Starting phenix.real_space_refine on Sat Feb 7 20:21:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9z7p_73876/02_2026/9z7p_73876.cif Found real_map, /net/cci-nas-00/data/ceres_data/9z7p_73876/02_2026/9z7p_73876.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9z7p_73876/02_2026/9z7p_73876.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9z7p_73876/02_2026/9z7p_73876.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9z7p_73876/02_2026/9z7p_73876.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9z7p_73876/02_2026/9z7p_73876.map" } resolution = 2.7 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= 0.030 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 96 5.16 5 C 11832 2.51 5 N 2856 2.21 5 O 3000 1.98 5 H 17784 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 132 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 35568 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2964 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 2964 Classifications: {'peptide': 182} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 174} Chain breaks: 1 Restraints were copied for chains: J, K, L, B, C, D, E, F, G, H, I Time building chain proxies: 3.93, per 1000 atoms: 0.11 Number of scatterers: 35568 At special positions: 0 Unit cell: (97.09, 95.76, 144.305, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 96 16.00 O 3000 8.00 N 2856 7.00 C 11832 6.00 H 17784 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 189 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 183 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 178 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 189 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 189 " distance=2.03 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 189 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 189 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 189 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 189 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 189 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 189 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 189 " distance=2.03 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 189 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 189 " distance=2.03 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 183 " distance=2.03 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 183 " distance=2.03 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS L 183 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 183 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 183 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 183 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 183 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 183 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 183 " distance=2.03 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 183 " distance=2.03 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 183 " distance=2.03 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 178 " distance=2.03 Simple disulfide: pdb=" SG CYS K 65 " - pdb=" SG CYS K 178 " distance=2.03 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 178 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 178 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 178 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 178 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 178 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 178 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 178 " distance=2.03 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 178 " distance=2.03 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 178 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.33 Conformation dependent library (CDL) restraints added in 883.7 milliseconds 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4104 Finding SS restraints... Secondary structure from input PDB file: 108 helices and 12 sheets defined 79.1% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 4 through 18 removed outlier: 4.084A pdb=" N LEU A 10 " --> pdb=" O PHE A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 33 Processing helix chain 'A' and resid 33 through 40 Processing helix chain 'A' and resid 40 through 45 Processing helix chain 'A' and resid 46 through 48 No H-bonds generated for 'chain 'A' and resid 46 through 48' Processing helix chain 'A' and resid 60 through 70 Processing helix chain 'A' and resid 73 through 100 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 142 through 169 Processing helix chain 'A' and resid 193 through 222 Processing helix chain 'J' and resid 4 through 18 removed outlier: 4.084A pdb=" N LEU J 10 " --> pdb=" O PHE J 6 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 33 Processing helix chain 'J' and resid 33 through 40 Processing helix chain 'J' and resid 40 through 45 Processing helix chain 'J' and resid 46 through 48 No H-bonds generated for 'chain 'J' and resid 46 through 48' Processing helix chain 'J' and resid 60 through 70 Processing helix chain 'J' and resid 73 through 100 Proline residue: J 88 - end of helix Processing helix chain 'J' and resid 142 through 169 Processing helix chain 'J' and resid 193 through 222 Processing helix chain 'K' and resid 4 through 18 removed outlier: 4.084A pdb=" N LEU K 10 " --> pdb=" O PHE K 6 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 33 Processing helix chain 'K' and resid 33 through 40 Processing helix chain 'K' and resid 40 through 45 Processing helix chain 'K' and resid 46 through 48 No H-bonds generated for 'chain 'K' and resid 46 through 48' Processing helix chain 'K' and resid 60 through 70 Processing helix chain 'K' and resid 73 through 100 Proline residue: K 88 - end of helix Processing helix chain 'K' and resid 142 through 169 Processing helix chain 'K' and resid 193 through 222 Processing helix chain 'L' and resid 4 through 18 removed outlier: 4.084A pdb=" N LEU L 10 " --> pdb=" O PHE L 6 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 33 Processing helix chain 'L' and resid 33 through 40 Processing helix chain 'L' and resid 40 through 45 Processing helix chain 'L' and resid 46 through 48 No H-bonds generated for 'chain 'L' and resid 46 through 48' Processing helix chain 'L' and resid 60 through 70 Processing helix chain 'L' and resid 73 through 100 Proline residue: L 88 - end