Starting phenix.real_space_refine on Thu Aug 6 10:12:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/36hu_77586/08_2026/36hu_77586.cif Found real_map, /net/cci-nas-00/data/ceres_data/36hu_77586/08_2026/36hu_77586.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/36hu_77586/08_2026/36hu_77586.cif" } default_model = "/net/cci-nas-00/data/ceres_data/36hu_77586/08_2026/36hu_77586.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/36hu_77586/08_2026/36hu_77586.map" default_real_map = "/net/cci-nas-00/data/ceres_data/36hu_77586/08_2026/36hu_77586.map" } resolution = 2.5 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= 0.006 sd= 0.051 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 118 5.16 5 C 9585 2.51 5 N 2237 2.21 5 O 2417 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14357 Number of models: 1 Model: "" Number of chains: 11 Chain: "A1" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1623 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 15, 'TRANS': 193} Chain: "B1" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1623 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 15, 'TRANS': 193} Chain: "C1" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1623 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 15, 'TRANS': 193} Chain: "D1" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1623 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 15, 'TRANS': 193} Chain: "E1" Number of atoms: 1623 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1623 Classifications: {'peptide': 209} Link IDs: {'PTRANS': 15, 'TRANS': 193} Chain: "F1" Number of atoms: 1925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 1925 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 15, 'TRANS': 234} Chain: "G1" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "H1" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "I1" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "J1" Number of atoms: 670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 670 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 5, 'TRANS': 83} Chain: "K1" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1637 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 12, 'TRANS': 201} Time building chain proxies: 2.59, per 1000 atoms: 0.18 Number of scatterers: 14357 At special positions: 0 Unit cell: (103.95, 105, 147, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 118 16.00 O 2417 8.00 N 2237 7.00 C 9585 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.84 Conformation dependent library (CDL) restraints added in 560.1 milliseconds 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3528 Finding SS restraints... Secondary structure from input PDB file: 93 helices and 0 sheets defined 87.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.19 Creating SS restraints... Processing helix chain 'A1' and resid 41 through 51 Processing helix chain 'A1' and resid 53 through 62 removed outlier: 3.990A pdb=" N THRA1 62 " --> pdb=" O LEUA1 58 " (cutoff:3.500A) Processing helix chain 'A1' and resid 63 through 77 Processing helix chain 'A1' and resid 78 through 80 No H-bonds generated for 'chain 'A1' and resid 78 through 80' Processing helix chain 'A1' and resid 85 through 112 Proline residue: A1 103 - end of helix Processing helix chain 'A1' and resid 112 through 118 Processing helix chain 'A1' and resid 124 through 142 removed outlier: 4.000A pdb=" N ASPA1 128 " --> pdb=" O GLNA1 124 " (cutoff:3.500A) Proline residue: A1 133 - end of helix Processing helix chain 'A1' and resid 143 through 154 Processing helix chain 'A1' and resid 161 through 165 removed outlier: 3.671A pdb=" N VALA1 165 " --> pdb=" O PROA1 162 " (cutoff:3.500A) Processing helix chain 'A1' and resid 169 through 207 Proline residue: A1 192 - end of helix removed outlier: 3.536A pdb=" N LEUA1 207 " --> pdb=" O VALA1 203 " (cutoff:3.500A) Processing helix chain 'A1' and resid 213 through 229 removed outlier: 3.878A pdb=" N ILEA1 217 " --> pdb=" O PROA1 213 " (cutoff:3.500A) Proline residue: A1 220 - end of helix Processing helix chain 'A1' and resid 230 through 242 Processing helix chain 'B1' and resid 40 through 52 removed outlier: 3.731A pdb=" N THRB1 52 " --> pdb=" O ILEB1 48 " (cutoff:3.500A) Processing helix chain 'B1' and resid 53 through 62 removed outlier: 3.806A pdb=" N THRB1 62 " --> pdb=" O LEUB1 58 " (cutoff:3.500A) Processing helix chain 'B1' and resid 63 through 77 Processing helix chain 'B1' and resid 78 through 80 No H-bonds generated for 'chain 'B1' and resid 78 through 80' Processing helix chain 'B1' and resid 88 through 112 Proline residue: B1 103 - end of helix Processing helix chain 'B1' and resid 112 through 118 Processing helix chain 'B1' and resid 124 through 141 removed outlier: 3.520A pdb=" N ASPB1 128 " --> pdb=" O GLNB1 124 " (cutoff:3.500A) Proline residue: B1 133 - end of helix removed outlier: 3.584A pdb=" N GLNB1 141 " --> pdb=" O PHEB1 137 " (cutoff:3.500A) Processing helix chain 'B1' and resid 143 through 155 Processing helix chain 'B1' and resid 161 through 165 Processing helix chain 'B1' and resid 166 through 207 Proline residue: B1 172 - end of helix Proline residue: B1 192 - end of helix Processing helix chain 'B1' and resid 213 through 229 removed outlier: 3.977A pdb=" N ILEB1 217 " --> pdb=" O PROB1 213 " (cutoff:3.500A) Proline residue: B1 220 - end of helix Processing helix chain 'B1' and resid 230 through 242 Processing helix chain 'C1' and resid 40 through 51 Processing helix chain 'C1' and resid 53 through 62 removed outlier: 3.778A pdb=" N THRC1 62 " --> pdb=" O LEUC1 58 " (cutoff:3.500A) Processing helix chain 'C1' and resid 63 through 77 Processing helix chain 'C1' and resid 78 through 80 No H-bonds generated for 'chain 'C1' and resid 78 through 80' Processing helix chain 'C1' and resid 88 through 112 Proline residue: C1 103 - end of helix Processing helix chain 'C1' and resid 112 through 118 removed outlier: 3.799A pdb=" N GLUC1 118 " --> pdb=" O GLNC1 114 " (cutoff:3.500A) Processing helix chain 'C1' and resid 124 through 142 removed outlier: 3.767A pdb=" N ASPC1 128 " --> pdb=" O GLNC1 124 " (cutoff:3.500A) Proline residue: C1 133 - end of helix removed outlier: 3.516A pdb=" N GLNC1 141 " --> pdb=" O PHEC1 137 " (cutoff:3.500A) Processing helix chain 'C1' and resid 143 through 154 Processing helix chain 'C1' and resid 161 through 165 Processing helix chain 'C1' and resid 166 through 206 Proline residue: C1 172 - end of helix Proline residue: C1 192 - end of helix Processing helix chain 'C1' and resid 213 through 229 removed outlier: 4.188A pdb=" N ILEC1 217 " --> pdb=" O PROC1 213 " (cutoff:3.500A) Proline residue: C1 220 - end of helix Processing helix chain 'C1' and resid 230 through 242 Processing helix chain 'D1' and resid 40 through 53 removed outlier: 3.512A pdb=" N THRD1 44 " --> pdb=" O LEUD1 40 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHED1 53 " --> pdb=" O THRD1 49 " (cutoff:3.500A) Processing helix chain 'D1' and resid 53 through 62 removed outlier: 3.696A pdb=" N THRD1 62 " --> pdb=" O LEUD1 58 " (cutoff:3.500A) Processing helix chain 'D1' and resid 63 through 77 Processing helix chain 'D1' and resid 78 through 80 No H-bonds generated for 'chain 'D1' and resid 78 through 80' Processing helix chain 'D1' and resid 88 through 112 Proline residue: D1 103 - end of helix Processing helix chain 'D1' and resid 112 through 118 Processing helix chain 'D1' and resid 124 through 141 removed outlier: 3.610A pdb=" N ASPD1 128 " --> pdb=" O GLND1 124 " (cutoff:3.500A) Proline residue: D1 133 - end of helix removed outlier: 3.605A pdb=" N GLND1 141 " --> pdb=" O PHED1 137 " (cutoff:3.500A) Processing helix chain 'D1' and resid 143 through 154 Processing helix chain 'D1' and resid 166 through 207 Proline residue: D1 172 - end of helix Proline residue: D1 192 - end of helix Processing helix chain 'D1' and resid 213 through 229 removed outlier: 3.794A pdb=" N ILED1 217 " --> pdb=" O PROD1 213 " (cutoff:3.500A) Proline residue: D1 220 - end of helix Processing helix chain 'D1' and resid 230 through 242 Processing helix chain 'E1' and resid 40 through 51 Processing helix chain 'E1' and resid 53 through 62 removed outlier: 3.757A pdb=" N THRE1 62 " --> pdb=" O LEUE1 58 " (cutoff:3.500A) Processing helix chain 'E1' and resid 63 through 77 Processing helix chain 'E1' and resid 78 through 80 No H-bonds generated for 'chain 'E1' and resid 78 through 80' Processing helix chain 'E1' and resid 88 through 112 Proline residue: E1 103 - end of helix Processing helix chain 'E1' and resid 112 through 118 removed outlier: 3.531A pdb=" N GLUE1 118 " --> pdb=" O GLNE1 114 " (cutoff:3.500A) Processing helix chain 'E1' and resid 124 through 142 removed outlier: 3.929A pdb=" N ASPE1 128 " --> pdb=" O GLNE1 124 " (cutoff:3.500A) Proline residue: E1 133 - end of helix Processing helix chain 'E1' and resid 143 through 155 Processing helix chain 'E1' and resid 161 through 165 removed outlier: 3.546A pdb=" N VALE1 165 " --> pdb=" O PROE1 162 " (cutoff:3.500A) Processing helix chain 'E1' and resid 166 through 