Starting phenix.real_space_refine on Sat Feb 7 09:40:32 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9d3i_46535/02_2026/9d3i_46535_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9d3i_46535/02_2026/9d3i_46535.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9d3i_46535/02_2026/9d3i_46535_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9d3i_46535/02_2026/9d3i_46535_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9d3i_46535/02_2026/9d3i_46535.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9d3i_46535/02_2026/9d3i_46535.map" } resolution = 3.11 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= 0.363 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 52 5.16 5 C 9940 2.51 5 N 2654 2.21 5 O 3027 1.98 5 H 15653 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 94 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 31326 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 3822 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 3822 Classifications: {'peptide': 242} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 231} Chain: "B" Number of atoms: 3799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 3799 Classifications: {'peptide': 247} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 234} Chain: "C" Number of atoms: 3625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 233, 3625 Classifications: {'peptide': 233} Link IDs: {'PTRANS': 5, 'TRANS': 227} Chain: "D" Number of atoms: 3665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3665 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 9, 'TRANS': 222} Chain: "G" Number of atoms: 3664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 235, 3664 Classifications: {'peptide': 235} Link IDs: {'PTRANS': 9, 'TRANS': 225} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "P" Number of atoms: 1439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1439 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 4, 'TRANS': 82} Chain breaks: 1 Chain: "H" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2274 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 3, 'TRANS': 142} Chain breaks: 4 Chain: "I" Number of atoms: 3229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 3229 Classifications: {'peptide': 214} Link IDs: {'PTRANS': 4, 'TRANS': 209} Chain breaks: 3 Chain: "J" Number of atoms: 2928 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 2928 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Chain: "K" Number of atoms: 2881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 179, 2881 Classifications: {'peptide': 179} Modifications used: {'NH1NOTPRO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 171} Chain breaks: 1 Time building chain proxies: 5.19, per 1000 atoms: 0.17 Number of scatterers: 31326 At special positions: 0 Unit cell: (126.024, 139.908, 133.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 O 3027 8.00 N 2654 7.00 C 9940 6.00 H 15653 1.00 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: 2.81 Conformation dependent library (CDL) restraints added in 737.3 milliseconds 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3712 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 0 sheets defined 43.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.67 Creating SS restraints... Processing helix chain 'A' and resid 11 through 15 removed outlier: 4.731A pdb=" N HIS A 15 " --> pdb=" O GLY A 11 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 11 through 15' Processing helix chain 'A' and resid 25 through 34 Processing helix chain 'A' and resid 35 through 37 No H-bonds generated for 'chain 'A' and resid 35 through 37' Processing helix chain 'A' and resid 86 through 109 Processing helix chain 'A' and resid 113 through 129 removed outlier: 3.508A pdb=" N TYR A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 190 removed outlier: 3.727A pdb=" N ILE A 178 " --> pdb=" O LYS A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 215 Processing helix chain 'A' and resid 237 through 252 removed outlier: 3.545A pdb=" N ASP A 252 " --> pdb=" O ILE A 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 30 Processing helix chain 'B' and resid 57 through 61 removed outlier: 4.412A pdb=" N LEU B 61 " --> pdb=" O MET B 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 57 through 61' Processing helix chain 'B' and resid 78 through 96 removed outlier: 3.681A pdb=" N ASP B 87 " --> pdb=" O ARG B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 102 Processing helix chain 'B' and resid 106 through 124 removed outlier: 3.558A pdb=" N THR B 122 " --> pdb=" O MET B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 179 Processing helix chain 'B' and resid 184 through 199 removed outlier: 3.654A pdb=" N HIS B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLU B 198 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N SER B 199 " --> pdb=" O THR B 195 " (cutoff:3.500A) Processing helix chain 'B' and resid 219 through 222 No H-bonds generated for 'chain 'B' and resid 219 through 222' Processing helix chain 'B' and resid 239 through 249 removed outlier: 3.713A pdb=" N ALA B 249 " --> pdb=" O ASP B 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 30 removed outlier: 3.742A pdb=" N SER C 30 " --> pdb=" O LEU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 103 removed outlier: 3.926A pdb=" N ILE C 86 " --> pdb=" O ALA C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 125 removed outlier: 3.523A pdb=" N LEU C 111 " --> pdb=" O PRO C 107 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N THR C 123 " --> pdb=" O LYS C 119 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N HIS C 125 " --> pdb=" O GLY C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 180 removed outlier: 3.508A pdb=" N MET C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 200 Processing helix chain 'C' and resid 231 through 242 Processing