Starting phenix.real_space_refine on Sun Aug 24 12:11:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rc3_19046/08_2025/8rc3_19046.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rc3_19046/08_2025/8rc3_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 { model { file = "/net/cci-nas-00/data/ceres_data/8rc3_19046/08_2025/8rc3_19046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rc3_19046/08_2025/8rc3_19046.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rc3_19046/08_2025/8rc3_19046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rc3_19046/08_2025/8rc3_19046.map" } 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-2.0-5787/lib/python3.9/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: 4.91, per 1000 atoms: 0.25 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: 1.95 Conformation dependent library (CDL) restraints added in 772.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 2.27 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: 3.70 Time building geometry restraints manager: 2.49 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=" C ASN D 30 " pdb=" O ASN D 30 " ideal model delta sigma weight residual 1.235 1.226 0.009 4.70e-03 4.53e+04 3.62e+00 bond pdb=" C3' DA I -3 " pdb=" O3' DA I -3 " ideal model delta sigma weight residual 1.422 1.462 -0.040 3.00e-02 1.11e+03 1.74e+00 bond pdb=" C3' U H 36 " pdb=" O3' U H 36 " ideal model delta sigma weight residual 1.427 1.446 -0.019 1.50e-02 4.44e+03 1.54e+00 bond pdb=" SD MET F 182 " pdb=" CE MET F 182 " ideal model delta sigma weight residual 1.791 1.763 0.028 2.50e-02 1.60e+03 1.22e+00 bond pdb=" C3' G H 33 " pdb=" O3' G H 33 " ideal model delta sigma weight residual 1.427 1.444 -0.017 1.50e-02 4.44e+03 1.21e+00 ... (remaining 20537 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 28004 2.16 - 4.32: 327 4.32 - 6.48: 32 6.48 - 8.64: 2 8.64 - 10.80: 6 Bond angle restraints: 28371 Sorted by residual: angle pdb=" C2' U H -6 " pdb=" C1' U H -6 " pdb=" N1 U H -6 " ideal model delta sigma weight residual 114.00 122.86 -8.86 1.50e+00 4.44e-01 3.49e+01 angle pdb=" O3' U H -6 " pdb=" C3' U H -6 " pdb=" C2' U H -6 " ideal model delta sigma weight residual 109.50 114.98 -5.48 1.50e+00 4.44e-01 1.33e+01 angle pdb=" OP1 U H -6 " pdb=" P U H -6 " pdb=" OP2 U H -6 " ideal model delta sigma weight residual 119.60 108.80 10.80 3.00e+00 1.11e-01 1.30e+01 angle pdb=" C3' U H 36 " pdb=" O3' U H 36 " pdb=" P U H 37 " ideal model delta sigma weight residual 120.20 125.43 -5.23 1.50e+00 4.44e-01 1.22e+01 angle pdb=" O3' G H -7 " pdb=" P U H -6 " pdb=" OP1 U H -6 " ideal model delta sigma weight residual 108.00 117.73 -9.73 3.00e+00 1.11e-01 1.05e+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 - 0.083: 2961 0.083 - 0.166: 243 0.166 - 0.249: 5 0.249 - 0.332: 1 0.332 - 0.415: 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 2.45 2.03 0.42 2.00e-01 2.50e+01 4.31e+00 chirality pdb=" C2' U H -6 " pdb=" C3' U H -6 " pdb=" O2' U H -6 " pdb=" C1' U H -6 " both_signs ideal model delta sigma weight residual False -2.52 -2.78 0.26 2.00e-01 2.50e+01 1.75e+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 ... (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: 3.010 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: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 22.990 Find NCS groups from input model: 0.300 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:6.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 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 0.040 20546 Z= 0.174 Angle : 0.569 10.803 28377 Z= 0.293 Chirality : 0.043 0.415 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 aren 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 covalent geometry : bond 0.00400 (20542) covalent geometry : angle 0.56601 (28371) hydrogen bonds : bond 0.16793 ( 840) hydrogen bonds : angle 7.90904 ( 2287) metal coordination : bond 0.00159 ( 4) metal coordination : angle 4.02242 ( 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 : 0.619 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: 0.6898 time to fit residues: 151.3837 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 : 