Starting phenix.real_space_refine on Tue Jun 17 09:12:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rc3_19046/06_2025/8rc3_19046.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rc3_19046/06_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_19046/06_2025/8rc3_19046.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rc3_19046/06_2025/8rc3_19046.map" model { file = "/net/cci-nas-00/data/ceres_data/8rc3_19046/06_2025/8rc3_19046.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rc3_19046/06_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-5710/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: 13.40, per 1000 atoms: 0.67 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: 5.18 Conformation dependent library (CDL) restraints added in 3.0 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: 8.43 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: 7.80 Time building geometry restraints manager: 6.13 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: 2.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.840 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 60.540 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.110 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: 0.020 Load rotamer database and sin/cos tables:18.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 83.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 20546 Z= 0.174 Angle : 0.569 10.803 28377 Z= 0.293 Chirality : 0.043 0.415 3211 Planarity : 0.004 0.037 3297 Dihedral : 18.295 176.566 8050 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.06 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 Details of bonding type rmsd hydrogen bonds : bond 0.16793 ( 840) hydrogen bonds : angle 7.90904 ( 2287) metal coordination : bond 0.00159 ( 4) metal coordination : angle 4.02242 ( 6) covalent geometry : bond 0.00400 (20542) covalent geometry : angle 0.56601 (28371) *********************** 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 : 2.023 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: 1.6585 time to fit residues: 364.9321 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 : 1.904 ------------------------------------------------------------------------------- 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 = 58)----------------| | 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: 0.2876 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 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 20546 Z= 0.201 Angle : 0.611 8.955 28377 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 Details of bonding type rmsd hydrogen bonds : bond 0.04316 ( 840) hydrogen bonds : angle 6.09913 ( 2287) metal coordination : bond 0.00657 ( 4) metal coordination : angle 4.72078 ( 6) covalent geometry : bond 0.00462 (20542) covalent geometry : angle 0.60760 (28371) *********************** 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 : 2.130 Fit side-chains revert: symmetry clash REVERT: B 145 MET cc_start: 0.8097 (mtt) cc_final: 0.7524 (mtt) REVERT: B 214 THR cc_start: 0.8646 (m) cc_final: 0.8371 (p) REVERT: C 163 ASP cc_start: 0.8509 (m-30) cc_final: 0.8296 (m-30) REVERT: C 305 GLU cc_start: 0.8556 (mm-30) cc_final: 0.8347 (mm-30) REVERT: C 332 MET cc_start: 0.8493 (ttm) cc_final: 0.8282 (ttp) REVERT: D 1 MET cc_start: 0.8627 (tmm) cc_final: 0.8368 (tpp) REVERT: E 1 MET cc_start: 0.7995 (pmm) cc_final: 0.7713 (pmm) REVERT: E 30 ASN cc_start: 0.8059 (m110) cc_final: 0.7662 (m110) REVERT: E 268 GLN cc_start: 0.8793 (OUTLIER) cc_final: 0.8422 (mt0) REVERT: F 14 MET cc_start: 0.9050 (ptm) cc_final: 0.8787 (ptm) REVERT: F 203 GLN cc_start: 0.8992 (mp-120) cc_final: 0.8776 (mp-120) REVERT: G 225 GLN cc_start: 0.8200 (mm-40) cc_final: 0.7940 (mm-40) REVERT: G 236 ILE cc_start: 0.8013 (mt) cc_final: 0.7705 (mp) REVERT: M 27 MET cc_start: 0.7120 (mmm) cc_final: 0.6473 (mmm) REVERT: M 31 GLN cc_start: 0.6428 (mp10) cc_final: 0.6139 (mp10) REVERT: M 193 LEU cc_start: 0.7130 (pt) cc_final: 0.6874 (tt) outliers start: 13 outliers final: 6 residues processed: 188 average time/residue: 