207 Proline residue: E1 172 - end of helix Proline residue: E1 192 - end of helix Processing helix chain 'E1' and resid 213 through 229 removed outlier: 4.383A pdb=" N ILEE1 217 " --> pdb=" O PROE1 213 " (cutoff:3.500A) Proline residue: E1 220 - end of helix Processing helix chain 'E1' and resid 230 through 242 Processing helix chain 'F1' and resid 8 through 28 removed outlier: 3.999A pdb=" N TRPF1 18 " --> pdb=" O HISF1 14 " (cutoff:3.500A) Proline residue: F1 19 - end of helix removed outlier: 3.602A pdb=" N ARGF1 22 " --> pdb=" O TRPF1 18 " (cutoff:3.500A) Processing helix chain 'F1' and resid 39 through 55 Processing helix chain 'F1' and resid 56 through 58 No H-bonds generated for 'chain 'F1' and resid 56 through 58' Processing helix chain 'F1' and resid 68 through 107 removed outlier: 3.863A pdb=" N TRPF1 72 " --> pdb=" O ILEF1 68 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N METF1 88 " --> pdb=" O LEUF1 84 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHEF1 90 " --> pdb=" O PHEF1 86 " (cutoff:3.500A) removed outlier: 4.598A pdb=" N ALAF1 91 " --> pdb=" O THRF1 87 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N PHEF1 92 " --> pdb=" O METF1 88 " (cutoff:3.500A) Processing helix chain 'F1' and resid 109 through 115 removed outlier: 3.965A pdb=" N PHEF1 113 " --> pdb=" O SERF1 109 " (cutoff:3.500A) Processing helix chain 'F1' and resid 123 through 140 Processing helix chain 'F1' and resid 141 through 157 removed outlier: 3.559A pdb=" N PHEF1 154 " --> pdb=" O LEUF1 150 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N HISF1 155 " --> pdb=" O VALF1 151 " (cutoff:3.500A) Processing helix chain 'F1' and resid 166 through 208 removed outlier: 3.684A pdb=" N METF1 170 " --> pdb=" O SERF1 166 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLYF1 176 " --> pdb=" O LEUF1 172 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLYF1 177 " --> pdb=" O ALAF1 173 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEUF1 178 " --> pdb=" O ARGF1 174 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILEF1 179 " --> pdb=" O ALAF1 175 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N PHEF1 180 " --> pdb=" O GLYF1 176 " (cutoff:3.500A) Proline residue: F1 189 - end of helix Processing helix chain 'F1' and resid 216 through 255 removed outlier: 3.658A pdb=" N LEUF1 220 " --> pdb=" O ILEF1 216 " (cutoff:3.500A) Proline residue: F1 234 - end of helix removed outlier: 4.471A pdb=" N ALAF1 237 " --> pdb=" O METF1 233 " (cutoff:3.500A) Proline residue: F1 238 - end of helix Processing helix chain 'G1' and resid 2 through 43 Proline residue: G1 23 - end of helix Processing helix chain 'G1' and resid 47 through 84 Proline residue: G1 53 - end of helix Proline residue: G1 67 - end of helix Processing helix chain 'G1' and resid 85 through 87 No H-bonds generated for 'chain 'G1' and resid 85 through 87' Processing helix chain 'H1' and resid 2 through 43 Proline residue: H1 23 - end of helix Processing helix chain 'H1' and resid 47 through 84 removed outlier: 3.607A pdb=" N PHEH1 51 " --> pdb=" O METH1 47 " (cutoff:3.500A) Proline residue: H1 53 - end of helix Proline residue: H1 67 - end of helix Processing helix chain 'H1' and resid 85 through 87 No H-bonds generated for 'chain 'H1' and resid 85 through 87' Processing helix chain 'I1' and resid 2 through 42 Proline residue: I1 23 - end of helix Processing helix chain 'I1' and resid 47 through 84 Proline residue: I1 53 - end of helix Proline residue: I1 67 - end of helix Processing helix chain 'I1' and resid 85 through 87 No H-bonds generated for 'chain 'I1' and resid 85 through 87' Processing helix chain 'J1' and resid 2 through 43 Proline residue: J1 23 - end of helix Processing helix chain 'J1' and resid 47 through 84 removed outlier: 3.762A pdb=" N PHEJ1 51 " --> pdb=" O METJ1 47 " (cutoff:3.500A) Proline residue: J1 53 - end of helix Proline residue: J1 67 - end of helix Processing helix chain 'J1' and resid 85 through 87 No H-bonds generated for 'chain 'J1' and resid 85 through 87' Processing helix chain 'K1' and resid 14 through 23 removed outlier: 3.737A pdb=" N GLUK1 23 " --> pdb=" O GLUK1 19 " (cutoff:3.500A) Processing helix chain 'K1' and resid 30 through 49 Processing helix chain 'K1' and resid 49 through 65 removed outlier: 3.604A pdb=" N LEUK1 53 " --> pdb=" O GLYK1 49 " (cutoff:3.500A) Processing helix chain 'K1' and resid 69 through 74 removed outlier: 3.960A pdb=" N ASNK1 73 " --> pdb=" O HISK1 69 " (cutoff:3.500A) Processing helix chain 'K1' and resid 76 through 107 removed outlier: 3.741A pdb=" N LEUK1 84 " --> pdb=" O GLYK1 80 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N METK1 90 " --> pdb=" O ILEK1 86 " (cutoff:3.500A) Proline residue: K1 95 - end of helix Processing helix chain 'K1' and resid 108 through 112 removed outlier: 4.234A pdb=" N GLYK1 112 " --> pdb=" O VALK1 109 " (cutoff:3.500A) Processing helix chain 'K1' and resid 117 through 121 removed outlier: 4.225A pdb=" N SERK1 120 " --> pdb=" O SERK1 117 " (cutoff:3.500A) Processing helix chain 'K1' and resid 124 through 128 removed outlier: 3.962A pdb=" N LYSK1 127 " --> pdb=" O LYSK1 124 " (cutoff:3.500A) Processing helix chain 'K1' and resid 129 through 136 removed outlier: 3.860A pdb=" N GLYK1 133 " --> pdb=" O ASNK1 129 " (cutoff:3.500A) Processing helix chain 'K1' and resid 139 through 174 Proline residue: K1 169 - end of helix Processing helix chain 'K1' and resid 175 through 177 No H-bonds generated for 'chain 'K1' and resid 175 through 177' Processing helix chain 'K1' and resid 178 through 201 Processing helix chain 'K1' and resid 201 through 220 1089 hydrogen bonds defined for protein. 3240 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.52 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 4293 1.34 - 1.46: 2514 1.46 - 1.58: 7640 1.58 - 1.70: 0 1.70 - 1.81: 232 Bond restraints: 14679 Sorted by residual: bond pdb=" C ALAF1 55 " pdb=" N PROF1 56 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.16e+00 bond pdb=" CA ILED1 191 " pdb=" C ILED1 191 " ideal model delta sigma weight residual 1.524 1.539 -0.014 1.05e-02 9.07e+03 1.82e+00 bond pdb=" CA ILEC1 191 " pdb=" C ILEC1 191 " ideal model delta sigma weight residual 1.524 1.538 -0.013 1.11e-02 8.12e+03 1.43e+00 bond pdb=" C ASNF1 162 " pdb=" N PROF1 163 " ideal model delta sigma weight residual 1.328 1.343 -0.015 1.25e-02 6.40e+03 1.43e+00 bond pdb=" CA ILEB1 191 " pdb=" C ILEB1 191 " ideal model delta sigma weight residual 1.524 1.538 -0.013 1.11e-02 8.12e+03 1.40e+00 ... (remaining 14674 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 19337 1.34 - 2.67: 484 2.67 - 4.01: 87 4.01 - 5.34: 79 5.34 - 6.68: 4 Bond angle restraints: 19991 Sorted by residual: angle pdb=" C GLYB1 186 " pdb=" N PHEB1 187 " pdb=" CA PHEB1 187 " ideal model delta sigma weight residual 120.31 115.86 4.45 1.52e+00 4.33e-01 8.56e+00 angle pdb=" N ILED1 191 " pdb=" CA ILED1 191 " pdb=" C ILED1 191 " ideal model delta sigma weight residual 108.88 114.41 -5.53 2.16e+00 2.14e-01 6.54e+00 angle pdb=" C ASNC1 86 " pdb=" N GLNC1 87 " pdb=" CA GLNC1 87 " ideal model delta sigma weight residual 121.54 126.26 -4.72 1.91e+00 2.74e-01 6.11e+00 angle pdb=" CA PROF1 163 " pdb=" C PROF1 163 " pdb=" N VALF1 164 " ideal model delta sigma weight residual 114.74 117.26 -2.52 1.03e+00 9.43e-01 6.00e+00 angle pdb=" N SERC1 39 " pdb=" CA SERC1 39 " pdb=" C SERC1 39 " ideal model delta sigma weight residual 110.65 113.48 -2.83 1.26e+00 6.30e-01 5.04e+00 ... (remaining 19986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.76: 7872 16.76 - 33.52: 785 33.52 - 50.27: 137 50.27 - 67.03: 29 67.03 - 83.79: 17 Dihedral angle restraints: 8840 sinusoidal: 3427 harmonic: 5413 Sorted by residual: dihedral pdb=" CA GLNB1 87 " pdb=" C GLNB1 87 " pdb=" N VALB1 88 " pdb=" CA VALB1 88 " ideal model delta harmonic sigma weight residual 180.00 153.71 26.29 0 5.00e+00 4.00e-02 2.77e+01 dihedral pdb=" CA GLND1 87 " pdb=" C GLND1 87 " pdb=" N VALD1 88 " pdb=" CA VALD1 88 " ideal model delta harmonic sigma weight residual 180.00 156.92 23.08 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA GLNC1 87 " pdb=" C GLNC1 87 " pdb=" N VALC1 88 " pdb=" CA VALC1 88 " ideal model delta harmonic sigma weight residual 180.00 159.28 20.72 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 8837 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 1673 0.037 - 0.074: 595 0.074 - 0.111: 190 0.111 - 0.148: 24 0.148 - 0.185: 3 Chirality restraints: 2485 Sorted by residual: chirality pdb=" CB ILEE1 191 " pdb=" CA ILEE1 191 " pdb=" CG1 ILEE1 191 " pdb=" CG2 ILEE1 191 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" CA GLNC1 87 " pdb=" N GLNC1 87 " pdb=" C GLNC1 87 " pdb=" CB GLNC1 87 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.15e-01 chirality pdb=" CA ILEE1 191 " pdb=" N ILEE1 191 " pdb=" C ILEE1 191 " pdb=" CB ILEE1 191 " both_signs ideal model delta sigma weight residual False 2.43 2.28 0.15 2.00e-01 2.50e+01 5.57e-01 ... (remaining 2482 not shown) Planarity restraints: 2430 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THRJ1 2 " 0.034 5.00e-02 