Starting phenix.real_space_refine on Thu Jan 23 05:51:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rc3_19046/01_2025/8rc3_19046.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rc3_19046/01_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8rc3_19046/01_2025/8rc3_19046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rc3_19046/01_2025/8rc3_19046.map" model { file = "/net/cci-nas-00/data/ceres_data/8rc3_19046/01_2025/8rc3_19046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rc3_19046/01_2025/8rc3_19046.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/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: 12.65, per 1000 atoms: 0.64 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: 5.51 Conformation dependent library (CDL) restraints added in 2.6 seconds 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: 7.32 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: 6.80 Time building geometry restraints manager: 6.11 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: 3.500 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: 0.020 Extract box with map and model: 0.610 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 54.050 Find NCS groups from input model: 0.760 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:13.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 72.510 ------------------------------------------------------------------------------- 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 20542 Z= 0.259 Angle : 0.566 10.803 28371 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 : 10.06 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.001 TRP A 207 HIS 0.006 0.001 HIS F 49 PHE 0.011 0.001 PHE D 133 TYR 0.011 0.001 TYR G 141 ARG 0.007 0.000 ARG C 263 *********************** 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 : 2.162 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: 1.6224 time to fit residues: 356.7356 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 : 1.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 200 optimal weight: 3.9990 chunk 179 optimal weight: 0.5980 chunk 99 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 185 optimal weight: 1.9990 chunk 71 optimal weight: 0.1980 chunk 112 optimal weight: 0.9990 chunk 138 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 = 0.3616 r_free = 0.3616 target = 0.096481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.071657 restraints weight = 40851.117| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.92 r_work: 0.3009 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.0909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 20542 Z= 0.300 Angle : 0.608 7.344 28371 Z= 0.315 Chirality : 0.044 0.230 3211 Planarity : 0.005 0.067 3297 Dihedral : 19.705 169.458 3961 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 0.70 % Allowed : 7.48 % Favored : 91.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.49 (0.17), residues: 2271 helix: 1.60 (0.19), residues: 738 sheet: 0.32 (0.25), residues: 393 loop : -0.49 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 255 HIS 0.005 0.001 HIS F 49 PHE 0.012 0.001 PHE E 133 TYR 0.011 0.001 TYR A 22 ARG 0.006 0.000 ARG E 88 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 180 time to evaluate : 1.975 Fit side-chains revert: symmetry clash REVERT: B 145 MET cc_start: 0.8100 (mtt) cc_final: 0.7525 (mtt) REVERT: B 214 THR cc_start: 0.8647 (m) cc_final: 0.8374 (p) REVERT: C 163 ASP cc_start: 0.8500 (m-30) cc_final: 0.8287 (m-30) REVERT: C 305 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8337 (mm-30) REVERT: C 332 MET cc_start: 0.8494 (ttm) cc_final: 0.8283 (ttp) REVERT: D 1 MET cc_start: 0.8633 (tmm) cc_final: 0.8376 (tpp) REVERT: E 1 MET cc_start: 0.7993 (pmm) cc_final: 0.7714 (pmm) REVERT: E 30 ASN cc_start: 0.8052 (m110) cc_final: 0.7657 (m110) REVERT: E 268 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8419 (mt0) REVERT: F 14 MET cc_start: 0.9046 (ptm) cc_final: 0.8783 (ptm) REVERT: F 203 GLN cc_start: 0.8991 (mp-120) cc_final: 0.8778 (mp-120) REVERT: G 225 GLN cc_start: 0.8185 (mm-40) cc_final: 0.7926 (mm-40) REVERT: G 236 ILE cc_start: 0.8024 (mt) cc_final: 0.7718 (mp) REVERT: M 27 MET cc_start: 0.7111 (mmm) cc_final: 0.6464 (mmm) REVERT: M 31 GLN cc_start: 0.6424 (mp10) cc_final: 0.6136 (mp10) REVERT: M 193 LEU cc_start: 0.7124 (pt) cc_final: 0.6869 (tt) outliers start: 13 outliers final: 6 residues processed: 188 average time/residue: 1.5415 time to fit residues: 323.9227 Evaluate side-chains 175 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 168 time to evaluate : 2.144 ------------------------------------------------------------------------------- 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 151 ILE 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 98 optimal weight: 1.9990 chunk 218 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 97 optimal weight: 2.9990 chunk 175 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 210 optimal weight: 3.9990 chunk 9 optimal weight: 0.0980 chunk 111 optimal weight: 0.8980 chunk 20 optimal weight: 3.