helix chain 'D' and resid 19 through 28 Processing helix chain 'D' and resid 56 through 60 removed outlier: 3.659A pdb=" N THR D 60 " --> pdb=" O ASP D 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 56 through 60' Processing helix chain 'D' and resid 78 through 101 removed outlier: 3.708A pdb=" N ILE D 84 " --> pdb=" O ALA D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 120 Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.587A pdb=" N VAL D 171 " --> pdb=" O ASN D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 201 Processing helix chain 'D' and resid 206 through 210 removed outlier: 4.951A pdb=" N ILE D 210 " --> pdb=" O GLY D 206 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 206 through 210' Processing helix chain 'D' and resid 225 through 246 Processing helix chain 'G' and resid 21 through 33 removed outlier: 3.839A pdb=" N LYS G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ASN G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 104 removed outlier: 3.597A pdb=" N LEU G 102 " --> pdb=" O SER G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 108 through 122 removed outlier: 3.523A pdb=" N ASP G 114 " --> pdb=" O PRO G 110 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG G 115 " --> pdb=" O ALA G 111 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU G 116 " --> pdb=" O PHE G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 123 through 125 No H-bonds generated for 'chain 'G' and resid 123 through 125' Processing helix chain 'G' and resid 168 through 183 Processing helix chain 'G' and resid 188 through 204 Processing helix chain 'G' and resid 205 through 208 No H-bonds generated for 'chain 'G' and resid 205 through 208' Processing helix chain 'G' and resid 233 through 248 Processing helix chain 'P' and resid 52 through 58 removed outlier: 5.137A pdb=" N THR P 56 " --> pdb=" O PRO P 52 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 76 Processing helix chain 'P' and resid 79 through 95 removed outlier: 5.037A pdb=" N ASP P 95 " --> pdb=" O VAL P 91 " (cutoff:3.500A) Processing helix chain 'P' and resid 104 through 111 removed outlier: 3.766A pdb=" N ASP P 108 " --> pdb=" O SER P 104 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE P 109 " --> pdb=" O ILE P 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 118 through 123 Processing helix chain 'P' and resid 140 through 146 Processing helix chain 'H' and resid 50 through 71 removed outlier: 3.567A pdb=" N GLN H 69 " --> pdb=" O LEU H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 89 removed outlier: 3.635A pdb=" N GLU H 84 " --> pdb=" O SER H 80 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU H 85 " --> pdb=" O VAL H 81 " (cutoff:3.500A) removed outlier: 5.063A pdb=" N GLU H 88 " --> pdb=" O GLU H 84 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASN H 89 " --> pdb=" O LEU H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 136 through 142 Processing helix chain 'H' and resid 147 through 160 removed outlier: 4.045A pdb=" N SER H 160 " --> pdb=" O LYS H 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 9 through 18 removed outlier: 5.774A pdb=" N ASN I 13 " --> pdb=" O TYR I 9 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 100 removed outlier: 3.518A pdb=" N GLU I 93 " --> pdb=" O GLY I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 104 through 119 Processing helix chain 'I' and resid 159 through 171 Processing helix chain 'I' and resid 176 through 192 removed outlier: 3.867A pdb=" N ILE I 192 " --> pdb=" O ILE I 188 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 79 Processing helix chain 'J' and resid 83 through 97 Processing helix chain 'J' and resid 142 through 154 removed outlier: 3.939A pdb=" N LEU J 146 " --> pdb=" O ALA J 142 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N GLY J 148 " --> pdb=" O ASP J 144 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 175 Processing helix chain 'K' and resid 51 through 72 removed outlier: 4.638A pdb=" N ASP K 72 " --> pdb=" O SER K 68 " (cutoff:3.500A) Processing helix chain 'K' and resid 76 through 91 Processing helix chain 'K' and resid 136 through 148 removed outlier: 5.597A pdb=" N THR K 140 " --> pdb=" O SER K 136 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N PHE K 141 " --> pdb=" O GLY K 137 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 172 579 hydrogen bonds defined for protein. 1737 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: 7.20 Time building geometry restraints manager: 3.71 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 4443 1.04 - 1.23: 12902 1.23 - 1.43: 5047 1.43 - 1.62: 9135 1.62 - 1.82: 82 Bond restraints: 31609 Sorted by residual: bond pdb=" CD1 TYR K 73 " pdb=" HD1 TYR K 73 " ideal model delta sigma weight residual 0.930 1.082 -0.152 2.00e-02 2.50e+03 5.77e+01 bond pdb=" N LEU G 151 " pdb=" H LEU G 151 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" NE ARG B 246 " pdb=" HE ARG B 246 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.76e+01 bond pdb=" N LYS A 232 " pdb=" H LYS A 232 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.75e+01 bond pdb=" N LYS G 41 " pdb=" H LYS G 41 " ideal model delta sigma weight residual 0.860 1.012 -0.152 2.00e-02 2.50e+03 5.75e+01 ... (remaining 31604 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.68: 48738 2.68 - 5.37: 6663 5.37 - 8.05: 1683 8.05 - 10.73: 30 10.73 - 13.42: 22 Bond angle restraints: 57136 Sorted by residual: angle pdb=" CA ASP A 147 " pdb=" CB ASP A 147 " pdb=" CG ASP A 147 " ideal model delta sigma weight residual 112.60 117.54 -4.94 1.00e+00 1.00e+00 2.44e+01 angle pdb=" C TRP J 183 " pdb=" N GLY J 184 " pdb=" CA GLY J 184 " ideal model delta sigma weight residual 120.98 125.42 -4.44 9.00e-01 1.23e+00 2.43e+01 angle pdb=" C CYS A 114 " pdb=" N ASP A 115 " pdb=" CA ASP A 115 " ideal model delta sigma weight residual 120.38 