1.4995 time to fit residues: 314.8341 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 : 2.076 ------------------------------------------------------------------------------- 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 = 0.3583 r_free = 0.3583 target = 0.095175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.070689 restraints weight = 41490.953| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.93 r_work: 0.2974 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 20546 Z= 0.195 Angle : 0.583 9.339 28377 Z= 0.300 Chirality : 0.043 0.220 3211 Planarity : 0.004 0.036 3297 Dihedral : 19.726 171.553 3961 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 1.52 % Allowed : 10.52 % Favored : 87.96 % 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: 0.43 (0.17), residues: 2271 helix: 1.52 (0.19), residues: 753 sheet: 0.21 (0.25), residues: 393 loop : -0.50 (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 0.012 0.001 PHE D 133 TYR 0.010 0.001 TYR G 141 ARG 0.007 0.000 ARG E 88 Details of bonding type rmsd hydrogen bonds : bond 0.04050 ( 840) hydrogen bonds : angle 5.73378 ( 2287) metal coordination : bond 0.00638 ( 4) metal coordination : angle 4.78387 ( 6) covalent geometry : bond 0.00452 (20542) covalent geometry : angle 0.57928 (28371) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 167 time to evaluate : 1.953 Fit side-chains revert: symmetry clash REVERT: C 163 ASP cc_start: 0.8481 (m-30) cc_final: 0.8231 (m-30) REVERT: C 332 MET cc_start: 0.8483 (ttm) cc_final: 0.8269 (ttp) REVERT: D 1 MET cc_start: 0.8638 (tmm) cc_final: 0.8350 (tpp) REVERT: E 30 ASN cc_start: 0.8002 (m110) cc_final: 0.7595 (m110) REVERT: E 268 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8331 (mt0) REVERT: F 1 MET cc_start: 0.7295 (pmm) cc_final: 0.6876 (pmm) REVERT: F 14 MET cc_start: 0.9071 (ptm) cc_final: 0.8776 (ptm) REVERT: G 225 GLN cc_start: 0.8309 (mm-40) cc_final: 0.8024 (mm-40) REVERT: G 236 ILE cc_start: 0.7993 (mt) cc_final: 0.7693 (mp) REVERT: M 27 MET cc_start: 0.7833 (mmm) cc_final: 0.7397 (mtt) REVERT: M 31 GLN cc_start: 0.6622 (mp10) cc_final: 0.6422 (mp10) REVERT: M 56 GLN cc_start: 0.7910 (pt0) cc_final: 0.7489 (pt0) REVERT: M 153 GLN cc_start: 0.8150 (OUTLIER) cc_final: 0.7938 (mp10) outliers start: 28 outliers final: 13 residues processed: 182 average time/residue: 1.5218 time to fit residues: 308.7744 Evaluate side-chains 175 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 160 time to evaluate : 1.980 ------------------------------------------------------------------------------- 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: 0.7980 chunk 122 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 150 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 62 optimal weight: 0.5980 chunk 231 optimal weight: 8.9990 chunk 66 optimal weight: 2.9990 chunk 128 optimal weight: 2.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 72 ASN E 281 ASN F 74 ASN ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.094066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.069771 restraints weight = 41846.184| |-----------------------------------------------------------------------------| r_work (start): 0.3054 rms_B_bonded: 1.82 r_work: 0.2953 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.1376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.061 20546 Z= 0.279 Angle : 0.625 9.122 28377 Z= 0.322 Chirality : 0.046 0.221 3211 Planarity : 0.005 0.041 3297 Dihedral : 19.834 179.325 3961 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.74 % Allowed : 12.20 % Favored : 86.06 % 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: 0.28 (0.17), residues: 2271 helix: 1.40 (0.19), residues: 753 sheet: 0.19 (0.26), residues: 372 loop : -0.61 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 207 HIS 0.007 0.002 HIS F 49 PHE 0.014 0.002 PHE C 38 TYR 0.014 0.002 TYR G 141 ARG 0.009 0.001 ARG E 88 Details of bonding type rmsd hydrogen bonds : bond 0.04187 ( 840) hydrogen bonds : angle 5.72558 ( 2287) metal coordination : bond 0.00717 ( 4) metal coordination : angle 4.87610 ( 6) covalent geometry : bond 0.00656 (20542) covalent geometry : angle 0.62112 (28371) *********************** 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 199 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 2.044 Fit side-chains revert: symmetry clash REVERT: B 214 THR cc_start: 0.8628 (m) cc_final: 0.8334 (p) REVERT: C 139 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8212 (mmt) REVERT: C 163 ASP cc_start: 0.8417 (m-30) cc_final: 0.8188 (m-30) REVERT: D 1 MET cc_start: 0.8679 (tmm) cc_final: 0.8471 (tpp) REVERT: E 30 ASN cc_start: 0.8028 (m110) cc_final: 0.7628 (m110) REVERT: E 154 GLN cc_start: 0.8188 (mp10) cc_final: 0.7932 (mp10) REVERT: E 268 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.8284 (mt0) REVERT: F 1 MET cc_start: 0.7381 (pmm) cc_final: 0.6904 (pmm) REVERT: G 225 GLN cc_start: 0.8330 (mm-40) cc_final: 0.8040 (mm-40) REVERT: G 236 ILE cc_start: 0.7981 (mt) cc_final: 0.7677 (mp) REVERT: M 31 GLN cc_start: 0.6698 (mp10) cc_final: 0.6470 (mp10) outliers start: 32 outliers final: 22 residues processed: 187 average time/residue: 1.5010 time to fit residues: 314.7352 Evaluate side-chains 188 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 1.848 ------------------------------------------------------------------------------- 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 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 G residue 162 ARG Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 193 LEU Chi-restraints excluded: chain M residue 197 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 228 optimal weight: 20.0000 chunk 234 optimal weight: 8.9990 chunk 43 optimal weight: 0.7980 chunk 142 optimal weight: 3.9990 chunk 215 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 231 optimal weight: 6.9990 chunk 26 optimal weight: 0.9980 chunk 158 optimal weight: 0.8980 chunk 146 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 = 0.3561 r_free = 0.3561 target = 0.094392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.069980 restraints weight = 41761.878| |-----------------------------------------------------------------------------| r_work (start): 0.3053 rms_B_bonded: 1.90 r_work: 0.2949 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 20546 Z= 0.190 Angle : 0.578 9.132 28377 Z= 0.298 Chirality : 0.043 0.215 3211 Planarity : 0.004 0.041 3297 Dihedral : 19.811 178.887 3961 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.28 % Allowed : 12.96 % Favored : 84.76 % 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: 1.45 (0.19), residues: 753 sheet: 0.20 (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 0.006 0.001 HIS F 49 PHE 0.012 0.001 PHE M 221 TYR 0.013 0.001 TYR G 141 ARG 0.009 0.000 ARG E 88 Details of bonding type rmsd hydrogen bonds : bond 0.03802 ( 840) hydrogen bonds : angle 5.58771 ( 2287) metal coordination : bond 0.00624 ( 4) metal coordination : angle 4.58040 ( 6) covalent geometry : bond 0.00438 (20542) covalent geometry : angle 0.57422 (28371) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4542 Ramachandran restraints generated. 2271 Oldfield, 0 Emsley, 2271 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 171 time to evaluate : 2.389 Fit side-chains revert: symmetry clash REVERT: B 214 THR cc_start: 0.8617 (m) cc_final: 0.8327 (p) REVERT: C 163 ASP cc_start: 0.8443 (m-30) cc_final: 0.8210 (m-30) REVERT: C 302 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8403 (tp) REVERT: D 1 MET cc_start: 0.8666 (tmm) cc_final: 0.8445 (tpp) REVERT: E 30 ASN cc_start: 0.7969 (m110) cc_final: 0.7571 (m110) REVERT: E 154 GLN cc_start: 0.8192 (mp10) cc_final: 0.7962 (mp10) REVERT: E 268 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8275 (mt0) REVERT: F 1 MET cc_start: 0.7373 (pmm) cc_final: 0.6910 (pmm) REVERT: G 225 GLN cc_start: 0.8367 (mm-40) cc_final: 0.8073 (mm-40) outliers start: 42 outliers final: 24 residues processed: 201 average time/residue: 1.3798 time to fit residues: 312.3462 Evaluate side-chains 186 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 1.970 ------------------------------------------------------------------------------- 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 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 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 193 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 180 optimal weight: 0.8980 chunk 69 optimal weight: 2.9990 chunk 189 optimal weight: 2.9990 chunk 139 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 111 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 136 optimal weight: 0.0980 chunk 101 optimal weight: 0.0470 chunk 24 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 overall best weight: 0.7880 ------------------------------------------------------------------------------- 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 = 0.3575 r_free = 0.3575 target = 0.095188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.070916 restraints weight = 41603.137| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 1.89 r_work: 0.2971 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20546 Z= 0.150 Angle : 0.553 8.970 28377 Z= 0.286 Chirality : 0.042 0.213 3211 Planarity : 0.004 0.042 3297 Dihedral : 19.690 178.702 3961 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.84 % Allowed : 13.72 % 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: 0.36 (0.17), residues: 2271 helix: 1.53 (0.19), residues: 761 sheet: 0.14 (0.25), residues: 385 loop : -0.59 (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 0.014 0.001 PHE E 38 TYR 0.015 0.001 TYR F 133 ARG 0.013 0.000 ARG E 88 Details of bonding type rmsd hydrogen bonds : bond 0.03539 ( 840) hydrogen bonds : angle 5.42908 ( 2287) metal coordination : bond 0.00584 ( 4) metal coordination : angle 4.33355 ( 6) covalent geometry : bond 0.00343 (20542) covalent geometry : angle 0.54987 (28371) *********************** 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 202 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 168 time to evaluate : 2.136 Fit side-chains revert: symmetry clash REVERT: B 214 THR cc_start: 0.8581 (m) cc_final: 0.8280 (p) REVERT: C 163 ASP cc_start: 0.8440 (m-30) cc_final: 0.8235 (m-30) REVERT: C 202 GLN cc_start: 0.7711 (tp40) cc_final: 0.7291 (tp-100) REVERT: C 302 LEU cc_start: 0.8653 (tm) cc_final: 0.8410 (tp) REVERT: D 1 MET cc_start: 0.8621 (tmm) cc_final: 0.8121 (tpp) REVERT: E 30 ASN cc_start: 0.7916 (m110) cc_final: 0.7501 (m110) REVERT: E 145 MET cc_start: 0.7224 (mtt) cc_final: 0.6535 (mtt) REVERT: E 154 GLN cc_start: 0.8152 (mp10) cc_final: 0.7890 (mp10) REVERT: F 1 MET cc_start: 0.7346 (pmm) cc_final: 0.6917 (pmm) REVERT: G 190 LYS cc_start: 0.8549 (mtpp) cc_final: 0.8095 (mppt) REVERT: G 225 GLN cc_start: 0.8328 (mm-40) cc_final: 0.8016 (mm-40) REVERT: M 213 MET cc_start: 0.6752 (pmm) cc_final: 0.6535 (ppp) outliers start: 34 outliers final: 22 residues processed: 192 average time/residue: 1.4777 time to fit residues: 317.9846 Evaluate side-chains 179 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 157 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 A residue 146 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 165 ILE 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 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 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: 5.9990 chunk 154 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 164 optimal weight: 2.9990 chunk 62 optimal weight: 0.4980 chunk 114 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 56 optimal weight: 0.6980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 72 ASN E 106 ASN F 74 ASN ** M 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.093261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.069826 restraints weight = 41559.832| |-----------------------------------------------------------------------------| r_work (start): 0.3042 rms_B_bonded: 1.97 r_work: 0.2896 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2760 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2760 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 20546 Z= 