of helix Processing helix chain 'L' and resid 142 through 169 Processing helix chain 'L' and resid 193 through 222 Processing helix chain 'B' and resid 4 through 18 removed outlier: 4.084A pdb=" N LEU B 10 " --> pdb=" O PHE B 6 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 33 Processing helix chain 'B' and resid 33 through 40 Processing helix chain 'B' and resid 40 through 45 Processing helix chain 'B' and resid 46 through 48 No H-bonds generated for 'chain 'B' and resid 46 through 48' Processing helix chain 'B' and resid 60 through 70 Processing helix chain 'B' and resid 73 through 100 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 142 through 169 Processing helix chain 'B' and resid 193 through 222 Processing helix chain 'C' and resid 4 through 18 removed outlier: 4.084A pdb=" N LEU C 10 " --> pdb=" O PHE C 6 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 33 Processing helix chain 'C' and resid 33 through 40 Processing helix chain 'C' and resid 40 through 45 Processing helix chain 'C' and resid 46 through 48 No H-bonds generated for 'chain 'C' and resid 46 through 48' Processing helix chain 'C' and resid 60 through 70 Processing helix chain 'C' and resid 73 through 100 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 142 through 169 Processing helix chain 'C' and resid 193 through 222 Processing helix chain 'D' and resid 4 through 18 removed outlier: 4.084A pdb=" N LEU D 10 " --> pdb=" O PHE D 6 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 33 Processing helix chain 'D' and resid 33 through 40 Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 46 through 48 No H-bonds generated for 'chain 'D' and resid 46 through 48' Processing helix chain 'D' and resid 60 through 70 Processing helix chain 'D' and resid 73 through 100 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 142 through 169 Processing helix chain 'D' and resid 193 through 222 Processing helix chain 'E' and resid 4 through 18 removed outlier: 4.084A pdb=" N LEU E 10 " --> pdb=" O PHE E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 33 Processing helix chain 'E' and resid 33 through 40 Processing helix chain 'E' and resid 40 through 45 Processing helix chain 'E' and resid 46 through 48 No H-bonds generated for 'chain 'E' and resid 46 through 48' Processing helix chain 'E' and resid 60 through 70 Processing helix chain 'E' and resid 73 through 100 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 142 through 169 Processing helix chain 'E' and resid 193 through 222 Processing helix chain 'F' and resid 4 through 18 removed outlier: 4.085A pdb=" N LEU F 10 " --> pdb=" O PHE F 6 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 33 Processing helix chain 'F' and resid 33 through 40 Processing helix chain 'F' and resid 40 through 45 Processing helix chain 'F' and resid 46 through 48 No H-bonds generated for 'chain 'F' and resid 46 through 48' Processing helix chain 'F' and resid 60 through 70 Processing helix chain 'F' and resid 73 through 100 Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 142 through 169 Processing helix chain 'F' and resid 193 through 222 Processing helix chain 'G' and resid 4 through 18 removed outlier: 4.085A pdb=" N LEU G 10 " --> pdb=" O PHE G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 33 Processing helix chain 'G' and resid 33 through 40 Processing helix chain 'G' and resid 40 through 45 Processing helix chain 'G' and resid 46 through 48 No H-bonds generated for 'chain 'G' and resid 46 through 48' Processing helix chain 'G' and resid 60 through 70 Processing helix chain 'G' and resid 73 through 100 Proline residue: G 88 - end of helix Processing helix chain 'G' and resid 142 through 169 Processing helix chain 'G' and resid 193 through 222 Processing helix chain 'H' and resid 4 through 18 removed outlier: 4.084A pdb=" N LEU H 10 " --> pdb=" O PHE H 6 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 33 Processing helix chain 'H' and resid 33 through 40 Processing helix chain 'H' and resid 40 through 45 Processing helix chain 'H' and resid 46 through 48 No H-bonds generated for 'chain 'H' and resid 46 through 48' Processing helix chain 'H' and resid 60 through 70 Processing helix chain 'H' and resid 73 through 100 Proline residue: H 88 - end of helix Processing helix chain 'H' and resid 142 through 169 Processing helix chain 'H' and resid 193 through 222 Processing helix chain 'I' and resid 4 through 18 removed outlier: 4.084A pdb=" N LEU I 10 " --> pdb=" O PHE I 6 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 33 Processing helix chain 'I' and resid 33 through 40 Processing helix chain 'I' and resid 40 through 45 Processing helix chain 'I' and resid 46 through 48 No H-bonds generated for 'chain 'I' and resid 46 through 48' Processing helix chain 'I' and resid 60 through 70 Processing helix chain 'I' and resid 73 through 100 Proline residue: I 88 - end of helix Processing helix chain 'I' and resid 142 through 169 Processing helix chain 'I' and resid 193 through 222 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA2, first strand: chain 'J' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'K' and resid 53 through 54 Processing sheet with id=AA4, first strand: chain 'L' and resid 53 through 54 Processing sheet with id=AA5, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA6, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AA7, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AA9, first strand: chain 'F' and resid 53 through 54 Processing sheet with id=AB1, first strand: chain 'G' and resid 53 through 54 Processing sheet with id=AB2, first strand: chain 'H' and resid 53 through 54 Processing sheet with id=AB3, first strand: chain 'I' and resid 53 through 54 1332 hydrogen bonds defined for protein. 3924 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: 8.64 Time building geometry restraints manager: 4.