4.00e+02 5.23e-02 4.37e+00 pdb=" N PROJ1 3 " -0.090 5.00e-02 4.00e+02 pdb=" CA PROJ1 3 " 0.027 5.00e-02 4.00e+02 pdb=" CD PROJ1 3 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA THRF1 192 " 0.010 2.00e-02 2.50e+03 1.96e-02 3.85e+00 pdb=" C THRF1 192 " -0.034 2.00e-02 2.50e+03 pdb=" O THRF1 192 " 0.013 2.00e-02 2.50e+03 pdb=" N LEUF1 193 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THRI1 2 " -0.028 5.00e-02 4.00e+02 4.24e-02 2.87e+00 pdb=" N PROI1 3 " 0.073 5.00e-02 4.00e+02 pdb=" CA PROI1 3 " -0.021 5.00e-02 4.00e+02 pdb=" CD PROI1 3 " -0.024 5.00e-02 4.00e+02 ... (remaining 2427 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 8467 3.02 - 3.49: 15923 3.49 - 3.96: 23825 3.96 - 4.43: 27933 4.43 - 4.90: 43309 Nonbonded interactions: 119457 Sorted by model distance: nonbonded pdb=" N THRH1 2 " pdb=" OG1 THRH1 2 " model vdw 2.547 2.496 nonbonded pdb=" O GLUD1 125 " pdb=" OD1 ASPD1 128 " model vdw 2.588 3.040 nonbonded pdb=" O SERE1 39 " pdb=" N SERE1 41 " model vdw 2.590 3.120 nonbonded pdb=" O ARGC1 75 " pdb=" O ALAC1 77 " model vdw 2.599 3.040 nonbonded pdb=" O SERB1 39 " pdb=" N SERB1 41 " model vdw 2.602 3.120 ... (remaining 119452 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A1' selection = chain 'B1' selection = chain 'C1' selection = chain 'D1' selection = chain 'E1' } ncs_group { reference = chain 'G1' selection = chain 'H1' selection = chain 'I1' selection = chain 'J1' } 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: 8.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 10.220 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14679 Z= 0.160 Angle : 0.593 6.680 19991 Z= 0.303 Chirality : 0.042 0.185 2485 Planarity : 0.004 0.052 2430 Dihedral : 14.129 83.789 5312 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.77 % Favored : 97.12 % Rotamer: Outliers : 0.19 % Allowed : 5.84 % Favored : 93.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.50 (0.20), residues: 1843 helix: 2.18 (0.13), residues: 1499 sheet: None (None), residues: 0 loop : -0.72 (0.36), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARGD1 75 TYR 0.008 0.001 TYRH1 86 PHE 0.019 0.002 PHEB1 187 TRP 0.006 0.001 TRPF1 9 HIS 0.003 0.001 HISK1 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.16 (14679) covalent geometry : angle 0.59276 / 0.30 (19991) hydrogen bonds : bond 0.10675 / 6.80 ( 1089) hydrogen bonds : angle 4.79527 / 3.37 ( 3240) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 496 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 493 time to evaluate : 0.737 Fit side-chains revert: symmetry clash REVERT: B1 101 MET cc_start: 0.8741 (mmm) cc_final: 0.8416 (mmm) REVERT: E1 118 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.7974 (pm20) REVERT: I1 4 GLU cc_start: 0.8225 (mp0) cc_final: 0.7960 (mp0) outliers start: 3 outliers final: 1 residues processed: 494 average time/residue: 0.5996 time to fit residues: 324.1500 Evaluate side-chains 406 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 404 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C1 residue 207 LEU Chi-restraints excluded: chain E1 residue 118 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 98 optimal weight: 0.5980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.0980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 chunk 77 optimal weight: 0.4980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1 76 ASN A1 141 GLN A1 160 GLN A1 184 GLN A1 241 GLN B1 132 GLN B1 141 GLN B1 155 ASN B1 241 GLN C1 114 GLN C1 141 GLN ** C1 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C1 241 GLN D1 76 ASN D1 141 GLN D1 155 ASN D1 184 GLN D1 241 GLN E1 76 ASN E1 86 ASN E1 119 GLN E1 141 GLN E1 233 GLN E1 241 GLN H1 39 GLN J1 39 GLN K1 56 GLN ** K1 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K1 122 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.100832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.080955 restraints weight = 22883.048| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 1.96 r_work: 0.2930 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14679 Z= 0.136 Angle : 0.599 7.937 19991 Z= 0.296 Chirality : 0.041 0.222 2485 Planarity : 0.005 0.056 2430 Dihedral : 4.596 53.368 1945 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.12 % Favored : 97.78 % Rotamer: Outliers : 2.92 % Allowed : 17.01 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.99 (0.20), residues: 1843 helix: 2.50 (0.13), residues: 1519 sheet: None (None), residues: 0 loop : -0.61 (0.38), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARGK1 55 TYR 0.011 0.001 TYRE1 109 PHE 0.024 0.001 PHEB1 187 TRP 0.008 0.001 TRPE1 232 HIS 0.003 0.001 HISK1 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.14 (14679) covalent geometry : angle 0.59911 / 0.30 (19991) hydrogen bonds : bond 0.04470 / 2.95 ( 1089) hydrogen bonds : angle 3.86725 / 2.75 ( 3240) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 420 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: A1 123 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8050 (tmt) REVERT: B1 101 MET cc_start: 0.9334 (mmm) cc_final: 0.8950 (mmm) REVERT: B1 140 ARG cc_start: 0.7385 (tpp-160) cc_final: 0.5909 (mtp85) REVERT: B1 210 MET cc_start: 0.9227 (OUTLIER) cc_final: 0.8889 (ptm) REVERT: C1 123 MET cc_start: 0.8670 (OUTLIER) cc_final: 0.8186 (ttt) REVERT: D1 60 MET cc_start: 0.9433 (OUTLIER) cc_final: 0.8879 (mmm) REVERT: D1 198 LEU cc_start: 0.8530 (mt) cc_final: 0.8272 (mm) REVERT: D1 210 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8643 (ptm) REVERT: E1 118 GLU cc_start: 0.8096 (OUTLIER) cc_final: 0.7744 (pm20) REVERT: E1 129 LYS cc_start: 0.7037 (mmpt) cc_final: 0.6785 (mtmp) REVERT: E1 168 ARG cc_start: 0.8687 (ptp90) cc_final: 0.8393 (ptt-90) REVERT: F1 35 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8144 (mp0) REVERT: G1 4 GLU cc_start: 0.8578 (mp0) cc_final: 0.8241 (mp0) REVERT: G1 51 PHE cc_start: 0.8911 (m-10) cc_final: 0.8656 (m-10) REVERT: H1 4 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8454 (mp0) REVERT: H1 76 TYR cc_start: 0.9420 (t80) cc_final: 0.9199 (t80) REVERT: I1 4 GLU cc_start: 0.8883 (mp0) cc_final: 0.8542 (mp0) REVERT: I1 15 LYS cc_start: 0.8749 (tppp) cc_final: 0.8488 (mttm) REVERT: K1 55 ARG cc_start: 0.8745 (ttm110) cc_final: 0.8436 (ttm-80) REVERT: K1 119 LYS cc_start: 0.7668 (tmtm) cc_final: 0.7146 (ptmt) REVERT: K1 121 LEU cc_start: 0.8144 (tm) cc_final: 0.7441 (mt) REVERT: K1 177 GLU cc_start: 0.8371 (mt-10) cc_final: 0.8171 (mt-10) REVERT: K1 211 PHE cc_start: 0.8606 (t80) cc_final: 0.8340 (t80) outliers start: 46 outliers final: 13 residues processed: 437 average time/residue: 0.6034 time to fit residues: 288.1228 Evaluate side-chains 426 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 406 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 123 MET Chi-restraints excluded: chain A1 residue 190 PHE Chi-restraints excluded: chain B1 residue 88 VAL Chi-restraints excluded: chain B1 residue 210 MET Chi-restraints excluded: chain C1 residue 123 MET Chi-restraints excluded: chain C1 residue 187 PHE Chi-restraints excluded: chain D1 residue 60 MET Chi-restraints excluded: chain D1 residue 210 MET Chi-restraints excluded: chain D1 residue 225 LEU Chi-restraints excluded: chain E1 residue 106 ASP Chi-restraints excluded: chain E1 residue 118 GLU Chi-restraints excluded: chain F1 residue 66 PHE Chi-restraints excluded: chain F1 residue 228 LEU Chi-restraints excluded: chain G1 residue 50 SER Chi-restraints excluded: chain H1 residue 4 GLU Chi-restraints excluded: chain I1 residue 18 LEU Chi-restraints excluded: chain I1 residue 27 VAL Chi-restraints excluded: chain J1 residue 9 MET Chi-restraints excluded: chain K1 residue 196 LEU Chi-restraints excluded: chain K1 residue 220 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 82 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 chunk 167 optimal weight: 0.4980 chunk 119 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 115 optimal weight: 0.0770 overall best weight: 0.6538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1 76 ASN B1 132 GLN ** C1 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 76 ASN D1 155 ASN E1 76 ASN E1 119 GLN E1 184 GLN F1 182 ASN F1 198 ASN G1 39 GLN J1 39 GLN K1 56 GLN K1 81 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.100364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.080270 restraints weight = 23310.821| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 2.00 r_work: 0.2922 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14679 Z= 0.136 Angle : 0.586 7.907 19991 Z= 0.288 Chirality : 0.041 0.152 2485 Planarity : 0.004 0.056 2430 Dihedral : 4.464 54.867 1943 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.39 % Favored : 97.50 % Rotamer: Outliers : 3.17 % Allowed : 18.78 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.15 (0.20), residues: 1843 helix: 2.62 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.69 (0.38), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGK1 55 TYR 0.009 0.001 TYRE1 109 PHE 0.021 0.001 PHEK1 210 TRP 0.008 0.001 TRPE1 232 