Starting phenix.real_space_refine on Fri Aug 7 05:33:46 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rc3_19046/08_2026/8rc3_19046.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rc3_19046/08_2026/8rc3_19046.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8rc3_19046/08_2026/8rc3_19046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rc3_19046/08_2026/8rc3_19046.map" model { file = "/net/cci-nas-00/data/ceres_data/8rc3_19046/08_2026/8rc3_19046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rc3_19046/08_2026/8rc3_19046.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.042 sd= 0.155 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 111 5.49 5 S 71 5.16 5 C 12179 2.51 5 N 3536 2.21 5 O 3995 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 19893 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 2491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 329, 2491 Classifications: {'peptide': 329} Link IDs: {'PTRANS': 18, 'TRANS': 310} Chain breaks: 1 Chain: "B" Number of atoms: 2510 Number of conformers: 1 Conformer: "" Number of residues, atoms: 332, 2510 Classifications: {'peptide': 332} Link IDs: {'PTRANS': 18, 'TRANS': 313} Chain breaks: 1 Chain: "C" Number of atoms: 2502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2502 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 18, 'TRANS': 312} Chain breaks: 1 Chain: "D" Number of atoms: 2504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 331, 2504 Classifications: {'peptide': 331} Link IDs: {'PTRANS': 18, 'TRANS': 312} Chain breaks: 1 Chain: "E" Number of atoms: 2153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2153 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 16, 'TRANS': 266} Chain breaks: 1 Chain: "F" Number of atoms: 1719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1719 Classifications: {'peptide': 222} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 208} Chain: "G" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1913 Classifications: {'peptide': 240} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 222} Chain: "H" Number of atoms: 1195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1195 Classifications: {'RNA': 56} Modifications used: {'5*END': 1, 'rna2p_pur': 15, 'rna2p_pyr': 10, 'rna3p_pur': 15, 'rna3p_pyr': 16} Link IDs: {'rna2p': 25, 'rna3p': 30} Chain breaks: 1 Chain: "I" Number of atoms: 821 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 821 Classifications: {'DNA': 40} Link IDs: {'rna3p': 39} Chain: "J" Number of atoms: 330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 330 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Chain: "M" Number of atoms: 1754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 229, 1754 Classifications: {'peptide': 229} Link IDs: {'PTRANS': 11, 'TRANS': 217} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 14118 SG CYS G 30 50.829 73.099 163.843 1.00 72.00 S ATOM 14140 SG CYS G 33 54.709 72.677 163.849 1.00 43.66 S ATOM 14387 SG CYS G 66 52.876 74.807 166.474 1.00 60.82 S ATOM 14418 SG CYS G 69 53.320 75.838 162.792 1.00 67.99 S Time building chain proxies: 4.55, per 1000 atoms: 0.23 Number of scatterers: 19893 At special positions: 0 Unit cell: (97.9, 133.1, 187, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 71 16.00 P 111 15.00 O 3995 8.00 N 3536 7.00 C 12179 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: 1.81 Conformation dependent library (CDL) restraints added in 702.4 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN G 301 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 66 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 33 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 69 " pdb="ZN ZN G 301 " - pdb=" SG CYS G 30 " Number of angles added : 6 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4168 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 32 sheets defined 37.0% alpha, 20.2% beta 37 base pairs and 44 stacking pairs defined. Time for finding SS restraints: 2.40 Creating SS restraints... Processing helix chain 'A' and resid 66 through 82 Processing helix chain 'A' and resid 83 through 90 removed outlier: 3.561A pdb=" N LYS A 90 " --> pdb=" O ALA A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 105 Processing helix chain 'A' and resid 117 through 126 Processing helix chain 'A' and resid 164 through 168 removed outlier: 3.564A pdb=" N SER A 168 " --> pdb=" O ILE A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 188 Processing helix chain 'A' and resid 200 through 221 removed outlier: 3.655A pdb=" N ALA A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 278 Processing helix chain 'A' and resid 279 through 282 Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 318 through 331 removed outlier: 3.571A pdb=" N PHE A 322 " --> pdb=" O THR A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 341 removed outlier: 4.051A pdb=" N PHE A 337 " --> pdb=" O THR A 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 82 Processing helix chain 'B' and resid 82 through 90 Processing helix chain 'B' and resid 95 through 105 Processing helix chain 'B' and resid 117 through 126 Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 153 through 155 No H-bonds generated for 'chain 'B' and resid 153 through 155' Processing helix chain 'B' and resid 156 through 161 Processing helix chain 'B' and resid 164 through 168 Processing helix chain 'B' and resid 183 through 188 removed outlier: 3.577A pdb=" N LEU B 188 " --> pdb=" O ILE B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 222 Processing helix chain 'B' and resid 265 through 278 Processing helix chain 'B' and resid 318 through 332 Processing helix chain 'B' and resid 333 through 342 removed outlier: 4.497A pdb=" N PHE B 337 " --> pdb=" O THR B 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 82 Processing helix chain 'C' and resid 82 through 90 removed outlier: 3.883A pdb=" N LYS C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 105 Processing helix chain 'C' and resid 117 through 126 Processing helix chain 'C' and resid 153 through 155 No H-bonds generated for 'chain 'C' and resid 153 through 155' Processing helix chain 'C' and resid 156 through 161 Processing helix chain 'C' and resid 183 through 188 Processing helix chain 'C' and resid 192 through 197 removed outlier: 3.966A pdb=" N VAL C 196 " --> pdb=" O ASP C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 222 removed outlier: 3.622A pdb=" N ALA C 204 " --> pdb=" O GLY C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 278 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 318 through 331 Processing helix chain 'C' and resid 334 through 342 Processing helix chain 'D' and resid 66 through 82 Processing helix chain 'D' and resid 82 through 90 removed outlier: 3.529A pdb=" N LYS D 90 " --> pdb=" O ALA D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 105 Processing helix chain 'D' and resid 117 through 126 Processing helix chain 'D' and resid 129 through 133 Processing helix chain 'D' and resid 156 through 161 Processing helix chain 'D' and resid 164 through 