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 153 GLN ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.095208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.070721 restraints weight = 41540.564| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.95 r_work: 0.2972 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20542 Z= 0.292 Angle : 0.579 6.821 28371 Z= 0.300 Chirality : 0.043 0.220 3211 Planarity : 0.004 0.036 3297 Dihedral : 19.731 171.701 3961 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.52 % Allowed : 10.79 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.17), residues: 2271 helix: 1.52 (0.19), residues: 753 sheet: 0.26 (0.25), residues: 385 loop : -0.49 (0.18), residues: 1133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 255 HIS 0.006 0.001 HIS F 49 PHE 0.012 0.001 PHE D 133 TYR 0.010 0.001 TYR G 141 ARG 0.007 0.000 ARG E 88 *********************** 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 196 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 168 time to evaluate : 2.310 Fit side-chains revert: symmetry clash REVERT: C 163 ASP cc_start: 0.8482 (m-30) cc_final: 0.8232 (m-30) REVERT: C 332 MET cc_start: 0.8487 (ttm) cc_final: 0.8270 (ttp) REVERT: D 1 MET cc_start: 0.8637 (tmm) cc_final: 0.8356 (tpp) REVERT: E 30 ASN cc_start: 0.7996 (m110) cc_final: 0.7607 (m110) REVERT: E 88 ARG cc_start: 0.8321 (ptp-110) cc_final: 0.8113 (ptp-110) REVERT: E 268 GLN cc_start: 0.8708 (OUTLIER) cc_final: 0.8331 (mt0) REVERT: F 1 MET cc_start: 0.7301 (pmm) cc_final: 0.6876 (pmm) REVERT: F 14 MET cc_start: 0.9074 (ptm) cc_final: 0.8781 (ptm) REVERT: G 225 GLN cc_start: 0.8311 (mm-40) cc_final: 0.8025 (mm-40) REVERT: G 236 ILE cc_start: 0.7992 (mt) cc_final: 0.7692 (mp) REVERT: M 27 MET cc_start: 0.7804 (mmm) cc_final: 0.7425 (mtt) REVERT: M 56 GLN cc_start: 0.7885 (pt0) cc_final: 0.7464 (pt0) REVERT: M 153 GLN cc_start: 0.8172 (OUTLIER) cc_final: 0.7957 (mp10) outliers start: 28 outliers final: 13 residues processed: 182 average time/residue: 1.5524 time to fit residues: 316.1430 Evaluate side-chains 174 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 159 time to evaluate : 2.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 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 162 ARG Chi-restraints excluded: chain M residue 153 GLN Chi-restraints excluded: chain M residue 197 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 106 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 122 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 150 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 231 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 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 = 0.3594 r_free = 0.3594 target = 0.095110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.070314 restraints weight = 41128.752| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 1.92 r_work: 0.2973 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.1389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.065 20542 Z= 0.453 Angle : 0.630 7.078 28371 Z= 0.326 Chirality : 0.046 0.222 3211 Planarity : 0.005 0.041 3297 Dihedral : 19.842 179.367 3961 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.95 % Allowed : 11.82 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.17), residues: 2271 helix: 1.35 (0.19), residues: 753 sheet: 0.20 (0.26), residues: 372 loop : -0.62 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 207 HIS 0.008 0.002 HIS F 49 PHE 0.014 0.002 PHE C 38 TYR 0.014 0.002 TYR G 141 ARG 0.008 0.001 ARG D 42 *********************** 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 202 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 166 time to evaluate : 2.088 Fit side-chains revert: symmetry clash REVERT: B 214 THR cc_start: 0.8653 (m) cc_final: 0.8361 (p) REVERT: C 1 MET cc_start: 0.8619 (tpp) cc_final: 0.8248 (tpt) REVERT: C 163 ASP cc_start: 0.8483 (m-30) cc_final: 0.8258 (m-30) REVERT: D 1 MET cc_start: 0.8665 (tmm) cc_final: 0.8458 (tpp) REVERT: E 30 ASN cc_start: 0.8016 (m110) cc_final: 0.7621 (m110) REVERT: E 268 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.8326 (mt0) REVERT: F 1 MET cc_start: 0.7341 (pmm) cc_final: 0.6834 (pmm) REVERT: G 225 GLN cc_start: 0.8378 (mm-40) cc_final: 0.8088 (mm-40) REVERT: G 236 ILE cc_start: 0.8023 (mt) cc_final: 0.7715 (mp) outliers start: 36 outliers final: 23 residues processed: 189 average time/residue: 1.4489 time to fit residues: 308.8633 Evaluate side-chains 185 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 1.982 ------------------------------------------------------------------------------- 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 145 MET Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 165 ILE 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 139 MET Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 302 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 F residue 151 ILE Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain G residue 85 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 228 optimal weight: 20.0000 chunk 234 optimal weight: 5.9990 chunk 43 optimal weight: 0.8980 chunk 142 optimal weight: 2.9990 chunk 215 optimal weight: 7.9990 chunk 183 optimal weight: 5.9990 chunk 231 optimal weight: 4.9990 chunk 26 optimal weight: 0.8980 chunk 158 optimal weight: 0.9990 chunk 146 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 201 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.094429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.070046 restraints weight = 41794.774| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.89 r_work: 0.2950 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20542 Z= 0.278 Angle : 0.573 7.146 28371 Z= 0.297 Chirality : 0.043 0.215 3211 Planarity : 0.004 0.042 3297 Dihedral : 19.813 178.823 3961 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.17 % Allowed : 12.96 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.17), residues: 2271 helix: 1.46 (0.19), residues: 753 sheet: 0.19 (0.26), residues: 367 loop : -0.59 (0.18), residues: 1151 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 255 HIS 0.007 0.001 HIS F 49 PHE 0.012 0.001 PHE E 133 TYR 0.013 0.001 TYR G 141 ARG 0.007 0.000 ARG E 88 *********************** 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 210 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 170 time to evaluate : 2.095 Fit side-chains revert: symmetry clash REVERT: B 214 THR cc_start: 0.8578 (m) cc_final: 0.8288 (p) REVERT: C 1 MET cc_start: 0.8673 (tpp) cc_final: 0.8430 (tpt) REVERT: C 163 ASP cc_start: 0.8440 (m-30) cc_final: 0.8235 (m-30) REVERT: C 302 LEU cc_start: 0.8698 (tm) cc_final: 0.8459 (tp) REVERT: D 1 MET cc_start: 0.8658 (tmm) cc_final: 0.8439 (tpp) REVERT: E 30 ASN cc_start: 0.7974 (m110) cc_final: 0.7555 (m110) REVERT: E 88 ARG cc_start: 0.8219 (ptp-110) cc_final: 0.7981 (ptp-110) REVERT: E 145 MET cc_start: 0.7189 (mtt) cc_final: 0.6508 (mtt) REVERT: E 268 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8268 (mt0) REVERT: F 1 MET cc_start: 0.7387 (pmm) cc_final: 0.6933 (pmm) REVERT: G 225 GLN cc_start: 0.8363 (mm-40) cc_final: 0.8070 (mm-40) outliers start: 40 outliers final: 23 residues processed: 198 average time/residue: 1.4050 time to fit residues: 313.9273 Evaluate side-chains 185 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 161 time to evaluate : 2.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 211 LEU 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 F residue 199 MET Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 193 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 180 optimal weight: 0.2980 chunk 69 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 139 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 136 optimal weight: 10.0000 chunk 101 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 = 0.3549 r_free = 0.3549 target = 0.093794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.069229 restraints weight = 41668.332| |-----------------------------------------------------------------------------| r_work (start): 0.3039 rms_B_bonded: 1.96 r_work: 0.2930 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 20542 Z= 0.347 Angle : 0.593 7.063 28371 Z= 0.307 Chirality : 0.044 0.215 3211 Planarity : 0.005 0.042 3297 Dihedral : 19.791 179.582 3961 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.01 % Allowed : 13.56 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.17), residues: 2271 helix: 1.35 (0.19), residues: 760 sheet: 0.16 (0.25), residues: 371 loop : -0.63 (0.18), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 207 HIS 0.006 0.001 HIS F 49 PHE 0.013 0.002 PHE E 38 TYR 0.015 0.001 TYR G 141 ARG 0.005 0.000 ARG D 42 *********************** 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 204 