0.776 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3611 r_free = 0.3611 target = 0.096763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.072360 restraints weight = 41752.512| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 1.95 r_work: 0.3011 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.0981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20546 Z= 0.137 Angle : 0.583 8.572 28377 Z= 0.301 Chirality : 0.042 0.225 3211 Planarity : 0.004 0.063 3297 Dihedral : 19.618 167.864 3961 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.60 % Allowed : 7.00 % Favored : 92.41 % 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 aren not related in a simple way. whole: 0.62 (0.17), residues: 2271 helix: 1.71 (0.20), residues: 745 sheet: 0.45 (0.25), residues: 384 loop : -0.44 (0.18), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 88 TYR 0.010 0.001 TYR A 22 PHE 0.012 0.001 PHE M 52 TRP 0.017 0.001 TRP D 255 HIS 0.003 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00293 (20542) covalent geometry : angle 0.57967 (28371) hydrogen bonds : bond 0.04105 ( 840) hydrogen bonds : angle 6.03129 ( 2287) metal coordination : bond 0.00559 ( 4) metal coordination : angle 4.23834 ( 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 197 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 186 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: B 145 MET cc_start: 0.7914 (mtt) cc_final: 0.7117 (mtt) REVERT: B 214 THR cc_start: 0.8601 (m) cc_final: 0.8329 (p) REVERT: C 163 ASP cc_start: 0.8455 (m-30) cc_final: 0.8199 (m-30) REVERT: C 202 GLN cc_start: 0.7714 (tp40) cc_final: 0.7393 (tp-100) REVERT: C 332 MET cc_start: 0.8364 (ttm) cc_final: 0.8120 (ttp) REVERT: D 1 MET cc_start: 0.8579 (tmm) cc_final: 0.8297 (tpp) REVERT: E 1 MET cc_start: 0.8014 (pmm) cc_final: 0.7758 (pmm) REVERT: E 30 ASN cc_start: 0.7994 (m110) cc_final: 0.7598 (m110) REVERT: E 268 GLN cc_start: 0.8705 (OUTLIER) cc_final: 0.8004 (mt0) REVERT: F 1 MET cc_start: 0.7176 (pmm) cc_final: 0.6844 (pmm) REVERT: F 14 MET cc_start: 0.9043 (ptm) cc_final: 0.8652 (ptm) REVERT: F 203 GLN cc_start: 0.8914 (mp-120) cc_final: 0.8688 (mp-120) REVERT: G 236 ILE cc_start: 0.7983 (mt) cc_final: 0.7669 (mp) REVERT: M 27 MET cc_start: 0.7343 (mmm) cc_final: 0.6666 (mtt) REVERT: M 31 GLN cc_start: 0.6403 (mp10) cc_final: 0.6121 (mp10) REVERT: M 56 GLN cc_start: 0.7715 (pt0) cc_final: 0.7316 (pt0) REVERT: M 193 LEU cc_start: 0.7047 (pt) cc_final: 0.6840 (pp) outliers start: 11 outliers final: 5 residues processed: 190 average time/residue: 0.6594 time to fit residues: 139.9693 Evaluate side-chains 178 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 172 time to evaluate : 0.697 ------------------------------------------------------------------------------- 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: 0.7980 chunk 131 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 100 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 169 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 194 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 221 optimal weight: 8.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3580 r_free = 0.3580 target = 0.095070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.070597 restraints weight = 41738.862| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.94 r_work: 0.2970 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20546 Z= 0.220 Angle : 0.592 9.026 28377 Z= 0.304 Chirality : 0.044 0.220 3211 Planarity : 0.004 0.036 3297 Dihedral : 19.667 171.127 3961 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.41 % Allowed : 10.25 % Favored : 88.34 % 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 aren not related in a simple way. whole: 0.51 (0.17), residues: 2271 helix: 1.59 (0.20), residues: 751 sheet: 0.33 (0.25), residues: 387 loop : -0.48 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 263 TYR 0.011 0.001 TYR G 141 PHE 0.013 0.001 PHE D 133 TRP 0.013 0.002 TRP D 255 HIS 0.005 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00513 (20542) covalent geometry : angle 0.58804 (28371) hydrogen bonds : bond 0.04134 ( 840) hydrogen bonds : angle 