168 removed outlier: 3.508A pdb=" N SER D 168 " --> pdb=" O ILE D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 188 Processing helix chain 'D' and resid 192 through 197 removed outlier: 4.537A pdb=" N VAL D 196 " --> pdb=" O ASP D 193 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 216 Processing helix chain 'D' and resid 265 through 278 Processing helix chain 'D' and resid 279 through 282 Processing helix chain 'D' and resid 315 through 317 No H-bonds generated for 'chain 'D' and resid 315 through 317' Processing helix chain 'D' and resid 318 through 330 Processing helix chain 'D' and resid 334 through 342 Processing helix chain 'E' and resid 66 through 82 Processing helix chain 'E' and resid 82 through 91 Processing helix chain 'E' and resid 95 through 105 Processing helix chain 'E' and resid 117 through 126 removed outlier: 3.552A pdb=" N ALA E 126 " --> pdb=" O VAL E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 134 Processing helix chain 'E' and resid 156 through 161 removed outlier: 3.545A pdb=" N GLY E 161 " --> pdb=" O GLN E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 279 Processing helix chain 'E' and resid 280 through 282 No H-bonds generated for 'chain 'E' and resid 280 through 282' Processing helix chain 'E' and resid 318 through 332 Processing helix chain 'E' and resid 334 through 342 Processing helix chain 'F' and resid 22 through 39 Processing helix chain 'F' and resid 44 through 48 removed outlier: 3.504A pdb=" N HIS F 48 " --> pdb=" O PRO F 45 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 99 Processing helix chain 'F' and resid 137 through 147 removed outlier: 3.918A pdb=" N GLN F 147 " --> pdb=" O ASP F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 154 through 158 Processing helix chain 'F' and resid 208 through 212 removed outlier: 3.598A pdb=" N HIS F 212 " --> pdb=" O ARG F 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 5 No H-bonds generated for 'chain 'G' and resid 3 through 5' Processing helix chain 'G' and resid 6 through 12 Processing helix chain 'G' and resid 67 through 73 Processing helix chain 'G' and resid 74 through 81 Processing helix chain 'G' and resid 96 through 106 Processing helix chain 'G' and resid 149 through 164 Processing helix chain 'G' and resid 189 through 194 Processing helix chain 'G' and resid 197 through 206 Processing helix chain 'G' and resid 208 through 219 removed outlier: 3.680A pdb=" N TYR G 217 " --> pdb=" O TRP G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 240 Processing helix chain 'M' and resid 15 through 30 removed outlier: 3.968A pdb=" N GLY M 29 " --> pdb=" O GLU M 25 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N VAL M 30 " --> pdb=" O LEU M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 39 Processing helix chain 'M' and resid 69 through 92 Proline residue: M 82 - end of helix Processing helix chain 'M' and resid 127 through 134 removed outlier: 3.743A pdb=" N ARG M 133 " --> pdb=" O ARG M 129 " (cutoff:3.500A) Processing helix chain 'M' and resid 136 through 160 removed outlier: 4.664A pdb=" N ALA M 142 " --> pdb=" O ALA M 138 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 144 through 146 removed outlier: 3.656A pdb=" N TYR A 150 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 144 through 146 removed outlier: 6.205A pdb=" N GLU A 4 " --> pdb=" O VAL A 300 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N VAL A 300 " --> pdb=" O GLU A 4 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N LEU A 6 " --> pdb=" O GLU A 298 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 21 through 23 removed outlier: 3.554A pdb=" N TYR A 21 " --> pdb=" O LEU A 40 " (cutoff:3.500A) removed outlier: 7.682A pdb=" N GLU A 247 " --> pdb=" O PRO A 39 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N THR A 41 " --> pdb=" O GLU A 247 " (cutoff:3.500A) removed outlier: 8.452A pdb=" N VAL A 249 " --> pdb=" O THR A 41 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 45 through 50 Processing sheet with id=AA5, first strand: chain 'A' and resid 94 through 95 removed outlier: 7.197A pdb=" N LEU A 94 " --> pdb=" O LEU F 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 308 through 309 Processing sheet with id=AA7, first strand: chain 'B' and resid 144 through 151 removed outlier: 5.410A pdb=" N ARG B 258 " --> pdb=" O ASP B 147 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N LEU B 149 " --> pdb=" O LEU B 256 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N LEU B 256 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N LYS B 254 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ASP B 299 " --> pdb=" O LEU B 6 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ARG B 8 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N ILE B 297 " --> pdb=" O ARG B 8 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 21 through 23 removed outlier: 3.588A pdb=" N TYR B 21 " --> pdb=" O LEU B 40 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N GLU B 247 " --> pdb=" O PRO B 39 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR B 41 " --> pdb=" O GLU B 247 " (cutoff:3.500A) removed outlier: 8.576A pdb=" N VAL B 249 " --> pdb=" O THR B 41 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 45 through 51 Processing sheet with id=AB1, first strand: chain 'C' and resid 144 through 151 removed outlier: 4.947A pdb=" N VAL C 146 " --> pdb=" O ASN C 260 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N ASN C 260 " --> pdb=" O VAL C 146 " (cutoff:3.500A) removed outlier: 5.520A pdb=" N SER C 148 " --> pdb=" O ARG C 258 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ARG C 258 " --> pdb=" O SER C 148 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ARG C 8 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N ILE C 297 " --> pdb=" O ARG C 8 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 21 through 23 removed outlier: 3.652A pdb=" N TYR C 21 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N GLU C 247 " --> pdb=" O PRO C 39 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N THR C 41 " --> pdb=" O GLU C 247 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N VAL C 249 " --> pdb=" O THR C 41 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 45 through 51 Processing sheet with id=AB4, first strand: chain 'C' and resid 308 through 309 Processing sheet with id=AB5, first strand: chain 'D' and resid 144 through 151 removed outlier: 5.185A pdb=" N ARG D 258 " --> pdb=" O ASP D 147 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU D 149 " --> pdb=" O LEU D 256 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LEU D 256 " --> pdb=" O LEU D 149 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N LYS D 254 " --> pdb=" O PRO D 151 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP D 299 " --> pdb=" O LEU D 6 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG D 8 " --> pdb=" O ILE D 297 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ILE D 297 " --> pdb=" O ARG D 8 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 21 through 23 removed outlier: 3.532A