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 167 time to evaluate : 2.025 Fit side-chains revert: symmetry clash REVERT: C 1 MET cc_start: 0.8674 (tpp) cc_final: 0.8471 (tpt) REVERT: C 163 ASP cc_start: 0.8469 (m-30) cc_final: 0.8267 (m-30) REVERT: C 302 LEU cc_start: 0.8730 (tm) cc_final: 0.8490 (tp) REVERT: D 1 MET cc_start: 0.8638 (tmm) cc_final: 0.8309 (tpt) REVERT: E 30 ASN cc_start: 0.8049 (m110) cc_final: 0.7662 (m110) REVERT: E 268 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8310 (mt0) REVERT: F 1 MET cc_start: 0.7403 (pmm) cc_final: 0.6933 (pmm) REVERT: G 225 GLN cc_start: 0.8398 (mm-40) cc_final: 0.8099 (mm-40) outliers start: 37 outliers final: 28 residues processed: 192 average time/residue: 1.3917 time to fit residues: 301.8880 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 : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 145 MET Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 165 ILE Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 16 optimal weight: 0.9980 chunk 154 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 164 optimal weight: 0.3980 chunk 62 optimal weight: 0.0970 chunk 114 optimal weight: 4.9990 chunk 66 optimal weight: 0.6980 chunk 124 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- 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 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 = 0.095418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.071321 restraints weight = 41363.713| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.85 r_work: 0.2982 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2856 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.2856 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 20542 Z= 0.201 Angle : 0.551 9.240 28371 Z= 0.286 Chirality : 0.042 0.211 3211 Planarity : 0.004 0.043 3297 Dihedral : 19.645 178.046 3961 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.52 % Allowed : 14.75 % Favored : 83.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.17), residues: 2271 helix: 1.49 (0.19), residues: 761 sheet: 0.13 (0.25), residues: 385 loop : -0.61 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 255 HIS 0.006 0.001 HIS F 49 PHE 0.010 0.001 PHE B 133 TYR 0.015 0.001 TYR G 141 ARG 0.008 0.000 ARG E 88 *********************** 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 192 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 2.138 Fit side-chains revert: symmetry clash REVERT: B 214 THR cc_start: 0.8532 (m) cc_final: 0.8274 (p) REVERT: C 163 ASP cc_start: 0.8443 (m-30) cc_final: 0.8203 (m-30) REVERT: C 202 GLN cc_start: 0.7733 (tp40) cc_final: 0.7329 (tp-100) REVERT: C 302 LEU cc_start: 0.8639 (tm) cc_final: 0.8399 (tp) REVERT: D 1 MET cc_start: 0.8605 (tmm) cc_final: 0.8127 (tpp) REVERT: E 30 ASN cc_start: 0.7870 (m110) cc_final: 0.7440 (m110) REVERT: E 88 ARG cc_start: 0.8145 (ptp-110) cc_final: 0.7945 (ptp-110) REVERT: F 1 MET cc_start: 0.7365 (pmm) cc_final: 0.6931 (pmm) REVERT: G 162 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7645 (ptp-170) REVERT: G 190 LYS cc_start: 0.8529 (mtpp) cc_final: 0.8090 (mppt) REVERT: G 225 GLN cc_start: 0.8330 (mm-40) cc_final: 0.8033 (mm-40) REVERT: M 9 ASN cc_start: 0.6925 (p0) cc_final: 0.6703 (p0) outliers start: 28 outliers final: 17 residues processed: 182 average time/residue: 1.5176 time to fit residues: 311.6302 Evaluate side-chains 177 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 159 time to evaluate : 2.045 ------------------------------------------------------------------------------- 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 261 VAL Chi-restraints excluded: chain C residue 91 SER Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain G residue 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 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 204 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 94 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 128 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 74 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 78 optimal weight: 0.0030 overall best weight: 0.8792 ------------------------------------------------------------------------------- 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 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 = 0.3593 r_free = 0.3593 target = 0.095567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.071088 restraints weight = 41778.129| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 1.96 r_work: 0.2980 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20542 Z= 0.240 Angle : 0.560 9.879 28371 Z= 0.290 Chirality : 0.042 