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 17772 1.03 - 1.23: 79 1.23 - 1.42: 7880 1.42 - 1.62: 10245 1.62 - 1.81: 108 Bond restraints: 36084 Sorted by residual: bond pdb=" NE2 HIS F 17 " pdb=" HE2 HIS F 17 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.73e+01 bond pdb=" NE2 HIS A 17 " pdb=" HE2 HIS A 17 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.72e+01 bond pdb=" NE2 HIS K 17 " pdb=" HE2 HIS K 17 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" NE2 HIS D 17 " pdb=" HE2 HIS D 17 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" ND1 HIS G 98 " pdb=" HD1 HIS G 98 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 36079 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 57922 1.49 - 2.97: 5811 2.97 - 4.46: 1224 4.46 - 5.94: 167 5.94 - 7.43: 12 Bond angle restraints: 65136 Sorted by residual: angle pdb=" CA PHE K 30 " pdb=" CB PHE K 30 " pdb=" CG PHE K 30 " ideal model delta sigma weight residual 113.80 117.69 -3.89 1.00e+00 1.00e+00 1.51e+01 angle pdb=" CA PHE H 30 " pdb=" CB PHE H 30 " pdb=" CG PHE H 30 " ideal model delta sigma weight residual 113.80 117.68 -3.88 1.00e+00 1.00e+00 1.51e+01 angle pdb=" CA PHE E 30 " pdb=" CB PHE E 30 " pdb=" CG PHE E 30 " ideal model delta sigma weight residual 113.80 117.66 -3.86 1.00e+00 1.00e+00 1.49e+01 angle pdb=" CA PHE A 30 " pdb=" CB PHE A 30 " pdb=" CG PHE A 30 " ideal model delta sigma weight residual 113.80 117.64 -3.84 1.00e+00 1.00e+00 1.48e+01 angle pdb=" CA PHE C 30 " pdb=" CB PHE C 30 " pdb=" CG PHE C 30 " ideal model delta sigma weight residual 113.80 117.64 -3.84 1.00e+00 1.00e+00 1.48e+01 ... (remaining 65131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.99: 14928 16.99 - 33.98: 1404 33.98 - 50.98: 470 50.98 - 67.97: 250 67.97 - 84.96: 48 Dihedral angle restraints: 17100 sinusoidal: 8856 harmonic: 8244 Sorted by residual: dihedral pdb=" CA ALA H 40 " pdb=" C ALA H 40 " pdb=" N ALA H 41 " pdb=" CA ALA H 41 " ideal model delta harmonic sigma weight residual 180.00 -164.18 -15.82 0 5.00e+00 4.00e-02 1.00e+01 dihedral pdb=" CA ALA G 40 " pdb=" C ALA G 40 " pdb=" N ALA G 41 " pdb=" CA ALA G 41 " ideal model delta harmonic sigma weight residual -180.00 -164.20 -15.80 0 5.00e+00 4.00e-02 9.99e+00 dihedral pdb=" CA ALA E 40 " pdb=" C ALA E 40 " pdb=" N ALA E 41 " pdb=" CA ALA E 41 " ideal model delta harmonic sigma weight residual -180.00 -164.20 -15.80 0 5.00e+00 4.00e-02 9.99e+00 ... (remaining 17097 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1762 0.049 - 0.099: 582 0.099 - 0.148: 317 0.148 - 0.197: 148 0.197 - 0.246: 47 Chirality restraints: 2856 Sorted by residual: chirality pdb=" CA VAL C 24 " pdb=" N VAL C 24 " pdb=" C VAL C 24 " pdb=" CB VAL C 24 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA VAL G 24 " pdb=" N VAL G 24 " pdb=" C VAL G 24 " pdb=" CB VAL G 24 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA VAL I 24 " pdb=" N VAL I 24 " pdb=" C VAL I 24 " pdb=" CB VAL I 24 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.51e+00 ... (remaining 2853 not shown) Planarity restraints: 5148 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN H 149 " 0.202 2.00e-02 2.50e+03 4.14e-01 2.57e+03 pdb=" CG ASN H 149 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN H 149 " -0.195 2.00e-02 2.50e+03 pdb=" ND2 ASN H 149 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN H 149 " 0.695 2.00e-02 2.50e+03 pdb="HD22 ASN H 149 " -0.683 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 149 " 0.202 2.00e-02 2.50e+03 4.14e-01 2.57e+03 pdb=" CG ASN I 149 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN I 149 " -0.195 2.00e-02 2.50e+03 pdb=" ND2 ASN I 149 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN I 149 " 0.695 2.00e-02 2.50e+03 pdb="HD22 ASN I 149 " -0.683 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN F 149 " -0.202 2.00e-02 2.50e+03 4.14e-01 2.57e+03 pdb=" CG ASN F 149 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN F 149 " 0.195 2.00e-02 2.50e+03 pdb=" ND2 ASN F 149 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN F 149 " -0.695 2.00e-02 2.50e+03 pdb="HD22 ASN F 149 " 0.683 2.00e-02 2.50e+03 ... (remaining 5145 not shown) Histogram of nonbonded interaction distances: 1.65 - 2.24: 3810 2.24 - 2.83: 78809 2.83 - 3.42: 100966 3.42 - 4.01: 133129 4.01 - 4.60: 205501 Nonbonded interactions: 522215 Sorted by model distance: nonbonded pdb="HE21 GLN J 57 " pdb=" H THR E 56 " model vdw 1.650 2.100 nonbonded pdb=" H THR K 56 " pdb="HE21 GLN D 57 " model vdw 1.679 2.100 nonbonded pdb=" H THR L 56 " pdb="HE21 GLN C 57 " model vdw 1.691 2.100 nonbonded pdb=" OD1 ASP J 188 " pdb="HD21 ASN E 185 " model vdw 1.691 2.450 nonbonded pdb=" O ILE D 72 " pdb=" HH TYR D 168 " model vdw 1.728 2.450 ... (remaining 522210 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'J' selection = chain 'K' selection = chain 'L' 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: 5.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.250 Extract box with map and model: 0.620 Check model and map are aligned: 0.100 Set scattering table: 0.100 Process input model: 30.380 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5873 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 : 0.007 0.039 18336 Z= 0.528 Angle : 1.178 7.430 25020 Z= 0.876 Chirality : 0.072 0.246 2856 Planarity : 0.005 0.031 3072 Dihedral : 14.779 84.959 6300 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.62 % Allowed : 12.96 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.16), residues: 2136 helix: -1.03 (0.11), residues: 1620 sheet: -0.20 (0.33), residues: 204 loop : -1.43 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG F 9 TYR 0.008 0.001 TYR L 176 PHE 0.012 0.001 PHE I 200 TRP 0.008 0.001 TRP H 78 HIS 0.003 0.001 HIS I 95 Details of bonding type rmsd covalent geometry : bond 0.00741 (18300) covalent geometry : angle 1.17845 (24948) SS BOND : bond 0.00143 ( 36) SS BOND : angle 1.19131 ( 72) hydrogen bonds : bond 0.18023 ( 1332) hydrogen bonds : angle 7.72202 ( 3924) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 305 time to evaluate : 0.918 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: A 166 PHE cc_start: 0.7324 (m-80) cc_final: 0.6969 (m-80) REVERT: A 173 LYS cc_start: 0.6218 (mttt) cc_final: 0.5721 (mmtt) REVERT: J 85 VAL cc_start: 0.6278 (t) cc_final: 0.5984 (m) REVERT: J 173 LYS cc_start: 0.5771 (mttt) cc_final: 0.5464 (mmtt) REVERT: J 205 LEU cc_start: 0.5943 (tt) cc_final: 0.5675 (tm) REVERT: K 166 PHE cc_start: 0.7298 (m-80) cc_final: 0.6957 (m-80) REVERT: K 173 LYS cc_start: 0.6289 (mttt) cc_final: 0.5790 (mmtt) REVERT: L 47 ASP cc_start: 0.6887 (p0) cc_final: 0.6465 (p0) REVERT: L 166 PHE cc_start: 0.7598 (m-80) cc_final: 0.7232 (m-80) REVERT: L 173 LYS cc_start: 0.6268 (mttt) cc_final: 0.5700 (mmtt) REVERT: B 155 LEU cc_start: 0.5635 (mm) cc_final: 0.5431 (mm) REVERT: B 164 GLN cc_start: 0.5664 (tp40) cc_final: 