HIS 0.003 0.001 HISK1 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (14679) covalent geometry : angle 0.58576 / 0.29 (19991) hydrogen bonds : bond 0.04374 / 2.88 ( 1089) hydrogen bonds : angle 3.74178 / 2.66 ( 3240) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 469 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 419 time to evaluate : 0.579 Fit side-chains REVERT: A1 118 GLU cc_start: 0.8773 (mm-30) cc_final: 0.8447 (mt-10) REVERT: A1 123 MET cc_start: 0.8494 (OUTLIER) cc_final: 0.7988 (tmt) REVERT: B1 101 MET cc_start: 0.9361 (mmm) cc_final: 0.9039 (mmm) REVERT: B1 140 ARG cc_start: 0.7250 (tpp-160) cc_final: 0.5879 (mtp85) REVERT: B1 230 ASP cc_start: 0.8668 (t0) cc_final: 0.8441 (t0) REVERT: C1 123 MET cc_start: 0.8709 (OUTLIER) cc_final: 0.8140 (ttt) REVERT: C1 152 ARG cc_start: 0.7421 (mtt180) cc_final: 0.7066 (mpt-90) REVERT: D1 60 MET cc_start: 0.9425 (OUTLIER) cc_final: 0.8873 (mmm) REVERT: D1 132 GLN cc_start: 0.8610 (OUTLIER) cc_final: 0.8369 (mm110) REVERT: E1 118 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7787 (mp0) REVERT: E1 129 LYS cc_start: 0.7099 (mmpt) cc_final: 0.6879 (mtmp) REVERT: E1 168 ARG cc_start: 0.8701 (ptp90) cc_final: 0.8397 (ptt-90) REVERT: F1 35 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8168 (mp0) REVERT: G1 4 GLU cc_start: 0.8628 (mp0) cc_final: 0.8270 (mp0) REVERT: G1 51 PHE cc_start: 0.8938 (m-10) cc_final: 0.8691 (m-10) REVERT: H1 4 GLU cc_start: 0.8877 (OUTLIER) cc_final: 0.8486 (mp0) REVERT: H1 76 TYR cc_start: 0.9474 (t80) cc_final: 0.9208 (t80) REVERT: I1 4 GLU cc_start: 0.8920 (mp0) cc_final: 0.8584 (mp0) REVERT: I1 15 LYS cc_start: 0.8778 (tppp) cc_final: 0.8485 (mttm) REVERT: I1 43 GLN cc_start: 0.8665 (mm-40) cc_final: 0.7749 (mp10) REVERT: J1 2 THR cc_start: 0.8234 (OUTLIER) cc_final: 0.8021 (t) REVERT: K1 119 LYS cc_start: 0.7689 (tmtm) cc_final: 0.7116 (ptmt) REVERT: K1 121 LEU cc_start: 0.8192 (tm) cc_final: 0.7525 (mt) REVERT: K1 148 LYS cc_start: 0.8699 (mtmt) cc_final: 0.8446 (ttpt) outliers start: 50 outliers final: 20 residues processed: 442 average time/residue: 0.5762 time to fit residues: 278.3818 Evaluate side-chains 427 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 400 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 123 MET Chi-restraints excluded: chain A1 residue 190 PHE Chi-restraints excluded: chain A1 residue 197 ASP Chi-restraints excluded: chain B1 residue 88 VAL Chi-restraints excluded: chain B1 residue 197 ASP Chi-restraints excluded: chain C1 residue 123 MET Chi-restraints excluded: chain C1 residue 187 PHE Chi-restraints excluded: chain C1 residue 207 LEU Chi-restraints excluded: chain D1 residue 60 MET Chi-restraints excluded: chain D1 residue 68 ILE Chi-restraints excluded: chain D1 residue 121 ILE Chi-restraints excluded: chain D1 residue 132 GLN Chi-restraints excluded: chain D1 residue 225 LEU Chi-restraints excluded: chain E1 residue 106 ASP Chi-restraints excluded: chain E1 residue 118 GLU Chi-restraints excluded: chain E1 residue 230 ASP Chi-restraints excluded: chain F1 residue 65 LEU Chi-restraints excluded: chain G1 residue 50 SER Chi-restraints excluded: chain H1 residue 4 GLU Chi-restraints excluded: chain I1 residue 18 LEU Chi-restraints excluded: chain I1 residue 27 VAL Chi-restraints excluded: chain J1 residue 2 THR Chi-restraints excluded: chain J1 residue 9 MET Chi-restraints excluded: chain J1 residue 84 LEU Chi-restraints excluded: chain K1 residue 146 LEU Chi-restraints excluded: chain K1 residue 196 LEU Chi-restraints excluded: chain K1 residue 220 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 142 optimal weight: 0.6980 chunk 129 optimal weight: 5.9990 chunk 67 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 118 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 70 optimal weight: 0.8980 chunk 158 optimal weight: 9.9990 chunk 13 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1 76 ASN B1 132 GLN B1 155 ASN ** C1 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 76 ASN E1 76 ASN E1 119 GLN E1 184 GLN F1 198 ASN G1 39 GLN J1 39 GLN K1 56 GLN K1 81 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.099833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.079831 restraints weight = 23293.542| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 1.98 r_work: 0.2913 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14679 Z= 0.143 Angle : 0.593 7.204 19991 Z= 0.291 Chirality : 0.041 0.258 2485 Planarity : 0.004 0.054 2430 Dihedral : 4.469 56.933 1943 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.44 % Favored : 97.45 % Rotamer: Outliers : 3.30 % Allowed : 19.99 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.22 (0.20), residues: 1843 helix: 2.69 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.72 (0.38), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGA1 152 TYR 0.010 0.001 TYRC1 109 PHE 0.022 0.001 PHEH1 59 TRP 0.007 0.001 TRPE1 232 HIS 0.003 0.001 HISK1 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (14679) covalent geometry : angle 0.59274 / 0.29 (19991) hydrogen bonds : bond 0.04356 / 2.88 ( 1089) hydrogen bonds : angle 3.71200 / 2.64 ( 3240) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 421 time to evaluate : 0.434 Fit side-chains REVERT: A1 118 GLU cc_start: 0.8788 (mm-30) cc_final: 0.8444 (mt-10) REVERT: A1 123 MET cc_start: 0.8474 (OUTLIER) cc_final: 0.7974 (tmt) REVERT: A1 222 LYS cc_start: 0.9113 (OUTLIER) cc_final: 0.8517 (mtpt) REVERT: B1 101 MET cc_start: 0.9376 (mmm) cc_final: 0.9058 (mmm) REVERT: B1 123 MET cc_start: 0.9006 (OUTLIER) cc_final: 0.8481 (ttt) REVERT: B1 140 ARG cc_start: 0.7111 (tpp-160) cc_final: 0.5778 (mtp85) REVERT: B1 230 ASP cc_start: 0.8697 (t0) cc_final: 0.8496 (t0) REVERT: C1 123 MET cc_start: 0.8700 (OUTLIER) cc_final: 0.8086 (ttt) REVERT: C1 152 ARG cc_start: 0.7426 (mtt180) cc_final: 0.7081 (mpt-90) REVERT: C1 210 MET cc_start: 0.9014 (ptm) cc_final: 0.8813 (ppp) REVERT: D1 60 MET cc_start: 0.9433 (OUTLIER) cc_final: 0.8911 (mmm) REVERT: D1 123 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8104 (ttt) REVERT: E1 114 GLN cc_start: 0.7252 (tm-30) cc_final: 0.6942 (tm-30) REVERT: E1 118 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: F1 35 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8188 (mp0) REVERT: F1 122 MET cc_start: 0.8462 (tpp) cc_final: 0.8164 (mmm) REVERT: G1 51 PHE cc_start: 0.8962 (m-10) cc_final: 0.8716 (m-10) REVERT: H1 4 GLU cc_start: 0.8881 (OUTLIER) cc_final: 0.8490 (mp0) REVERT: H1 76 TYR cc_start: 0.9494 (t80) cc_final: 0.9198 (t80) REVERT: I1 4 GLU cc_start: 0.8923 (mp0) cc_final: 0.8578 (mp0) REVERT: I1 15 LYS cc_start: 0.8760 (tppp) cc_final: 0.8480 (mttm) REVERT: I1 43 GLN cc_start: 0.8705 (mm-40) cc_final: 0.7840 (mp10) REVERT: J1 2 THR cc_start: 0.8242 (OUTLIER) cc_final: 0.8034 (t) REVERT: J1 62 ILE cc_start: 0.9162 (mt) cc_final: 0.8958 (tt) REVERT: K1 119 LYS cc_start: 0.7691 (tmtm) cc_final: 0.7147 (ptmt) REVERT: K1 121 LEU cc_start: 0.8234 (tm) cc_final: 0.7463 (mt) REVERT: K1 141 GLN cc_start: 0.8088 (mp10) cc_final: 0.7794 (mm-40) outliers start: 52 outliers final: 24 residues processed: 449 average time/residue: 0.5173 time to fit residues: 254.8000 Evaluate side-chains 436 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 403 time to evaluate : 0.579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 88 VAL Chi-restraints excluded: chain A1 residue 123 MET Chi-restraints excluded: chain A1 residue 190 PHE Chi-restraints excluded: chain A1 residue 197 ASP Chi-restraints excluded: chain A1 residue 222 LYS Chi-restraints excluded: chain B1 residue 40 LEU Chi-restraints excluded: chain B1 residue 88 VAL Chi-restraints excluded: chain B1 residue 121 ILE Chi-restraints excluded: chain B1 residue 123 MET Chi-restraints excluded: chain B1 residue 197 ASP Chi-restraints excluded: chain C1 residue 123 MET Chi-restraints excluded: chain C1 residue 187 PHE Chi-restraints excluded: chain C1 residue 227 VAL Chi-restraints excluded: chain D1 residue 60 MET Chi-restraints excluded: chain D1 residue 68 ILE Chi-restraints excluded: chain D1 residue 123 MET Chi-restraints excluded: chain D1 residue 225 LEU Chi-restraints excluded: chain D1 residue 235 LEU Chi-restraints excluded: chain E1 residue 106 ASP Chi-restraints excluded: chain E1 residue 118 GLU Chi-restraints excluded: chain E1 residue 230 ASP Chi-restraints excluded: chain F1 residue 65 LEU Chi-restraints excluded: chain G1 residue 50 SER Chi-restraints excluded: chain H1 residue 4 GLU Chi-restraints excluded: chain H1 residue 18 LEU Chi-restraints excluded: chain I1 residue 11 THR Chi-restraints excluded: chain I1 residue 18 LEU Chi-restraints excluded: chain I1 residue 27 VAL Chi-restraints excluded: chain J1 residue 2 THR Chi-restraints excluded: chain J1 residue 9 MET Chi-restraints excluded: chain J1 residue 84 LEU Chi-restraints excluded: chain K1 residue 196 LEU Chi-restraints excluded: chain K1 residue 220 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 176 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 chunk 34 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 152 optimal weight: 0.7980 chunk 91 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 69 optimal weight: 0.0050 chunk 21 optimal weight: 1.9990 chunk 153 optimal weight: 1.9990 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1 76 ASN B1 119 GLN B1 132 GLN B1 155 ASN ** C1 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 76 ASN D1 132 GLN E1 76 ASN E1 184 GLN F1 141 ASN F1 198 ASN G1 39 GLN J1 39 GLN K1 56 GLN K1 81 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.100298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.080318 restraints weight = 23345.216| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 1.99 r_work: 0.2923 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14679 Z= 0.135 Angle : 0.600 7.800 19991 Z= 0.293 Chirality : 0.041 0.247 2485 Planarity : 0.004 0.052 2430 Dihedral : 4.455 59.133 1943 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.33 % Favored : 97.56 % Rotamer: Outliers : 3.55 % Allowed : 20.69 % Favored : 75.