole: -0.59 (0.22), residues: 1630 helix: 0.16 (0.21), residues: 550 sheet: -1.21 (0.35), residues: 270 loop : -0.34 (0.24), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 91 TYR 0.017 0.002 TYR H 67 PHE 0.015 0.002 PHE I 71 TRP 0.021 0.003 TRP I 116 HIS 0.004 0.001 HIS J 113 Details of bonding type rmsd covalent geometry : bond 0.00286 (13170) covalent geometry : angle 0.57566 (17830) hydrogen bonds : bond 0.03309 ( 550) hydrogen bonds : angle 5.43023 ( 1500) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 237 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 98 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7301 (tt) REVERT: A 40 GLU cc_start: 0.7011 (OUTLIER) cc_final: 0.5923 (mp0) REVERT: A 91 ARG cc_start: 0.7184 (mmm-85) cc_final: 0.6892 (mtp-110) REVERT: B 40 GLU cc_start: 0.7012 (mp0) cc_final: 0.6809 (mp0) REVERT: D 140 GLU cc_start: 0.7615 (pt0) cc_final: 0.7307 (mt-10) REVERT: E 91 ARG cc_start: 0.7185 (mmm-85) cc_final: 0.6829 (mtp-110) REVERT: E 140 GLU cc_start: 0.7304 (pt0) cc_final: 0.6990 (mt-10) REVERT: F 40 GLU cc_start: 0.6675 (mt-10) cc_final: 0.6438 (mp0) REVERT: G 91 ARG cc_start: 0.7354 (mtm-85) cc_final: 0.7000 (mtp180) REVERT: H 91 ARG cc_start: 0.7426 (mtp-110) cc_final: 0.7215 (mtm-85) REVERT: I 62 ASP cc_start: 0.6499 (m-30) cc_final: 0.6076 (t0) REVERT: I 91 ARG cc_start: 0.7241 (mmm-85) cc_final: 0.6790 (mtp-110) outliers start: 46 outliers final: 27 residues processed: 262 average time/residue: 0.4982 time to fit residues: 143.8544 Evaluate side-chains 234 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 205 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 98 LEU Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 176 LEU Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 75 MET Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain C residue 75 MET Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 98 LEU Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 75 MET Chi-restraints excluded: chain F residue 85 ILE Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 109 SER Chi-restraints excluded: chain I residue 176 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 159 optimal weight: 9.9990 chunk 12 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 31 optimal weight: 8.9990 chunk 157 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 101 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 158 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: ** J 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 193 GLN ** D 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 193 GLN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 GLN ** I 174 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.198770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.175159 restraints weight = 14384.484| |-----------------------------------------------------------------------------| r_work (start): 0.3886 rms_B_bonded: 1.60 r_work: 0.3738 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3608 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 13170 Z= 0.288 Angle : 0.734 13.219 17830 Z= 0.379 Chirality : 0.052 0.157 2000 Planarity : 0.006 0.060 2320 Dihedral : 5.277 20.158 1780 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 3.77 % Allowed : 16.52 % Favored : 79.71 % 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 aren not related in a simple way. whole: -0.94 (0.22), residues: 1630 helix: -0.47 (0.20), residues: 550 sheet: -1.39 (0.35), residues: 270 loop : -0.28 (0.24), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 157 TYR 0.024 0.003 TYR D 67 PHE 0.018 0.003 PHE B 88 TRP 0.036 0.006 TRP I 116 HIS 0.005 0.001 HIS J 113 Details of bonding type rmsd covalent geometry : bond 0.00693 (13170) covalent geometry : angle 0.73379 (17830) hydrogen bonds : bond 0.04271 ( 550) hydrogen bonds : angle 6.07801 ( 1500) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 228 time to evaluate : 0.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 165 LYS cc_start: 0.6461 (mttt) cc_final: 0.5976 (mmmt) REVERT: A 40 GLU cc_start: 0.7327 (OUTLIER) cc_final: 0.6173 (mp0) REVERT: A 165 LYS cc_start: 0.6024 (mtmm) cc_final: 0.5264 (mmmt) REVERT: B 165 LYS cc_start: 0.6602 (mttt) cc_final: 0.5814 (mmmt) REVERT: C 129 MET cc_start: 0.7477 (tpp) cc_final: 0.7107 (tpt) REVERT: C 165 LYS cc_start: 0.6517 (mttt) cc_final: 0.5940 (mmmt) REVERT: D 138 SER cc_start: 0.8884 (p) cc_final: 0.8643 (t) REVERT: D 165 LYS cc_start: 0.5998 (mtmm) cc_final: 0.5578 (mmmt) REVERT: E 165 LYS cc_start: 0.6583 (mttt) cc_final: 0.5960 (mmmt) REVERT: F 129 MET cc_start: 0.7551 (tpp) cc_final: 0.7197 (tpt) REVERT: F 165 LYS cc_start: 0.6497 (mttt) cc_final: 0.5930 (mmmt) REVERT: G 91 ARG cc_start: 0.7345 (mtm-85) cc_final: 0.6981 (mtp-110) REVERT: H 75 MET cc_start: 0.8193 (OUTLIER) cc_final: 0.7887 (ptm) REVERT: H 165 LYS cc_start: 0.6517 (mttt) cc_final: 0.5737 (mmmt) REVERT: I 140 GLU cc_start: 0.7620 (mt-10) cc_final: 0.7408 (mt-10) REVERT: I 165 LYS cc_start: 0.6618 (mttt) cc_final: 0.6000 (mmmt) outliers start: 52 outliers final: 33 residues processed: 250 average time/residue: 0.5203 time to fit residues: 142.6388 Evaluate side-chains 258 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 223 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 83 THR Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 68 ILE Chi-restraints excluded: chain B residue 83 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain D residue 152 SER Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 83 THR Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 68 ILE Chi-restraints excluded: chain G residue 83 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 83 THR Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain H residue 157 ARG Chi-restraints excluded: chain I residue 83 THR Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 109 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 110 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 7.9990 chunk 79 optimal weight: 0.6980 chunk 132 optimal weight: 0.7980 chunk 101 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 99 ASN F 99 ASN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 99 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4219 r_free = 0.4219 target = 0.207378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.182829 restraints weight = 14219.836| |-----------------------------------------------------------------------------| r_work (start): 0.3968 rms_B_bonded: 1.73 r_work: 0.3820 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 13170 Z= 0.126 Angle : 0.616 14.975 17830 Z= 0.315 Chirality : 0.046 0.136 2000 Planarity : 0.005 0.053 2320 Dihedral : 4.610 18.040 1780 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 13.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 2.32 % Allowed : 18.55 % Favored : 79.13 % 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 aren not related in a simple way. whole: -0.61 (0.22), residues: 1630 helix: 0.14 (0.20), residues: 550 sheet: -1.27 (0.35), residues: 270 loop : -0.32 (0.24), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 157 TYR 0.028 0.002 TYR J 67 PHE 0.016 0.002 PHE B 71 TRP 0.016 0.003 TRP J 116 HIS 0.006 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00285 (13170) covalent geometry : angle 0.61641 (17830) hydrogen bonds : bond 0.03359 ( 550) hydrogen bonds : angle 5.48476 ( 1500) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 212 time to evaluate : 0.497 Fit side-chains revert: symmetry clash REVERT: A 40 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.5908 (mp0) REVERT: A 75 MET cc_start: 0.8000 (ptp) cc_final: 0.7681 (ptm) REVERT: A 91 ARG cc_start: 0.7156 (mmm-85) cc_final: 0.6874 (mtp180) REVERT: A 123 LYS cc_start: 0.7878 (mttt) cc_final: 0.7587 (mmtp) REVERT: D 140 GLU cc_start: 0.7462 (pt0) cc_final: 0.6920 (mp0) REVERT: E 91 ARG cc_start: 0.7244 (mmm-85) cc_final: 0.6996 (mtp-110) REVERT: F 40 GLU cc_start: 0.6743 (mt-10) cc_final: 0.6477 (mp0) REVERT: F 129 MET cc_start: 0.7167 (tpp) cc_final: 0.6941 (tpt) REVERT: G 91 ARG cc_start: 0.7251 (mtm-85) cc_final: 0.6908 (mtp180) REVERT: H 91 ARG cc_start: 0.7363 (mtp-110) cc_final: 0.7137 (mtm-85) REVERT: I 62 ASP cc_start: 0.6492 (m-30) cc_final: 0.6037 (t0) REVERT: I 91 ARG cc_start: 0.7166 (mmm-85) cc_final: 0.6827 (mtp-110) REVERT: I 138 SER cc_start: 0.8536 (p) cc_final: 0.8206 (p) REVERT: I 140 GLU cc_start: 0.7361 (mt-10) cc_final: 0.6991 (mt-10) outliers start: 32 outliers final: 25 residues processed: 225 average time/residue: 0.5071 time to fit residues: 125.3207 Evaluate side-chains 226 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain B residue 37 THR Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain F residue 37 THR Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain G residue 37 THR Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain G residue 140 GLU Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 75 MET Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 109 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 20 optimal weight: 0.9990 chunk 148 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 135 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 30 optimal weight: 8.9990 chunk 16 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 93 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 99 ASN ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 193 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.208690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.183977 restraints weight = 14139.178| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 1.74 r_work: 0.3835 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 13170 Z= 0.121 Angle : 0.610 15.655 17830 Z= 0.310 Chirality : 0.045 0.139 2000 Planarity : 0.005 0.052 2320 Dihedral : 4.449 17.590 1780 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 12.