5.78169 ( 2287) metal coordination : bond 0.00603 ( 4) metal coordination : angle 4.62992 ( 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 194 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: B 146 VAL cc_start: 0.8819 (OUTLIER) cc_final: 0.8605 (t) REVERT: C 163 ASP cc_start: 0.8486 (m-30) cc_final: 0.8233 (m-30) REVERT: D 1 MET cc_start: 0.8641 (tmm) cc_final: 0.8359 (tpp) REVERT: E 30 ASN cc_start: 0.7992 (m110) cc_final: 0.7596 (m110) REVERT: E 268 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.8346 (mt0) REVERT: F 1 MET cc_start: 0.7303 (pmm) cc_final: 0.6920 (pmm) REVERT: F 14 MET cc_start: 0.9077 (ptm) cc_final: 0.8801 (ptm) REVERT: F 203 GLN cc_start: 0.9008 (mp-120) cc_final: 0.8794 (mp-120) REVERT: G 225 GLN cc_start: 0.8175 (mm-40) cc_final: 0.7908 (mm-40) REVERT: G 236 ILE cc_start: 0.7999 (mt) cc_final: 0.7689 (mp) REVERT: M 27 MET cc_start: 0.7910 (mmm) cc_final: 0.7372 (mtt) REVERT: M 31 GLN cc_start: 0.6643 (mp10) cc_final: 0.6434 (mp10) REVERT: M 56 GLN cc_start: 0.7933 (pt0) cc_final: 0.7556 (pt0) REVERT: M 153 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7930 (mp10) outliers start: 26 outliers final: 11 residues processed: 183 average time/residue: 0.6305 time to fit residues: 128.8595 Evaluate side-chains 177 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 163 time to evaluate : 0.537 ------------------------------------------------------------------------------- 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 146 VAL 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 179 THR Chi-restraints excluded: chain E residue 268 GLN Chi-restraints excluded: chain E residue 278 LYS Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain M residue 153 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 229 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 159 optimal weight: 2.9990 chunk 169 optimal weight: 0.9980 chunk 150 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 209 optimal weight: 20.0000 chunk 157 optimal weight: 6.9990 chunk 185 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 74 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.094311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.069713 restraints weight = 41731.892| |-----------------------------------------------------------------------------| r_work (start): 0.3051 rms_B_bonded: 1.93 r_work: 0.2946 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 20546 Z= 0.270 Angle : 0.616 8.957 28377 Z= 0.317 Chirality : 0.045 0.221 3211 Planarity : 0.005 0.043 3297 Dihedral : 19.778 177.960 3961 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.90 % Allowed : 11.77 % Favored : 86.33 % 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 aren not related in a simple way. whole: 0.37 (0.17), residues: 2271 helix: 1.48 (0.19), residues: 752 sheet: 0.32 (0.26), residues: 367 loop : -0.58 (0.18), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 42 TYR 0.012 0.002 TYR G 141 PHE 0.013 0.002 PHE B 133 TRP 0.014 0.002 TRP A 207 HIS 0.007 0.002 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00635 (20542) covalent geometry : angle 0.61234 (28371) hydrogen bonds : bond 0.04124 ( 840) hydrogen bonds : angle 5.70689 ( 2287) metal coordination : bond 0.00727 ( 4) metal coordination : angle 4.75637 ( 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 201 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 166 time to evaluate : 0.581 Fit side-chains revert: symmetry clash REVERT: B 214 THR cc_start: 0.8644 (m) cc_final: 0.8351 (p) REVERT: C 139 MET cc_start: 0.8725 (OUTLIER) cc_final: 0.8091 (mmt) REVERT: C 332 MET cc_start: 0.8571 (ttm) cc_final: 0.8363 (ttp) REVERT: E 30 ASN cc_start: 0.8008 (m110) cc_final: 0.7613 (m110) REVERT: E 268 GLN cc_start: 0.8755 (OUTLIER) cc_final: 0.8309 (mt0) REVERT: F 1 MET cc_start: 0.7497 (pmm) cc_final: 0.7101 (pmm) REVERT: G 162 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7718 (ptp-170) REVERT: G 225 GLN cc_start: 0.8329 (mm-40) cc_final: 0.8038 (mm-40) REVERT: G 236 ILE cc_start: 0.8022 (mt) cc_final: 0.7721 (mp) REVERT: M 31 GLN cc_start: 0.6721 (mp10) cc_final: 0.6477 (mp10) REVERT: M 56 GLN cc_start: 0.7942 (pt0) cc_final: 0.7571 (pt0) outliers start: 35 outliers final: 21 residues processed: 189 average time/residue: 0.6102 time to fit residues: 129.1880 Evaluate side-chains 186 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 162 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 37 ARG Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 46 MET Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 46 MET Chi-restraints excluded: chain D residue 174 THR 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 E residue 278 LYS 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 81 VAL Chi-restraints excluded: chain M residue 193 LEU Chi-restraints excluded: chain M residue 197 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 24 optimal weight: 0.5980 chunk 221 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 80 optimal weight: 0.8980 chunk 217 optimal weight: 0.9990 chunk 138 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 233 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 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** M 201 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.094592 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.070054 restraints weight = 41503.380| |-----------------------------------------------------------------------------| r_work (start): 0.3057 rms_B_bonded: 1.94 r_work: 0.2951 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20546 Z= 0.185 Angle : 0.577 11.306 28377 Z= 0.297 Chirality : 0.043 0.216 3211 Planarity : 0.004 0.039 3297 Dihedral : 19.764 178.653 3961 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 2.28 % Allowed : 12.69 % Favored : 85.03 % 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 aren not related in a simple way. whole: 0.33 (0.17), residues: 2271 helix: 1.49 (0.19), residues: 760 sheet: 0.14 (0.26), residues: 374 loop : -0.60 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG E 88 TYR 0.012 0.001 TYR G 141 PHE 0.011 0.001 PHE E 133 TRP 0.014 0.001 TRP D 255 HIS 0.006 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00428 (20542) covalent geometry : angle 0.57303 (28371) hydrogen bonds : bond 0.03770 ( 840) hydrogen bonds : angle 5.55409 ( 2287) metal coordination : bond 0.00625 ( 4) metal coordination : angle 4.51388 ( 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 213 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 171 time to evaluate : 0.698 Fit side-chains revert: symmetry clash REVERT: B 214 THR cc_start: 0.8587 (m) cc_final: 0.8290 (p) REVERT: C 302 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8395 (tp) REVERT: C 332 MET cc_start: 0.8477 (ttm) cc_final: 0.8271 (ttp) REVERT: E 30 ASN cc_start: 0.7967 (m110) cc_final: 0.7569 (m110) REVERT: E 268 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.8321 (mt0) REVERT: F 1 MET cc_start: 0.7492 (pmm) cc_final: 0.7101 (pmm) REVERT: G 162 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7713 (ptp-170) REVERT: G 225 GLN cc_start: 0.8347 (mm-40) cc_final: 0.8045 (mm-40) REVERT: M 56 GLN cc_start: 0.7999 (pt0) cc_final: 0.7642 (pt0) outliers start: 42 outliers final: 24 residues processed: 200 average time/residue: 0.6358 time to fit residues: 142.4736 Evaluate side-chains 188 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.645 ------------------------------------------------------------------------------- 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 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 46 MET Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 174 THR 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 E residue 278 LYS Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 85 LEU 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 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: 4.9990 chunk 71 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 119 optimal weight: 8.9990 chunk 125 optimal weight: 0.9980 chunk 171 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 214 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3564 r_free = 0.3564 target = 0.094561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.070371 restraints weight = 