Starting phenix.real_space_refine on Sat Sep 12 10:04:17 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/5tc1_8397/09_2026/5tc1_8397.cif Found real_map, /net/cci-nas-00/data/ceres_data/5tc1_8397/09_2026/5tc1_8397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5tc1_8397/09_2026/5tc1_8397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5tc1_8397/09_2026/5tc1_8397.map" model { file = "/net/cci-nas-00/data/ceres_data/5tc1_8397/09_2026/5tc1_8397.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5tc1_8397/09_2026/5tc1_8397.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/5tc1_8397/09_2026/5tc1_8397.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/5tc1_8397/09_2026/5tc1_8397.cif" } resolution = 3.6 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 ------------------------------------------------------------------------------- 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= 0.000 sd= 1.000 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 P 242 5.49 5 S 43 5.16 5 C 8768 2.51 5 N 2671 2.21 5 O 3669 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 15393 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 965 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "B" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 965 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 122} Chain: "C" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 965 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "D" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 965 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "E" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 965 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 122} Chain: "F" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 965 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "G" Number of atoms: 898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 898 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 112} Chain breaks: 1 Chain: "H" Number of atoms: 965 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 965 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 122} Chain: "M" Number of atoms: 2608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2608 Classifications: {'peptide': 330} Link IDs: {'PTRANS': 13, 'TRANS': 316} Chain breaks: 4 Chain: "R" Number of atoms: 5132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 5132 Classifications: {'RNAv2': 242} Modifications used: {'rna2p_pur': 27, 'rna2p_pyr': 34, 'rna3p_pur': 92, 'rna3p_pyr': 89} Link IDs: {'rna2p': 61, 'rna3p': 180} Chain breaks: 15 Residues with excluded nonbonded symmetry interactions: 17 residue: pdb=" P A R1748 " occ=0.80 ... (20 atoms not shown) pdb=" C4 A R1748 " occ=0.80 residue: pdb=" P U R1749 " occ=0.80 ... (18 atoms not shown) pdb=" C6 U R1749 " occ=0.80 residue: pdb=" P G R1750 " occ=0.80 ... (21 atoms not shown) pdb=" C4 G R1750 " occ=0.80 residue: pdb=" P A R1751 " occ=0.80 ... (20 atoms not shown) pdb=" C4 A R1751 " occ=0.80 residue: pdb=" P G R1752 " occ=0.80 ... (21 atoms not shown) pdb=" C4 G R1752 " occ=0.80 residue: pdb=" P G R1753 " occ=0.80 ... (21 atoms not shown) pdb=" C4 G R1753 " occ=0.80 residue: pdb=" P A R1754 " occ=0.80 ... (20 atoms not shown) pdb=" C4 A R1754 " occ=0.80 residue: pdb=" P U R1755 " occ=0.80 ... (18 atoms not shown) pdb=" C6 U R1755 " occ=0.80 residue: pdb=" P U R1756 " occ=0.80 ... (18 atoms not shown) pdb=" C6 U R1756 " occ=0.80 residue: pdb=" P A R1757 " occ=0.80 ... (20 atoms not shown) pdb=" C4 A R1757 " occ=0.80 residue: pdb=" P C R1758 " occ=0.80 ... (18 atoms not shown) pdb=" C6 C R1758 " occ=0.80 residue: pdb=" P C R1759 " occ=0.80 ... (18 atoms not shown) pdb=" C6 C R1759 " occ=0.80 ... (remaining 5 not shown) Time building chain proxies: 3.06, per 1000 atoms: 0.20 Number of scatterers: 15393 At special positions: 0 Unit cell: (206.7, 216.24, 261.82, 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 43 16.00 P 242 15.00 O 3669 8.00 N 2671 7.00 C 8768 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: 0.99 Conformation dependent library (CDL) restraints added in 519.2 milliseconds 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2522 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 9 sheets defined 26.6% alpha, 40.5% beta 17 base pairs and 71 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 25 through 29 Processing helix chain 'A' and resid 97 through 111 removed outlier: 3.829A pdb=" N LEU A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.603A pdb=" N GLY B 28 " --> pdb=" O PHE B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 112 removed outlier: 3.692A pdb=" N VAL B 105 " --> pdb=" O CYS B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 123 removed outlier: 3.532A pdb=" N ILE B 122 " --> pdb=" O ILE B 118 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 29 removed outlier: 3.847A pdb=" N GLY C 28 " --> pdb=" O PHE C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 41 removed outlier: 3.623A pdb=" N ALA C 41 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 112 removed outlier: 3.554A pdb=" N LEU C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 123 Processing helix chain 'D' and resid 25 through 27 No H-bonds generated for 'chain 'D' and resid 25 through 27' Processing helix chain 'D' and resid 97 through 112 removed outlier: 3.603A pdb=" N LEU D 103 " --> pdb=" O SER D 99 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU D 112 " --> pdb=" O MET D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 124 removed outlier: 3.514A pdb=" N ALA D 123 " --> pdb=" O PRO D 119 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA D 124 " --> pdb=" O SER D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 81 removed outlier: 3.552A pdb=" N ALA E 81 " --> pdb=" O PRO E 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 78 through 81' Processing helix chain 'E' and resid 97 through 112 removed outlier: 3.585A pdb=" N LEU E 103 " --> pdb=" O SER E 99 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU E 111 " --> pdb=" O ALA E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 123 Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.890A pdb=" N GLY F 28 " --> pdb=" O PHE F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 112 removed outlier: 3.687A pdb=" N ILE F 104 " --> pdb=" O ASP F 100 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU F 112 " --> pdb=" O MET F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 116 through 124 removed outlier: 3.530A pdb=" N ALA F 124 " --> pdb=" O SER F 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 29 removed outlier: 4.044A pdb=" N GLY G 28 " --> pdb=" O PHE G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 41 removed outlier: 3.573A pdb=" N ALA G 41 " --> pdb=" O ARG G 38 " (cutoff:3.500A) Processing helix chain 'G' and resid 97 through 112 removed outlier: 3.949A pdb=" N LEU G 103 " --> pdb=" O SER G 99 " (cutoff:3.500A) Processing helix chain 'G' and resid 116 through 123 removed outlier: 3.623A pdb=" N ALA G 123 " --> pdb=" O PRO G 119 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 29 removed outlier: 4.362A pdb=" N GLY H 28 " --> pdb=" O PHE H 25 " (cutoff:3.500A) Processing helix chain 'H' and resid 97 through 110 