0.301 Angle : 0.636 9.146 28377 Z= 0.328 Chirality : 0.046 0.216 3211 Planarity : 0.005 0.051 3297 Dihedral : 19.779 178.293 3961 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.84 % Allowed : 14.26 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.19 (0.17), residues: 2271 helix: 1.27 (0.19), residues: 760 sheet: 0.18 (0.26), residues: 365 loop : -0.65 (0.18), residues: 1146 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 207 HIS 0.007 0.002 HIS A 288 PHE 0.021 0.002 PHE C 38 TYR 0.015 0.002 TYR G 141 ARG 0.014 0.001 ARG E 88 Details of bonding type rmsd hydrogen bonds : bond 0.04094 ( 840) hydrogen bonds : angle 5.59424 ( 2287) metal coordination : bond 0.00725 ( 4) metal coordination : angle 4.65397 ( 6) covalent geometry : bond 0.00711 (20542) covalent geometry : angle 0.63265 (28371) *********************** 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 193 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 2.055 Fit side-chains revert: symmetry clash REVERT: C 302 LEU cc_start: 0.8741 (tm) cc_final: 0.8508 (tp) REVERT: D 1 MET cc_start: 0.8671 (tmm) cc_final: 0.8323 (tpt) REVERT: E 30 ASN cc_start: 0.8117 (m110) cc_final: 0.7719 (m110) REVERT: E 154 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.7947 (mp10) REVERT: F 1 MET cc_start: 0.7427 (pmm) cc_final: 0.6857 (pmm) REVERT: F 14 MET cc_start: 0.9122 (ptm) cc_final: 0.8703 (ptt) REVERT: G 225 GLN cc_start: 0.8436 (mm-40) cc_final: 0.8126 (mm-40) outliers start: 34 outliers final: 27 residues processed: 183 average time/residue: 1.4784 time to fit residues: 304.0819 Evaluate side-chains 183 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 2.200 ------------------------------------------------------------------------------- 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 A residue 263 ARG Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 169 ILE 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 154 GLN Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 196 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 193 LEU Chi-restraints excluded: chain M residue 197 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 204 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 chunk 94 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 128 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 56 optimal weight: 0.6980 chunk 78 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 72 ASN E 106 ASN F 74 ASN ** 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 = 0.095381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.070981 restraints weight = 41672.374| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.92 r_work: 0.2980 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 20546 Z= 0.161 Angle : 0.561 10.376 28377 Z= 0.290 Chirality : 0.042 0.212 3211 Planarity : 0.004 0.042 3297 Dihedral : 19.618 178.262 3961 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.06 % Allowed : 14.75 % 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: 0.30 (0.17), residues: 2271 helix: 1.47 (0.19), residues: 760 sheet: 0.10 (0.25), residues: 385 loop : -0.62 (0.18), residues: 1126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 255 HIS 0.005 0.001 HIS F 49 PHE 0.015 0.001 PHE E 38 TYR 0.015 0.001 TYR G 141 ARG 0.014 0.000 ARG E 88 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 840) hydrogen bonds : angle 5.42204 ( 2287) metal coordination : bond 0.00641 ( 4) metal coordination : angle 4.24501 ( 6) covalent geometry : bond 0.00370 (20542) covalent geometry : angle 0.55770 (28371) *********************** 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 200 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 162 time to evaluate : 1.960 Fit side-chains revert: symmetry clash REVERT: A 263 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7940 (mtm-85) REVERT: B 214 THR cc_start: 0.8567 (m) cc_final: 0.8305 (p) REVERT: C 1 MET cc_start: 0.8706 (tpp) cc_final: 0.8490 (tpt) REVERT: C 202 GLN cc_start: 0.7708 (tp40) cc_final: 0.7316 (tp-100) REVERT: C 302 LEU cc_start: 0.8706 (tm) cc_final: 