0.5045 (tt0) REVERT: B 166 PHE cc_start: 0.6951 (m-80) cc_final: 0.6697 (m-80) REVERT: B 173 LYS cc_start: 0.6030 (mttt) cc_final: 0.5567 (mmtt) REVERT: B 188 ASP cc_start: 0.6562 (m-30) cc_final: 0.6299 (m-30) REVERT: C 155 LEU cc_start: 0.5682 (mm) cc_final: 0.5480 (mm) REVERT: C 173 LYS cc_start: 0.5954 (mttt) cc_final: 0.5547 (mmpt) REVERT: D 164 GLN cc_start: 0.5426 (tp40) cc_final: 0.4810 (tt0) REVERT: D 173 LYS cc_start: 0.6103 (mttt) cc_final: 0.5730 (mmtt) REVERT: E 30 PHE cc_start: 0.6371 (m-10) cc_final: 0.6008 (m-80) REVERT: E 47 ASP cc_start: 0.6737 (p0) cc_final: 0.6307 (p0) REVERT: E 173 LYS cc_start: 0.6429 (mttt) cc_final: 0.5864 (mmtt) REVERT: F 30 PHE cc_start: 0.6344 (m-10) cc_final: 0.6046 (m-80) REVERT: F 47 ASP cc_start: 0.6380 (p0) cc_final: 0.6076 (p0) REVERT: F 173 LYS cc_start: 0.5495 (mttt) cc_final: 0.5253 (mmpt) REVERT: G 85 VAL cc_start: 0.6398 (t) cc_final: 0.6192 (m) REVERT: G 173 LYS cc_start: 0.6229 (mttt) cc_final: 0.5815 (mmtt) REVERT: H 165 TYR cc_start: 0.6756 (t80) cc_final: 0.6519 (t80) REVERT: H 166 PHE cc_start: 0.7202 (m-80) cc_final: 0.6991 (m-80) REVERT: H 173 LYS cc_start: 0.6300 (mttt) cc_final: 0.5823 (mmtt) REVERT: I 155 LEU cc_start: 0.5864 (mm) cc_final: 0.5591 (mm) REVERT: I 157 GLU cc_start: 0.6659 (tp30) cc_final: 0.6434 (tp30) REVERT: I 164 GLN cc_start: 0.6014 (tp40) cc_final: 0.5448 (tt0) REVERT: I 166 PHE cc_start: 0.7226 (m-80) cc_final: 0.6966 (m-80) REVERT: I 173 LYS cc_start: 0.5888 (mttt) cc_final: 0.5483 (mmtt) REVERT: I 188 ASP cc_start: 0.6714 (m-30) cc_final: 0.6436 (m-30) REVERT: I 205 LEU cc_start: 0.5801 (tt) cc_final: 0.5525 (tm) outliers start: 12 outliers final: 9 residues processed: 314 average time/residue: 0.7823 time to fit residues: 295.3981 Evaluate side-chains 267 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 258 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain C residue 149 ASN Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain H residue 149 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 0.5980 chunk 194 optimal weight: 0.4980 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 0.9980 chunk 212 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 57 GLN J 57 GLN J 149 ASN K 149 ASN L 49 GLN L 149 ASN C 57 GLN C 149 ASN D 57 GLN E 57 GLN E 149 ASN F 49 GLN F 57 GLN F 149 ASN G 49 GLN H 49 GLN H 57 GLN H 149 ASN I 49 GLN I 57 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.206774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.136772 restraints weight = 47295.008| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.58 r_work: 0.3277 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3156 rms_B_bonded: 3.54 restraints_weight: 0.2500 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 18336 Z= 0.162 Angle : 0.579 4.296 25020 Z= 0.317 Chirality : 0.040 0.142 2856 Planarity : 0.003 0.021 3072 Dihedral : 5.251 57.978 2358 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 2.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.87 % Allowed : 16.00 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.17), residues: 2136 helix: 1.05 (0.12), residues: 1632 sheet: -0.07 (0.32), residues: 204 loop : -0.86 (0.34), residues: 300 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 180 TYR 0.012 0.002 TYR G 146 PHE 0.017 0.002 PHE K 190 TRP 0.010 0.001 TRP C 25 HIS 0.004 0.001 HIS B 17 Details of bonding type rmsd covalent geometry : bond 0.00343 (18300) covalent geometry : angle 0.57704 (24948) SS BOND : bond 0.00094 ( 36) SS BOND : angle 1.14258 ( 72) hydrogen bonds : bond 0.04732 ( 1332) hydrogen bonds : angle 5.06393 ( 3924) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 248 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: J 205 LEU cc_start: 0.8232 (tt) cc_final: 0.8004 (tm) REVERT: K 166 PHE cc_start: 0.8105 (m-80) cc_final: 0.7905 (m-80) REVERT: L 47 ASP cc_start: 0.8427 (p0) cc_final: 0.7682 (p0) REVERT: B 164 GLN cc_start: 0.7285 (tp40) cc_final: 0.6726 (tt0) REVERT: C 47 ASP cc_start: 0.7794 (p0) cc_final: 0.7105 (p0) REVERT: C 155 LEU cc_start: 0.6811 (mm) cc_final: 0.6533 (mm) REVERT: D 164 GLN cc_start: 0.7025 (tp40) cc_final: 0.6523 (tt0) REVERT: E 47 ASP cc_start: 0.8415 (p0) cc_final: 0.7912 (p0) REVERT: E 213 LEU cc_start: 0.7175 (tm) cc_final: 0.6854 (tp) REVERT: F 47 ASP cc_start: 0.8385 (p0) cc_final: 0.7725 (p0) REVERT: I 164 GLN cc_start: 0.7512 (tp40) cc_final: 0.7042 (tt0) REVERT: I 205 LEU cc_start: 0.8185 (tt) cc_final: 0.7940 (tm) outliers start: 17 outliers final: 9 residues processed: 259 average time/residue: 0.8405 time to fit residues: 260.5886 Evaluate side-chains 246 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 237 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain B residue 152 PHE Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain H residue 149 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 94 optimal weight: 0.0970 chunk 64 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 111 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 123 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 131 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 110 optimal weight: 0.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 149 ASN K 57 GLN L 57 GLN B 57 GLN G 57 GLN G 149 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.202697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.129865 restraints weight = 46349.581| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 1.64 r_work: 0.3135 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.2664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 18336 Z= 0.138 Angle : 0.517 7.197 25020 Z= 0.277 Chirality : 0.038 0.134 2856 Planarity : 0.003 0.021 3072 Dihedral : 4.855 59.079 2356 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.87 % Allowed : 15.59 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.19 (0.17), residues: 2136 helix: 2.04 (0.12), residues: 1632 sheet: 0.45 (0.37), residues: 132 loop : -0.82 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 180 TYR 0.010 0.001 TYR J 66 PHE 0.019 0.001 PHE I 190 TRP 0.007 0.001 TRP C 181 HIS 0.003 0.001 HIS E 17 Details of bonding type rmsd covalent geometry : bond 0.00317 (18300) covalent geometry : angle 0.51370 (24948) SS BOND : bond 0.00118 ( 36) SS BOND : angle 1.15635 ( 72) hydrogen bonds : bond 0.03855 ( 1332) hydrogen bonds : angle 4.81893 ( 