pdb=" N TYR D 21 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N GLU D 247 " --> pdb=" O PRO D 39 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N THR D 41 " --> pdb=" O GLU D 247 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N VAL D 249 " --> pdb=" O THR D 41 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 45 through 51 Processing sheet with id=AB8, first strand: chain 'D' and resid 134 through 135 Processing sheet with id=AB9, first strand: chain 'D' and resid 308 through 309 Processing sheet with id=AC1, first strand: chain 'E' and resid 144 through 151 removed outlier: 5.314A pdb=" N ARG E 258 " --> pdb=" O ASP E 147 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N LEU E 149 " --> pdb=" O LEU E 256 " (cutoff:3.500A) removed outlier: 5.500A pdb=" N LEU E 256 " --> pdb=" O LEU E 149 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N LYS E 254 " --> pdb=" O PRO E 151 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASP E 299 " --> pdb=" O LEU E 6 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ARG E 8 " --> pdb=" O ILE E 297 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N ILE E 297 " --> pdb=" O ARG E 8 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 21 through 23 removed outlier: 7.608A pdb=" N GLU E 247 " --> pdb=" O PRO E 39 " (cutoff:3.500A) removed outlier: 7.236A pdb=" N THR E 41 " --> pdb=" O GLU E 247 " (cutoff:3.500A) removed outlier: 9.467A pdb=" N VAL E 249 " --> pdb=" O THR E 41 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 45 through 51 removed outlier: 3.708A pdb=" N LYS E 58 " --> pdb=" O ALA E 50 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 72 through 75 removed outlier: 4.122A pdb=" N ASN F 74 " --> pdb=" O THR F 129 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N ALA F 128 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU F 10 " --> pdb=" O ALA F 128 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 14 through 15 Processing sheet with id=AC6, first strand: chain 'F' and resid 56 through 58 Processing sheet with id=AC7, first strand: chain 'F' and resid 195 through 200 Processing sheet with id=AC8, first strand: chain 'G' and resid 21 through 22 Processing sheet with id=AC9, first strand: chain 'G' and resid 28 through 29 removed outlier: 3.589A pdb=" N VAL G 28 " --> pdb=" O ILE G 37 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 91 through 93 removed outlier: 3.639A pdb=" N ALA G 84 " --> pdb=" O MET G 115 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N VAL G 114 " --> pdb=" O LYS G 138 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'M' and resid 55 through 56 removed outlier: 3.546A pdb=" N ILE M 7 " --> pdb=" O GLU M 100 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N GLU M 100 " --> pdb=" O ILE M 7 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'M' and resid 108 through 122 removed outlier: 10.684A pdb=" N ARG M 111 " --> pdb=" O LEU M 204 " (cutoff:3.500A) removed outlier: 9.482A pdb=" N LEU M 204 " --> pdb=" O ARG M 111 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N TYR M 113 " --> pdb=" O ALA M 202 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA M 202 " --> pdb=" O TYR M 113 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG M 121 " --> pdb=" O ARG M 194 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARG M 194 " --> pdb=" O ARG M 121 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N VAL M 197 " --> pdb=" O LYS M 172 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'M' and resid 108 through 122 removed outlier: 10.684A pdb=" N ARG M 111 " --> pdb=" O LEU M 204 " (cutoff:3.500A) removed outlier: 9.482A pdb=" N LEU M 204 " --> pdb=" O ARG M 111 " (cutoff:3.500A) removed outlier: 8.271A pdb=" N TYR M 113 " --> pdb=" O ALA M 202 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ALA M 202 " --> pdb=" O TYR M 113 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ARG M 121 " --> pdb=" O ARG M 194 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N ARG M 194 " --> pdb=" O ARG M 121 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'M' and resid 207 through 209 753 hydrogen bonds defined for protein. 2097 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 95 hydrogen bonds 190 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 44 stacking parallelities Total time for adding SS restraints: 3.67 Time building geometry restraints manager: 2.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5115 1.33 - 1.45: 4242 1.45 - 1.57: 10836 1.57 - 1.69: 219 1.69 - 1.81: 130 Bond restraints: 20542 Sorted by residual: bond pdb=" C3' DG I -23 " pdb=" C2' DG I -23 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DT I 1 " pdb=" C2' DT I 1 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DC I -26 " pdb=" C2' DC I -26 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.78e+00 bond pdb=" C3' DA I -10 " pdb=" C2' DA I -10 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.78e+00 bond pdb=" C3' DA I -9 " pdb=" C2' DA I -9 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.55e+00 ... (remaining 20537 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 27870 2.16 - 4.32: 460 4.32 - 6.48: 33 6.48 - 8.64: 2 8.64 - 10.80: 6 Bond angle restraints: 28371 Sorted by residual: angle pdb=" N1 C H 39 " pdb=" C2 C H 39 " pdb=" O2 C H 39 " ideal model delta sigma weight residual 118.90 127.99 -9.09 6.00e-01 2.78e+00 2.30e+02 angle pdb=" O2 C H 39 " pdb=" C2 C H 39 " pdb=" N3 C H 39 " ideal model delta sigma weight residual 121.90 112.89 9.01 7.00e-01 2.04e+00 1.66e+02 angle pdb=" N2 G H 52 " pdb=" C2 G H 52 " pdb=" N3 G H 52 " ideal model delta sigma weight residual 119.90 126.47 -6.57 7.00e-01 2.04e+00 8.81e+01 angle pdb=" C2 C H 39 " pdb=" N1 C H 39 " pdb=" C6 C H 39 " ideal model delta sigma weight residual 120.30 117.46 2.84 4.00e-01 6.25e+00 5.03e+01 angle pdb=" N1 G H 52 " pdb=" C2 G H 52 " pdb=" N2 G H 52 " ideal model delta sigma weight residual 116.20 109.94 6.26 9.00e-01 1.23e+00 4.84e+01 ... (remaining 28366 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.31: 11639 35.31 - 70.63: 527 70.63 - 105.94: 42 105.94 - 141.25: 4 141.25 - 176.57: 6 Dihedral angle restraints: 12218 sinusoidal: 5713 harmonic: 6505 Sorted by residual: dihedral pdb=" C4' U H -6 " pdb=" C3' U H -6 " pdb=" C2' U H -6 " pdb=" C1' U H -6 " ideal model delta sinusoidal sigma weight residual -35.00 32.80 -67.80 1 8.00e+00 1.56e-02 9.33e+01 dihedral pdb=" C5' U H -6 " pdb=" C4' U H -6 " pdb=" C3' U H -6 " pdb=" O3' U H -6 " ideal model delta sinusoidal sigma weight residual 147.00 81.64 65.36 1 8.00e+00 1.56e-02 8.75e+01 dihedral pdb=" O4' U H -6 " pdb=" C4' U H -6 " pdb=" C3' U H -6 " pdb=" C2' U H -6 " ideal model delta sinusoidal sigma weight residual 24.00 -33.50 57.50 1 8.00e+00 1.56e-02 6.94e+01 ... (remaining 12215 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.081: 2866 0.081 - 0.162: 338 0.162 - 0.243: 6 0.243 - 0.324: 0 0.324 - 0.405: 1 Chirality restraints: 3211 Sorted by residual: chirality pdb=" C1' U H -6 " pdb=" O4' U H -6 " pdb=" C2' U H -6 " pdb=" N1 U H -6 " both_signs