41693.877| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.86 r_work: 0.2959 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20546 Z= 0.187 Angle : 0.577 8.927 28377 Z= 0.297 Chirality : 0.043 0.215 3211 Planarity : 0.004 0.038 3297 Dihedral : 19.749 179.210 3961 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.17 % Allowed : 13.23 % Favored : 84.60 % 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 aren not related in a simple way. whole: 0.35 (0.17), residues: 2271 helix: 1.52 (0.19), residues: 760 sheet: 0.11 (0.25), residues: 384 loop : -0.59 (0.18), residues: 1127 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 88 TYR 0.014 0.001 TYR G 141 PHE 0.012 0.001 PHE E 38 TRP 0.013 0.001 TRP D 255 HIS 0.006 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00433 (20542) covalent geometry : angle 0.57308 (28371) hydrogen bonds : bond 0.03722 ( 840) hydrogen bonds : angle 5.49486 ( 2287) metal coordination : bond 0.00604 ( 4) metal coordination : angle 4.43932 ( 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 201 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 161 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: B 214 THR cc_start: 0.8593 (m) cc_final: 0.8298 (p) REVERT: C 302 LEU cc_start: 0.8711 (tm) cc_final: 0.8468 (tp) REVERT: C 332 MET cc_start: 0.8456 (ttm) cc_final: 0.8253 (ttp) REVERT: E 30 ASN cc_start: 0.7933 (m110) cc_final: 0.7533 (m110) REVERT: E 145 MET cc_start: 0.7192 (mtt) cc_final: 0.6517 (mtt) REVERT: E 268 GLN cc_start: 0.8748 (OUTLIER) cc_final: 0.8316 (mt0) REVERT: F 1 MET cc_start: 0.7499 (pmm) cc_final: 0.7111 (pmm) REVERT: G 162 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7708 (ptp-170) REVERT: G 190 LYS cc_start: 0.8593 (mtpp) cc_final: 0.8135 (mppt) REVERT: G 225 GLN cc_start: 0.8341 (mm-40) cc_final: 0.8041 (mm-40) REVERT: M 27 MET cc_start: 0.7099 (mmm) cc_final: 0.6863 (mtt) outliers start: 40 outliers final: 27 residues processed: 191 average time/residue: 0.6624 time to fit residues: 141.6729 Evaluate side-chains 183 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.463 ------------------------------------------------------------------------------- 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 146 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 263 ARG 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 46 MET Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 197 ILE 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 85 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 194 optimal weight: 2.9990 chunk 180 optimal weight: 0.9990 chunk 202 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 199 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 236 optimal weight: 0.0770 overall best weight: 1.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3557 r_free = 0.3557 target = 0.094224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.069917 restraints weight = 41773.587| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 1.86 r_work: 0.2945 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20546 Z= 0.223 Angle : 0.595 8.767 28377 Z= 0.307 Chirality : 0.044 0.215 3211 Planarity : 0.005 0.050 3297 Dihedral : 19.750 179.748 3961 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.39 % Allowed : 13.77 % 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 aren not related in a simple way. whole: 0.27 (0.17), residues: 2271 helix: 1.39 (0.19), residues: 761 sheet: 0.18 (0.26), residues: 367 loop : -0.61 (0.18), residues: 1143 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG E 88 TYR 0.015 0.001 TYR G 141 PHE 0.014 0.001 PHE M 221 TRP 0.012 0.002 TRP A 207 HIS 0.007 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00523 (20542) covalent geometry : angle 0.59176 (28371) hydrogen bonds : bond 0.03821 ( 840) hydrogen bonds : angle 5.52194 ( 2287) metal coordination : bond 0.00637 ( 4) metal coordination : angle 4.49961 ( 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 208 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 164 time to evaluate : 0.681 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.8717 (tpp) cc_final: 0.8456 (tpt) REVERT: C 302 LEU cc_start: 0.8726 (tm) cc_final: 0.8483 (tp) REVERT: E 30 ASN cc_start: 0.8014 (m110) cc_final: 0.7627 (m110) REVERT: E 268 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8319 (mt0) REVERT: F 1 MET cc_start: 0.7562 (pmm) cc_final: 0.7162 (pmm) REVERT: G 162 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7708 (ptp-170) REVERT: G 190 LYS cc_start: 0.8576 (mtpp) cc_final: 0.8121 (mppt) REVERT: G 225 GLN cc_start: 0.8370 (mm-40) cc_final: 0.8079 (mm-40) REVERT: M 213 MET cc_start: 0.6922 (pmm) cc_final: 0.5857 (ppp) outliers start: 44 outliers final: 31 residues processed: 194 average time/residue: 0.6466 time to fit residues: 140.2870 Evaluate side-chains 193 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 160 time to evaluate : 0.701 ------------------------------------------------------------------------------- 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 146 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 263 ARG 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 46 MET Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 169 ILE Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain D residue 197 ILE 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 85 LEU Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 162 ARG Chi-restraints excluded: chain G residue 196 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 134 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 17 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 129 optimal weight: 4.9990 chunk 26 optimal weight: 0.5980 chunk 73 optimal weight: 0.6980 chunk 54 optimal weight: 0.9990 chunk 176 optimal weight: 2.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3588 r_free = 0.3588 target = 0.095344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.070919 restraints weight = 41542.873| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.92 r_work: 0.2978 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20546 Z= 0.175 Angle : 0.569 9.862 28377 Z= 0.294 Chirality : 0.043 0.213 3211 Planarity : 0.004 0.042 3297 Dihedral : 19.657 179.142 3961 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.11 % Allowed : 14.21 % Favored : 83.68 % 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 aren not related in a simple way. whole: 0.30 (0.17), residues: 2271 helix: 1.44 (0.19), residues: 761 sheet: 0.13 (0.25), residues: 379 loop : -0.62 (0.18), residues: 1131 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 E 38 TRP 0.013 0.001 TRP D 255 HIS 0.006 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00406 (20542) covalent geometry : angle 0.56587 (28371) hydrogen bonds : bond 0.03605 ( 840) hydrogen bonds : angle 5.43851 ( 2287) metal coordination : bond 0.00628 ( 4) metal coordination : angle 4.33459 ( 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: 39 poor density : 163 time to evaluate : 0.537 Fit side-chains revert: symmetry clash REVERT: A 263 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7955 (mtm-85) REVERT: B 214 THR cc_start: 0.8626 (m) cc_final: 0.8358 (p) REVERT: C 1 MET cc_start: 0.8730 (tpp) cc_final: 0.8500 (tpt) REVERT: C 139 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8342 (mmt) REVERT: C 202 GLN cc_start: 0.7724 (tp40) cc_final: 0.7330 (tp-100) REVERT: C 302 LEU cc_start: 0.8672 (tm) cc_final: 0.8427 (tp) REVERT: E 30 ASN cc_start: 0.7903 (m110) cc_final: 0.7483 (m110) REVERT: E 268 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.8320 (mt0) REVERT: F 1 MET cc_start: 0.7572 (pmm) cc_final: 0.7073 (pmm) REVERT: G 162 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7695 (ptp-170) REVERT: G 190 LYS cc_start: 0.8540 (mtpp) cc_final: 0.8100 (mppt) REVERT: G 225 GLN cc_start: 0.8349 (mm-40) cc_final: 0.8055 (mm-40) REVERT: M 92 MET cc_start: 0.7330 (mtm) cc_final: 0.6768 (mpp) outliers start: 39 outliers final: 25 residues processed: 189 average time/residue: 0.7126 time to fit residues: 150.5393 Evaluate side-chains 187 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 158 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 146 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 263 ARG 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 46 