127.12 -6.74 1.37e+00 5.33e-01 2.42e+01 angle pdb=" CB HIS I 122 " pdb=" CG HIS I 122 " pdb=" CD2 HIS I 122 " ideal model delta sigma weight residual 131.20 124.81 6.39 1.30e+00 5.92e-01 2.42e+01 angle pdb=" OE1 GLN K 118 " pdb=" CD GLN K 118 " pdb=" NE2 GLN K 118 " ideal model delta sigma weight residual 122.60 117.71 4.89 1.00e+00 1.00e+00 2.39e+01 ... (remaining 57131 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 13564 17.80 - 35.61: 853 35.61 - 53.41: 271 53.41 - 71.21: 115 71.21 - 89.02: 26 Dihedral angle restraints: 14829 sinusoidal: 8104 harmonic: 6725 Sorted by residual: dihedral pdb=" CA TYR J 96 " pdb=" C TYR J 96 " pdb=" N GLU J 97 " pdb=" CA GLU J 97 " ideal model delta harmonic sigma weight residual 180.00 150.73 29.27 0 5.00e+00 4.00e-02 3.43e+01 dihedral pdb=" CA GLY J 182 " pdb=" C GLY J 182 " pdb=" N TRP J 183 " pdb=" CA TRP J 183 " ideal model delta harmonic sigma weight residual 180.00 150.77 29.23 0 5.00e+00 4.00e-02 3.42e+01 dihedral pdb=" CA TYR I 126 " pdb=" C TYR I 126 " pdb=" N LEU I 127 " pdb=" CA LEU I 127 " ideal model delta harmonic sigma weight residual -180.00 -151.08 -28.92 0 5.00e+00 4.00e-02 3.35e+01 ... (remaining 14826 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.122: 1958 0.122 - 0.244: 446 0.244 - 0.367: 36 0.367 - 0.489: 4 0.489 - 0.611: 2 Chirality restraints: 2446 Sorted by residual: chirality pdb=" CB ILE I 246 " pdb=" CA ILE I 246 " pdb=" CG1 ILE I 246 " pdb=" CG2 ILE I 246 " both_signs ideal model delta sigma weight residual False 2.64 2.03 0.61 2.00e-01 2.50e+01 9.33e+00 chirality pdb=" CB VAL I 247 " pdb=" CA VAL I 247 " pdb=" CG1 VAL I 247 " pdb=" CG2 VAL I 247 " both_signs ideal model delta sigma weight residual False -2.63 -2.05 -0.58 2.00e-01 2.50e+01 8.37e+00 chirality pdb=" CA ARG J 98 " pdb=" N ARG J 98 " pdb=" C ARG J 98 " pdb=" CB ARG J 98 " both_signs ideal model delta sigma weight residual False 2.51 2.05 0.46 2.00e-01 2.50e+01 5.33e+00 ... (remaining 2443 not shown) Planarity restraints: 4679 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN B 123 " -0.113 2.00e-02 2.50e+03 4.36e-01 2.85e+03 pdb=" CD GLN B 123 " 0.003 2.00e-02 2.50e+03 pdb=" OE1 GLN B 123 " 0.114 2.00e-02 2.50e+03 pdb=" NE2 GLN B 123 " -0.001 2.00e-02 2.50e+03 pdb="HE21 GLN B 123 " 0.745 2.00e-02 2.50e+03 pdb="HE22 GLN B 123 " -0.749 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN I 38 " -0.133 2.00e-02 2.50e+03 1.41e-01 2.97e+02 pdb=" CG ASN I 38 " 0.011 2.00e-02 2.50e+03 pdb=" OD1 ASN I 38 " 0.125 2.00e-02 2.50e+03 pdb=" ND2 ASN I 38 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN I 38 " -0.210 2.00e-02 2.50e+03 pdb="HD22 ASN I 38 " 0.203 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 28 " -0.380 9.50e-02 1.11e+02 1.64e-01 2.59e+02 pdb=" NE ARG J 28 " -0.039 2.00e-02 2.50e+03 pdb=" CZ ARG J 28 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG J 28 " -0.016 2.00e-02 2.50e+03 pdb=" NH2 ARG J 28 " 0.025 2.00e-02 2.50e+03 pdb="HH11 ARG J 28 " 0.190 2.00e-02 2.50e+03 pdb="HH12 ARG J 28 " -0.208 2.00e-02 2.50e+03 pdb="HH21 ARG J 28 " 0.118 2.00e-02 2.50e+03 pdb="HH22 ARG J 28 " -0.040 2.00e-02 2.50e+03 ... (remaining 4676 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.20: 2341 2.20 - 2.80: 59406 2.80 - 3.40: 87974 3.40 - 4.00: 117970 4.00 - 4.60: 173288 Nonbonded interactions: 440979 Sorted by model distance: nonbonded pdb="HG23 THR B 122 " pdb="HH21 ARG C 129 " model vdw 1.606 2.270 nonbonded pdb=" HG SER H 48 " pdb=" OD1 ASP H 51 " model vdw 1.607 2.450 nonbonded pdb=" OD2 ASP C 222 " pdb=" HH TYR C 226 " model vdw 1.620 2.450 nonbonded pdb=" OD2 ASP A 147 " pdb="HH21 ARG I 101 " model vdw 1.621 2.450 nonbonded pdb=" OE2 GLU B 103 " pdb=" HG1 THR J 86 " model vdw 1.626 2.450 ... (remaining 440974 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.440 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: 0.210 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 28.590 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 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 : 0.012 0.082 15956 Z= 0.738 Angle : 1.865 8.044 21571 Z= 1.246 Chirality : 0.100 0.611 2446 Planarity : 0.014 0.121 2764 Dihedral : 13.978 89.018 5896 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 1.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.23 % Allowed : 5.47 % Favored : 93.30 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.78 (0.17), residues: 1964 helix: -0.70 (0.15), residues: 812 sheet: 0.90 (0.24), residues: 425 loop : -1.00 (0.21), residues: 727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 185 TYR 0.114 0.022 TYR H 124 PHE 0.083 0.014 PHE J 67 TRP 0.101 0.022 TRP J 183 HIS 0.016 0.003 HIS P 51 Details of bonding type rmsd covalent geometry : bond 0.01177 (15956) covalent geometry : angle 1.86471 (21571) hydrogen bonds : bond 0.20243 ( 579) hydrogen bonds : angle 7.23477 ( 1737) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 305 time to evaluate : 0.768 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASN cc_start: 0.8784 (m-40) cc_final: 0.8346 (t0) REVERT: A 112 MET cc_start: 0.8584 (tpp) cc_final: 0.8267 (tpp) REVERT: B 245 ASP cc_start: 0.7888 (m-30) cc_final: 0.7505 (m-30) REVERT: C 39 MET cc_start: 0.8870 (ttt) cc_final: 0.8515 (ttm) REVERT: C 61 THR cc_start: 0.8630 (m) cc_final: 0.8344 (m) REVERT: C 226 TYR cc_start: 0.7641 (m-80) cc_final: 0.7186 (m-80) REVERT: D 102 ASP cc_start: 0.8587 (m-30) cc_final: 0.8296 (m-30) REVERT: G 127 ASN cc_start: 0.8770 (p0) cc_final: 0.8134 (p0) REVERT: P 114 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7780 (mp0) REVERT: H 186 LEU cc_start: 0.7476 (mt) cc_final: 0.7260 (mt) REVERT: I 164 MET cc_start: 0.8191 (mmm) cc_final: 0.7904 (mmm) REVERT: I 201 ASN cc_start: 0.7816 (m110) cc_final: 0.7593 (m-40) REVERT: I 247 VAL cc_start: 0.2517 (OUTLIER) cc_final: 0.1488 (t) REVERT: J 162 ASP cc_start: 0.8784 (m-30) cc_final: 0.8575 (m-30) REVERT: K 11 ASP cc_start: 0.8654 (p0) cc_final: 0.8162 (t0) REVERT: K 66 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7826 (tt) REVERT: K 174 MET cc_start: 0.8810 (mmm) cc_final: 0.8481 (pmm) outliers start: 21 outliers final: 8 residues processed: 324 average time/residue: 0.4630 time to fit residues: 195.7383 Evaluate side-chains 213 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 202 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 THR Chi-restraints excluded: chain B residue 210 GLU Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain P residue 82 MET Chi-restraints excluded: chain P residue 114 GLU Chi-restraints excluded: chain P residue 117 ILE Chi-restraints excluded: chain I residue 247 VAL Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 183 TRP Chi-restraints excluded: chain K residue 66 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 98 optimal weight: 6.9990 chunk 194 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 0.9980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 36 ASN A 126 GLN B 20 GLN B 123 GLN B 190 HIS P 102 ASN H 141 ASN K 78 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.047683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.039148 restraints weight = 174633.816| |-----------------------------------------------------------------------------| r_work (start): 0.2591 rms_B_bonded: 2.79 r_work: 0.2500 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2392 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 moved from start: 0.2936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 15956 Z= 0.184 Angle : 0.665 5.764 21571 Z= 0.365 Chirality : 0.045 0.160 2446 Planarity : 0.005 0.076 2764 Dihedral : 7.725 85.050 2191 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.59 % Allowed : 9.17 % Favored : 89.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.18), residues: 1964 helix: 0.59 (0.17), residues: 828 sheet: 0.14 (0.22), residues: 494 loop : -0.94 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 14 TYR 0.017 0.002 TYR J 188 PHE 0.016 0.002 PHE A 19 TRP 0.014 0.001 TRP A 199 HIS 0.010 0.002 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00402 (15956) covalent geometry : angle 0.66544 (21571) hydrogen bonds : bond 0.06801 ( 579) hydrogen bonds : angle 5.15235 ( 1737) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 209 time to evaluate : 0.863 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ASP cc_start: 0.8983 (t0) cc_final: 0.8777 (t0) REVERT: C 16 GLU cc_start: 0.3971 (OUTLIER) cc_final: 0.3277 (tm-30) REVERT: C 39 MET cc_start: 0.9535 (ttt) cc_final: 0.9272 (ttm) REVERT: C 125 HIS cc_start: 0.8545 (t-90) cc_final: 0.8158 (t-90) REVERT: C 202 ASP cc_start: 0.8329 (p0) cc_final: 0.8100 (p0) REVERT: G 213 GLU cc_start: 0.8552 (mt-10) cc_final: 0.8189 (mp0) REVERT: P 143 GLU cc_start: 0.6924 (tp30) cc_final: 0.6570 (tp30) REVERT: H 4 MET cc_start: 0.8521 (ttm) cc_final: 0.8296 (ttm) REVERT: H 184 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7378 (tm-30) REVERT: H 186 LEU cc_start: 0.8470 (mt) cc_final: 0.8189 (mt) REVERT: I 164 MET cc_start: 0.9547 (mmm) cc_final: 0.9317 (mmm) REVERT: I 174 ASP cc_start: 0.8710 (p0) cc_final: 0.8293 (p0) REVERT: K 11 ASP cc_start: 0.8794 (p0) cc_final: 0.8489 (t0) REVERT: K 66 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9129 (tt) outliers start: 27 outliers final: 12 residues processed: 229 average time/residue: 0.4001 time to fit residues: 125.3883 Evaluate side-chains 205 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain P residue 49 ASP Chi-restraints excluded: chain P residue 117 ILE Chi-restraints excluded: chain P residue 120 GLU Chi-restraints excluded: chain P residue 140 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 174 ARG Chi-restraints excluded: chain I residue 102 GLU Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 183 TRP Chi-restraints excluded: chain K residue 66 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 104 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 134 optimal weight: 0.0370 chunk 139 optimal weight: 2.9990 chunk 174 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 117 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 overall best weight: 1.1464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 GLN C 147 GLN H 106 ASN I 10 GLN I 38 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.046676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.038244 restraints weight = 175077.229| |-----------------------------------------------------------------------------| r_work (start): 0.2562 rms_B_bonded: 2.72 r_work: 0.2474 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2370 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15956 Z= 0.163 Angle : 0.577 6.306 21571 Z= 0.313 Chirality : 0.044 0.146 2446 Planarity : 0.005 0.083 2764 Dihedral : 6.507 86.093 2179 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.41 % Allowed : 10.17 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.18), residues: 1964 helix: 1.10 (0.17), residues: 829 sheet: 0.12 (0.23), residues: 482 loop : -0.92 (0.22), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 190 TYR 0.019 0.001 TYR H 137 PHE 0.017 0.002 PHE I 37 TRP 0.011 0.001 TRP A 199 HIS 0.010 0.002 HIS G 204 Details of bonding type rmsd covalent geometry : bond 0.00365 (15956) covalent geometry : angle 0.57662 (21571) hydrogen bonds : bond 0.05350 ( 579) hydrogen bonds : angle 4.61919 ( 1737) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASN cc_start: 0.8834 (t0) cc_final: 0.8556 (t0) REVERT: A 210 MET cc_start: 0.9323 (tpp) cc_final: 0.9067 (tpp) REVERT: C 39 MET cc_start: 0.9513 (ttt) cc_final: 0.9285 (ttm) REVERT: D 21 GLU cc_start: 0.8458 (mp0) cc_final: 0.8178 (mp0) REVERT: H 184 GLU cc_start: 0.7879 (tm-30) cc_final: 0.7512 (tm-30) REVERT: H 186 LEU cc_start: 0.8506 (mt) cc_final: 