0.212 3211 Planarity : 0.004 0.043 3297 Dihedral : 19.585 178.586 3961 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.68 % Allowed : 15.18 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.17), residues: 2271 helix: 1.48 (0.19), residues: 761 sheet: 0.15 (0.25), residues: 385 loop : -0.58 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 255 HIS 0.006 0.001 HIS F 49 PHE 0.014 0.001 PHE C 38 TYR 0.016 0.001 TYR G 141 ARG 0.008 0.000 ARG C 263 *********************** 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 196 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 2.130 Fit side-chains revert: symmetry clash REVERT: B 214 THR cc_start: 0.8576 (m) cc_final: 0.8299 (p) REVERT: C 163 ASP cc_start: 0.8456 (m-30) cc_final: 0.8251 (m-30) REVERT: C 202 GLN cc_start: 0.7716 (tp40) cc_final: 0.7306 (tp-100) REVERT: C 332 MET cc_start: 0.8271 (OUTLIER) cc_final: 0.8033 (ttm) REVERT: D 1 MET cc_start: 0.8607 (tmm) cc_final: 0.8150 (tpp) REVERT: E 30 ASN cc_start: 0.7886 (m110) cc_final: 0.7479 (m110) REVERT: E 88 ARG cc_start: 0.8151 (ptp-110) cc_final: 0.7856 (ptp-110) REVERT: F 1 MET cc_start: 0.7356 (OUTLIER) cc_final: 0.6903 (pmm) REVERT: G 162 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7645 (ptp-170) REVERT: G 190 LYS cc_start: 0.8500 (mtpp) cc_final: 0.8065 (mppt) REVERT: G 225 GLN cc_start: 0.8353 (mm-40) cc_final: 0.8050 (mm-40) REVERT: M 92 MET cc_start: 0.7293 (mtm) cc_final: 0.6833 (mpp) outliers start: 31 outliers final: 17 residues processed: 185 average time/residue: 1.5193 time to fit residues: 314.5494 Evaluate side-chains 181 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 161 time to evaluate : 2.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain C residue 332 MET Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 162 ARG Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 193 LEU Chi-restraints excluded: chain M residue 197 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 50 optimal weight: 1.9990 chunk 197 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 213 optimal weight: 3.9990 chunk 190 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 139 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 overall best weight: 0.8584 ------------------------------------------------------------------------------- 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 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 = 0.3598 r_free = 0.3598 target = 0.095789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.071339 restraints weight = 41464.641| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.95 r_work: 0.2987 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20542 Z= 0.235 Angle : 0.568 12.771 28371 Z= 0.292 Chirality : 0.042 0.212 3211 Planarity : 0.004 0.042 3297 Dihedral : 19.536 178.087 3961 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.57 % Allowed : 15.24 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.18), residues: 2271 helix: 1.51 (0.20), residues: 761 sheet: 0.13 (0.25), residues: 385 loop : -0.56 (0.18), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 255 HIS 0.006 0.001 HIS F 49 PHE 0.012 0.001 PHE C 38 TYR 0.017 0.001 TYR G 141 ARG 0.008 0.000 ARG C 263 *********************** 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 193 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 2.163 Fit side-chains revert: symmetry clash REVERT: B 214 THR cc_start: 0.8555 (m) cc_final: 0.8275 (p) REVERT: C 163 ASP cc_start: 0.8468 (m-30) cc_final: 0.8264 (m-30) REVERT: C 202 GLN cc_start: 0.7734 (tp40) cc_final: 0.7327 (tp-100) REVERT: D 1 MET cc_start: 0.8586 (tmm) cc_final: 0.8127 (tpp) REVERT: E 30 ASN cc_start: 0.7939 (m110) cc_final: 0.7519 (m110) REVERT: E 88 ARG cc_start: 0.8160 (ptp-110) cc_final: 0.7960 (ptp-110) REVERT: E 332 MET cc_start: 0.7370 (ppp) cc_final: 0.5961 (ptt) REVERT: F 1 MET cc_start: 0.7406 (OUTLIER) cc_final: 0.6980 (pmm) REVERT: G 162 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7666 (ptp-170) REVERT: G 190 LYS cc_start: 0.8499 (mtpp) cc_final: 0.8066 (mppt) REVERT: G 225 GLN cc_start: 0.8353 (mm-40) cc_final: 0.8054 (mm-40) REVERT: M 92 MET cc_start: 0.7235 (mtm) cc_final: 0.6769 (mpp) REVERT: M 213 MET cc_start: 0.6605 (pmm) cc_final: 0.6269 (pmm) outliers start: 29 outliers final: 21 residues processed: 183 average time/residue: 1.4604 time to fit residues: 301.1880 Evaluate side-chains 183 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 160 time to evaluate : 2.080 ------------------------------------------------------------------------------- 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 