ideal model delta sigma weight residual False 2.44 2.03 0.41 2.00e-01 2.50e+01 4.10e+00 chirality pdb=" C3' U H -6 " pdb=" C4' U H -6 " pdb=" O3' U H -6 " pdb=" C2' U H -6 " both_signs ideal model delta sigma weight residual False -2.74 -2.51 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" C1' A H 7 " pdb=" O4' A H 7 " pdb=" C2' A H 7 " pdb=" N9 A H 7 " both_signs ideal model delta sigma weight residual False 2.47 2.24 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 3208 not shown) Planarity restraints: 3297 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C H 39 " 0.024 2.00e-02 2.50e+03 1.73e-02 6.70e+00 pdb=" N1 C H 39 " -0.024 2.00e-02 2.50e+03 pdb=" C2 C H 39 " -0.035 2.00e-02 2.50e+03 pdb=" O2 C H 39 " 0.014 2.00e-02 2.50e+03 pdb=" N3 C H 39 " 0.010 2.00e-02 2.50e+03 pdb=" C4 C H 39 " 0.003 2.00e-02 2.50e+03 pdb=" N4 C H 39 " 0.006 2.00e-02 2.50e+03 pdb=" C5 C H 39 " 0.001 2.00e-02 2.50e+03 pdb=" C6 C H 39 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A H 11 " -0.022 2.00e-02 2.50e+03 1.00e-02 2.76e+00 pdb=" N9 A H 11 " 0.023 2.00e-02 2.50e+03 pdb=" C8 A H 11 " 0.002 2.00e-02 2.50e+03 pdb=" N7 A H 11 " -0.001 2.00e-02 2.50e+03 pdb=" C5 A H 11 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A H 11 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A H 11 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A H 11 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A H 11 " 0.001 2.00e-02 2.50e+03 pdb=" N3 A H 11 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A H 11 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A H 7 " 0.020 2.00e-02 2.50e+03 9.88e-03 2.68e+00 pdb=" N9 A H 7 " -0.024 2.00e-02 2.50e+03 pdb=" C8 A H 7 " 0.001 2.00e-02 2.50e+03 pdb=" N7 A H 7 " 0.003 2.00e-02 2.50e+03 pdb=" C5 A H 7 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A H 7 " 0.001 2.00e-02 2.50e+03 pdb=" N6 A H 7 " 0.004 2.00e-02 2.50e+03 pdb=" N1 A H 7 " 0.005 2.00e-02 2.50e+03 pdb=" C2 A H 7 " -0.004 2.00e-02 2.50e+03 pdb=" N3 A H 7 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A H 7 " -0.002 2.00e-02 2.50e+03 ... (remaining 3294 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 302 2.64 - 3.20: 17574 3.20 - 3.77: 32393 3.77 - 4.33: 44773 4.33 - 4.90: 74645 Nonbonded interactions: 169687 Sorted by model distance: nonbonded pdb=" O2' C H 41 " pdb=" OG1 THR M 50 " model vdw 2.075 3.040 nonbonded pdb=" OG SER E 24 " pdb=" OD1 ASP E 26 " model vdw 2.110 3.040 nonbonded pdb=" OG SER F 86 " pdb=" OG SER F 119 " model vdw 2.134 3.040 nonbonded pdb=" O2' U H 37 " pdb=" OP2 U H 38 " model vdw 2.152 3.040 nonbonded pdb=" OG SER D 190 " pdb=" OD1 ASP D 192 " model vdw 2.168 3.040 ... (remaining 169682 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 179 or resid 242 through 343)) selection = (chain 'B' and (resid 1 through 179 or resid 242 through 343)) selection = (chain 'C' and (resid 1 through 179 or resid 242 through 343)) selection = (chain 'D' and (resid 1 through 179 or resid 242 through 343)) selection = (chain 'E' and resid 1 through 343) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.750 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20546 Z= 0.270 Angle : 0.613 10.803 28377 Z= 0.443 Chirality : 0.047 0.405 3211 Planarity : 0.004 0.037 3297 Dihedral : 18.295 176.566 8050 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: 0.49 (0.17), residues: 2271 helix: 1.47 (0.20), residues: 737 sheet: 0.41 (0.25), residues: 387 loop : -0.43 (0.18), residues: 1147 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 263 TYR 0.011 0.001 TYR G 141 PHE 0.011 0.001 PHE D 133 TRP 0.012 0.001 TRP A 207 HIS 0.006 0.001 HIS F 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00427 / 0.27 (20542) covalent geometry : angle 0.61057 / 0.44 (28371) hydrogen bonds : bond 0.16793 / 11.40 ( 840) hydrogen bonds : angle 7.90904 / 5.51 ( 2287) metal coordination : bond 0.00159 / 0.08 ( 4) metal coordination : angle 4.02242 / 1.94 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 198 time to evaluate : 0.705 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 163 ASP cc_start: 0.8261 (m-30) cc_final: 0.8023 (m-30) REVERT: C 332 MET cc_start: 0.8451 (ttm) cc_final: 0.8249 (ttp) REVERT: D 1 MET cc_start: 0.8442 (tmm) cc_final: 0.8202 (tpp) REVERT: E 1 MET cc_start: 0.7926 (pmm) cc_final: 0.7668 (pmm) REVERT: E 30 ASN cc_start: 0.8035 (m110) cc_final: 0.7825 (m110) REVERT: F 14 MET cc_start: 0.9103 (ptm) cc_final: 0.8711 (ptm) REVERT: F 203 GLN cc_start: 0.8907 (mp-120) cc_final: 0.8702 (mp-120) REVERT: G 76 GLN cc_start: 0.8549 (mp10) cc_final: 0.8110 (mp10) REVERT: G 236 ILE cc_start: 0.8117 (mt) cc_final: 0.7816 (mp) REVERT: M 56 GLN cc_start: 0.8041 (pt0) cc_final: 0.7605 (pt0) outliers start: 0 outliers final: 0 residues processed: 198 average time/residue: 0.7333 time to fit residues: 161.6972 Evaluate side-chains 164 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 216 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 0.0980 chunk 227 optimal weight: 5.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.9990 chunk 124 optimal weight: 0.2980 chunk 103 optimal weight: 5.9990 chunk 235 optimal weight: 0.0370 overall best weight: 0.4260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 157 GLN ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 147 GLN G 164 ASN ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 GLN ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.097961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.073213 restraints weight = 41063.653| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 1.93 r_work: 0.3046 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.0958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 20546 Z= 0.138 Angle : 0.597 8.808 28377 Z= 0.321 Chirality : 0.046 0.408 3211 Planarity : 0.004 0.055 3297 Dihedral : 19.673 170.922 3961 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 8.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 0.54 % Allowed : 7.43 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.17), residues: 2271 helix: 1.66 (0.20), residues: 740 sheet: 0.30 (0.25), residues: 392 loop : -0.46 (0.18), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 88 TYR 0.011 0.001 TYR A 22 PHE 0.012 0.001 PHE M 8 TRP 0.021 0.001 TRP D 255 HIS 0.005 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.14 (20542) covalent geometry : angle 0.59393 / 0.32 (28371) hydrogen bonds : bond 0.04520 / 2.97 ( 840) hydrogen bonds : angle 6.15017 / 4.41 ( 2287) metal coordination : bond 0.00538 / 0.27 ( 4) metal coordination : angle 4.30821 / 2.