removed outlier: 3.590A pdb=" N LEU H 103 " --> pdb=" O SER H 99 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ILE H 104 " --> pdb=" O ASP H 100 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL H 105 " --> pdb=" O CYS H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 123 Processing helix chain 'M' and resid 98 through 104 removed outlier: 3.696A pdb=" N CYS M 101 " --> pdb=" O ALA M 98 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N TYR M 102 " --> pdb=" O ARG M 99 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER M 103 " --> pdb=" O SER M 100 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LEU M 104 " --> pdb=" O CYS M 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 98 through 104' Processing helix chain 'M' and resid 117 through 135 removed outlier: 4.056A pdb=" N ARG M 123 " --> pdb=" O ASN M 119 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LYS M 131 " --> pdb=" O GLU M 127 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR M 133 " --> pdb=" O LEU M 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 145 Processing helix chain 'M' and resid 145 through 150 Processing helix chain 'M' and resid 152 through 169 removed outlier: 3.580A pdb=" N GLN M 156 " --> pdb=" O GLN M 152 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA M 159 " --> pdb=" O THR M 155 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL M 161 " --> pdb=" O THR M 157 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA M 166 " --> pdb=" O LYS M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 176 Processing helix chain 'M' and resid 191 through 199 removed outlier: 3.717A pdb=" N LEU M 199 " --> pdb=" O ARG M 195 " (cutoff:3.500A) Processing helix chain 'M' and resid 199 through 220 Proline residue: M 205 - end of helix removed outlier: 3.663A pdb=" N GLN M 211 " --> pdb=" O MET M 207 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N MET M 216 " --> pdb=" O GLY M 212 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU M 217 " --> pdb=" O ALA M 213 " (cutoff:3.500A) Processing helix chain 'M' and resid 221 through 224 Processing helix chain 'M' and resid 294 through 300 removed outlier: 3.741A pdb=" N ASP M 298 " --> pdb=" O SER M 294 " (cutoff:3.500A) Processing helix chain 'M' and resid 300 through 312 removed outlier: 3.503A pdb=" N MET M 306 " --> pdb=" O PRO M 302 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLU M 308 " --> pdb=" O GLY M 304 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR M 311 " --> pdb=" O LEU M 307 " (cutoff:3.500A) Processing helix chain 'M' and resid 379 through 388 removed outlier: 3.722A pdb=" N ILE M 387 " --> pdb=" O ALA M 383 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 10 removed outlier: 6.710A pdb=" N VAL A 18 " --> pdb=" O LEU A 9 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N GLU A 31 " --> pdb=" O SER A 23 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS A 61 " --> pdb=" O THR A 45 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ARG A 56 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N THR A 91 " --> pdb=" O ARG A 56 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N TYR A 58 " --> pdb=" O GLU A 89 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N GLU A 89 " --> pdb=" O TYR A 58 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N ILE A 60 " --> pdb=" O ASN A 87 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ASN A 87 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL A 62 " --> pdb=" O TYR A 85 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N TYR A 85 " --> pdb=" O VAL A 62 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL A 64 " --> pdb=" O ARG A 83 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ARG A 83 " --> pdb=" O VAL A 64 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N LYS A 66 " --> pdb=" O ALA A 81 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL A 79 " --> pdb=" O ALA A 68 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 7 through 10 removed outlier: 7.131A pdb=" N VAL B 18 " --> pdb=" O LEU B 9 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLU B 31 " --> pdb=" O SER B 23 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ARG D 83 " --> pdb=" O PRO B 93 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N GLU D 76 " --> pdb=" O VAL D 72 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL D 72 " --> pdb=" O GLU D 76 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N GLN D 70 " --> pdb=" O PRO D 78 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N ALA D 80 " --> pdb=" O ALA D 68 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ALA D 68 " --> pdb=" O ALA D 80 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N TRP D 82 " --> pdb=" O LYS D 66 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG D 49 " --> pdb=" O LYS D 57 " (cutoff:3.500A) removed outlier: 7.261A pdb=" N GLU D 31 " --> pdb=" O SER D 23 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N VAL D 18 " --> pdb=" O LEU D 9 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 7 through 10 removed outlier: 6.891A pdb=" N VAL C 18 " --> pdb=" O LEU C 9 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N GLU C 31 " --> pdb=" O SER C 23 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS C 61 " --> pdb=" O THR C 45 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N TRP C 82 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ALA C 68 " --> pdb=" O ALA C 80 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N ALA C 80 " --> pdb=" O ALA C 68 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N GLN C 70 " --> pdb=" O PRO C 78 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N VAL C 72 " --> pdb=" O GLU C 76 " (cutoff:3.500A) removed outlier: 5.650A pdb=" N GLU C 76 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 7 through 10 removed outlier: 5.262A pdb=" N VAL E 8 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL E 20 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL E 10 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU E 31 " --> pdb=" O SER E 23 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE E 25 " --> pdb=" O VAL E 29 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N VAL E 29 " --> pdb=" O PHE E 25 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA E 30 " --> pdb=" O CYS E 46 " (cutoff:3.500A) removed outlier: 8.691A pdb=" N ARG F 83 " --> pdb=" O PRO E 93 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N GLU F 76 " --> pdb=" O VAL F 72 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N VAL F 72 " --> pdb=" O GLU F 76 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLN F 70 " --> pdb=" O PRO F 78 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ALA F 80 " --> pdb=" O ALA F 68 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA F 68 " --> pdb=" O ALA F 80 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N TRP F 82 " --> pdb=" O LYS F 66 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS F 61 " --> pdb=" O THR F 45 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLU F 31 " --> pdb=" O SER F 23 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL F 18 " --> pdb=" O LEU F 9 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE F 7 " --> pdb=" O VAL F 20 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 7 through 10 removed outlier: 5.262A pdb=" N VAL E 8 " --> pdb=" O VAL E 20 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL E 20 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL E 10 " --> pdb=" O VAL E 18 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU E 31 " --> pdb=" O SER E 23 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N PHE E 25 " --> pdb=" O VAL E 29 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N VAL E 29 " --> pdb=" O PHE E 25 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA E 30 " --> pdb=" O CYS E 46 " (cutoff:3.500A) removed outlier: 8.195A pdb=" N ARG E 83 " --> pdb=" O PRO F 93 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N LYS F 61 " --> pdb=" O THR F 45 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N GLU F 31 " --> pdb=" O SER F 23 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N VAL F 18 " --> pdb=" O LEU F 9 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE F 7 " --> pdb=" O VAL F 20 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 7 through 10 removed outlier: 6.858A pdb=" N VAL G 18 " --> pdb=" O LEU G 9 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N GLU G 31 " --> pdb=" O SER G 23 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS G 46 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS G 61 " --> pdb=" O THR G 45 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ARG G 49 " --> pdb=" O LYS G 57 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N SER G 51 " --> pdb=" O ASN G 55 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N ASN G 55 " --> pdb=" O SER G 51 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU G 90 " --> pdb=" O TYR G 58 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 7 through 10 removed outlier: 6.662A pdb=" N VAL H 18 " --> pdb=" O LEU H 9 " (cutoff:3.500A) removed outlier: 7.250A pdb=" N GLU H 31 " --> pdb=" O SER H 23 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS H 43 " --> pdb=" O GLU H 63 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS H 61 " --> pdb=" O THR H 45 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N GLN H 70 " --> pdb=" O PRO H 78 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'M' and resid 38 through 39 removed outlier: 6.745A pdb=" N LYS M 350 " --> pdb=" O THR M 68 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA M 351 " --> pdb=" O SER M 331 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE M 327 " --> pdb=" O ALA M 355 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N TRP M 264 " --> pdb=" O MET M 319 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N GLY M 321 " --> pdb=" O VAL M 262 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N VAL M 262 " --> pdb=" O GLY M 321 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL M 323 " --> pdb=" O ARG M 260 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG M 260 " --> pdb=" O VAL M 323 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N ASP M 325 " --> pdb=" O SER M 258 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N SER M 258 " --> pdb=" O ASP M 325 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE M 327 " --> pdb=" O ASN M 256 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N ASN M 256 " --> pdb=" O ILE M 327 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N GLY M 329 " --> pdb=" O THR M 254 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR M 254 " --> pdb=" O GLY M 329 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE M 261 " --> pdb=" O ARG M 232 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'M' and resid 44 through 45 removed outlier: 4.067A pdb=" N PHE M 44 " --> pdb=" O SER M 61 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N SER M 61 " --> pdb=" O PHE M 44 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR M 60 " --> pdb=" O ARG M 358 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA M 351 " --> pdb=" O SER M 331 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE M 327 " --> pdb=" O ALA M 355 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ALA M 369 " --> pdb=" O CYS M 316 " (cutoff:3.500A) 469 hydrogen bonds defined for protein. 1284 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 39 hydrogen bonds 78 hydrogen bond angles 0 basepair planarities 17 basepair parallelities 71 stacking parallelities Total time for adding SS restraints: 2.28 Time building geometry restraints manager: 1.41 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: 3967 1.34 - 1.45: 4322 1.45 - 1.57: 7348 1.57 - 1.69: 468 1.69 - 1.81: 67 Bond restraints: 16172 Sorted by residual: bond pdb=" C LEU M 104 " pdb=" N PHE M 105 " ideal model delta sigma weight residual 1.330 1.232 0.098 1.47e-02 4.63e+03 4.49e+01 bond pdb=" C VAL E 20 " pdb=" N ALA E 21 " ideal model delta sigma weight residual 1.331 1.390 -0.059 1.59e-02 3.96e+03 1.37e+01 bond pdb=" C TYR F 129 " pdb=" O TYR F 129 " ideal model delta sigma weight residual 1.231 1.277 -0.046 2.00e-02 2.50e+03 5.40e+00 bond pdb=" C TYR F 129 " pdb=" OXT TYR F 129 " ideal model delta sigma weight residual 1.231 1.277 -0.046 2.00e-02 2.50e+03 5.26e+00 bond pdb=" C ILE G 118 " pdb=" N PRO G 119 " ideal model delta sigma weight residual 1.335 1.350 -0.015 9.40e-03 1.13e+04 2.53e+00 ... (remaining 16167 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.92: 23046 3.92 - 7.83: 48 7.83 - 11.75: 5 11.75 - 15.67: 0 15.67 - 19.59: 1 Bond angle restraints: 23100 Sorted by residual: angle pdb=" C LEU M 104 " pdb=" N PHE M 105 " pdb=" CA PHE M 105 " ideal model delta sigma weight residual 120.68 140.27 -19.59 1.52e+00 4.33e-01 1.66e+02 angle pdb=" C LEU M 179 " pdb=" N ALA M 180 " pdb=" CA ALA M 180 " ideal model delta sigma weight residual 122.40 127.50 -5.10 1.45e+00 4.76e-01 1.24e+01 angle pdb=" N VAL B 67 " pdb=" CA VAL B 67 " pdb=" C VAL B 67 " ideal model delta sigma weight residual 112.96 109.49 3.47 1.00e+00 1.00e+00 1.21e+01 angle pdb=" C ASN M 110 " pdb=" N LEU M 111 " pdb=" CA LEU M 111 " ideal model delta sigma weight residual 123.05 128.30 -5.25 1.57e+00 4.06e-01 1.12e+01 angle pdb=" C ALA H 26 " pdb=" N ASN H 27 " pdb=" CA ASN H 27 " ideal model delta sigma weight residual 122.40 127.18 -4.78 1.45e+00 4.76e-01 1.09e+01 ... (remaining 23095 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.49: 8417 34.49 - 68.99: 616 68.99 - 103.48: 70 103.48 - 137.97: 0 137.97 - 172.46: 10 Dihedral angle restraints: 9113 sinusoidal: 5210 harmonic: 3903 Sorted by residual: dihedral pdb=" C4' U R 190 " pdb=" C3' U R 190 " pdb=" C2' U R 190 " pdb=" C1' U R 190 " ideal model delta sinusoidal sigma weight residual 36.34 -36.29 72.64 1 3.10e+00 1.04e-01 7.01e+02 dihedral pdb=" C4' U R 188 " pdb=" C3' U R 188 " pdb=" C2' U R 188 " pdb=" C1' U R 188 " ideal model delta sinusoidal sigma weight residual 36.34 -36.29 72.63 1 3.10e+00 1.04e-01 7.01e+02 dihedral pdb=" C4' U R2845 " pdb=" C3' U R2845 " pdb=" C2' U R2845 " pdb=" C1' U R2845 " ideal model delta sinusoidal sigma weight residual 36.34 -36.27 72.61 1 3.10e+00 1.04e-01 7.00e+02 ... (remaining 9110 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 1720 0.054 - 0.109: 302 0.109 - 0.163: 324 0.163 - 0.217: 506 0.217 - 0.271: 19 Chirality restraints: 2871 Sorted by residual: chirality pdb=" CB VAL H 20 " pdb=" CA VAL H 20 " pdb=" CG1 VAL H 20 " pdb=" CG2 VAL H 20 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.84e+00 chirality pdb=" CB VAL F 20 " pdb=" CA VAL F 20 " pdb=" CG1 VAL F 20 " pdb=" CG2 VAL F 20 " both_signs ideal model delta sigma weight residual False -2.63 -2.40 -0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" P C R2374 " pdb=" OP1 C R2374 " pdb=" OP2 C R2374 " pdb=" O5' C R2374 " both_signs ideal model delta sigma weight residual True 2.17 -2.40 -0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 2868 not shown) Planarity restraints: 2074 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 64 " -0.045 5.00e-02 4.00e+02 6.75e-02 7.30e+00 pdb=" N PRO F 65 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO F 65 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 65 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU M 204 " 0.045 5.00e-02 4.00e+02 6.71e-02 7.20e+00 pdb=" N PRO M 205 " -0.116 5.00e-02 4.00e+02 pdb=" CA PRO M 205 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO M 205 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 64 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.37e+00 pdb=" N PRO H 65 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO H 65 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 65 " -0.035 5.00e-02 4.00e+02 ... (remaining 2071 not shown) Histogram of nonbonded interaction distances: 1.13 - 1.88: 14 1.88 - 2.64: 394 2.64 - 3.39: 19273 3.39 - 4.15: 37897 4.15 - 4.90: 61108 Nonbonded interactions: 118686 Sorted by model distance: nonbonded pdb=" NH1 ARG E 56 " pdb=" OD1 ASN F 125 " model vdw 1.126 3.120 nonbonded pdb=" OG SER M 58 " pdb=" O6 G R3555 " model vdw 1.430 3.040 nonbonded pdb=" O ALA B 1 " pdb=" CE2 TYR D 129 " model vdw 1.444 3.340 nonbonded pdb=" CB ALA B 1 " pdb=" OH TYR D 129 " model vdw 1.483 3.460 nonbonded pdb=" OD1 ASP E 114 " pdb=" NE2 GLN F 109 " model vdw 1.649 3.120 ... (remaining 118681 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 'A' and (resid 1 through 67 or resid 78 through 129)) selection = (chain 'B' and (resid 1 through 67 or resid 78 through 129)) selection = (chain 'C' and (resid 1 through 67 or resid 78 through 129)) selection = (chain 'D' and (resid 1 through 67 or resid 78 through 129)) selection = (chain 'E' and (resid 1 through 67 or resid 78 through 129)) selection = (chain 'F' and (resid 1 through 67 or resid 78 through 129)) selection = chain 'G' selection = (chain 'H' and (resid 1 through 67 or resid 78 through 129)) } 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=0.80 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 2.790 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: 0.460 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.950 Find NCS groups from input model: 0.180 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:1.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 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 : 0.006 0.098 16172 Z= 0.267 Angle : 0.969 19.587 23100 Z= 0.493 Chirality : 0.102 0.271 2871 Planarity : 0.007 0.068 2074 Dihedral : 20.956 172.464 6591 Min Nonbonded Distance : 1.126 Molprobity Statistics. All-atom Clashscore : 33.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.27 % Allowed : 1.25 % Favored : 98.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -3.80 (0.19), residues: 1324 helix: -4.62 (0.09), residues: 332 sheet: -0.77 (0.25), residues: 423 loop : -2.45 (0.21), residues: 569 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 195 TYR 0.022 0.003 TYR A 42 PHE 0.028 0.004 PHE A 4 TRP 0.018 0.002 TRP F 32 HIS 0.008 0.002 HIS M 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.27 (16172) covalent geometry : angle 0.96900 / 0.49 (23100) hydrogen bonds : bond 0.30493 / 20.59 ( 459) hydrogen bonds : angle 10.96330 / 7.54 ( 1362) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 333 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 57 LYS cc_start: 0.8996 (tttt) cc_final: 0.8783 (tttm) REVERT: A 66 LYS cc_start: 0.8203 (tptt) cc_final: 0.7890 (tptm) REVERT: A 88 MET cc_start: 0.8541 (ptp) cc_final: 0.6644 (mmt) REVERT: A 100 ASP cc_start: 0.8671 (m-30) cc_final: 0.8392 (m-30) REVERT: A 106 LYS cc_start: 0.8835 (mttm) cc_final: 0.7469 (tmtt) REVERT: E 97 THR cc_start: 0.8850 (p) cc_final: 0.8602 (p) REVERT: E 128 ILE cc_start: 0.8729 (mm) cc_final: 0.8325 (mm) REVERT: F 12 ASN cc_start: 0.7832 (m-40) cc_final: 0.7523 (t0) REVERT: G 38 ARG cc_start: 0.8012 (tpm-80) cc_final: 0.6293 (ptt-90) REVERT: H 100 ASP cc_start: 0.8231 (m-30) cc_final: 0.7689 (m-30) REVERT: M 308 GLU cc_start: 0.7479 (mt-10) cc_final: 0.7240 (mt-10) REVERT: M 350 LYS cc_start: 0.8329 (mttt) cc_final: 0.8079 (mtpp) outliers start: 3 outliers final: 1 residues processed: 335 average time/residue: 0.1109 time to fit residues: 55.4425 Evaluate side-chains 210 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 129 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 130 optimal weight: 20.0000 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 9.9990 chunk 149 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN B 3 ASN B 116 ASN C 98 ASN D 36 ASN F 6 GLN F 109 GLN F 116 ASN G 54 GLN G 116 ASN H 70 GLN M 11 ASN ** M 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 221 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 352 GLN M 357 HIS M 389 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.121577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.097503 restraints weight = 29753.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.099422 restraints weight = 15460.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.099901 restraints weight = 10333.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.099993 restraints weight = 8254.023| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.100861 restraints weight = 8081.888| |-----------------------------------------------------------------------------| r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.80 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3176 r_free = 0.3176 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 13 (19 function evaluations) r_final: 0.3176 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.3217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 16172 Z= 0.297 Angle : 1.323 18.863 23100 Z= 0.540 Chirality : 0.101 0.954 2871 Planarity : 0.006 0.051 2074 Dihedral : 20.055 178.093 4303 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.03 % Allowed : 10.62 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -2.54 (0.20), residues: 1324 helix: -2.74 (0.20), residues: 327 sheet: -0.54 (0.24), residues: 449 loop : -1.85 (0.24), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 123 TYR 0.018 0.002 TYR F 58 PHE 0.030 0.003 PHE M 105 TRP 0.020 0.002 TRP M 54 HIS 0.005 0.001 HIS M 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00650 / 0.30 (16172) covalent geometry : angle 1.32346 / 0.54 (23100) hydrogen bonds : bond 0.06472 / 4.62 ( 459) hydrogen bonds : angle 5.75669 / 4.05 ( 1362) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 197 time to evaluate : 0.421 Fit side-chains REVERT: A 88 