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.27 (0.20), residues: 1843 helix: 2.72 (0.13), residues: 1520 sheet: None (None), residues: 0 loop : -0.69 (0.38), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGA1 152 TYR 0.008 0.001 TYRE1 109 PHE 0.023 0.001 PHEH1 59 TRP 0.007 0.001 TRPE1 232 HIS 0.003 0.001 HISK1 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.14 (14679) covalent geometry : angle 0.59966 / 0.29 (19991) hydrogen bonds : bond 0.04183 / 2.77 ( 1089) hydrogen bonds : angle 3.68416 / 2.61 ( 3240) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 480 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 424 time to evaluate : 0.578 Fit side-chains REVERT: A1 105 ILE cc_start: 0.9181 (OUTLIER) cc_final: 0.8970 (mp) REVERT: A1 118 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8471 (mt-10) REVERT: A1 123 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8121 (tmt) REVERT: A1 222 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8482 (mtpt) REVERT: B1 101 MET cc_start: 0.9393 (mmm) cc_final: 0.9079 (mmm) REVERT: B1 123 MET cc_start: 0.8951 (OUTLIER) cc_final: 0.8396 (ttt) REVERT: B1 140 ARG cc_start: 0.7158 (tpp-160) cc_final: 0.5915 (mtm110) REVERT: C1 123 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8029 (ttt) REVERT: C1 152 ARG cc_start: 0.7392 (mtt180) cc_final: 0.7045 (mpt-90) REVERT: D1 60 MET cc_start: 0.9345 (OUTLIER) cc_final: 0.8749 (mmm) REVERT: D1 123 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8084 (ttt) REVERT: E1 118 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7806 (mp0) REVERT: E1 129 LYS cc_start: 0.6937 (mmpt) cc_final: 0.6730 (mtmp) REVERT: E1 168 ARG cc_start: 0.8704 (ptp90) cc_final: 0.8454 (ptt-90) REVERT: F1 35 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8899 (mm-30) REVERT: F1 207 MET cc_start: 0.8796 (mtp) cc_final: 0.8487 (mtt) REVERT: G1 51 PHE cc_start: 0.8959 (m-10) cc_final: 0.8749 (m-10) REVERT: H1 4 GLU cc_start: 0.8900 (OUTLIER) cc_final: 0.8440 (mp0) REVERT: H1 76 TYR cc_start: 0.9497 (t80) cc_final: 0.9212 (t80) REVERT: I1 4 GLU cc_start: 0.8943 (mp0) cc_final: 0.8589 (mp0) REVERT: I1 15 LYS cc_start: 0.8768 (tppp) cc_final: 0.8494 (mttm) REVERT: I1 43 GLN cc_start: 0.8730 (mm-40) cc_final: 0.7885 (mp10) REVERT: I1 46 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: K1 114 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7186 (pp) REVERT: K1 119 LYS cc_start: 0.7586 (tmtm) cc_final: 0.7330 (ptpp) REVERT: K1 121 LEU cc_start: 0.8154 (tm) cc_final: 0.7408 (mt) REVERT: K1 148 LYS cc_start: 0.8723 (mtpt) cc_final: 0.8498 (ttpp) outliers start: 56 outliers final: 29 residues processed: 451 average time/residue: 0.5334 time to fit residues: 263.0908 Evaluate side-chains 453 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 413 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 88 VAL Chi-restraints excluded: chain A1 residue 105 ILE Chi-restraints excluded: chain A1 residue 123 MET Chi-restraints excluded: chain A1 residue 190 PHE Chi-restraints excluded: chain A1 residue 197 ASP Chi-restraints excluded: chain A1 residue 222 LYS Chi-restraints excluded: chain B1 residue 40 LEU Chi-restraints excluded: chain B1 residue 88 VAL Chi-restraints excluded: chain B1 residue 123 MET Chi-restraints excluded: chain B1 residue 197 ASP Chi-restraints excluded: chain C1 residue 123 MET Chi-restraints excluded: chain C1 residue 171 LEU Chi-restraints excluded: chain C1 residue 187 PHE Chi-restraints excluded: chain C1 residue 207 LEU Chi-restraints excluded: chain C1 residue 227 VAL Chi-restraints excluded: chain D1 residue 60 MET Chi-restraints excluded: chain D1 residue 121 ILE Chi-restraints excluded: chain D1 residue 123 MET Chi-restraints excluded: chain D1 residue 223 LEU Chi-restraints excluded: chain D1 residue 225 LEU Chi-restraints excluded: chain D1 residue 235 LEU Chi-restraints excluded: chain E1 residue 106 ASP Chi-restraints excluded: chain E1 residue 118 GLU Chi-restraints excluded: chain E1 residue 223 LEU Chi-restraints excluded: chain E1 residue 230 ASP Chi-restraints excluded: chain F1 residue 65 LEU Chi-restraints excluded: chain F1 residue 84 LEU Chi-restraints excluded: chain G1 residue 50 SER Chi-restraints excluded: chain H1 residue 4 GLU Chi-restraints excluded: chain H1 residue 9 MET Chi-restraints excluded: chain H1 residue 18 LEU Chi-restraints excluded: chain H1 residue 33 LEU Chi-restraints excluded: chain I1 residue 18 LEU Chi-restraints excluded: chain I1 residue 27 VAL Chi-restraints excluded: chain I1 residue 46 GLU Chi-restraints excluded: chain J1 residue 9 MET Chi-restraints excluded: chain J1 residue 84 LEU Chi-restraints excluded: chain K1 residue 114 LEU Chi-restraints excluded: chain K1 residue 196 LEU Chi-restraints excluded: chain K1 residue 220 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 78 optimal weight: 0.6980 chunk 127 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 2 optimal weight: 0.6980 chunk 65 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 chunk 174 optimal weight: 4.9990 chunk 163 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1 76 ASN B1 132 GLN B1 233 GLN ** C1 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 76 ASN E1 76 ASN F1 198 ASN G1 39 GLN J1 39 GLN K1 56 GLN K1 81 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.099899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.079910 restraints weight = 23337.893| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 1.98 r_work: 0.2917 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2806 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14679 Z= 0.141 Angle : 0.605 8.002 19991 Z= 0.297 Chirality : 0.041 0.228 2485 Planarity : 0.004 0.049 2430 Dihedral : 4.448 57.835 1943 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.50 % Favored : 97.40 % Rotamer: Outliers : 3.49 % Allowed : 20.88 % Favored : 75.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.33 (0.20), residues: 1843 helix: 2.75 (0.13), residues: 1525 sheet: None (None), residues: 0 loop : -0.67 (0.39), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARGA1 152 TYR 0.010 0.001 TYRC1 109 PHE 0.027 0.001 PHEK1 210 TRP 0.007 0.001 TRPH1 68 HIS 0.003 0.001 HISK1 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 (14679) covalent geometry : angle 0.60525 / 0.30 (19991) hydrogen bonds : bond 0.04221 / 2.78 ( 1089) hydrogen bonds : angle 3.68233 / 2.61 ( 3240) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 413 time to evaluate : 0.504 Fit side-chains REVERT: A1 105 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8967 (mp) REVERT: A1 118 GLU cc_start: 0.8827 (mm-30) cc_final: 0.8459 (mt-10) REVERT: A1 123 MET cc_start: 0.8666 (OUTLIER) cc_final: 0.8115 (tmt) REVERT: A1 222 LYS cc_start: 0.9115 (OUTLIER) cc_final: 0.8538 (mtpt) REVERT: B1 101 MET cc_start: 0.9381 (mmm) cc_final: 0.9057 (mmm) REVERT: B1 140 ARG cc_start: 0.7133 (tpp-160) cc_final: 0.5937 (mtp85) REVERT: B1 230 ASP cc_start: 0.8806 (t0) cc_final: 0.8321 (t0) REVERT: B1 233 GLN cc_start: 0.8834 (pt0) cc_final: 0.8193 (pt0) REVERT: C1 123 MET cc_start: 0.8693 (OUTLIER) cc_final: 0.8085 (ttt) REVERT: C1 152 ARG cc_start: 0.7429 (mtt180) cc_final: 0.7083 (mpt-90) REVERT: D1 60 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.8767 (mmm) REVERT: D1 123 MET cc_start: 0.8762 (OUTLIER) cc_final: 0.8007 (ttt) REVERT: E1 118 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7866 (mp0) REVERT: E1 168 ARG cc_start: 0.8715 (ptp90) cc_final: 0.8466 (ptt-90) REVERT: E1 202 SER cc_start: 0.9306 (t) cc_final: 0.9061 (m) REVERT: F1 35 GLU cc_start: 0.9054 (mm-30) cc_final: 0.8838 (mm-30) REVERT: G1 51 PHE cc_start: 0.8961 (m-10) cc_final: 0.8741 (m-10) REVERT: H1 2 THR cc_start: 0.9135 (m) cc_final: 0.8882 (t) REVERT: H1 76 TYR cc_start: 0.9507 (t80) cc_final: 0.9260 (t80) REVERT: I1 4 GLU cc_start: 0.8954 (mp0) cc_final: 0.8599 (mp0) REVERT: I1 15 LYS cc_start: 0.8777 (tppp) cc_final: 0.8508 (mttm) REVERT: I1 43 GLN cc_start: 0.8727 (mm-40) cc_final: 0.7902 (mp10) REVERT: I1 46 GLU cc_start: 0.7802 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: J1 44 ILE cc_start: 0.8676 (mt) cc_final: 0.8380 (mm) REVERT: K1 114 LEU cc_start: 0.7438 (OUTLIER) cc_final: 0.7229 (pp) REVERT: K1 119 LYS cc_start: 0.7570 (tmtm) cc_final: 0.7058 (pttt) REVERT: K1 121 LEU cc_start: 0.8108 (tm) cc_final: 0.7470 (mt) REVERT: K1 148 LYS cc_start: 0.8666 (mtpt) cc_final: 0.8376 (ttpt) REVERT: K1 158 CYS cc_start: 0.9055 (m) cc_final: 0.8695 (m) outliers start: 55 outliers final: 29 residues processed: 437 average time/residue: 0.5250 time to fit residues: 251.4372 Evaluate side-chains 443 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 405 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 88 VAL Chi-restraints excluded: chain A1 residue 105 ILE Chi-restraints excluded: chain A1 residue 123 MET Chi-restraints excluded: chain A1 residue 190 PHE Chi-restraints excluded: chain A1 residue 222 LYS Chi-restraints excluded: chain B1 residue 40 LEU Chi-restraints excluded: chain B1 residue 88 VAL Chi-restraints excluded: chain B1 residue 197 ASP Chi-restraints excluded: chain C1 residue 123 MET Chi-restraints excluded: chain C1 residue 171 LEU Chi-restraints excluded: chain C1 residue 187 PHE Chi-restraints excluded: chain C1 residue 227 VAL Chi-restraints excluded: chain D1 residue 60 MET Chi-restraints excluded: chain D1 residue 68 ILE Chi-restraints excluded: chain D1 residue 121 ILE Chi-restraints excluded: chain D1 residue 123 MET Chi-restraints excluded: chain D1 residue 223 LEU Chi-restraints excluded: chain D1 residue 225 LEU Chi-restraints excluded: chain D1 residue 235 LEU Chi-restraints excluded: chain E1 residue 106 ASP Chi-restraints excluded: chain E1 residue 118 GLU Chi-restraints excluded: chain E1 residue 223 LEU Chi-restraints excluded: chain F1 residue 65 LEU Chi-restraints excluded: chain F1 residue 84 LEU Chi-restraints excluded: chain G1 residue 50 SER Chi-restraints excluded: chain H1 residue 18 LEU Chi-restraints excluded: chain H1 residue 33 LEU Chi-restraints excluded: chain I1 residue 18 LEU Chi-restraints excluded: chain I1 residue 27 VAL Chi-restraints excluded: chain I1 residue 46 GLU Chi-restraints excluded: chain J1 residue 9 MET Chi-restraints excluded: chain J1 residue 82 SER Chi-restraints excluded: chain J1 residue 84 LEU Chi-restraints excluded: chain K1 residue 109 VAL Chi-restraints excluded: chain K1 residue 114 LEU Chi-restraints excluded: chain K1 residue 146 LEU Chi-restraints excluded: chain K1 residue 196 LEU Chi-restraints excluded: chain K1 residue 220 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 51 optimal weight: 0.9980 chunk 136 optimal weight: 0.2980 chunk 135 optimal weight: 0.0970 chunk 120 optimal weight: 0.9990 chunk 128 optimal weight: 0.7980 chunk 80 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 111 optimal weight: 0.6980 chunk 20 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 71 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1 76 ASN B1 132 GLN B1 155 ASN ** C1 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 76 ASN E1 76 ASN E1 241 GLN F1 198 ASN G1 39 GLN J1 39 GLN K1 56 GLN K1 81 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.100910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.080982 restraints weight = 23107.435| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 1.97 r_work: 0.2938 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 14679 Z= 0.129 Angle : 0.604 8.331 19991 Z= 0.295 Chirality : 0.041 0.206 2485 Planarity : 0.004 0.051 2430 Dihedral : 4.404 55.109 1943 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.33 % Favored : 97.56 % Rotamer: Outliers : 3.17 % Allowed : 21.57 % Favored : 75.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.35 (0.20), residues: 1843 helix: 2.76 (0.13), residues: 1525 sheet: None (None), residues: 0 loop : -0.69 (0.39), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGA1 152 TYR 0.009 0.001 TYRE1 109 PHE 0.024 0.001 PHEH1 59 TRP 0.008 0.001 TRPH1 68 HIS 0.003 0.001 HISK1 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (14679) covalent geometry : angle 0.60399 / 0.30 (19991) hydrogen bonds : bond 0.03972 / 2.62 ( 1089) hydrogen bonds : angle 3.65272 / 2.58 ( 3240) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 418 time to evaluate : 0.594 Fit side-chains REVERT: A1 118 GLU cc_start: 0.8789 (mm-30) cc_final: 0.8066 (tp30) REVERT: A1 123 MET cc_start: 0.8629 (OUTLIER) cc_final: 0.8048 (tmt) REVERT: A1 222 LYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8552 (mtpt) REVERT: B1 101 MET cc_start: 0.9386 (mmm) cc_final: 0.9076 (mmm) REVERT: B1 140 ARG cc_start: 0.7033 (tpp-160) cc_final: 0.5874 (mtm110) REVERT: C1 123 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.7969 (ttt) REVERT: C1 152 ARG cc_start: 0.7388 (mtt180) cc_final: 0.7034 (mpt-90) REVERT: D1 60 MET cc_start: 0.9320 (OUTLIER) cc_final: 0.8773 (mmm) REVERT: D1 123 MET cc_start: 0.8782 (OUTLIER) cc_final: 0.7993 (ttt) REVERT: E1 118 GLU cc_start: 0.8242 (OUTLIER) cc_final: 0.7683 (mp0) REVERT: E1 168 ARG cc_start: 0.8707 (ptp90) cc_final: 0.8456 (ptt-90) REVERT: E1 202 SER cc_start: 0.9316 (t) cc_final: 0.9066 (m) REVERT: F1 35 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8743 (mm-30) REVERT: G1 51 PHE cc_start: 0.8943 (m-10) cc_final: 0.8707 (m-10) REVERT: H1 76 TYR cc_start: 0.9519 (t80) cc_final: 0.9282 (t80) REVERT: I1 4 GLU cc_start: 0.8945 (mp0) cc_final: 0.8596 (mp0) REVERT: I1 15 LYS cc_start: 0.8804 (tppp) cc_final: 0.8536 (mttm) REVERT: I1 43 GLN cc_start: 0.8798 (mm-40) cc_final: 0.7972 (mp10) REVERT: I1 46 GLU cc_start: 0.7798 (OUTLIER) cc_final: 0.7453 (mp0) REVERT: J1 44 ILE cc_start: 0.8653 (mt) cc_final: 0.8384 (mm) REVERT: K1 119 LYS cc_start: 0.7567 (tmtm) cc_final: 0.7322 (ptpp) REVERT: K1 121 LEU cc_start: 0.8130 (tm) cc_final: 0.7493 (mt) REVERT: K1 148 LYS cc_start: 0.8680 (mtpt) cc_final: 0.8394 (ttpt) REVERT: K1 158 CYS cc_start: 0.9052 (m) cc_final: 0.8679 (m) outliers start: 50 outliers final: 26 residues processed: 447 average time/residue: 0.5000 time to fit residues: 245.8548 Evaluate side-chains 448 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 415 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 88 VAL Chi-restraints excluded: chain A1 residue 123 MET Chi-restraints excluded: chain A1 residue 190 PHE Chi-restraints excluded: chain A1 residue 197 ASP Chi-restraints excluded: chain A1 residue 222 LYS Chi-restraints excluded: chain B1 residue 40 LEU Chi-restraints excluded: chain B1 residue 88 VAL Chi-restraints excluded: chain C1 residue 123 MET Chi-restraints excluded: chain C1 residue 187 PHE Chi-restraints excluded: chain C1 residue 207 LEU Chi-restraints excluded: chain C1 residue 227 VAL Chi-restraints excluded: chain D1 residue 60 MET Chi-restraints excluded: chain D1 residue 68 ILE Chi-restraints excluded: chain D1 residue 121 ILE Chi-restraints excluded: chain D1 residue 123 MET Chi-restraints excluded: chain D1 residue 225 LEU Chi-restraints excluded: chain D1 residue 235 LEU Chi-restraints excluded: chain E1 residue 106 ASP Chi-restraints excluded: chain E1 residue 118 GLU Chi-restraints excluded: chain E1 residue 230 ASP Chi-restraints excluded: chain F1 residue 65 LEU Chi-restraints excluded: chain G1 residue 50 SER Chi-restraints excluded: chain H1 residue 33 LEU Chi-restraints excluded: chain I1 residue 11 THR Chi-restraints excluded: chain I1 residue 18 LEU Chi-restraints excluded: chain I1 residue 27 VAL Chi-restraints excluded: chain I1 residue 46 GLU Chi-restraints excluded: chain J1 residue 9 MET Chi-restraints excluded: chain J1 residue 63 ILE Chi-restraints excluded: chain J1 residue 82 SER Chi-restraints excluded: chain J1 residue 84 LEU Chi-restraints excluded: chain K1 residue 109 VAL Chi-restraints excluded: chain K1 residue 220 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 124 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 168 optimal weight: 0.2980 chunk 37 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 118 optimal weight: 0.0870 chunk 82 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 160 optimal weight: 0.9980 overall best weight: 0.8360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1 132 GLN B1 155 ASN C1 76 ASN ** C1 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 76 ASN D1 132 GLN E1 76 ASN F1 198 ASN G1 39 GLN J1 39 GLN K1 56 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.099751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.079652 restraints weight = 23150.187| |-----------------------------------------------------------------------------| r_work (start): 0.3030 rms_B_bonded: 1.99 r_work: 0.2914 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2803 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.2447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14679 Z= 0.148 Angle : 0.618 8.225 19991 Z= 0.302 Chirality : 0.042 0.192 2485 Planarity : 0.004 0.049 2430 Dihedral : 4.414 51.391 1943 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.71 % Favored : 97.18 % Rotamer: Outliers : 2.92 % Allowed : 22.34 % Favored : 74.