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 183 time to evaluate : 0.732 Fit side-chains revert: symmetry clash REVERT: B 145 MET cc_start: 0.7872 (mtt) cc_final: 0.7180 (mtt) REVERT: B 214 THR cc_start: 0.8626 (m) cc_final: 0.8380 (p) REVERT: C 163 ASP cc_start: 0.8477 (m-30) cc_final: 0.8227 (m-30) REVERT: C 202 GLN cc_start: 0.7774 (tp40) cc_final: 0.7455 (tp-100) REVERT: C 332 MET cc_start: 0.8385 (ttm) cc_final: 0.8143 (ttp) REVERT: D 1 MET cc_start: 0.8610 (tmm) cc_final: 0.8359 (tpp) REVERT: E 1 MET cc_start: 0.7995 (pmm) cc_final: 0.7740 (pmm) REVERT: E 30 ASN cc_start: 0.8065 (m110) cc_final: 0.7690 (m110) REVERT: E 268 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8097 (mt0) REVERT: E 330 ASP cc_start: 0.7732 (m-30) cc_final: 0.7505 (p0) REVERT: F 14 MET cc_start: 0.9029 (ptm) cc_final: 0.8723 (ptm) REVERT: F 203 GLN cc_start: 0.8917 (mp-120) cc_final: 0.8707 (mp-120) REVERT: G 76 GLN cc_start: 0.8493 (mp10) cc_final: 0.8096 (mp10) REVERT: G 225 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7904 (mm-40) REVERT: G 236 ILE cc_start: 0.7996 (mt) cc_final: 0.7673 (mp) REVERT: M 31 GLN cc_start: 0.6415 (mp10) cc_final: 0.6078 (mp10) REVERT: M 56 GLN cc_start: 0.7690 (pt0) cc_final: 0.7318 (pt0) outliers start: 10 outliers final: 5 residues processed: 188 average time/residue: 0.7157 time to fit residues: 150.5988 Evaluate side-chains 179 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 173 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain E residue 268 GLN Chi-restraints excluded: chain F residue 199 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 90 optimal weight: 0.9990 chunk 131 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 100 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 169 optimal weight: 2.9990 chunk 129 optimal weight: 4.9990 chunk 120 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 221 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 98 GLN M 153 GLN ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.095584 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.071108 restraints weight = 41688.628| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.93 r_work: 0.2984 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20546 Z= 0.176 Angle : 0.566 8.918 28377 Z= 0.304 Chirality : 0.045 0.402 3211 Planarity : 0.004 0.040 3297 Dihedral : 19.744 171.733 3961 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.36 % Allowed : 10.14 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: 0.49 (0.17), residues: 2271 helix: 1.60 (0.19), residues: 753 sheet: 0.21 (0.25), residues: 392 loop : -0.48 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 88 TYR 0.009 0.001 TYR A 150 PHE 0.012 0.001 PHE E 133 TRP 0.014 0.001 TRP D 255 HIS 0.007 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00393 / 0.18 (20542) covalent geometry : angle 0.56178 / 0.30 (28371) hydrogen bonds : bond 0.04501 / 2.99 ( 840) hydrogen bonds : angle 5.87757 / 4.23 ( 2287) metal coordination : bond 0.00559 / 0.28 ( 4) metal coordination : angle 4.55817 / 2.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 163 ASP cc_start: 0.8456 (m-30) cc_final: 0.8251 (m-30) REVERT: C 332 MET cc_start: 0.8460 (ttm) cc_final: 0.8227 (ttp) REVERT: D 1 MET cc_start: 0.8639 (tmm) cc_final: 0.8423 (tpp) REVERT: E 30 ASN cc_start: 0.8014 (m110) cc_final: 0.7612 (m110) REVERT: E 72 ASN cc_start: 0.7488 (OUTLIER) cc_final: 0.7174 (t0) REVERT: E 145 MET cc_start: 0.7380 (mtt) cc_final: 0.6677 (mtt) REVERT: E 154 GLN cc_start: 0.8128 (OUTLIER) cc_final: 0.7786 (mp10) REVERT: E 268 GLN cc_start: 0.8709 (OUTLIER) cc_final: 0.8278 (mt0) REVERT: E 330 ASP cc_start: 0.7734 (m-30) cc_final: 0.7450 (m-30) REVERT: F 1 MET cc_start: 0.7222 (pmm) cc_final: 0.6838 (pmm) REVERT: F 14 MET cc_start: 0.9071 (ptm) cc_final: 0.8789 (ptm) REVERT: G 225 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7904 (mm-40) REVERT: G 236 ILE cc_start: 0.7989 (mt) cc_final: 0.7678 (mp) REVERT: M 27 MET cc_start: 0.7498 (mmm) cc_final: 0.6747 (mtt) REVERT: M 31 GLN cc_start: 0.6608 (mp10) cc_final: 0.6281 (mp10) REVERT: M 56 GLN cc_start: 0.7863 (pt0) cc_final: 0.7472 (pt0) REVERT: M 92 MET cc_start: 0.7407 (mtm) cc_final: 0.6767 (mpp) outliers start: 25 outliers final: 12 residues processed: 184 average time/residue: 0.6591 time to fit residues: 136.1030 Evaluate side-chains 180 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 165 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 268 GLN Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain M residue 153 GLN Chi-restraints excluded: chain M residue 193 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 229 optimal weight: 10.0000 chunk 46 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 169 optimal weight: 1.9990 chunk 150 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 176 optimal weight: 0.5980 chunk 37 optimal weight: 0.0170 chunk 209 optimal weight: 50.0000 chunk 157 optimal weight: 5.9990 chunk 185 optimal weight: 1.9990 overall best weight: 1.0622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.095640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.071212 restraints weight = 41704.223| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.94 r_work: 0.2984 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2857 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2857 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 20546 Z= 0.173 Angle : 0.559 8.794 28377 Z= 0.299 Chirality : 0.045 0.402 3211 Planarity : 0.004 0.036 3297 Dihedral : 19.756 174.728 3961 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.46 % Allowed : 11.28 % Favored : 87.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: 0.46 (0.17), residues: 2271 helix: 1.62 (0.20), residues: 752 sheet: 0.18 (0.26), residues: 380 loop : -0.52 (0.18), residues: 1139 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 88 TYR 0.010 0.001 TYR F 133 PHE 0.011 0.001 PHE E 133 TRP 0.013 0.001 TRP D 255 HIS 0.005 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (20542) covalent geometry : angle 0.55539 / 0.30 (28371) hydrogen bonds : bond 0.04110 / 2.72 ( 840) hydrogen bonds : angle 5.70485 / 4.12 ( 2287) metal coordination : bond 0.00574 / 0.28 ( 4) metal coordination : angle 4.45317 / 2.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 166 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 214 THR cc_start: 0.8619 (m) cc_final: 0.8349 (p) REVERT: C 163 ASP cc_start: 0.8470 (m-30) cc_final: 0.8217 (m-30) REVERT: C 202 GLN cc_start: 0.7749 (tp40) cc_final: 0.7433 (tp-100) REVERT: C 332 MET cc_start: 0.8480 (ttm) cc_final: 0.8239 (ttp) REVERT: D 1 MET cc_start: 0.8663 (tmm) cc_final: 0.8386 (tpp) REVERT: E 2 GLN cc_start: 0.8637 (mp10) cc_final: 0.7587 (tt0) REVERT: E 30 ASN cc_start: 0.7974 (m110) cc_final: 0.7580 (m110) REVERT: E 72 ASN cc_start: 0.7471 (OUTLIER) cc_final: 0.7153 (t0) REVERT: E 154 GLN cc_start: 0.8096 (OUTLIER) cc_final: 0.7709 (mp10) REVERT: E 268 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8274 (mt0) REVERT: E 330 ASP cc_start: 0.7734 (m-30) cc_final: 0.7521 (m-30) REVERT: F 1 MET cc_start: 0.7233 (pmm) cc_final: 0.6846 (pmm) REVERT: F 14 MET cc_start: 0.9068 (ptm) cc_final: 0.8729 (ptm) REVERT: G 162 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7677 (ptp-170) REVERT: G 225 GLN cc_start: 0.8161 (mm-40) cc_final: 0.7893 (mm-40) REVERT: M 27 MET cc_start: 0.7630 (mmm) cc_final: 0.7251 (mtt) REVERT: M 31 GLN cc_start: 0.6597 (mp10) cc_final: 0.6350 (mp10) REVERT: M 56 GLN cc_start: 0.7907 (pt0) cc_final: 0.7521 (pt0) outliers start: 