MET cc_start: 0.8054 (ptp) cc_final: 0.6708 (mmt) REVERT: A 106 LYS cc_start: 0.8938 (mttm) cc_final: 0.7448 (tmtt) REVERT: F 33 ILE cc_start: 0.8531 (OUTLIER) cc_final: 0.8219 (pp) REVERT: F 56 ARG cc_start: 0.8270 (mtp-110) cc_final: 0.7556 (mtp180) REVERT: G 38 ARG cc_start: 0.8337 (tpm-80) cc_final: 0.6647 (ptt-90) REVERT: H 100 ASP cc_start: 0.8008 (m-30) cc_final: 0.7798 (m-30) REVERT: M 127 GLU cc_start: 0.8057 (mt-10) cc_final: 0.7804 (mt-10) outliers start: 34 outliers final: 25 residues processed: 220 average time/residue: 0.0993 time to fit residues: 34.2416 Evaluate side-chains 185 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 19 THR Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 114 ASP Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 145 GLU Chi-restraints excluded: chain M residue 319 MET Chi-restraints excluded: chain M residue 324 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 64 optimal weight: 8.9990 chunk 141 optimal weight: 20.0000 chunk 92 optimal weight: 0.9980 chunk 3 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 60 optimal weight: 5.9990 chunk 119 optimal weight: 9.9990 chunk 111 optimal weight: 10.0000 chunk 113 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 98 optimal weight: 9.9990 overall best weight: 6.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 3 ASN ** C 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 116 ASN H 27 ASN M 109 GLN ** M 211 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 221 HIS ** M 282 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.117956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.096752 restraints weight = 29979.721| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.098374 restraints weight = 15019.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.099610 restraints weight = 10567.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.099766 restraints weight = 7430.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.100043 restraints weight = 7421.602| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 37 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3200 r_free = 0.3200 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 65 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (15 function evaluations) r_final: 0.3200 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 16172 Z= 0.235 Angle : 1.050 15.725 23100 Z= 0.439 Chirality : 0.080 0.806 2871 Planarity : 0.005 0.044 2074 Dihedral : 19.658 179.887 4303 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 3.66 % Allowed : 13.11 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.75 (0.22), residues: 1324 helix: -1.55 (0.25), residues: 325 sheet: -0.21 (0.24), residues: 448 loop : -1.60 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 123 TYR 0.020 0.002 TYR F 58 PHE 0.024 0.003 PHE M 105 TRP 0.016 0.002 TRP F 32 HIS 0.007 0.002 HIS M 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00528 / 0.23 (16172) covalent geometry : angle 1.04981 / 0.44 (23100) hydrogen bonds : bond 0.05168 / 3.69 ( 459) hydrogen bonds : angle 5.16297 / 3.63 ( 1362) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 163 time to evaluate : 0.449 Fit side-chains REVERT: A 106 LYS cc_start: 0.8994 (mttm) cc_final: 0.7564 (tmtt) REVERT: D 33 ILE cc_start: 0.8932 (pp) cc_final: 0.8659 (pt) REVERT: F 33 ILE cc_start: 0.8486 (OUTLIER) cc_final: 0.8133 (pp) REVERT: G 38 ARG cc_start: 0.8404 (tpm-80) cc_final: 0.6607 (ptt-90) outliers start: 41 outliers final: 26 residues processed: 192 average time/residue: 0.0936 time to fit residues: 28.9560 Evaluate side-chains 175 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 148 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 100 ASP Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain H residue 97 THR Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 145 GLU Chi-restraints excluded: chain M residue 183 GLU Chi-restraints excluded: chain M residue 324 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 110 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 5 optimal weight: 0.0470 chunk 9 optimal weight: 0.0470 chunk 3 optimal weight: 5.9990 chunk 99 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 32 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 80 optimal weight: 9.9990 overall best weight: 2.1980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 40 GLN A 87 ASN B 3 ASN C 36 ASN D 6 GLN G 40 GLN H 27 ASN M 211 GLN M 282 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.119520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.099165 restraints weight = 30045.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.100788 restraints weight = 15273.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.101919 restraints weight = 10683.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.102064 restraints weight = 7548.385| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.102238 restraints weight = 7557.973| |-----------------------------------------------------------------------------| r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3243 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 65 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3241 r_free = 0.3241 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 88 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 7 (15 function evaluations) r_final: 0.3241 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16172 Z= 0.135 Angle : 0.922 13.980 23100 Z= 0.380 Chirality : 0.071 0.624 2871 Planarity : 0.004 0.037 2074 Dihedral : 19.143 179.666 4303 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 2.59 % Allowed : 15.08 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.06 (0.22), residues: 1324 helix: -0.82 (0.27), residues: 323 sheet: 0.18 (0.24), residues: 442 loop : -1.27 (0.25), residues: 559 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 56 TYR 0.014 0.001 TYR B 42 PHE 0.020 0.002 PHE H 4 TRP 0.014 0.001 TRP F 32 HIS 0.003 0.001 HIS M 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (16172) covalent geometry : angle 0.92150 / 0.38 (23100) hydrogen bonds : bond 0.04202 / 3.01 ( 459) hydrogen bonds : angle 4.59133 / 3.22 ( 1362) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 0.434 Fit side-chains REVERT: A 88 MET cc_start: 0.7896 (ptp) cc_final: 0.6283 (mmt) REVERT: A 106 LYS cc_start: 0.8979 (mttm) cc_final: 0.7427 (tmtt) REVERT: E 29 VAL cc_start: 0.9449 (t) cc_final: 0.9101 (m) REVERT: E 128 ILE cc_start: 0.8860 (mm) cc_final: 0.8397 (mm) REVERT: F 33 ILE cc_start: 0.8413 (OUTLIER) cc_final: 0.8095 (pp) REVERT: F 56 ARG cc_start: 0.8220 (mtp-110) cc_final: 0.7446 (mtp180) REVERT: G 38 ARG cc_start: 0.8368 (tpm-80) cc_final: 0.6568 (ptt-90) REVERT: M 388 ARG cc_start: 0.8273 (mtt180) cc_final: 0.7912 (ttm110) outliers start: 29 outliers final: 16 residues processed: 196 average time/residue: 0.1008 time to fit residues: 30.7810 Evaluate side-chains 178 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 161 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 ASP Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 6 GLN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 319 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 72 optimal weight: 10.0000 chunk 109 optimal weight: 9.9990 chunk 103 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 20 optimal weight: 10.0000 chunk 92 optimal weight: 0.0030 chunk 149 optimal weight: 20.0000 chunk 15 optimal weight: 20.0000 chunk 64 optimal weight: 8.9990 chunk 70 optimal weight: 6.9990 overall best weight: 3.