MET Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 139 MET Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 40 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 174 THR 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 85 LEU Chi-restraints excluded: chain G residue 93 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 153 GLN 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: 0.9990 chunk 0 optimal weight: 3.9990 chunk 116 optimal weight: 0.6980 chunk 55 optimal weight: 0.0000 chunk 94 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 226 optimal weight: 0.3980 chunk 213 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 111 optimal weight: 0.9990 chunk 151 optimal weight: 8.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 106 ASN F 74 ASN ** 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 = 0.3606 r_free = 0.3606 target = 0.096287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.072023 restraints weight = 41362.119| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 1.92 r_work: 0.2999 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 20546 Z= 0.137 Angle : 0.564 12.765 28377 Z= 0.290 Chirality : 0.042 0.211 3211 Planarity : 0.004 0.042 3297 Dihedral : 19.553 177.660 3961 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.46 % Allowed : 15.13 % Favored : 83.41 % 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 aren not related in a simple way. whole: 0.39 (0.18), residues: 2271 helix: 1.54 (0.20), residues: 762 sheet: 0.19 (0.26), residues: 379 loop : -0.57 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 88 TYR 0.016 0.001 TYR G 141 PHE 0.010 0.001 PHE B 133 TRP 0.014 0.001 TRP D 255 HIS 0.005 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00311 (20542) covalent geometry : angle 0.56078 (28371) hydrogen bonds : bond 0.03403 ( 840) hydrogen bonds : angle 5.35059 ( 2287) metal coordination : bond 0.00571 ( 4) metal coordination : angle 4.18475 ( 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 188 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 0.722 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 263 ARG cc_start: 0.8244 (OUTLIER) cc_final: 0.7906 (mtm-85) REVERT: B 214 THR cc_start: 0.8551 (m) cc_final: 0.8283 (p) REVERT: C 1 MET cc_start: 0.8728 (tpp) cc_final: 0.8507 (tpt) REVERT: C 202 GLN cc_start: 0.7720 (tp40) cc_final: 0.7329 (tp-100) REVERT: C 302 LEU cc_start: 0.8605 (tm) cc_final: 0.8371 (tp) REVERT: E 30 ASN cc_start: 0.7941 (m110) cc_final: 0.7504 (m110) REVERT: E 145 MET cc_start: 0.7327 (mtt) cc_final: 0.6611 (mtt) REVERT: E 268 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8298 (mt0) REVERT: E 332 MET cc_start: 0.7302 (ppp) cc_final: 0.5907 (ptt) REVERT: F 1 MET cc_start: 0.7592 (pmm) cc_final: 0.7082 (pmm) REVERT: G 162 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7624 (ptp-170) REVERT: G 190 LYS cc_start: 0.8502 (mtpp) cc_final: 0.8067 (mppt) REVERT: G 225 GLN cc_start: 0.8312 (mm-40) cc_final: 0.8008 (mm-40) REVERT: M 9 ASN cc_start: 0.7008 (p0) cc_final: 0.6714 (p0) REVERT: M 92 MET cc_start: 0.7265 (mtm) cc_final: 0.6792 (mpp) outliers start: 27 outliers final: 19 residues processed: 181 average time/residue: 0.6746 time to fit residues: 135.8622 Evaluate side-chains 178 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 156 time to evaluate : 0.586 ------------------------------------------------------------------------------- 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 A residue 263 ARG 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 46 MET Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 40 LEU 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 85 LEU 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 60 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 36 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 9 optimal weight: 0.0000 chunk 123 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 223 optimal weight: 0.5980 chunk 35 optimal weight: 0.2980 overall best weight: 0.