27 outliers final: 14 residues processed: 184 average time/residue: 0.6428 time to fit residues: 133.2789 Evaluate side-chains 180 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain E residue 268 GLN Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain G residue 162 ARG Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 193 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 24 optimal weight: 2.9990 chunk 221 optimal weight: 3.9990 chunk 143 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 217 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 88 optimal weight: 1.9990 chunk 233 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 74 ASN ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 201 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.095073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.070639 restraints weight = 41479.288| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.96 r_work: 0.2963 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20546 Z= 0.172 Angle : 0.555 8.746 28377 Z= 0.296 Chirality : 0.044 0.400 3211 Planarity : 0.004 0.038 3297 Dihedral : 19.743 177.452 3961 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.95 % Allowed : 12.20 % Favored : 85.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: 0.42 (0.17), residues: 2271 helix: 1.59 (0.19), residues: 758 sheet: 0.12 (0.26), residues: 380 loop : -0.54 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 88 TYR 0.011 0.001 TYR F 133 PHE 0.011 0.001 PHE B 133 TRP 0.013 0.001 TRP D 255 HIS 0.005 0.001 HIS F 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 (20542) covalent geometry : angle 0.55165 / 0.30 (28371) hydrogen bonds : bond 0.03951 / 2.62 ( 840) hydrogen bonds : angle 5.56282 / 4.02 ( 2287) metal coordination : bond 0.00567 / 0.28 ( 4) metal coordination : angle 4.43023 / 2.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 145 MET cc_start: 0.8194 (mtt) cc_final: 0.7588 (mtt) REVERT: B 214 THR cc_start: 0.8573 (m) cc_final: 0.8276 (p) REVERT: C 163 ASP cc_start: 0.8487 (m-30) cc_final: 0.8271 (m-30) REVERT: C 202 GLN cc_start: 0.7744 (tp40) cc_final: 0.7347 (tp-100) REVERT: D 1 MET cc_start: 0.8666 (tmm) cc_final: 0.8427 (tpp) REVERT: E 2 GLN cc_start: 0.8631 (mp10) cc_final: 0.7625 (tt0) REVERT: E 30 ASN cc_start: 0.7940 (m110) cc_final: 0.7535 (m110) REVERT: E 72 ASN cc_start: 0.7491 (OUTLIER) cc_final: 0.7174 (t0) REVERT: E 154 GLN cc_start: 0.8093 (OUTLIER) cc_final: 0.7761 (mp10) REVERT: E 268 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8264 (mt0) REVERT: E 330 ASP cc_start: 0.7703 (m-30) cc_final: 0.7488 (m-30) REVERT: F 1 MET cc_start: 0.7262 (pmm) cc_final: 0.6856 (pmm) REVERT: F 14 MET cc_start: 0.9077 (ptm) cc_final: 0.8786 (ptm) REVERT: G 162 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7652 (ptp-170) REVERT: G 225 GLN cc_start: 0.8205 (mm-40) cc_final: 0.7930 (mm-40) REVERT: M 27 MET cc_start: 0.7664 (mmm) cc_final: 0.7438 (mtt) REVERT: M 56 GLN cc_start: 0.7912 (pt0) cc_final: 0.7553 (pt0) REVERT: M 153 GLN cc_start: 0.8200 (OUTLIER) cc_final: 0.7820 (mm110) outliers start: 36 outliers final: 18 residues processed: 188 average time/residue: 0.6513 time to fit residues: 138.2536 Evaluate side-chains 185 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain E residue 268 GLN Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 162 ARG Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 153 GLN Chi-restraints excluded: chain M residue 193 LEU Chi-restraints excluded: chain M residue 197 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 226 optimal weight: 0.9980 chunk 71 optimal weight: 0.0970 chunk 100 optimal weight: 0.8980 chunk 119 optimal weight: 6.9990 chunk 125 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 158 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 214 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 110 ASN E 106 ASN F 74 ASN ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.095761 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.071355 restraints weight = 41637.377| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.96 r_work: 0.2980 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 20546 Z= 0.138 Angle : 0.541 8.602 28377 Z= 0.288 Chirality : 0.043 0.393 3211 Planarity : 0.004 0.043 3297 Dihedral : 19.653 178.228 3961 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.68 % Allowed : 12.91 % Favored : 85.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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 (0.17), residues: 2271 helix: 1.67 (0.20), residues: 758 sheet: 0.18 (0.26), residues: 379 loop : -0.53 (0.18), residues: 1134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG E 88 TYR 0.013 0.001 TYR G 141 PHE 0.010 0.001 PHE B 133 TRP 0.013 0.001 TRP D 255 HIS 0.005 0.001 HIS F 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 (20542) covalent geometry : angle 0.53722 / 0.29 (28371) hydrogen bonds : bond 0.03689 / 2.44 ( 840) hydrogen bonds : angle 5.42663 / 3.92 ( 2287) metal coordination : bond 0.00535 / 0.26 ( 4) metal coordination : angle 4.18884 / 2.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 169 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 214 THR cc_start: 0.8583 (m) cc_final: 0.8283 (p) REVERT: C 1 MET cc_start: 0.8608 (tpp) cc_final: 0.8260 (tpt) REVERT: C 163 ASP cc_start: 0.8484 (m-30) cc_final: 0.8270 (m-30) REVERT: C 202 GLN cc_start: 0.7743 (tp40) cc_final: 0.7352 (tp-100) REVERT: C 302 LEU cc_start: 0.8660 (tm) cc_final: 0.8385 (tp) REVERT: D 1 MET cc_start: 0.8637 (tmm) cc_final: 0.8258 (tpt) REVERT: E 2 GLN cc_start: 0.8573 (mp10) cc_final: 0.7592 (tt0) REVERT: E 30 ASN cc_start: 0.7928 (m110) cc_final: 0.7521 (m110) REVERT: E 72 ASN cc_start: 0.7462 (OUTLIER) cc_final: 0.7152 (t0) REVERT: E 154 GLN cc_start: 0.8092 (OUTLIER) cc_final: 0.7762 (mp10) REVERT: E 268 GLN cc_start: 0.8647 (OUTLIER) cc_final: 0.8261 (mt0) REVERT: F 1 MET cc_start: 0.7236 (pmm) cc_final: 0.6830 (pmm) REVERT: G 162 ARG cc_start: 0.8205 (OUTLIER) cc_final: 0.7685 (ptp-170) REVERT: G 190 LYS cc_start: 0.8455 (mtpp) cc_final: 0.8168 (mppt) REVERT: G 225 GLN cc_start: 0.8305 (mm-40) cc_final: 0.8024 (mm-40) REVERT: M 153 GLN cc_start: 0.8190 (mp10) cc_final: 0.7609 (mp10) outliers start: 31 outliers final: 18 residues processed: 190 average time/residue: 0.5940 time to fit residues: 127.1933 Evaluate side-chains 186 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 164 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain E residue 268 GLN Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain G residue 162 ARG Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 193 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 194 optimal weight: 0.7980 chunk 180 optimal weight: 0.0000 chunk 202 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 186 optimal weight: 0.0070 chunk 24 optimal weight: 0.7980 chunk 141 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 chunk 9 optimal weight: 0.4980 chunk 236 optimal weight: 7.9990 overall best weight: 0.4202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 106 ASN F 74 ASN ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.096750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.072446 restraints weight = 41799.069| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.95 r_work: 0.3005 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 20546 Z= 0.115 Angle : 0.527 8.422 28377 Z= 0.281 Chirality : 0.043 0.390 3211 Planarity : 0.004 0.044 3297 Dihedral : 19.568 177.860 3961 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.68 % Allowed : 13.77 % Favored : 84.