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 56 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 162 ARG Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 193 LEU Chi-restraints excluded: chain M residue 197 VAL Chi-restraints excluded: chain M residue 200 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 12 optimal weight: 0.0070 chunk 96 optimal weight: 3.9990 chunk 151 optimal weight: 9.9990 chunk 72 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 117 optimal weight: 0.0970 chunk 188 optimal weight: 1.9990 chunk 219 optimal weight: 8.9990 chunk 145 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.1400 ------------------------------------------------------------------------------- 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 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 = 0.3587 r_free = 0.3587 target = 0.095260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.070765 restraints weight = 41742.968| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.93 r_work: 0.2972 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20542 Z= 0.288 Angle : 0.590 12.108 28371 Z= 0.303 Chirality : 0.043 0.214 3211 Planarity : 0.004 0.043 3297 Dihedral : 19.543 179.152 3961 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.74 % Allowed : 15.29 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.17), residues: 2271 helix: 1.46 (0.20), residues: 761 sheet: 0.14 (0.25), residues: 373 loop : -0.56 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 255 HIS 0.006 0.001 HIS F 49 PHE 0.015 0.001 PHE C 38 TYR 0.018 0.001 TYR G 141 ARG 0.010 0.000 ARG C 263 ********************** 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 192 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 160 time to evaluate : 2.241 Fit side-chains revert: symmetry clash REVERT: B 214 THR cc_start: 0.8555 (m) cc_final: 0.8269 (p) REVERT: C 163 ASP cc_start: 0.8463 (m-30) cc_final: 0.8260 (m-30) REVERT: C 202 GLN cc_start: 0.7713 (tp40) cc_final: 0.7321 (tp-100) REVERT: D 1 MET cc_start: 0.8574 (tmm) cc_final: 0.8098 (tpp) REVERT: E 30 ASN cc_start: 0.7999 (m110) cc_final: 0.7560 (m110) REVERT: E 332 MET cc_start: 0.7480 (ppp) cc_final: 0.5965 (ptt) REVERT: F 61 SER cc_start: 0.9063 (t) cc_final: 0.8776 (p) REVERT: G 162 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7664 (ptp-170) REVERT: G 190 LYS cc_start: 0.8443 (mtpp) cc_final: 0.8029 (mppt) REVERT: G 225 GLN cc_start: 0.8362 (mm-40) cc_final: 0.8071 (mm-40) REVERT: M 92 MET cc_start: 0.7241 (mtm) cc_final: 0.6697 (mpp) REVERT: M 213 MET cc_start: 0.6845 (pmm) cc_final: 0.6618 (pmm) outliers start: 32 outliers final: 25 residues processed: 178 average time/residue: 1.4836 time to fit residues: 297.3331 Evaluate side-chains 185 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 159 time to evaluate : 2.257 ------------------------------------------------------------------------------- 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 B residue 26 ASP Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain B residue 332 MET Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 174 THR Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain G residue 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 Chi-restraints excluded: chain M residue 200 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 130 optimal weight: 0.7980 chunk 211 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 192 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 95 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 194 optimal weight: 0.7980 chunk 207 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 106 ASN E 339 GLN F 74 ASN ** M 153 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.095391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.070791 restraints weight = 41945.714| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 1.96 r_work: 0.2972 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.114 20542 Z= 0.288 Angle : 0.759 59.199 28371 Z= 0.423 Chirality : 0.044 0.619 3211 Planarity : 0.004 0.043 3297 Dihedral : 19.544 179.079 3961 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.46 % Allowed : 15.51 % Favored : 83.03 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.33 (0.17), residues: 2271 helix: 1.43 (0.20), residues: 761 sheet: 0.14 (0.25), residues: 373 loop : -0.56 (0.18), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 255 HIS 0.005 0.001 HIS F 49 PHE 0.015 0.001 PHE C 38 TYR 0.017 0.001 TYR G 141 ARG 0.011 0.000 ARG E 88 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12855.40 seconds wall clock time: 227 minutes 57.24 seconds (13677.24 seconds total)