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.32 (0.20), residues: 1843 helix: 2.74 (0.13), residues: 1526 sheet: None (None), residues: 0 loop : -0.69 (0.39), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARGA1 152 TYR 0.013 0.001 TYRC1 109 PHE 0.030 0.001 PHEK1 210 TRP 0.009 0.001 TRPH1 68 HIS 0.003 0.001 HISK1 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.15 (14679) covalent geometry : angle 0.61810 / 0.30 (19991) hydrogen bonds : bond 0.04253 / 2.80 ( 1089) hydrogen bonds : angle 3.67641 / 2.60 ( 3240) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 418 time to evaluate : 0.404 Fit side-chains REVERT: A1 105 ILE cc_start: 0.9151 (OUTLIER) cc_final: 0.8943 (mp) REVERT: A1 118 GLU cc_start: 0.8782 (mm-30) cc_final: 0.8038 (tp30) REVERT: A1 123 MET cc_start: 0.8638 (OUTLIER) cc_final: 0.8048 (tmt) REVERT: A1 222 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8539 (mtpt) REVERT: B1 101 MET cc_start: 0.9359 (mmm) cc_final: 0.9021 (mmm) REVERT: B1 140 ARG cc_start: 0.6971 (tpp-160) cc_final: 0.5855 (mtp85) REVERT: B1 233 GLN cc_start: 0.8805 (pt0) cc_final: 0.8590 (pt0) REVERT: C1 123 MET cc_start: 0.8687 (OUTLIER) cc_final: 0.8048 (ttt) REVERT: C1 152 ARG cc_start: 0.7367 (mtt180) cc_final: 0.7020 (mpt-90) REVERT: D1 60 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.8765 (mmm) REVERT: D1 123 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8017 (ttt) REVERT: E1 118 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7725 (mp0) REVERT: E1 168 ARG cc_start: 0.8699 (ptp90) cc_final: 0.8444 (ptt-90) REVERT: E1 202 SER cc_start: 0.9283 (t) cc_final: 0.9057 (m) REVERT: F1 35 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8724 (mm-30) REVERT: F1 207 MET cc_start: 0.8868 (mtp) cc_final: 0.8517 (mtt) REVERT: G1 51 PHE cc_start: 0.8933 (m-10) cc_final: 0.8706 (m-10) REVERT: H1 12 GLU cc_start: 0.8699 (tt0) cc_final: 0.8403 (pt0) REVERT: H1 76 TYR cc_start: 0.9518 (t80) cc_final: 0.9307 (t80) REVERT: I1 4 GLU cc_start: 0.8954 (mp0) cc_final: 0.8590 (mp0) REVERT: I1 15 LYS cc_start: 0.8800 (tppp) cc_final: 0.8537 (mttm) REVERT: I1 43 GLN cc_start: 0.8799 (mm-40) cc_final: 0.7955 (mp10) REVERT: I1 46 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: K1 119 LYS cc_start: 0.7555 (tmtm) cc_final: 0.7314 (ptpp) REVERT: K1 148 LYS cc_start: 0.8643 (mtpt) cc_final: 0.8333 (ttpt) REVERT: K1 158 CYS cc_start: 0.9051 (m) cc_final: 0.8681 (m) outliers start: 46 outliers final: 31 residues processed: 442 average time/residue: 0.5461 time to fit residues: 264.2302 Evaluate side-chains 452 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 413 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 88 VAL Chi-restraints excluded: chain A1 residue 105 ILE Chi-restraints excluded: chain A1 residue 123 MET Chi-restraints excluded: chain A1 residue 190 PHE Chi-restraints excluded: chain A1 residue 197 ASP Chi-restraints excluded: chain A1 residue 222 LYS Chi-restraints excluded: chain B1 residue 40 LEU Chi-restraints excluded: chain B1 residue 88 VAL Chi-restraints excluded: chain B1 residue 197 ASP Chi-restraints excluded: chain B1 residue 207 LEU Chi-restraints excluded: chain C1 residue 123 MET Chi-restraints excluded: chain C1 residue 171 LEU Chi-restraints excluded: chain C1 residue 187 PHE Chi-restraints excluded: chain C1 residue 207 LEU Chi-restraints excluded: chain C1 residue 227 VAL Chi-restraints excluded: chain D1 residue 60 MET Chi-restraints excluded: chain D1 residue 68 ILE Chi-restraints excluded: chain D1 residue 121 ILE Chi-restraints excluded: chain D1 residue 123 MET Chi-restraints excluded: chain D1 residue 225 LEU Chi-restraints excluded: chain D1 residue 235 LEU Chi-restraints excluded: chain E1 residue 106 ASP Chi-restraints excluded: chain E1 residue 118 GLU Chi-restraints excluded: chain E1 residue 230 ASP Chi-restraints excluded: chain F1 residue 65 LEU Chi-restraints excluded: chain F1 residue 157 LEU Chi-restraints excluded: chain G1 residue 50 SER Chi-restraints excluded: chain H1 residue 33 LEU Chi-restraints excluded: chain I1 residue 11 THR Chi-restraints excluded: chain I1 residue 18 LEU Chi-restraints excluded: chain I1 residue 27 VAL Chi-restraints excluded: chain I1 residue 46 GLU Chi-restraints excluded: chain J1 residue 9 MET Chi-restraints excluded: chain J1 residue 49 LEU Chi-restraints excluded: chain J1 residue 63 ILE Chi-restraints excluded: chain J1 residue 82 SER Chi-restraints excluded: chain J1 residue 84 LEU Chi-restraints excluded: chain K1 residue 146 LEU Chi-restraints excluded: chain K1 residue 220 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 150 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 41 optimal weight: 0.0670 chunk 110 optimal weight: 0.7980 chunk 14 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 171 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 overall best weight: 0.6922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1 132 GLN B1 155 ASN C1 76 ASN ** C1 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 76 ASN D1 132 GLN E1 76 ASN E1 132 GLN F1 198 ASN G1 39 GLN J1 39 GLN K1 56 GLN K1 81 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.100189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.080068 restraints weight = 23055.718| |-----------------------------------------------------------------------------| r_work (start): 0.3037 rms_B_bonded: 1.99 r_work: 0.2921 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2811 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 14679 Z= 0.141 Angle : 0.628 8.759 19991 Z= 0.305 Chirality : 0.042 0.176 2485 Planarity : 0.004 0.048 2430 Dihedral : 4.392 48.426 1943 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.60 % Favored : 97.29 % Rotamer: Outliers : 2.98 % Allowed : 22.97 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.31 (0.20), residues: 1843 helix: 2.73 (0.13), residues: 1526 sheet: None (None), residues: 0 loop : -0.69 (0.39), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGK1 70 TYR 0.012 0.001 TYRC1 109 PHE 0.026 0.001 PHEH1 59 TRP 0.010 0.001 TRPH1 68 HIS 0.003 0.001 HISK1 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 (14679) covalent geometry : angle 0.62787 / 0.31 (19991) hydrogen bonds : bond 0.04141 / 2.73 ( 1089) hydrogen bonds : angle 3.66953 / 2.59 ( 3240) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 419 time to evaluate : 0.566 Fit side-chains REVERT: A1 105 ILE cc_start: 0.9166 (OUTLIER) cc_final: 0.8959 (mp) REVERT: A1 118 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8068 (tp30) REVERT: A1 222 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8544 (mtpt) REVERT: B1 101 MET cc_start: 0.9382 (mmm) cc_final: 0.9046 (mmm) REVERT: B1 114 GLN cc_start: 0.8180 (tp40) cc_final: 0.7802 (tm-30) REVERT: B1 140 ARG cc_start: 0.6954 (tpp-160) cc_final: 0.5878 (mtp85) REVERT: B1 233 GLN cc_start: 0.8808 (pt0) cc_final: 0.8577 (pt0) REVERT: C1 119 GLN cc_start: 0.8678 (mp10) cc_final: 0.8141 (mp10) REVERT: C1 123 MET cc_start: 0.8662 (OUTLIER) cc_final: 0.8020 (ttt) REVERT: C1 152 ARG cc_start: 0.7394 (mtt180) cc_final: 0.7052 (mpt-90) REVERT: D1 60 MET cc_start: 0.9339 (OUTLIER) cc_final: 0.8740 (mmm) REVERT: D1 123 MET cc_start: 0.8786 (OUTLIER) cc_final: 0.8030 (ttt) REVERT: E1 118 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7672 (mp0) REVERT: E1 168 ARG cc_start: 0.8714 (ptp90) cc_final: 0.8466 (ptt-90) REVERT: E1 202 SER cc_start: 0.9343 (t) cc_final: 0.9074 (m) REVERT: E1 209 MET cc_start: 0.9107 (OUTLIER) cc_final: 0.8309 (mtm) REVERT: F1 35 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8679 (mm-30) REVERT: G1 51 PHE cc_start: 0.8938 (m-10) cc_final: 0.8712 (m-10) REVERT: H1 4 GLU cc_start: 0.8764 (pm20) cc_final: 0.8445 (mp0) REVERT: H1 12 GLU cc_start: 0.8712 (tt0) cc_final: 0.8413 (pt0) REVERT: H1 76 TYR cc_start: 0.9525 (t80) cc_final: 0.9312 (t80) REVERT: I1 4 GLU cc_start: 0.8966 (mp0) cc_final: 0.8617 (mp0) REVERT: I1 15 LYS cc_start: 0.8815 (tppp) cc_final: 0.8554 (mttm) REVERT: I1 43 GLN cc_start: 0.8791 (mm-40) cc_final: 0.7976 (mp10) REVERT: I1 46 GLU cc_start: 0.7870 (OUTLIER) cc_final: 0.7547 (mp0) REVERT: K1 119 LYS cc_start: 0.7536 (tmtm) cc_final: 0.7276 (ptpp) REVERT: K1 148 LYS cc_start: 0.8676 (mtpt) cc_final: 0.8369 (ttpt) REVERT: K1 158 CYS cc_start: 0.9069 (m) cc_final: 0.8743 (m) REVERT: K1 183 MET cc_start: 0.8678 (OUTLIER) cc_final: 0.8421 (mtp) outliers start: 47 outliers final: 29 residues processed: 443 average time/residue: 0.5894 time to fit residues: 286.1446 Evaluate side-chains 446 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 408 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 88 VAL Chi-restraints excluded: chain A1 residue 105 ILE Chi-restraints excluded: chain A1 residue 190 PHE Chi-restraints excluded: chain A1 residue 197 ASP Chi-restraints excluded: chain A1 residue 222 LYS Chi-restraints excluded: chain B1 residue 40 LEU Chi-restraints excluded: chain B1 residue 88 VAL Chi-restraints excluded: chain C1 residue 123 MET Chi-restraints excluded: chain C1 residue 171 LEU Chi-restraints excluded: chain C1 residue 187 PHE Chi-restraints excluded: chain C1 residue 227 VAL