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: 0.57 (0.18), residues: 2271 helix: 1.78 (0.20), residues: 752 sheet: 0.23 (0.26), residues: 379 loop : -0.50 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 88 TYR 0.012 0.001 TYR G 141 PHE 0.014 0.001 PHE M 221 TRP 0.014 0.001 TRP D 255 HIS 0.004 0.001 HIS F 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (20542) covalent geometry : angle 0.52406 / 0.28 (28371) hydrogen bonds : bond 0.03485 / 2.30 ( 840) hydrogen bonds : angle 5.29724 / 3.84 ( 2287) metal coordination : bond 0.00503 / 0.25 ( 4) metal coordination : angle 4.04047 / 1.91 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 170 time to evaluate : 0.729 Fit side-chains revert: symmetry clash REVERT: B 214 THR cc_start: 0.8590 (m) cc_final: 0.8283 (p) REVERT: C 1 MET cc_start: 0.8627 (tpp) cc_final: 0.8343 (tpt) REVERT: C 163 ASP cc_start: 0.8479 (m-30) cc_final: 0.8256 (m-30) REVERT: C 202 GLN cc_start: 0.7740 (tp40) cc_final: 0.7351 (tp-100) REVERT: C 302 LEU cc_start: 0.8593 (tm) cc_final: 0.8331 (tp) REVERT: D 1 MET cc_start: 0.8605 (tmm) cc_final: 0.8259 (tpt) REVERT: E 2 GLN cc_start: 0.8542 (mp10) cc_final: 0.7565 (tt0) REVERT: E 30 ASN cc_start: 0.7917 (m110) cc_final: 0.7532 (m110) REVERT: E 145 MET cc_start: 0.7242 (mtt) cc_final: 0.6528 (mtt) REVERT: E 154 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7726 (mp10) REVERT: F 1 MET cc_start: 0.7169 (pmm) cc_final: 0.6777 (pmm) REVERT: F 14 MET cc_start: 0.9064 (ptm) cc_final: 0.8819 (ptm) REVERT: G 76 GLN cc_start: 0.8287 (mp10) cc_final: 0.7969 (mp10) REVERT: G 162 ARG cc_start: 0.8186 (OUTLIER) cc_final: 0.7594 (ptp-170) REVERT: G 190 LYS cc_start: 0.8575 (mtpp) cc_final: 0.8095 (mppt) REVERT: G 225 GLN cc_start: 0.8284 (mm-40) cc_final: 0.8010 (mm-40) outliers start: 31 outliers final: 14 residues processed: 189 average time/residue: 0.6087 time to fit residues: 129.9276 Evaluate side-chains 181 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 218 LYS Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain G residue 162 ARG Chi-restraints excluded: chain M residue 193 LEU Chi-restraints excluded: chain M residue 197 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 134 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 210 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 230 optimal weight: 6.9990 chunk 129 optimal weight: 4.9990 chunk 26 optimal weight: 0.2980 chunk 73 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 176 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 72 ASN E 106 ASN F 74 ASN ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.094841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.070786 restraints weight = 41714.342| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.04 r_work: 0.2953 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20546 Z= 0.218 Angle : 0.585 10.321 28377 Z= 0.307 Chirality : 0.045 0.398 3211 Planarity : 0.005 0.052 3297 Dihedral : 19.628 179.825 3961 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.90 % Allowed : 13.77 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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 (0.18), residues: 2271 helix: 1.57 (0.20), residues: 762 sheet: 0.13 (0.25), residues: 384 loop : -0.51 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG E 88 TYR 0.015 0.001 TYR G 141 PHE 0.013 0.002 PHE E 38 TRP 0.011 0.002 TRP A 207 HIS 0.006 0.001 HIS F 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.22 (20542) covalent geometry : angle 0.58142 / 0.31 (28371) hydrogen bonds : bond 0.03817 / 2.54 ( 840) hydrogen bonds : angle 5.41079 / 3.91 ( 2287) metal coordination : bond 0.00536 / 0.26 ( 4) metal coordination : angle 4.23922 / 2.00 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 167 time to evaluate : 0.657 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.8667 (tpp) cc_final: 0.8425 (tpt) REVERT: C 163 ASP cc_start: 0.8492 (m-30) cc_final: 0.8242 (m-30) REVERT: C 202 GLN cc_start: 0.7729 (tp40) cc_final: 0.7286 (tp-100) REVERT: C 302 LEU cc_start: 0.8685 (tm) cc_final: 0.8458 (tp) REVERT: D 1 MET cc_start: 0.8617 (tmm) cc_final: 0.8231 (tpt) REVERT: E 2 GLN cc_start: 0.8611 (mp10) cc_final: 0.7591 (tt0) REVERT: E 30 ASN cc_start: 0.8017 (m110) cc_final: 0.7575 (m110) REVERT: E 72 ASN cc_start: 0.7444 (OUTLIER) cc_final: 0.7139 (t0) REVERT: E 154 GLN cc_start: 0.8074 (OUTLIER) cc_final: 0.7660 (mp10) REVERT: E 339 GLN cc_start: 0.8039 (mp10) cc_final: 0.7541 (mp10) REVERT: F 1 MET cc_start: 0.7283 (pmm) cc_final: 0.6841 (pmm) REVERT: G 162 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7669 (ptp-170) REVERT: G 190 LYS cc_start: 0.8517 (mtpp) cc_final: 0.8051 (mppt) REVERT: G 225 GLN cc_start: 0.8315 (mm-40) cc_final: 0.8024 (mm-40) REVERT: M 10 MET cc_start: 0.6357 (ttt) cc_final: 0.6026 (tpp) REVERT: M 92 MET cc_start: 0.7264 (mpp) cc_final: 0.6928 (mpp) outliers start: 35 outliers final: 24 residues processed: 188 average time/residue: 0.6612 time to fit residues: 140.1480 Evaluate side-chains 190 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain E residue 72 ASN Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain G residue 10 GLN Chi-restraints excluded: chain G residue 162 ARG Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 193 LEU Chi-restraints excluded: chain M residue 197 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 150 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 116 optimal weight: 0.7980 chunk 55 optimal weight: 0.3980 chunk 94 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 226 optimal weight: 5.9990 chunk 213 optimal weight: 10.0000 chunk 142 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 151 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 106 ASN F 74 ASN ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 153 GLN ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.096161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.071630 restraints weight = 41332.855| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.93 r_work: 0.2994 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20546 Z= 0.147 Angle : 0.561 11.927 28377 Z= 0.295 Chirality : 0.044 0.394 3211 Planarity : 0.004 0.042 3297 Dihedral : 19.608 179.050 3961 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.63 % Allowed : 14.53 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: 0.46 (0.18), residues: 2271 helix: 1.62 (0.20), residues: 761 sheet: 0.12 (0.25), residues: 390 loop : -0.52 (0.18), residues: 1120 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.000 