0.8231 (mt) REVERT: I 164 MET cc_start: 0.9537 (mmm) cc_final: 0.9322 (mmm) REVERT: I 168 GLU cc_start: 0.8857 (tm-30) cc_final: 0.8468 (tm-30) REVERT: J 26 ASP cc_start: 0.8527 (m-30) cc_final: 0.7678 (p0) REVERT: K 11 ASP cc_start: 0.8788 (p0) cc_final: 0.8464 (t0) REVERT: K 44 MET cc_start: 0.9420 (ttt) cc_final: 0.9082 (ttt) outliers start: 24 outliers final: 18 residues processed: 209 average time/residue: 0.3836 time to fit residues: 109.7755 Evaluate side-chains 207 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 189 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain P residue 49 ASP Chi-restraints excluded: chain P residue 115 CYS Chi-restraints excluded: chain P residue 120 GLU Chi-restraints excluded: chain P residue 140 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain I residue 11 ARG Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 66 MET Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 183 TRP Chi-restraints excluded: chain K residue 169 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 155 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 120 optimal weight: 0.6980 chunk 182 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 106 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.046171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.037873 restraints weight = 173553.322| |-----------------------------------------------------------------------------| r_work (start): 0.2545 rms_B_bonded: 2.63 r_work: 0.2458 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2354 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9059 moved from start: 0.3794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15956 Z= 0.172 Angle : 0.557 6.452 21571 Z= 0.301 Chirality : 0.043 0.144 2446 Planarity : 0.005 0.064 2764 Dihedral : 6.191 87.706 2175 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.41 % Allowed : 11.05 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.36 (0.18), residues: 1964 helix: 1.29 (0.18), residues: 826 sheet: 0.12 (0.23), residues: 474 loop : -0.93 (0.22), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 171 TYR 0.016 0.001 TYR H 137 PHE 0.013 0.001 PHE H 154 TRP 0.012 0.001 TRP A 199 HIS 0.008 0.002 HIS G 204 Details of bonding type rmsd covalent geometry : bond 0.00391 (15956) covalent geometry : angle 0.55726 (21571) hydrogen bonds : bond 0.05019 ( 579) hydrogen bonds : angle 4.49807 ( 1737) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 189 time to evaluate : 0.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASN cc_start: 0.8921 (t0) cc_final: 0.8680 (t0) REVERT: A 49 ASP cc_start: 0.8889 (t0) cc_final: 0.8593 (t0) REVERT: C 39 MET cc_start: 0.9494 (ttt) cc_final: 0.9285 (ttm) REVERT: D 21 GLU cc_start: 0.8580 (mp0) cc_final: 0.8280 (mp0) REVERT: G 71 ASP cc_start: 0.8857 (t0) cc_final: 0.8567 (t0) REVERT: G 213 GLU cc_start: 0.8456 (mt-10) cc_final: 0.7963 (mp0) REVERT: H 84 GLU cc_start: 0.8668 (mm-30) cc_final: 0.8379 (mp0) REVERT: I 168 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8461 (tm-30) REVERT: J 26 ASP cc_start: 0.8474 (m-30) cc_final: 0.7750 (p0) REVERT: K 44 MET cc_start: 0.9423 (ttt) cc_final: 0.9060 (ttt) outliers start: 24 outliers final: 19 residues processed: 204 average time/residue: 0.3572 time to fit residues: 100.9915 Evaluate side-chains 200 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain P residue 49 ASP Chi-restraints excluded: chain P residue 115 CYS Chi-restraints excluded: chain P residue 120 GLU Chi-restraints excluded: chain P residue 140 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain I residue 11 ARG Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 126 LEU Chi-restraints excluded: chain J residue 183 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 54 optimal weight: 0.0970 chunk 35 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 chunk 136 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 237 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.046464 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2565 r_free = 0.2565 target = 0.038189 restraints weight = 174189.896| |-----------------------------------------------------------------------------| r_work (start): 0.2560 rms_B_bonded: 2.65 r_work: 0.2474 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2371 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2371 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9044 moved from start: 0.3998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15956 Z= 0.127 Angle : 0.521 6.341 21571 Z= 0.280 Chirality : 0.042 0.143 2446 Planarity : 0.004 0.059 2764 Dihedral : 5.888 89.261 2175 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.41 % Allowed : 11.76 % Favored : 86.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.18), residues: 1964 helix: 1.59 (0.18), residues: 826 sheet: -0.04 (0.23), residues: 491 loop : -0.86 (0.23), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG P 73 TYR 0.013 0.001 TYR H 137 PHE 0.013 0.001 PHE G 212 TRP 0.010 0.001 TRP A 199 HIS 0.007 0.001 HIS K 146 Details of bonding type rmsd covalent geometry : bond 0.00286 (15956) covalent geometry : angle 0.52080 (21571) hydrogen bonds : bond 0.04518 ( 579) hydrogen bonds : angle 4.32440 ( 1737) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 183 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASN cc_start: 0.8888 (t0) cc_final: 0.8658 (t0) REVERT: A 49 ASP cc_start: 0.8888 (t0) cc_final: 0.8617 (t0) REVERT: C 16 GLU cc_start: 0.4320 (OUTLIER) cc_final: 0.3925 (tm-30) REVERT: C 39 MET cc_start: 0.9472 (ttt) cc_final: 0.9268 (ttm) REVERT: D 21 GLU cc_start: 0.8600 (mp0) cc_final: 0.8180 (mp0) REVERT: H 84 GLU cc_start: 0.8634 (mm-30) cc_final: 0.8382 (mp0) REVERT: H 121 LYS cc_start: 0.8833 (tttt) cc_final: 0.8469 (tttp) REVERT: H 184 GLU cc_start: 0.7923 (tm-30) cc_final: 0.7530 (tm-30) REVERT: I 168 GLU cc_start: 