3924) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 256 time to evaluate : 0.844 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: J 205 LEU cc_start: 0.8249 (tt) cc_final: 0.8027 (tm) REVERT: L 43 GLU cc_start: 0.7845 (mt-10) cc_final: 0.7622 (mt-10) REVERT: L 47 ASP cc_start: 0.8534 (p0) cc_final: 0.7818 (p0) REVERT: L 85 VAL cc_start: 0.7698 (t) cc_final: 0.7435 (m) REVERT: B 164 GLN cc_start: 0.7498 (tp40) cc_final: 0.6875 (tt0) REVERT: B 166 PHE cc_start: 0.7930 (m-80) cc_final: 0.7718 (m-80) REVERT: C 47 ASP cc_start: 0.8045 (p0) cc_final: 0.7373 (p0) REVERT: C 205 LEU cc_start: 0.7954 (tt) cc_final: 0.7721 (tm) REVERT: D 164 GLN cc_start: 0.7224 (tp40) cc_final: 0.6660 (tt0) REVERT: D 166 PHE cc_start: 0.7897 (m-80) cc_final: 0.7681 (m-80) REVERT: D 205 LEU cc_start: 0.8278 (tp) cc_final: 0.8035 (tm) REVERT: E 47 ASP cc_start: 0.8517 (p0) cc_final: 0.8018 (p0) REVERT: E 213 LEU cc_start: 0.7101 (tm) cc_final: 0.6781 (tp) REVERT: F 47 ASP cc_start: 0.8450 (p0) cc_final: 0.7788 (p0) REVERT: I 164 GLN cc_start: 0.7638 (tp40) cc_final: 0.7082 (tt0) REVERT: I 166 PHE cc_start: 0.8114 (m-80) cc_final: 0.7897 (m-80) REVERT: I 205 LEU cc_start: 0.8147 (tt) cc_final: 0.7905 (tm) outliers start: 17 outliers final: 10 residues processed: 267 average time/residue: 1.0168 time to fit residues: 317.3183 Evaluate side-chains 257 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 247 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain I residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 110 optimal weight: 6.9990 chunk 142 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 215 optimal weight: 7.9990 chunk 111 optimal weight: 2.9990 chunk 203 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 117 optimal weight: 20.0000 chunk 74 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 GLN J 58 GLN K 58 GLN L 58 GLN B 58 GLN C 58 GLN D 58 GLN E 58 GLN F 58 GLN G 58 GLN H 58 GLN I 58 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.192333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.116486 restraints weight = 45445.218| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 1.83 r_work: 0.2963 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 3.67 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.3642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 18336 Z= 0.254 Angle : 0.615 6.703 25020 Z= 0.328 Chirality : 0.043 0.136 2856 Planarity : 0.004 0.034 3072 Dihedral : 5.092 57.031 2356 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 1.59 % Allowed : 15.17 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.11 (0.17), residues: 2136 helix: 2.04 (0.12), residues: 1632 sheet: 0.44 (0.37), residues: 132 loop : -1.16 (0.28), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG K 33 TYR 0.015 0.002 TYR E 66 PHE 0.027 0.002 PHE D 190 TRP 0.015 0.002 TRP B 181 HIS 0.003 0.001 HIS I 74 Details of bonding type rmsd covalent geometry : bond 0.00611 (18300) covalent geometry : angle 0.60877 (24948) SS BOND : bond 0.00187 ( 36) SS BOND : angle 1.68439 ( 72) hydrogen bonds : bond 0.03974 ( 1332) hydrogen bonds : angle 5.00173 ( 3924) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 254 time to evaluate : 0.995 Fit side-chains REVERT: A 85 VAL cc_start: 0.7716 (t) cc_final: 0.7490 (m) REVERT: J 30 PHE cc_start: 0.7780 (m-10) cc_final: 0.7524 (m-80) REVERT: J 205 LEU cc_start: 0.8206 (tt) cc_final: 0.7923 (tm) REVERT: L 43 GLU cc_start: 0.7948 (mt-10) cc_final: 0.7721 (mt-10) REVERT: L 47 ASP cc_start: 0.8571 (p0) cc_final: 0.7849 (p0) REVERT: L 85 VAL cc_start: 0.7786 (t) cc_final: 0.7554 (m) REVERT: B 83 ILE cc_start: 0.7640 (mp) cc_final: 0.7423 (mt) REVERT: B 164 GLN cc_start: 0.7851 (tp40) cc_final: 0.7113 (tt0) REVERT: B 166 PHE cc_start: 0.8309 (m-80) cc_final: 0.8018 (m-80) REVERT: C 47 ASP cc_start: 0.8520 (p0) cc_final: 0.7861 (p0) REVERT: C 166 PHE cc_start: 0.8297 (m-80) cc_final: 0.8062 (m-80) REVERT: C 205 LEU cc_start: 0.8243 (tt) cc_final: 0.7971 (tm) REVERT: D 164 GLN cc_start: 0.7696 (tp40) cc_final: 0.7038 (tt0) REVERT: D 205 LEU cc_start: 0.8466 (tp) cc_final: 0.8213 (tm) REVERT: E 47 ASP cc_start: 0.8594 (p0) cc_final: 0.7915 (p0) REVERT: E 85 VAL cc_start: 0.7724 (t) cc_final: 0.7385 (m) REVERT: E 213 LEU cc_start: 0.7156 (tm) cc_final: 0.6855 (tp) REVERT: F 47 ASP cc_start: 0.8546 (p0) cc_final: 0.7852 (p0) REVERT: F 85 VAL cc_start: 0.7879 (t) cc_final: 0.7611 (m) REVERT: G 30 PHE cc_start: 0.7825 (m-10) cc_final: 0.7490 (m-80) REVERT: I 166 PHE cc_start: 0.8425 (m-80) cc_final: 0.8144 (m-80) REVERT: I 205 LEU cc_start: 0.8242 (tt) cc_final: 0.7946 (tm) outliers start: 31 outliers final: 25 residues processed: 269 average time/residue: 0.9392 time to fit residues: 297.6322 Evaluate side-chains 262 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 237 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 87 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 211 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 206 optimal weight: 0.9980 chunk 16 optimal weight: 0.8980 chunk 181 optimal weight: 7.9990 chunk 185 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 125 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.194337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.116584 restraints weight = 45371.715| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.88 r_work: 0.2964 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18336 Z= 0.153 Angle : 0.515 3.741 25020 Z= 0.274 Chirality : 0.038 0.127 2856 Planarity : 0.003 0.032 3072 Dihedral : 4.910 54.735 2356 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.03 % Allowed : 16.87 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.45 (0.17), residues: 2136 helix: 2.36 (0.12), residues: 1632 sheet: 0.28 (0.36), residues: 132 loop : -1.30 (0.28), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 33 TYR 0.015 0.002 TYR E 66 PHE 0.020 0.002 PHE F 190 TRP 0.009 0.001 TRP G 181 HIS 0.002 0.000 HIS E 221 Details of bonding type rmsd covalent geometry : bond 0.00350 (18300) covalent geometry : angle 0.51106 (24948) SS BOND : bond 0.00135 ( 36) SS BOND : angle 1.26535 ( 72) hydrogen bonds : bond 0.03550 ( 1332) hydrogen bonds : angle 4.83490 ( 3924) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 237 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: A 85 VAL cc_start: 0.7673 (t) cc_final: 0.7457 (m) REVERT: J 30 PHE cc_start: 0.7721 (m-10) cc_final: 