ARG E 88 TYR 0.015 0.001 TYR G 141 PHE 0.012 0.001 PHE B 133 TRP 0.012 0.001 TRP D 255 HIS 0.005 0.001 HIS F 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.15 (20542) covalent geometry : angle 0.55746 / 0.29 (28371) hydrogen bonds : bond 0.03542 / 2.34 ( 840) hydrogen bonds : angle 5.35346 / 3.87 ( 2287) metal coordination : bond 0.00523 / 0.26 ( 4) metal coordination : angle 4.05487 / 1.94 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 164 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 214 THR cc_start: 0.8593 (m) cc_final: 0.8318 (p) REVERT: C 1 MET cc_start: 0.8667 (tpp) cc_final: 0.8421 (tpt) REVERT: C 163 ASP cc_start: 0.8461 (m-30) cc_final: 0.8241 (m-30) REVERT: C 202 GLN cc_start: 0.7735 (tp40) cc_final: 0.7365 (tp-100) REVERT: C 302 LEU cc_start: 0.8681 (tm) cc_final: 0.8431 (tp) REVERT: D 1 MET cc_start: 0.8596 (tmm) cc_final: 0.8247 (tpt) REVERT: E 2 GLN cc_start: 0.8586 (mp10) cc_final: 0.7610 (tt0) REVERT: E 30 ASN cc_start: 0.7986 (m110) cc_final: 0.7583 (m110) REVERT: E 145 MET cc_start: 0.7308 (mtt) cc_final: 0.6542 (mtt) REVERT: E 154 GLN cc_start: 0.8094 (OUTLIER) cc_final: 0.7751 (mp10) REVERT: F 1 MET cc_start: 0.7268 (pmm) cc_final: 0.6858 (pmm) REVERT: G 162 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7674 (ptp-170) REVERT: G 190 LYS cc_start: 0.8511 (mtpp) cc_final: 0.8060 (mppt) REVERT: G 225 GLN cc_start: 0.8253 (mm-40) cc_final: 0.7978 (mm-40) REVERT: M 10 MET cc_start: 0.6535 (ttt) cc_final: 0.6185 (tpp) REVERT: M 92 MET cc_start: 0.7222 (mpp) cc_final: 0.6897 (mpp) REVERT: M 213 MET cc_start: 0.6342 (pmm) cc_final: 0.5906 (pmm) outliers start: 30 outliers final: 23 residues processed: 183 average time/residue: 0.5980 time to fit residues: 123.3279 Evaluate side-chains 185 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain G residue 10 GLN Chi-restraints excluded: chain G residue 162 ARG Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 153 GLN Chi-restraints excluded: chain M residue 193 LEU Chi-restraints excluded: chain M residue 197 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 60 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 36 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 9 optimal weight: 0.0870 chunk 123 optimal weight: 3.9990 chunk 97 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 129 optimal weight: 3.9990 chunk 223 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 106 ASN E 339 GLN F 74 ASN ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.096130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.071592 restraints weight = 41384.586| |-----------------------------------------------------------------------------| r_work (start): 0.3099 rms_B_bonded: 1.92 r_work: 0.2995 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 20546 Z= 0.161 Angle : 0.723 59.198 28377 Z= 0.399 Chirality : 0.044 0.394 3211 Planarity : 0.004 0.039 3297 Dihedral : 19.608 179.189 3961 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.63 % Allowed : 14.64 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: 0.45 (0.18), residues: 2271 helix: 1.59 (0.20), residues: 761 sheet: 0.17 (0.25), residues: 383 loop : -0.52 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 88 TYR 0.016 0.001 TYR G 141 PHE 0.012 0.001 PHE B 133 TRP 0.012 0.001 TRP D 255 HIS 0.005 0.001 HIS F 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (20542) covalent geometry : angle 0.72023 / 0.40 (28371) hydrogen bonds : bond 0.03584 / 2.38 ( 840) hydrogen bonds : angle 5.36206 / 3.88 ( 2287) metal coordination : bond 0.00533 / 0.26 ( 4) metal coordination : angle 4.05132 / 1.93 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 160 time to evaluate : 0.779 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 214 THR cc_start: 0.8623 (m) cc_final: 0.8344 (p) REVERT: C 1 MET cc_start: 0.8671 (tpp) cc_final: 0.8418 (tpt) REVERT: C 163 ASP cc_start: 0.8461 (m-30) cc_final: 0.8241 (m-30) REVERT: C 202 GLN cc_start: 0.7724 (tp40) cc_final: 0.7359 (tp-100) REVERT: C 302 LEU cc_start: 0.8681 (tm) cc_final: 0.8432 (tp) REVERT: D 1 MET cc_start: 0.8583 (tmm) cc_final: 0.8236 (tpt) REVERT: E 2 GLN cc_start: 0.8576 (mp10) cc_final: 0.7615 (tt0) REVERT: E 30 ASN cc_start: 0.7972 (m110) cc_final: 0.7572 (m110) REVERT: E 145 MET cc_start: 0.7312 (mtt) cc_final: 0.6561 (mtt) REVERT: E 154 GLN cc_start: 0.8095 (OUTLIER) cc_final: 0.7752 (mp10) REVERT: F 1 MET cc_start: 0.7264 (pmm) cc_final: 0.6852 (pmm) REVERT: G 162 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7669 (ptp-170) REVERT: G 190 LYS cc_start: 0.8498 (mtpp) cc_final: 0.8054 (mppt) REVERT: G 225 GLN cc_start: 0.8252 (mm-40) cc_final: 0.7978 (mm-40) REVERT: M 92 MET cc_start: 0.7229 (mpp) cc_final: 0.6893 (mpp) REVERT: M 213 MET cc_start: 0.6361 (pmm) cc_final: 0.5932 (pmm) outliers start: 30 outliers final: 23 residues processed: 178 average time/residue: 0.6960 time to fit residues: 139.2429 Evaluate side-chains 185 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 160 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 311 SER Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain G residue 10 GLN Chi-restraints excluded: chain G residue 162 ARG Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 193 LEU Chi-restraints excluded: chain M residue 197 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 68 optimal weight: 0.8980 chunk 134 optimal weight: 9.9990 chunk 88 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 3 optimal weight: 0.6980 chunk 117 optimal weight: 0.2980 chunk 28 optimal weight: 0.7980 chunk 212 optimal weight: 6.9990 chunk 55 optimal weight: 0.0020 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 106 ASN E 339 GLN F 74 ASN ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 153 GLN ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.096133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.071568 restraints weight = 41604.072| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.93 r_work: 0.2994 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 20546 Z= 0.161 Angle : 0.723 59.198 28377 Z= 0.399 Chirality : 0.044 0.394 3211 Planarity : 0.004 0.039 3297 Dihedral : 19.608 179.189 3961 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 1.41 % Allowed : 14.70 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % 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: 0.45 (0.18), residues: 2271 helix: 1.59 (0.20), residues: 761 sheet: 0.17 (0.25), residues: 383 loop : -0.52 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG E 88 TYR 0.016 0.001 TYR G 141 PHE 0.012 0.001 PHE B 133 TRP 0.012 0.001 TRP D 255 HIS 0.005 0.001 HIS F 49 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.16 (20542) covalent geometry : angle 0.72023 / 0.40 (28371) hydrogen bonds : bond 0.03584 / 2.38 ( 840) hydrogen bonds : angle 5.36206 / 3.88 ( 2287) metal coordination : bond 0.00533 / 0.26 ( 4) metal coordination : angle 4.05132 / 1.93 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5983.88 seconds wall clock time: 102 minutes 49.48 seconds (6169.48 seconds total)