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 ASN 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.096641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.072328 restraints weight = 41396.242| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 1.92 r_work: 0.3013 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.1913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20546 Z= 0.131 Angle : 0.559 10.461 28377 Z= 0.287 Chirality : 0.041 0.212 3211 Planarity : 0.004 0.041 3297 Dihedral : 19.471 177.688 3961 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.63 % Allowed : 15.29 % Favored : 83.08 % 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 aren not related in a simple way. whole: 0.48 (0.18), residues: 2271 helix: 1.62 (0.20), residues: 762 sheet: 0.29 (0.26), residues: 372 loop : -0.55 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 88 TYR 0.018 0.001 TYR G 141 PHE 0.014 0.001 PHE E 38 TRP 0.013 0.001 TRP D 255 HIS 0.005 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00296 (20542) covalent geometry : angle 0.55539 (28371) hydrogen bonds : bond 0.03270 ( 840) hydrogen bonds : angle 5.27525 ( 2287) metal coordination : bond 0.00544 ( 4) metal coordination : angle 4.10828 ( 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 197 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 167 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 214 THR cc_start: 0.8546 (m) cc_final: 0.8277 (p) REVERT: C 1 MET cc_start: 0.8725 (tpp) cc_final: 0.8437 (tpt) REVERT: C 202 GLN cc_start: 0.7728 (tp40) cc_final: 0.7382 (tp-100) REVERT: C 302 LEU cc_start: 0.8599 (tm) cc_final: 0.8351 (tp) REVERT: E 30 ASN cc_start: 0.7894 (m110) cc_final: 0.7466 (m110) REVERT: E 145 MET cc_start: 0.7268 (mtt) cc_final: 0.6510 (mtt) REVERT: E 268 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8277 (mt0) REVERT: E 332 MET cc_start: 0.7494 (ppp) cc_final: 0.5795 (ptt) REVERT: F 1 MET cc_start: 0.7571 (pmm) cc_final: 0.7050 (pmm) REVERT: F 61 SER cc_start: 0.9042 (t) cc_final: 0.8784 (p) REVERT: G 190 LYS cc_start: 0.8453 (mtpp) cc_final: 0.8061 (mppt) REVERT: G 225 GLN cc_start: 0.8307 (mm-40) cc_final: 0.8007 (mm-40) REVERT: M 92 MET cc_start: 0.7300 (mtm) cc_final: 0.6830 (mpp) outliers start: 30 outliers final: 20 residues processed: 185 average time/residue: 0.5922 time to fit residues: 122.8991 Evaluate side-chains 179 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 158 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 A residue 263 ARG 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 46 MET Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 40 LEU 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 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: 0.1980 chunk 134 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 58 optimal weight: 0.7980 chunk 3 optimal weight: 0.9990 chunk 117 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 288 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3602 r_free = 0.3602 target = 0.096031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.071683 restraints weight = 41695.324| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.93 r_work: 0.2993 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2865 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 20546 Z= 0.172 Angle : 0.582 13.332 28377 Z= 0.298 Chirality : 0.042 0.214 3211 Planarity : 0.004 0.041 3297 Dihedral : 19.473 178.697 3961 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.52 % Allowed : 15.46 % Favored : 83.03 % 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 aren not related in a simple way. whole: 0.43 (0.18), residues: 2271 helix: 1.56 (0.20), residues: 762 sheet: 0.23 (0.26), residues: 379 loop : -0.55 (0.18), residues: 1130 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG E 88 TYR 0.017 0.001 TYR G 141 PHE 0.018 0.001 PHE E 243 TRP 0.011 0.001 TRP D 255 HIS 0.005 0.001 HIS F 49 Details of bonding type rmsd covalent geometry : bond 0.00399 (20542) covalent geometry : angle 0.57876 (28371) hydrogen bonds : bond 0.03398 ( 840) hydrogen bonds : angle 5.30447 ( 2287) metal coordination : bond 0.00565 ( 4) metal coordination : angle 4.17150 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6157.46 seconds wall clock time: 105 minutes 45.46 seconds (6345.46 seconds total)