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN M 211 GLN M 252 GLN M 282 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.119615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.098758 restraints weight = 29871.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.100840 restraints weight = 14828.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.102193 restraints weight = 9391.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.103053 restraints weight = 6910.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.103670 restraints weight = 5595.126| |-----------------------------------------------------------------------------| r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3280 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3280 r_free = 0.3280 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 88 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3278 r_free = 0.3278 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 100 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (13 function evaluations) r_final: 0.3278 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 16172 Z= 0.160 Angle : 0.906 13.407 23100 Z= 0.377 Chirality : 0.070 0.615 2871 Planarity : 0.004 0.040 2074 Dihedral : 18.827 179.880 4303 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.03 % Allowed : 14.72 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.69 (0.23), residues: 1324 helix: -0.41 (0.28), residues: 324 sheet: 0.49 (0.25), residues: 428 loop : -1.17 (0.25), residues: 572 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 49 TYR 0.015 0.001 TYR B 42 PHE 0.014 0.002 PHE C 4 TRP 0.013 0.001 TRP H 32 HIS 0.004 0.001 HIS M 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.16 (16172) covalent geometry : angle 0.90585 / 0.38 (23100) hydrogen bonds : bond 0.04159 / 2.99 ( 459) hydrogen bonds : angle 4.59692 / 3.24 ( 1362) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 169 time to evaluate : 0.485 Fit side-chains REVERT: A 106 LYS cc_start: 0.9169 (mttm) cc_final: 0.7666 (tmtt) REVERT: F 33 ILE cc_start: 0.8496 (OUTLIER) cc_final: 0.8182 (pp) REVERT: F 129 TYR cc_start: 0.6125 (OUTLIER) cc_final: 0.4486 (t80) REVERT: G 38 ARG cc_start: 0.8377 (tpm-80) cc_final: 0.6590 (ptt-90) REVERT: M 228 MET cc_start: 0.8908 (mtm) cc_final: 0.8675 (mtm) REVERT: M 388 ARG cc_start: 0.8287 (mtt180) cc_final: 0.7993 (ttm110) outliers start: 34 outliers final: 22 residues processed: 188 average time/residue: 0.1029 time to fit residues: 30.5544 Evaluate side-chains 184 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 160 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 87 ASN Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 319 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 60 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 68 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 108 optimal weight: 0.0570 chunk 86 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 78 optimal weight: 0.5980 chunk 42 optimal weight: 10.0000 overall best weight: 3.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.120205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.099393 restraints weight = 29673.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.101505 restraints weight = 14262.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.102906 restraints weight = 8898.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.103811 restraints weight = 6472.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.104332 restraints weight = 5169.881| |-----------------------------------------------------------------------------| r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3286 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 100 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3286 r_free = 0.3286 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 100 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3286 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16172 Z= 0.151 Angle : 0.879 11.863 23100 Z= 0.366 Chirality : 0.069 0.591 2871 Planarity : 0.004 0.038 2074 Dihedral : 18.710 178.473 4303 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 3.39 % Allowed : 14.81 % Favored : 81.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.44 (0.23), residues: 1324 helix: -0.13 (0.28), residues: 323 sheet: 0.61 (0.26), residues: 410 loop : -0.98 (0.25), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 56 TYR 0.014 0.001 TYR B 42 PHE 0.016 0.002 PHE H 4 TRP 0.014 0.001 TRP H 32 HIS 0.004 0.001 HIS M 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.15 (16172) covalent geometry : angle 0.87903 / 0.37 (23100) hydrogen bonds : bond 0.03948 / 2.81 ( 459) hydrogen bonds : angle 4.44824 / 3.14 ( 1362) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 171 time to evaluate : 0.450 Fit side-chains REVERT: A 106 LYS cc_start: 0.9126 (mttm) cc_final: 0.7543 (tmtt) REVERT: F 33 ILE cc_start: 0.8371 (OUTLIER) cc_final: 0.8022 (pp) REVERT: F 56 ARG cc_start: 0.8306 (mtp-110) cc_final: 0.7653 (mtp180) REVERT: F 129 TYR cc_start: 0.6037 (OUTLIER) cc_final: 0.4319 (t80) REVERT: G 38 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.6600 (ptt-90) REVERT: M 228 MET cc_start: 0.8925 (mtm) cc_final: 0.8689 (mtm) REVERT: M 388 ARG cc_start: 0.8342 (mtt180) cc_final: 0.8017 (ttm110) outliers start: 38 outliers final: 28 residues processed: 194 average time/residue: 0.1029 time to fit residues: 31.0321 Evaluate side-chains 192 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 161 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 318 TYR Chi-restraints excluded: chain M residue 319 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 18 optimal weight: 7.9990 chunk 103 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 112 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 3 optimal weight: 9.9990 chunk 32 optimal weight: 6.9990 chunk 41 optimal weight: 20.0000 chunk 15 optimal weight: 10.0000 chunk 64 optimal weight: 4.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 GLN A 87 ASN F 109 GLN M 379 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.116177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.096208 restraints weight = 29764.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.097775 restraints weight = 14935.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.098913 restraints weight = 10595.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.099429 restraints weight = 7631.