0.8813 (tm-30) cc_final: 0.8430 (tm-30) REVERT: J 26 ASP cc_start: 0.8401 (m-30) cc_final: 0.7891 (p0) REVERT: K 44 MET cc_start: 0.9392 (ttt) cc_final: 0.9043 (ttt) outliers start: 24 outliers final: 19 residues processed: 199 average time/residue: 0.3889 time to fit residues: 106.5772 Evaluate side-chains 198 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 178 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain P residue 49 ASP Chi-restraints excluded: chain P residue 120 GLU Chi-restraints excluded: chain P residue 140 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 137 TYR Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain I residue 11 ARG Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 66 MET Chi-restraints excluded: chain J residue 183 TRP Chi-restraints excluded: chain K residue 168 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 12 optimal weight: 0.9980 chunk 101 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 180 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 84 optimal weight: 0.7980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.046073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.037773 restraints weight = 173182.956| |-----------------------------------------------------------------------------| r_work (start): 0.2547 rms_B_bonded: 2.67 r_work: 0.2457 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2352 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9056 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15956 Z= 0.146 Angle : 0.521 7.118 21571 Z= 0.279 Chirality : 0.042 0.141 2446 Planarity : 0.005 0.057 2764 Dihedral : 5.784 88.590 2173 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.70 % Allowed : 11.99 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.18), residues: 1964 helix: 1.71 (0.18), residues: 820 sheet: 0.01 (0.23), residues: 474 loop : -0.86 (0.22), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG P 73 TYR 0.015 0.001 TYR G 201 PHE 0.014 0.001 PHE G 212 TRP 0.010 0.001 TRP A 199 HIS 0.007 0.001 HIS K 146 Details of bonding type rmsd covalent geometry : bond 0.00334 (15956) covalent geometry : angle 0.52107 (21571) hydrogen bonds : bond 0.04516 ( 579) hydrogen bonds : angle 4.27376 ( 1737) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 180 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASN cc_start: 0.8899 (t0) cc_final: 0.8655 (t0) REVERT: A 49 ASP cc_start: 0.8931 (t0) cc_final: 0.8725 (t0) REVERT: C 16 GLU cc_start: 0.4558 (OUTLIER) cc_final: 0.4356 (mm-30) REVERT: G 71 ASP cc_start: 0.8855 (t0) cc_final: 0.8607 (t0) REVERT: G 213 GLU cc_start: 0.8428 (mt-10) cc_final: 0.7894 (mp0) REVERT: H 84 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8411 (mp0) REVERT: H 184 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7673 (tm-30) REVERT: I 168 GLU cc_start: 0.8831 (tm-30) cc_final: 0.8450 (tm-30) REVERT: I 203 ASP cc_start: 0.7984 (m-30) cc_final: 0.7705 (m-30) REVERT: J 26 ASP cc_start: 0.8402 (m-30) cc_final: 0.7980 (p0) REVERT: K 44 MET cc_start: 0.9395 (ttt) cc_final: 0.8990 (ttt) outliers start: 29 outliers final: 22 residues processed: 200 average time/residue: 0.3844 time to fit residues: 106.2380 Evaluate side-chains 200 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 177 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain G residue 18 ASP Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain P residue 49 ASP Chi-restraints excluded: chain P residue 115 CYS Chi-restraints excluded: chain P residue 120 GLU Chi-restraints excluded: chain P residue 140 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 118 SER Chi-restraints excluded: chain H residue 137 TYR Chi-restraints excluded: chain H residue 187 ILE Chi-restraints excluded: chain I residue 11 ARG Chi-restraints excluded: chain I residue 17 GLU Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 66 MET Chi-restraints excluded: chain J residue 135 ASP Chi-restraints excluded: chain J residue 183 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 65 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 174 optimal weight: 0.4980 chunk 151 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 163 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 87 optimal weight: 0.0060 chunk 46 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.5796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.046598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.038241 restraints weight = 173416.840| |-----------------------------------------------------------------------------| r_work (start): 0.2560 rms_B_bonded: 2.68 r_work: 0.2473 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2370 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 15956 Z= 0.114 Angle : 0.512 7.072 21571 Z= 0.273 Chirality : 0.042 0.142 2446 Planarity : 0.004 0.062 2764 Dihedral : 5.588 86.687 2173 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 3.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.23 % Allowed : 13.05 % Favored : 85.71 % 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: 0.73 (0.18), residues: 1964 helix: 1.83 (0.18), residues: 820 sheet: -0.03 (0.23), residues: 477 loop : -0.77 (0.22), residues: 667 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG P 73 TYR 0.014 0.001 TYR G 201 PHE 0.013 0.001 PHE G 212 TRP 0.008 0.001 TRP A 199 HIS 0.005 0.001 HIS K 146 Details of bonding type rmsd covalent geometry : bond 0.00256 (15956) covalent geometry : angle 0.51204 (21571) hydrogen bonds : bond 0.04243 ( 579) hydrogen bonds : angle 4.16990 ( 1737) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASN cc_start: 0.8910 (t0) cc_final: 0.8674 (t0) REVERT: C 16 GLU cc_start: 0.4612 (OUTLIER) cc_final: 0.4391 (mm-30) REVERT: G 213 GLU cc_start: 0.8402 (mt-10) cc_final: 0.7945 (mp0) REVERT: I 168 GLU cc_start: 0.8802 (tm-30) cc_final: 0.8415 (tm-30) REVERT: I 203 ASP