0.7447 (m-80) REVERT: J 205 LEU cc_start: 0.8156 (tt) cc_final: 0.7847 (tm) REVERT: L 43 GLU cc_start: 0.7811 (mt-10) cc_final: 0.7594 (mt-10) REVERT: L 47 ASP cc_start: 0.8561 (p0) cc_final: 0.7879 (p0) REVERT: L 85 VAL cc_start: 0.7677 (t) cc_final: 0.7418 (m) REVERT: B 164 GLN cc_start: 0.7868 (tp40) cc_final: 0.7147 (tt0) REVERT: B 166 PHE cc_start: 0.8325 (m-80) cc_final: 0.8029 (m-80) REVERT: C 47 ASP cc_start: 0.8526 (p0) cc_final: 0.7832 (p0) REVERT: C 205 LEU cc_start: 0.8160 (tt) cc_final: 0.7870 (tm) REVERT: D 205 LEU cc_start: 0.8432 (tp) cc_final: 0.8183 (tm) REVERT: E 47 ASP cc_start: 0.8582 (p0) cc_final: 0.7923 (p0) REVERT: E 85 VAL cc_start: 0.7690 (t) cc_final: 0.7377 (m) REVERT: E 218 GLU cc_start: 0.7057 (tt0) cc_final: 0.6844 (mt-10) REVERT: F 47 ASP cc_start: 0.8521 (p0) cc_final: 0.7858 (p0) REVERT: F 85 VAL cc_start: 0.7775 (t) cc_final: 0.7538 (m) REVERT: G 30 PHE cc_start: 0.7709 (m-10) cc_final: 0.7362 (m-80) REVERT: I 166 PHE cc_start: 0.8432 (m-80) cc_final: 0.8131 (m-80) REVERT: I 205 LEU cc_start: 0.8166 (tt) cc_final: 0.7864 (tm) outliers start: 20 outliers final: 15 residues processed: 250 average time/residue: 1.0321 time to fit residues: 303.4820 Evaluate side-chains 249 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 234 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain J residue 51 ASP Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain I residue 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 10.0000 chunk 144 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 5 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 0.0970 chunk 179 optimal weight: 5.9990 chunk 2 optimal weight: 4.9990 chunk 192 optimal weight: 2.9990 chunk 171 optimal weight: 9.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 164 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.193701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.116259 restraints weight = 45110.656| |-----------------------------------------------------------------------------| r_work (start): 0.3139 rms_B_bonded: 1.55 r_work: 0.2969 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.4121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 18336 Z= 0.187 Angle : 0.537 3.948 25020 Z= 0.285 Chirality : 0.039 0.124 2856 Planarity : 0.004 0.029 3072 Dihedral : 4.845 51.812 2356 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.90 % Allowed : 16.98 % Favored : 81.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.57 (0.17), residues: 2136 helix: 2.46 (0.12), residues: 1632 sheet: 0.30 (0.35), residues: 132 loop : -1.36 (0.28), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 33 TYR 0.015 0.002 TYR E 66 PHE 0.022 0.002 PHE D 190 TRP 0.011 0.002 TRP G 181 HIS 0.001 0.000 HIS D 74 Details of bonding type rmsd covalent geometry : bond 0.00447 (18300) covalent geometry : angle 0.53250 (24948) SS BOND : bond 0.00145 ( 36) SS BOND : angle 1.37150 ( 72) hydrogen bonds : bond 0.03527 ( 1332) hydrogen bonds : angle 4.88146 ( 3924) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 242 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 VAL cc_start: 0.7840 (t) cc_final: 0.7630 (m) REVERT: J 30 PHE cc_start: 0.7845 (m-10) cc_final: 0.7612 (m-80) REVERT: J 205 LEU cc_start: 0.8327 (tt) cc_final: 0.8008 (tm) REVERT: L 43 GLU cc_start: 0.7876 (mt-10) cc_final: 0.7664 (mt-10) REVERT: L 47 ASP cc_start: 0.8590 (p0) cc_final: 0.7889 (p0) REVERT: L 85 VAL cc_start: 0.7814 (t) cc_final: 0.7580 (m) REVERT: B 166 PHE cc_start: 0.8482 (m-80) cc_final: 0.8262 (m-80) REVERT: C 47 ASP cc_start: 0.8536 (p0) cc_final: 0.7855 (p0) REVERT: C 205 LEU cc_start: 0.8360 (tt) cc_final: 0.8076 (tm) REVERT: E 47 ASP cc_start: 0.8602 (p0) cc_final: 0.7897 (p0) REVERT: E 85 VAL cc_start: 0.7844 (t) cc_final: 0.7555 (m) REVERT: F 43 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7624 (mt-10) REVERT: F 47 ASP cc_start: 0.8541 (p0) cc_final: 0.7871 (p0) REVERT: F 85 VAL cc_start: 0.7899 (t) cc_final: 0.7658 (m) REVERT: G 30 PHE cc_start: 0.7834 (m-10) cc_final: 0.7546 (m-80) REVERT: I 205 LEU cc_start: 0.8357 (tt) cc_final: 0.8060 (tm) outliers start: 37 outliers final: 31 residues processed: 262 average time/residue: 1.0142 time to fit residues: 313.2230 Evaluate side-chains 264 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 233 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain J residue 51 ASP Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 87 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 199 optimal weight: 5.9990 chunk 33 optimal weight: 0.0980 chunk 124 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 155 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 72 optimal weight: 9.9990 chunk 143 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 166 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.192382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.116471 restraints weight = 45301.510| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 1.96 r_work: 0.2945 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.4277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 18336 Z= 0.175 Angle : 0.521 3.977 25020 Z= 0.276 Chirality : 0.039 0.213 2856 Planarity : 0.003 0.027 3072 Dihedral : 4.735 50.009 2356 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.95 % Allowed : 17.85 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.17), residues: 2136 helix: 2.54 (0.12), residues: 1632 sheet: 0.26 (0.35), residues: 132 loop : -1.45 (0.27), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG J 33 TYR 0.015 0.002 TYR G 66 PHE 0.020 0.002 PHE F 190 TRP 0.010 0.001 TRP G 181 HIS 0.001 0.000 HIS F 74 Details of bonding type rmsd covalent geometry : bond 0.00410 (18300) covalent geometry : angle 0.51688 (24948) SS BOND : bond 0.00126 ( 36) SS BOND : angle 1.26913 ( 72) hydrogen bonds : bond 0.03426 ( 1332) hydrogen bonds : angle 4.85720 ( 3924) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 85 VAL cc_start: 0.7732 (t) cc_final: 0.7478 (m) REVERT: J 30 PHE cc_start: 0.7743 (m-10) cc_final: 0.7513 (m-80) REVERT: J 205 LEU cc_start: 0.8198 (tt) cc_final: 0.7841 (tm) REVERT: L 43 GLU cc_start: 0.7789 (mt-10) cc_final: 0.7581 (mt-10) REVERT: L 47 ASP cc_start: 0.8602 (p0) cc_final: 0.7930 (p0) REVERT: L 85 VAL cc_start: 0.7721 (t) cc_final: 0.7474 (m) REVERT: C 47 ASP cc_start: 0.8542 (p0) cc_final: 0.7883 (p0) REVERT: C 205 