Chi-restraints excluded: chain D1 residue 60 MET Chi-restraints excluded: chain D1 residue 68 ILE Chi-restraints excluded: chain D1 residue 121 ILE Chi-restraints excluded: chain D1 residue 123 MET Chi-restraints excluded: chain D1 residue 225 LEU Chi-restraints excluded: chain D1 residue 235 LEU Chi-restraints excluded: chain E1 residue 106 ASP Chi-restraints excluded: chain E1 residue 118 GLU Chi-restraints excluded: chain E1 residue 209 MET Chi-restraints excluded: chain E1 residue 230 ASP Chi-restraints excluded: chain F1 residue 65 LEU Chi-restraints excluded: chain F1 residue 157 LEU Chi-restraints excluded: chain F1 residue 170 MET Chi-restraints excluded: chain H1 residue 9 MET Chi-restraints excluded: chain H1 residue 33 LEU Chi-restraints excluded: chain I1 residue 11 THR Chi-restraints excluded: chain I1 residue 18 LEU Chi-restraints excluded: chain I1 residue 27 VAL Chi-restraints excluded: chain I1 residue 46 GLU Chi-restraints excluded: chain J1 residue 9 MET Chi-restraints excluded: chain J1 residue 49 LEU Chi-restraints excluded: chain J1 residue 63 ILE Chi-restraints excluded: chain J1 residue 82 SER Chi-restraints excluded: chain K1 residue 109 VAL Chi-restraints excluded: chain K1 residue 146 LEU Chi-restraints excluded: chain K1 residue 183 MET Chi-restraints excluded: chain K1 residue 220 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 99 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 105 optimal weight: 0.2980 chunk 5 optimal weight: 0.7980 chunk 118 optimal weight: 0.0770 chunk 120 optimal weight: 0.6980 chunk 142 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 4 optimal weight: 0.2980 chunk 151 optimal weight: 0.9980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1 155 ASN C1 76 ASN C1 114 GLN ** C1 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 76 ASN D1 132 GLN D1 184 GLN E1 76 ASN F1 198 ASN J1 39 GLN K1 56 GLN K1 129 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.101317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.081296 restraints weight = 23069.488| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 2.00 r_work: 0.2947 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8737 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 14679 Z= 0.128 Angle : 0.620 9.752 19991 Z= 0.301 Chirality : 0.042 0.315 2485 Planarity : 0.004 0.048 2430 Dihedral : 4.335 43.826 1943 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.50 % Favored : 97.40 % Rotamer: Outliers : 2.47 % Allowed : 23.48 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.34 (0.20), residues: 1843 helix: 2.75 (0.13), residues: 1526 sheet: None (None), residues: 0 loop : -0.67 (0.39), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGK1 70 TYR 0.009 0.001 TYRE1 109 PHE 0.035 0.001 PHEK1 210 TRP 0.011 0.001 TRPH1 68 HIS 0.003 0.001 HISK1 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.13 (14679) covalent geometry : angle 0.61959 / 0.30 (19991) hydrogen bonds : bond 0.03862 / 2.56 ( 1089) hydrogen bonds : angle 3.63341 / 2.57 ( 3240) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3686 Ramachandran restraints generated. 1843 Oldfield, 0 Emsley, 1843 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 463 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 424 time to evaluate : 0.548 Fit side-chains REVERT: A1 105 ILE cc_start: 0.9167 (OUTLIER) cc_final: 0.8964 (mp) REVERT: A1 118 GLU cc_start: 0.8783 (mm-30) cc_final: 0.8133 (tp30) REVERT: A1 222 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8561 (mtpt) REVERT: B1 101 MET cc_start: 0.9387 (mmm) cc_final: 0.9082 (mmm) REVERT: B1 114 GLN cc_start: 0.8143 (tp40) cc_final: 0.7844 (tm-30) REVERT: B1 140 ARG cc_start: 0.7082 (tpp-160) cc_final: 0.5948 (mtp85) REVERT: B1 233 GLN cc_start: 0.8792 (pt0) cc_final: 0.8553 (pt0) REVERT: C1 119 GLN cc_start: 0.8681 (mp10) cc_final: 0.8145 (mp10) REVERT: C1 123 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.7881 (ttt) REVERT: C1 152 ARG cc_start: 0.7342 (mtt180) cc_final: 0.6997 (mpt-90) REVERT: C1 210 MET cc_start: 0.8736 (ppp) cc_final: 0.7834 (ppp) REVERT: D1 60 MET cc_start: 0.9301 (OUTLIER) cc_final: 0.8761 (mmm) REVERT: D1 123 MET cc_start: 0.8763 (OUTLIER) cc_final: 0.7977 (ttt) REVERT: E1 118 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.7631 (mp0) REVERT: E1 168 ARG cc_start: 0.8705 (ptp90) cc_final: 0.8457 (ptt-90) REVERT: E1 202 SER cc_start: 0.9358 (t) cc_final: 0.9100 (m) REVERT: F1 35 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8685 (mm-30) REVERT: F1 134 MET cc_start: 0.9357 (mtp) cc_final: 0.9077 (mtp) REVERT: F1 165 ASN cc_start: 0.8766 (p0) cc_final: 0.8349 (p0) REVERT: F1 207 MET cc_start: 0.8809 (mtp) cc_final: 0.8442 (mtt) REVERT: H1 4 GLU cc_start: 0.8760 (pm20) cc_final: 0.8472 (mp0) REVERT: H1 12 GLU cc_start: 0.8730 (tt0) cc_final: 0.8437 (pt0) REVERT: H1 76 TYR cc_start: 0.9520 (t80) cc_final: 0.9302 (t80) REVERT: I1 4 GLU cc_start: 0.8963 (mp0) cc_final: 0.8615 (mp0) REVERT: I1 15 LYS cc_start: 0.8795 (tppp) cc_final: 0.8543 (mttm) REVERT: I1 43 GLN cc_start: 0.8783 (mm-40) cc_final: 0.7983 (mp10) REVERT: I1 46 GLU cc_start: 0.7861 (OUTLIER) cc_final: 0.7542 (mp0) REVERT: K1 119 LYS cc_start: 0.7494 (tmtm) cc_final: 0.7216 (ptpp) REVERT: K1 148 LYS cc_start: 0.8659 (mtpt) cc_final: 0.8322 (ttpt) REVERT: K1 158 CYS cc_start: 0.9087 (m) cc_final: 0.8746 (m) REVERT: K1 183 MET cc_start: 0.8613 (OUTLIER) cc_final: 0.8371 (mtp) outliers start: 39 outliers final: 25 residues processed: 444 average time/residue: 0.5758 time to fit residues: 280.2289 Evaluate side-chains 450 residues out of total 1576 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 417 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A1 residue 88 VAL Chi-restraints excluded: chain A1 residue 105 ILE Chi-restraints excluded: chain A1 residue 171 LEU Chi-restraints excluded: chain A1 residue 190 PHE Chi-restraints excluded: chain A1 residue 197 ASP Chi-restraints excluded: chain A1 residue 222 LYS Chi-restraints excluded: chain B1 residue 40 LEU Chi-restraints excluded: chain B1 residue 88 VAL Chi-restraints excluded: chain C1 residue 123 MET Chi-restraints excluded: chain C1 residue 171 LEU Chi-restraints excluded: chain C1 residue 187 PHE Chi-restraints excluded: chain C1 residue 227 VAL Chi-restraints excluded: chain D1 residue 60 MET Chi-restraints excluded: chain D1 residue 121 ILE Chi-restraints excluded: chain D1 residue 123 MET Chi-restraints excluded: chain D1 residue 225 LEU Chi-restraints excluded: chain E1 residue 106 ASP Chi-restraints excluded: chain E1 residue 118 GLU Chi-restraints excluded: chain E1 residue 230 ASP Chi-restraints excluded: chain F1 residue 65 LEU Chi-restraints excluded: chain F1 residue 157 LEU Chi-restraints excluded: chain H1 residue 9 MET Chi-restraints excluded: chain H1 residue 33 LEU Chi-restraints excluded: chain I1 residue 18 LEU Chi-restraints excluded: chain I1 residue 27 VAL Chi-restraints excluded: chain I1 residue 46 GLU Chi-restraints excluded: chain J1 residue 9 MET Chi-restraints excluded: chain J1 residue 49 LEU Chi-restraints excluded: chain J1 residue 63 ILE Chi-restraints excluded: chain J1 residue 82 SER Chi-restraints excluded: chain K1 residue 109 VAL Chi-restraints excluded: chain K1 residue 183 MET Chi-restraints excluded: chain K1 residue 220 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 178 random chunks: chunk 96 optimal weight: 0.7980 chunk 173 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 83 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 164 optimal weight: 0.0060 chunk 33 optimal weight: 0.9980 chunk 66 optimal weight: 0.4980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B1 132 GLN B1 155 ASN C1 76 ASN C1 114 GLN ** C1 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D1 76 ASN D1 132 GLN D1 184 GLN E1 76 ASN F1 198 ASN J1 39 GLN K1 56 GLN K1 129 ASN K1 141 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.100935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.080796 restraints weight = 23137.982| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.00 r_work: 0.2938 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 14679 Z= 0.135 Angle : 0.635 10.678 19991 Z= 0.307 Chirality : 0.042 0.289 2485 Planarity : 0.004 0.048 2430 Dihedral : 4.335 40.275 1943 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.44 % Favored : 97.45 % Rotamer: Outliers : 2.47 % Allowed : 23.86 % Favored : 73.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.33 (0.20), residues: 1843 helix: 2.74 (0.13), residues: 1526 sheet: None (None), residues: 0 loop : -0.67 (0.39), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARGK1 70 TYR 0.009 0.001 TYRJ1 76 PHE 0.026 0.001 PHEH1 59 TRP 0.012 0.001 TRPH1 68 HIS 0.003 0.001 HISK1 16 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.14 (14679) covalent geometry : angle 0.63475 / 0.31 (19991) hydrogen bonds : bond 0.04002 / 2.64 ( 1089) hydrogen bonds : angle 3.64222 / 2.58 ( 3240) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6634.76 seconds wall clock time: 113 minutes 16.85 seconds (6796.85 seconds total)