cc_start: 0.7903 (m-30) cc_final: 0.7603 (m-30) REVERT: J 26 ASP cc_start: 0.8337 (m-30) cc_final: 0.7995 (p0) REVERT: K 44 MET cc_start: 0.9369 (ttt) cc_final: 0.8994 (ttt) outliers start: 21 outliers final: 17 residues processed: 197 average time/residue: 0.4260 time to fit residues: 113.7704 Evaluate side-chains 195 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 177 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain G residue 29 LYS Chi-restraints excluded: chain P residue 49 ASP Chi-restraints excluded: chain P residue 120 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 137 TYR Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 183 TRP Chi-restraints excluded: chain J residue 191 LYS Chi-restraints excluded: chain K residue 1 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 181 optimal weight: 0.0870 chunk 165 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 130 optimal weight: 0.0470 chunk 172 optimal weight: 1.9990 chunk 190 optimal weight: 3.9990 chunk 88 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 154 optimal weight: 1.9990 overall best weight: 1.0262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.046092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2555 r_free = 0.2555 target = 0.037865 restraints weight = 173953.910| |-----------------------------------------------------------------------------| r_work (start): 0.2551 rms_B_bonded: 2.64 r_work: 0.2465 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2361 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9054 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15956 Z= 0.148 Angle : 0.527 7.145 21571 Z= 0.281 Chirality : 0.042 0.139 2446 Planarity : 0.005 0.084 2764 Dihedral : 5.583 84.818 2173 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.18 % Allowed : 13.76 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.70 (0.18), residues: 1964 helix: 1.82 (0.18), residues: 820 sheet: -0.06 (0.23), residues: 481 loop : -0.80 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 14 TYR 0.021 0.001 TYR G 201 PHE 0.015 0.001 PHE G 212 TRP 0.009 0.001 TRP A 199 HIS 0.005 0.001 HIS K 146 Details of bonding type rmsd covalent geometry : bond 0.00342 (15956) covalent geometry : angle 0.52677 (21571) hydrogen bonds : bond 0.04368 ( 579) hydrogen bonds : angle 4.17530 ( 1737) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASN cc_start: 0.8919 (t0) cc_final: 0.8677 (t0) REVERT: A 49 ASP cc_start: 0.8748 (t0) cc_final: 0.8535 (t0) REVERT: C 16 GLU cc_start: 0.4559 (OUTLIER) cc_final: 0.4322 (mm-30) REVERT: C 184 MET cc_start: 0.8511 (OUTLIER) cc_final: 0.8193 (mtm) REVERT: G 213 GLU cc_start: 0.8331 (mt-10) cc_final: 0.7789 (mp0) REVERT: H 45 ARG cc_start: 0.8405 (mtm110) cc_final: 0.8193 (mtm110) REVERT: H 184 GLU cc_start: 0.7621 (tm-30) cc_final: 0.7326 (tm-30) REVERT: H 186 LEU cc_start: 0.8167 (mt) cc_final: 0.7955 (mt) REVERT: I 168 GLU cc_start: 0.8782 (tm-30) cc_final: 0.8387 (tm-30) REVERT: I 203 ASP cc_start: 0.8008 (m-30) cc_final: 0.7742 (m-30) REVERT: J 26 ASP cc_start: 0.8339 (m-30) cc_final: 0.8029 (p0) REVERT: K 44 MET cc_start: 0.9399 (ttt) cc_final: 0.9002 (ttt) outliers start: 20 outliers final: 16 residues processed: 185 average time/residue: 0.3852 time to fit residues: 97.0054 Evaluate side-chains 190 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 172 time to evaluate : 0.885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain G residue 25 GLU Chi-restraints excluded: chain P residue 49 ASP Chi-restraints excluded: chain P residue 115 CYS Chi-restraints excluded: chain P residue 120 GLU Chi-restraints excluded: chain P residue 140 SER Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 137 TYR Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 183 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 178 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 chunk 63 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 163 optimal weight: 1.9990 chunk 91 optimal weight: 0.8980 chunk 95 optimal weight: 1.9990 chunk 142 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.046153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2560 r_free = 0.2560 target = 0.037977 restraints weight = 173342.174| |-----------------------------------------------------------------------------| r_work (start): 0.2555 rms_B_bonded: 2.62 r_work: 0.2469 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2367 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 moved from start: 0.4416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15956 Z= 0.128 Angle : 0.522 7.220 21571 Z= 0.278 Chirality : 0.042 0.139 2446 Planarity : 0.005 0.080 2764 Dihedral : 5.493 82.574 2173 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.18 % Allowed : 13.87 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.19), residues: 1964 helix: 1.91 (0.18), residues: 819 sheet: -0.06 (0.23), residues: 481 loop : -0.76 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 14 TYR 0.021 0.001 TYR G 201 PHE 0.016 0.001 PHE G 212 TRP 0.008 0.001 TRP A 199 HIS 0.005 0.001 HIS K 146 Details of bonding type rmsd covalent geometry : bond 0.00295 (15956) covalent geometry : angle 0.52175 (21571) hydrogen bonds : bond 0.04226 ( 579) hydrogen bonds : angle 4.16127 ( 1737) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASN cc_start: 0.8937 (t0) cc_final: 0.8700 (t0) REVERT: A 49 ASP cc_start: 0.8844 (t0) cc_final: 0.8633 (t0) REVERT: C 16 GLU cc_start: 0.4610 (OUTLIER) cc_final: 0.4396 (mm-30) REVERT: C 184 MET cc_start: 0.8468 (OUTLIER) cc_final: 0.8136 (mtm) REVERT: G 213 GLU cc_start: 0.8300 (mt-10) cc_final: 0.7863 (mp0) REVERT: H 45 ARG cc_start: 0.8403 (mtm110) cc_final: 0.8179 (mtm110) REVERT: H 184 GLU cc_start: 0.7820 (tm-30) cc_final: 0.7546 (tm-30) REVERT: H 186 LEU cc_start: 0.8212 (mt) cc_final: 0.7993 (mt) REVERT: I 17 GLU cc_start: 0.8956 (tt0) cc_final: 