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.099595 restraints weight = 7507.435| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3205 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 100 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3205 r_free = 0.3205 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 101 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3205 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.067 16172 Z= 0.239 Angle : 0.977 16.804 23100 Z= 0.411 Chirality : 0.075 0.646 2871 Planarity : 0.005 0.042 2074 Dihedral : 18.792 178.610 4303 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 3.75 % Allowed : 14.72 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.56 (0.23), residues: 1324 helix: -0.32 (0.28), residues: 323 sheet: 0.55 (0.25), residues: 423 loop : -1.04 (0.25), residues: 578 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 56 TYR 0.016 0.002 TYR E 129 PHE 0.016 0.002 PHE C 4 TRP 0.015 0.002 TRP B 32 HIS 0.008 0.002 HIS M 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00550 / 0.24 (16172) covalent geometry : angle 0.97666 / 0.41 (23100) hydrogen bonds : bond 0.04519 / 3.22 ( 459) hydrogen bonds : angle 4.80334 / 3.40 ( 1362) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 165 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 106 LYS cc_start: 0.9164 (mttm) cc_final: 0.7646 (tmtt) REVERT: B 6 GLN cc_start: 0.8417 (pt0) cc_final: 0.8214 (pt0) REVERT: F 33 ILE cc_start: 0.8499 (OUTLIER) cc_final: 0.8166 (pp) REVERT: G 38 ARG cc_start: 0.8536 (OUTLIER) cc_final: 0.6658 (ptt-90) REVERT: M 388 ARG cc_start: 0.8305 (mtt180) cc_final: 0.8019 (ttm110) outliers start: 42 outliers final: 32 residues processed: 190 average time/residue: 0.0940 time to fit residues: 28.1669 Evaluate side-chains 191 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain G residue 92 ILE Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 183 GLU Chi-restraints excluded: chain M residue 216 MET Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 318 TYR Chi-restraints excluded: chain M residue 319 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 93 optimal weight: 2.9990 chunk 95 optimal weight: 8.9990 chunk 143 optimal weight: 10.0000 chunk 147 optimal weight: 30.0000 chunk 3 optimal weight: 5.9990 chunk 134 optimal weight: 30.0000 chunk 37 optimal weight: 8.9990 chunk 67 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 43 optimal weight: 7.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN C 36 ASN H 27 ASN M 252 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.117185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.096719 restraints weight = 30167.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.098713 restraints weight = 15208.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.100025 restraints weight = 9739.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.100887 restraints weight = 7190.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.101459 restraints weight = 5819.924| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 101 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 104 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (11 function evaluations) r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.4949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 16172 Z= 0.202 Angle : 0.935 13.565 23100 Z= 0.391 Chirality : 0.073 0.632 2871 Planarity : 0.004 0.042 2074 Dihedral : 18.647 177.965 4303 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 3.21 % Allowed : 16.32 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.48 (0.23), residues: 1324 helix: -0.17 (0.28), residues: 323 sheet: 0.64 (0.25), residues: 434 loop : -1.11 (0.26), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 56 TYR 0.016 0.002 TYR E 129 PHE 0.017 0.002 PHE H 4 TRP 0.019 0.002 TRP B 32 HIS 0.006 0.001 HIS M 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.20 (16172) covalent geometry : angle 0.93538 / 0.39 (23100) hydrogen bonds : bond 0.04273 / 3.04 ( 459) hydrogen bonds : angle 4.63499 / 3.27 ( 1362) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 163 time to evaluate : 0.529 Fit side-chains REVERT: A 106 LYS cc_start: 0.9137 (mttm) cc_final: 0.7656 (tmtt) REVERT: F 33 ILE cc_start: 0.8449 (OUTLIER) cc_final: 0.8110 (pp) REVERT: G 38 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.6711 (ptt-90) REVERT: M 388 ARG cc_start: 0.8326 (mtt180) cc_final: 0.8033 (ttm110) outliers start: 36 outliers final: 32 residues processed: 185 average time/residue: 0.1098 time to fit residues: 31.9085 Evaluate side-chains 192 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 158 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 70 GLN Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain F residue 33 ILE Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 103 LEU Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain G residue 6 GLN Chi-restraints excluded: chain G residue 38 ARG Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 20 VAL Chi-restraints excluded: chain H residue 33 ILE Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 110 ASN Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 183 GLU Chi-restraints excluded: chain M residue 216 MET Chi-restraints excluded: chain M residue 231 VAL Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 318 TYR Chi-restraints excluded: chain M residue 319 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 75 optimal weight: 5.9990 chunk 6 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 89 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 122 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN C 36 ASN D 109 GLN F 109 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.122158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.101605 restraints weight = 29503.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.103695 restraints weight = 14546.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.105049 restraints weight = 9125.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.105871 restraints weight = 6655.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.106503 restraints weight = 5382.408| |-----------------------------------------------------------------------------| r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3318 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 104 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3318 r_free = 0.3318 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 104 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3318 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8203 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16172 Z= 0.124 Angle : 0.842 11.491 23100 Z= 0.349 Chirality : 0.066 0.556 2871 Planarity : 0.004 0.039 2074 Dihedral : 18.388 178.265 4303 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.77 % Allowed : 16.86 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.09 (0.23), residues: 1324 helix: 0.38 (0.30), residues: 323 sheet: 0.85 (0.26), residues: 402 loop : -0.91 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 229 TYR 0.014 0.001 TYR B 42 PHE 0.016 0.001 PHE H 4 TRP 0.020 0.002 TRP H 32 HIS 0.002 0.001 HIS M 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 (16172) covalent geometry : angle 0.84153 / 0.35 (23100) hydrogen bonds : bond 0.03635 / 2.56 ( 459) hydrogen bonds : angle 4.25054 / 2.98 ( 1362) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 182 time to evaluate : 0.466 Fit side-chains REVERT: A 49 ARG cc_start: 0.8139 (ptt-90) cc_final: 0.7924 (ptt-90) REVERT: A 106 LYS cc_start: 0.9177 (mttm) cc_final: 0.7637 (tmtt) REVERT: B 15 THR cc_start: 0.8365 (t) cc_final: 0.8102 (m) REVERT: C 88 MET cc_start: 0.7868 (OUTLIER) cc_final: 0.7615 (ptp) REVERT: E 106 LYS cc_start: 0.8651 (mttp) cc_final: 0.8418 (mtpt) REVERT: F 56 ARG cc_start: 0.8190 (mtp-110) cc_final: 0.7855 (ttm170) REVERT: F 129 TYR cc_start: 0.5728 (OUTLIER) cc_final: 0.4274 (t80) REVERT: G 36 ASN cc_start: 0.6699 (t0) cc_final: 0.6425 (m-40) REVERT: G 38 ARG cc_start: 0.8402 (tpm-80) cc_final: 0.6571 (ptt-90) REVERT: M 388 ARG cc_start: 0.8312 (mtt180) cc_final: 0.7975 (ttm110) outliers start: 31 outliers final: 19 residues processed: 200 average time/residue: 0.1113 time to fit residues: 34.7339 Evaluate side-chains 189 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 88 MET Chi-restraints excluded: chain A residue 97 THR Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 183 GLU Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 318 TYR Chi-restraints excluded: chain M residue 319 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 123 optimal weight: 0.8980 chunk 5 optimal weight: 7.9990 chunk 133 optimal weight: 20.0000 chunk 77 optimal weight: 8.9990 chunk 24 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 chunk 132 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 45 optimal weight: 9.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 109 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.117471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.096841 restraints weight = 30066.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.098942 restraints weight = 14713.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.100319 restraints weight = 9236.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.101189 restraints weight = 6737.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.101791 restraints weight = 5416.331| |-----------------------------------------------------------------------------| r_work (final): 0.3239 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 104 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 103 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3239 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 0.5134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16172 Z= 0.211 Angle : 0.940 14.515 23100 Z= 0.396 Chirality : 0.072 0.592 2871 Planarity : 0.004 0.041 2074 Dihedral : 18.472 177.996 4303 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 2.50 % Allowed : 17.57 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % 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: -0.31 (0.23), residues: 1324 helix: 0.10 (0.29), residues: 323 sheet: 0.77 (0.26), residues: 408 loop : -1.05 (0.25), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 56 TYR 0.020 0.002 TYR B 129 PHE 0.021 0.002 PHE M 265 TRP 0.020 0.002 TRP B 32 HIS 0.007 0.002 HIS M 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00482 / 0.21 (16172) covalent geometry : angle 0.93962 / 0.40 (23100) hydrogen bonds : bond 0.04302 / 3.04 ( 459) hydrogen bonds : angle 4.64315 / 3.27 ( 1362) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2648 Ramachandran restraints generated. 1324 Oldfield, 0 Emsley, 1324 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 157 time to evaluate : 0.475 Fit side-chains REVERT: A 106 LYS cc_start: 0.9148 (mttm) cc_final: 0.7628 (tmtt) REVERT: B 15 THR cc_start: 0.8454 (t) cc_final: 0.8210 (m) REVERT: E 50 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7147 (mp10) REVERT: G 38 ARG cc_start: 0.8459 (tpm-80) cc_final: 0.6768 (ptt90) REVERT: M 388 ARG cc_start: 0.8382 (mtt180) cc_final: 0.8040 (ttm110) outliers start: 28 outliers final: 22 residues processed: 176 average time/residue: 0.1113 time to fit residues: 30.8155 Evaluate side-chains 176 residues out of total 1121 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 153 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 VAL Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 118 ILE Chi-restraints excluded: chain C residue 15 THR Chi-restraints excluded: chain C residue 18 VAL Chi-restraints excluded: chain C residue 20 VAL Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 88 MET Chi-restraints excluded: chain C residue 112 LEU Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 35 SER Chi-restraints excluded: chain E residue 50 GLN Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 114 ASP Chi-restraints excluded: chain F residue 129 TYR Chi-restraints excluded: chain H residue 15 THR Chi-restraints excluded: chain H residue 35 SER Chi-restraints excluded: chain M residue 58 SER Chi-restraints excluded: chain M residue 141 VAL Chi-restraints excluded: chain M residue 183 GLU Chi-restraints excluded: chain M residue 253 THR Chi-restraints excluded: chain M residue 318 TYR Chi-restraints excluded: chain M residue 319 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 43 optimal weight: 5.9990 chunk 48 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 150 optimal weight: 20.0000 chunk 36 optimal weight: 9.9990 chunk 137 optimal weight: 20.0000 chunk 19 optimal weight: 0.0070 chunk 2 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 145 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 overall best weight: 3.2004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 36 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.120073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.099328 restraints weight = 29621.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.101460 restraints weight = 14256.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.102765 restraints weight = 8869.844| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.103701 restraints weight = 6519.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.104238 restraints weight = 5218.358| |-----------------------------------------------------------------------------| r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3281 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 103 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3281 r_free = 0.3281 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 102 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3281 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.5271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16172 Z= 0.146 Angle : 0.871 12.380 23100 Z= 0.365 Chirality : 0.068 0.591 2871 Planarity : 0.004 0.040 2074 Dihedral : 18.363 178.096 4303 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.05 % Allowed : 17.57 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.10 (0.23), residues: 1324 helix: 0.36 (0.30), residues: 323 sheet: 0.86 (0.26), residues: 402 loop : -0.93 (0.25), residues: 599 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG H 56 TYR 0.016 0.001 TYR B 129 PHE 0.017 0.002 PHE E 7 TRP 0.019 0.002 TRP B 32 HIS 0.003 0.001 HIS M 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.15 (16172) covalent geometry : angle 0.87123 / 0.36 (23100) hydrogen bonds : bond 0.03870 / 2.74 ( 459) hydrogen bonds : angle 4.38377 / 3.07 ( 1362) =============================================================================== Job complete usr+sys time: 4278.15 seconds wall clock time: 73 minutes 52.40 seconds (4432.40 seconds total)