LEU cc_start: 0.8242 (tt) cc_final: 0.7923 (tm) REVERT: E 47 ASP cc_start: 0.8612 (p0) cc_final: 0.7934 (p0) REVERT: E 85 VAL cc_start: 0.7742 (t) cc_final: 0.7446 (m) REVERT: F 43 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7577 (mt-10) REVERT: F 47 ASP cc_start: 0.8536 (p0) cc_final: 0.7884 (p0) REVERT: F 85 VAL cc_start: 0.7803 (t) cc_final: 0.7536 (m) REVERT: G 30 PHE cc_start: 0.7732 (m-10) cc_final: 0.7441 (m-80) REVERT: H 213 LEU cc_start: 0.6947 (tm) cc_final: 0.6704 (tp) REVERT: I 205 LEU cc_start: 0.8249 (tt) cc_final: 0.7912 (tm) outliers start: 38 outliers final: 30 residues processed: 258 average time/residue: 1.0142 time to fit residues: 308.1678 Evaluate side-chains 258 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 228 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 24 VAL Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain E residue 218 GLU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 87 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 102 optimal weight: 2.9990 chunk 189 optimal weight: 20.0000 chunk 169 optimal weight: 1.9990 chunk 198 optimal weight: 4.9990 chunk 153 optimal weight: 8.9990 chunk 52 optimal weight: 1.9990 chunk 55 optimal weight: 9.9990 chunk 210 optimal weight: 2.9990 chunk 154 optimal weight: 4.9990 chunk 212 optimal weight: 0.8980 chunk 27 optimal weight: 20.0000 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.194234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3238 r_free = 0.3238 target = 0.119947 restraints weight = 45059.823| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.66 r_work: 0.2922 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2794 rms_B_bonded: 3.42 restraints_weight: 0.2500 r_work (final): 0.2794 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8428 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 18336 Z= 0.234 Angle : 0.565 3.862 25020 Z= 0.300 Chirality : 0.041 0.149 2856 Planarity : 0.004 0.035 3072 Dihedral : 4.787 47.809 2356 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Rotamer: Outliers : 2.26 % Allowed : 17.64 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.51 (0.17), residues: 2136 helix: 2.42 (0.12), residues: 1632 sheet: 0.31 (0.35), residues: 132 loop : -1.42 (0.28), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 33 TYR 0.016 0.002 TYR E 66 PHE 0.023 0.002 PHE D 190 TRP 0.013 0.002 TRP F 181 HIS 0.001 0.000 HIS H 74 Details of bonding type rmsd covalent geometry : bond 0.00558 (18300) covalent geometry : angle 0.56050 (24948) SS BOND : bond 0.00171 ( 36) SS BOND : angle 1.48642 ( 72) hydrogen bonds : bond 0.03634 ( 1332) hydrogen bonds : angle 4.97782 ( 3924) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 225 time to evaluate : 1.039 Fit side-chains REVERT: A 85 VAL cc_start: 0.7802 (t) cc_final: 0.7529 (m) REVERT: J 30 PHE cc_start: 0.7834 (m-10) cc_final: 0.7574 (m-80) REVERT: J 205 LEU cc_start: 0.8215 (tt) cc_final: 0.7835 (tm) REVERT: L 43 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7597 (mt-10) REVERT: L 47 ASP cc_start: 0.8601 (p0) cc_final: 0.7923 (p0) REVERT: L 85 VAL cc_start: 0.7756 (t) cc_final: 0.7498 (m) REVERT: L 149 ASN cc_start: 0.6367 (OUTLIER) cc_final: 0.6003 (t0) REVERT: C 47 ASP cc_start: 0.8545 (p0) cc_final: 0.7881 (p0) REVERT: C 205 LEU cc_start: 0.8255 (tt) cc_final: 0.7907 (tm) REVERT: E 47 ASP cc_start: 0.8593 (p0) cc_final: 0.7919 (p0) REVERT: E 85 VAL cc_start: 0.7799 (t) cc_final: 0.7525 (m) REVERT: F 43 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7594 (mt-10) REVERT: F 47 ASP cc_start: 0.8556 (p0) cc_final: 0.7901 (p0) REVERT: F 85 VAL cc_start: 0.7846 (t) cc_final: 0.7563 (m) REVERT: G 30 PHE cc_start: 0.7829 (m-10) cc_final: 0.7551 (m-80) REVERT: H 213 LEU cc_start: 0.7103 (tm) cc_final: 0.6866 (tp) outliers start: 44 outliers final: 32 residues processed: 253 average time/residue: 0.9958 time to fit residues: 297.2827 Evaluate side-chains 258 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 225 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain F residue 51 ASP Chi-restraints excluded: chain F residue 86 SER Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 87 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 140 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 95 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 162 optimal weight: 8.9990 chunk 156 optimal weight: 2.9990 chunk 153 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 163 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.191647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 91)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.118188 restraints weight = 46170.984| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.62 r_work: 0.2933 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 18336 Z= 0.212 Angle : 0.549 4.019 25020 Z= 0.291 Chirality : 0.040 0.189 2856 Planarity : 0.004 0.033 3072 Dihedral : 4.715 45.801 2356 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.16 % Allowed : 17.80 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.17), residues: 2136 helix: 2.42 (0.12), residues: 1632 sheet: 0.32 (0.35), residues: 132 loop : -1.47 (0.27), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 33 TYR 0.016 0.002 TYR I 66 PHE 0.021 0.002 PHE F 190 TRP 0.012 0.002 TRP J 181 HIS 0.001 0.000 HIS F 74 Details of bonding type rmsd covalent geometry : bond 0.00503 (18300) covalent geometry : angle 0.54513 (24948) SS BOND : bond 0.00158 ( 36) SS BOND : angle 1.38615 ( 72) hydrogen bonds : bond 0.03553 ( 1332) hydrogen bonds : angle 4.96612 ( 3924) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 221 time to evaluate : 1.035 Fit side-chains REVERT: A 85 VAL cc_start: 0.7878 (t) cc_final: 0.7607 (m) REVERT: J 30 PHE cc_start: 0.7909 (m-10) cc_final: 0.7656 (m-80) REVERT: J 205 LEU cc_start: 0.8333 (tt) cc_final: 0.7952 (tm) REVERT: L 47 ASP cc_start: 0.8593 (p0) cc_final: 0.7880 (p0) REVERT: L 85 VAL cc_start: 0.7830 (t) cc_final: 0.7576 (m) REVERT: L 149 ASN cc_start: 0.6490 (OUTLIER) cc_final: 0.6055 (t0) REVERT: C 47 ASP cc_start: 0.8544 (p0) cc_final: 0.7880 (p0) REVERT: C 205 LEU cc_start: 0.8336 (tt) cc_final: 0.7987 (tm) REVERT: E 47 ASP cc_start: 0.8596 (p0) cc_final: 0.7907 (p0) REVERT: E 85 VAL cc_start: 0.7863 (t) cc_final: 0.7572 (m) REVERT: F 43 GLU cc_start: 0.7931 (mt-10) cc_final: 0.7659 (mt-10) REVERT: F 47 ASP cc_start: 