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.96 % Allowed : 20.00 % Favored : 78.04 % 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 aren not related in a simple way. whole: -0.48 (0.22), residues: 1630 helix: 0.38 (0.21), residues: 550 sheet: -1.27 (0.34), residues: 270 loop : -0.33 (0.24), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 157 TYR 0.030 0.002 TYR J 67 PHE 0.016 0.002 PHE B 71 TRP 0.016 0.003 TRP J 116 HIS 0.005 0.001 HIS J 113 Details of bonding type rmsd covalent geometry : bond 0.00275 (13170) covalent geometry : angle 0.61043 (17830) hydrogen bonds : bond 0.03221 ( 550) hydrogen bonds : angle 5.35508 ( 1500) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3260 Ramachandran restraints generated. 1630 Oldfield, 0 Emsley, 1630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 207 time to evaluate : 0.485 Fit side-chains revert: symmetry clash REVERT: A 40 GLU cc_start: 0.7032 (OUTLIER) cc_final: 0.5936 (mp0) REVERT: A 123 LYS cc_start: 0.7834 (mttt) cc_final: 0.7566 (mmtp) REVERT: C 76 ASP cc_start: 0.8229 (m-30) cc_final: 0.7709 (m-30) REVERT: C 98 LEU cc_start: 0.7237 (mp) cc_final: 0.6764 (tt) REVERT: D 140 GLU cc_start: 0.7438 (pt0) cc_final: 0.6885 (mp0) REVERT: E 91 ARG cc_start: 0.7306 (mmm-85) cc_final: 0.7103 (mtp-110) REVERT: F 40 GLU cc_start: 0.6647 (mt-10) cc_final: 0.6435 (mp0) REVERT: F 129 MET cc_start: 0.7143 (tpp) cc_final: 0.6896 (tpt) REVERT: G 91 ARG cc_start: 0.7308 (mtm-85) cc_final: 0.6963 (mtp180) REVERT: H 40 GLU cc_start: 0.7137 (OUTLIER) cc_final: 0.5996 (mp0) REVERT: I 62 ASP cc_start: 0.6415 (m-30) cc_final: 0.6008 (t0) REVERT: I 91 ARG cc_start: 0.7188 (mmm-85) cc_final: 0.6852 (mtp-110) REVERT: I 138 SER cc_start: 0.8520 (p) cc_final: 0.8265 (p) REVERT: I 140 GLU cc_start: 0.7271 (mt-10) cc_final: 0.6815 (mt-10) outliers start: 27 outliers final: 19 residues processed: 217 average time/residue: 0.5346 time to fit residues: 127.6865 Evaluate side-chains 225 residues out of total 1380 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain J residue 109 SER Chi-restraints excluded: chain J residue 182 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 40 GLU Chi-restraints excluded: chain A residue 109 SER Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 140 GLU Chi-restraints excluded: chain C residue 109 SER Chi-restraints excluded: chain D residue 37 THR Chi-restraints excluded: chain D residue 109 SER Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 75 MET Chi-restraints excluded: chain E residue 109 SER Chi-restraints excluded: chain F residue 78 THR Chi-restraints excluded: chain F residue 109 SER Chi-restraints excluded: chain G residue 109 SER Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 40 GLU Chi-restraints excluded: chain H residue 109 SER Chi-restraints excluded: chain I residue 98 LEU Chi-restraints excluded: chain I residue 109 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 48 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 127 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 chunk 46 optimal weight: 0.9980 chunk 78 optimal weight: 1.9990 chunk 67 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 99 ASN ** C 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.204086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.179216 restraints weight = 14211.389| |-----------------------------------------------------------------------------| r_work (start): 0.3929 rms_B_bonded: 1.73 r_work: 0.3781 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 moved from start: 0.3858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13170 Z= 0.168 Angle : 0.671 18.435 17830 Z= 0.336 Chirality : 0.047 0.142 2000 Planarity : 0.005 0.052 2320 Dihedral : 4.688 18.936 1780 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 13.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.88 % Allowed : 20.87 % Favored : 77.25 % 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 aren not related in a simple way. whole: -0.54 (0.21), residues: 1630 helix: 0.28 (0.21), residues: 550 sheet: -1.31 (0.35), residues: 270 loop : -0.32 (0.24), residues: 810 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG H 157 TYR 0.030 0.002 TYR J 67 PHE 0.015 0.002 PHE E 71 TRP 0.024 0.004 TRP J 116 HIS 0.005 0.001 HIS J 113 Details of bonding type rmsd covalent geometry : bond 0.00396 (13170) covalent geometry : angle 0.67084 (17830) hydrogen bonds : bond 0.03567 ( 550) hydrogen bonds : angle 5.60749 ( 1500) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4043.51 seconds wall clock time: 69 minutes 55.46 seconds (4195.46 seconds total)