0.8750 (tt0) REVERT: I 168 GLU cc_start: 0.8758 (tm-30) cc_final: 0.8359 (tm-30) REVERT: I 203 ASP cc_start: 0.7974 (m-30) cc_final: 0.7735 (m-30) REVERT: J 26 ASP cc_start: 0.8382 (m-30) cc_final: 0.8090 (p0) REVERT: K 44 MET cc_start: 0.9389 (ttt) cc_final: 0.8986 (ttt) outliers start: 20 outliers final: 16 residues processed: 188 average time/residue: 0.4135 time to fit residues: 106.4560 Evaluate side-chains 188 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 170 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain P residue 49 ASP Chi-restraints excluded: chain P residue 115 CYS Chi-restraints excluded: chain P residue 120 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 137 TYR Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 183 TRP Chi-restraints excluded: chain J residue 191 LYS Chi-restraints excluded: chain K residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 94 optimal weight: 0.7980 chunk 191 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 137 optimal weight: 0.5980 chunk 29 optimal weight: 0.4980 chunk 147 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 162 optimal weight: 2.9990 chunk 175 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.046348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2567 r_free = 0.2567 target = 0.038178 restraints weight = 172744.363| |-----------------------------------------------------------------------------| r_work (start): 0.2564 rms_B_bonded: 2.62 r_work: 0.2477 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2374 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9045 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15956 Z= 0.117 Angle : 0.517 6.840 21571 Z= 0.274 Chirality : 0.042 0.139 2446 Planarity : 0.005 0.128 2764 Dihedral : 5.378 79.516 2173 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.12 % Allowed : 13.82 % Favored : 85.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.19), residues: 1964 helix: 2.00 (0.18), residues: 820 sheet: -0.07 (0.23), residues: 481 loop : -0.71 (0.23), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 14 TYR 0.021 0.001 TYR G 201 PHE 0.015 0.001 PHE G 212 TRP 0.008 0.001 TRP A 199 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00269 (15956) covalent geometry : angle 0.51712 (21571) hydrogen bonds : bond 0.04077 ( 579) hydrogen bonds : angle 4.13564 ( 1737) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 174 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 ASN cc_start: 0.8933 (t0) cc_final: 0.8704 (t0) REVERT: A 49 ASP cc_start: 0.8824 (t0) cc_final: 0.8612 (t0) REVERT: C 16 GLU cc_start: 0.4680 (OUTLIER) cc_final: 0.4463 (mm-30) REVERT: C 184 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.8109 (mtm) REVERT: H 45 ARG cc_start: 0.8397 (mtm110) cc_final: 0.8174 (mtm110) REVERT: H 184 GLU cc_start: 0.7843 (tm-30) cc_final: 0.7497 (tm-30) REVERT: H 186 LEU cc_start: 0.8213 (mt) cc_final: 0.7963 (mt) REVERT: I 17 GLU cc_start: 0.8952 (tt0) cc_final: 0.8746 (tt0) REVERT: I 168 GLU cc_start: 0.8753 (tm-30) cc_final: 0.8352 (tm-30) REVERT: I 203 ASP cc_start: 0.7923 (m-30) cc_final: 0.7698 (m-30) REVERT: J 26 ASP cc_start: 0.8350 (m-30) cc_final: 0.8112 (p0) REVERT: K 44 MET cc_start: 0.9376 (ttt) cc_final: 0.8972 (ttt) outliers start: 19 outliers final: 17 residues processed: 185 average time/residue: 0.4153 time to fit residues: 104.6357 Evaluate side-chains 189 residues out of total 1702 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 50 LYS Chi-restraints excluded: chain B residue 58 SER Chi-restraints excluded: chain C residue 16 GLU Chi-restraints excluded: chain C residue 184 MET Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 238 GLN Chi-restraints excluded: chain P residue 49 ASP Chi-restraints excluded: chain P residue 115 CYS Chi-restraints excluded: chain P residue 120 GLU Chi-restraints excluded: chain H residue 74 SER Chi-restraints excluded: chain H residue 105 LYS Chi-restraints excluded: chain H residue 137 TYR Chi-restraints excluded: chain I residue 47 THR Chi-restraints excluded: chain I residue 67 SER Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 183 TRP Chi-restraints excluded: chain J residue 191 LYS Chi-restraints excluded: chain K residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 195 random chunks: chunk 125 optimal weight: 0.0470 chunk 120 optimal weight: 0.0970 chunk 131 optimal weight: 2.9990 chunk 160 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 91 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 overall best weight: 0.7678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.046205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.038058 restraints weight = 174253.281| |-----------------------------------------------------------------------------| r_work (start): 0.2558 rms_B_bonded: 2.62 r_work: 0.2473 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2370 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9047 moved from start: 0.4531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15956 Z= 0.128 Angle : 0.526 6.962 21571 Z= 0.280 Chirality : 0.042 0.139 2446 Planarity : 0.005 0.095 2764 Dihedral : 5.336 77.274 2173 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.06 % Allowed : 13.99 % Favored : 84.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.19), residues: 1964 helix: 2.02 (0.18), residues: 819 sheet: -0.07 (0.23), residues: 481 loop : -0.74 (0.23), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG A 14 TYR 0.019 0.001 TYR G 201 PHE 0.018 0.001 PHE G 212 TRP 0.008 0.001 TRP A 199 HIS 0.005 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00294 (15956) covalent geometry : angle 0.52622 (21571) hydrogen bonds : bond 0.04105 ( 579) hydrogen bonds : angle 4.14070 ( 1737) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7591.67 seconds wall clock time: 129 minutes 35.89 seconds (7775.89 seconds total)