0.8540 (p0) cc_final: 0.7883 (p0) REVERT: F 85 VAL cc_start: 0.7905 (t) cc_final: 0.7620 (m) REVERT: G 30 PHE cc_start: 0.7912 (m-10) cc_final: 0.7599 (m-80) REVERT: H 149 ASN cc_start: 0.6256 (OUTLIER) cc_final: 0.5929 (t0) REVERT: H 213 LEU cc_start: 0.7193 (tm) cc_final: 0.6955 (tp) outliers start: 42 outliers final: 32 residues processed: 246 average time/residue: 1.0276 time to fit residues: 297.9842 Evaluate side-chains 251 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 217 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain K residue 51 ASP Chi-restraints excluded: chain K residue 86 SER Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain F residue 205 LEU Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 51 ASP Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 86 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 117 optimal weight: 5.9990 chunk 82 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 165 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 193 optimal weight: 0.5980 chunk 83 optimal weight: 0.0370 chunk 198 optimal weight: 10.0000 overall best weight: 1.3462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.193135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.120833 restraints weight = 46528.456| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 1.76 r_work: 0.2953 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.4637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 18336 Z= 0.168 Angle : 0.517 3.667 25020 Z= 0.273 Chirality : 0.038 0.145 2856 Planarity : 0.003 0.029 3072 Dihedral : 4.622 44.011 2356 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.01 % Allowed : 17.95 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.64 (0.17), residues: 2136 helix: 2.54 (0.12), residues: 1632 sheet: 0.26 (0.35), residues: 132 loop : -1.46 (0.27), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG I 33 TYR 0.015 0.002 TYR I 66 PHE 0.019 0.002 PHE D 190 TRP 0.010 0.001 TRP F 181 HIS 0.001 0.000 HIS F 74 Details of bonding type rmsd covalent geometry : bond 0.00392 (18300) covalent geometry : angle 0.51325 (24948) SS BOND : bond 0.00116 ( 36) SS BOND : angle 1.21437 ( 72) hydrogen bonds : bond 0.03358 ( 1332) hydrogen bonds : angle 4.89280 ( 3924) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4272 Ramachandran restraints generated. 2136 Oldfield, 0 Emsley, 2136 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 219 time to evaluate : 1.042 Fit side-chains REVERT: J 30 PHE cc_start: 0.7803 (m-10) cc_final: 0.7555 (m-80) REVERT: J 43 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7524 (mt-10) REVERT: J 205 LEU cc_start: 0.8199 (tt) cc_final: 0.7800 (tm) REVERT: L 47 ASP cc_start: 0.8586 (p0) cc_final: 0.7911 (p0) REVERT: L 85 VAL cc_start: 0.7737 (t) cc_final: 0.7464 (m) REVERT: L 149 ASN cc_start: 0.6438 (OUTLIER) cc_final: 0.6024 (t0) REVERT: B 33 ARG cc_start: 0.8593 (mtp180) cc_final: 0.8338 (mtt180) REVERT: C 47 ASP cc_start: 0.8503 (p0) cc_final: 0.7851 (p0) REVERT: C 205 LEU cc_start: 0.8227 (tt) cc_final: 0.7850 (tm) REVERT: E 47 ASP cc_start: 0.8576 (p0) cc_final: 0.7914 (p0) REVERT: E 85 VAL cc_start: 0.7776 (t) cc_final: 0.7488 (m) REVERT: F 43 GLU cc_start: 0.7827 (mt-10) cc_final: 0.7551 (mt-10) REVERT: F 47 ASP cc_start: 0.8521 (p0) cc_final: 0.7844 (p0) REVERT: F 85 VAL cc_start: 0.7810 (t) cc_final: 0.7508 (m) REVERT: G 30 PHE cc_start: 0.7800 (m-10) cc_final: 0.7526 (m-80) REVERT: H 149 ASN cc_start: 0.6187 (OUTLIER) cc_final: 0.5856 (t0) REVERT: H 213 LEU cc_start: 0.7050 (tm) cc_final: 0.6828 (tp) outliers start: 39 outliers final: 26 residues processed: 242 average time/residue: 1.0591 time to fit residues: 299.5834 Evaluate side-chains 245 residues out of total 1944 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 217 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 149 ASN Chi-restraints excluded: chain J residue 50 SER Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 149 ASN Chi-restraints excluded: chain K residue 149 ASN Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain L residue 87 THR Chi-restraints excluded: chain L residue 149 ASN Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 51 ASP Chi-restraints excluded: chain C residue 50 SER Chi-restraints excluded: chain C residue 87 THR Chi-restraints excluded: chain D residue 50 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 149 ASN Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 149 ASN Chi-restraints excluded: chain E residue 205 LEU Chi-restraints excluded: chain F residue 149 ASN Chi-restraints excluded: chain G residue 50 SER Chi-restraints excluded: chain G residue 87 THR Chi-restraints excluded: chain G residue 149 ASN Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 149 ASN Chi-restraints excluded: chain I residue 50 SER Chi-restraints excluded: chain I residue 87 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 206 optimal weight: 3.9990 chunk 99 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 117 optimal weight: 8.9990 chunk 165 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 172 optimal weight: 0.9990 chunk 134 optimal weight: 0.7980 chunk 139 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4056 r_free = 0.4056 target = 0.192875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.119051 restraints weight = 46488.966| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 1.66 r_work: 0.2936 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 18336 Z= 0.183 Angle : 0.529 3.949 25020 Z= 0.279 Chirality : 0.039 0.174 2856 Planarity : 0.004 0.054 3072 Dihedral : 4.602 42.561 2356 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 1.80 % Allowed : 18.16 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.17), residues: 2136 helix: 2.54 (0.12), residues: 1632 sheet: 0.26 (0.35), residues: 132 loop : -1.45 (0.27), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 33 TYR 0.015 0.002 TYR I 66 PHE 0.021 0.002 PHE D 190 TRP 0.010 0.002 TRP J 181 HIS 0.001 0.000 HIS F 74 Details of bonding type rmsd covalent geometry : bond 0.00433 (18300) covalent geometry : angle 0.52501 (24948) SS BOND : bond 0.00131 ( 36) SS BOND : angle 1.28349 ( 72) hydrogen bonds : bond 0.03392 ( 1332) hydrogen bonds : angle 4.90686 ( 3924) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12836.39 seconds wall clock time: 217 minutes 41.34 seconds (13061.34 seconds total)