0.8483 (tp) REVERT: D 1 MET cc_start: 0.8597 (tmm) cc_final: 0.8144 (tpp) REVERT: E 30 ASN cc_start: 0.7917 (m110) cc_final: 0.7490 (m110) REVERT: E 145 MET cc_start: 0.7101 (mtt) cc_final: 0.6432 (mtt) REVERT: E 154 GLN cc_start: 0.8164 (OUTLIER) cc_final: 0.7927 (mp10) REVERT: E 268 GLN cc_start: 0.8682 (OUTLIER) cc_final: 0.8257 (mt0) REVERT: F 1 MET cc_start: 0.7399 (pmm) cc_final: 0.6944 (pmm) REVERT: G 190 LYS cc_start: 0.8530 (mtpp) cc_final: 0.8084 (mppt) REVERT: G 225 GLN cc_start: 0.8353 (mm-40) cc_final: 0.8062 (mm-40) REVERT: M 92 MET cc_start: 0.7268 (mtm) cc_final: 0.6783 (mpp) outliers start: 38 outliers final: 24 residues processed: 187 average time/residue: 1.3824 time to fit residues: 290.2874 Evaluate side-chains 185 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 158 time to evaluate : 1.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 169 ILE 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 154 GLN Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain E residue 268 GLN Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain G residue 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 Chi-restraints excluded: chain M residue 197 VAL Chi-restraints excluded: chain M residue 200 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 237 random chunks: chunk 50 optimal weight: 0.9990 chunk 197 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 113 optimal weight: 0.2980 chunk 213 optimal weight: 3.9990 chunk 190 optimal weight: 4.9990 chunk 69 optimal weight: 3.9990 chunk 139 optimal weight: 0.2980 chunk 80 optimal weight: 0.4980 chunk 3 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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 = 0.3606 r_free = 0.3606 target = 0.096285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.071972 restraints weight = 41326.950| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 1.92 r_work: 0.3003 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2876 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.1841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 20546 Z= 0.132 Angle : 0.554 13.862 28377 Z= 0.286 Chirality : 0.041 0.212 3211 Planarity : 0.004 0.044 3297 Dihedral : 19.520 177.606 3961 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.63 % Allowed : 15.29 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.78 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 0.39 (0.18), residues: 2271 helix: 1.55 (0.20), residues: 762 sheet: 0.15 (0.26), residues: 385 loop : -0.57 (0.18), residues: 1124 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 0.011 0.001 PHE C 38 TYR 0.017 0.001 TYR G 141 ARG 0.013 0.000 ARG E 88 Details of bonding type rmsd hydrogen bonds : bond 0.03343 ( 840) hydrogen bonds : angle 5.31188 ( 2287) metal coordination : bond 0.00574 ( 4) metal coordination : angle 4.08667 ( 6) covalent geometry : bond 0.00299 (20542) covalent geometry : angle 0.55126 (28371) *********************** 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 201 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 171 time to evaluate : 1.993 Fit side-chains revert: symmetry clash REVERT: A 263 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7916 (mtm-85) REVERT: B 214 THR cc_start: 0.8535 (m) cc_final: 0.8264 (p) REVERT: C 1 MET cc_start: 0.8706 (tpp) cc_final: 0.8493 (tpt) REVERT: C 202 GLN cc_start: 0.7724 (tp40) cc_final: 0.7373 (tp-100) REVERT: C 302 LEU cc_start: 0.8605 (tm) cc_final: 0.8363 (tp) REVERT: D 1 MET cc_start: 0.8587 (tmm) cc_final: 0.8300 (tpt) REVERT: E 1 MET cc_start: 0.7608 (pmm) cc_final: 0.6525 (pmm) REVERT: E 30 ASN cc_start: 0.7930 (m110) cc_final: 0.7490 (m110) REVERT: E 145 MET cc_start: 0.7121 (mtt) cc_final: 0.6469 (mtt) REVERT: E 154 GLN cc_start: 0.8106 (OUTLIER) cc_final: 0.7837 (mp10) REVERT: E 332 MET cc_start: 0.7277 (ppp) cc_final: 0.5882 (ptt) REVERT: E 339 GLN cc_start: 0.8029 (mp10) cc_final: 0.7416 (mp10) REVERT: F 1 MET cc_start: 0.7403 (OUTLIER) cc_final: 0.6988 (pmm) REVERT: F 61 SER cc_start: 0.9043 (t) cc_final: 0.8778 (p) REVERT: F 199 MET cc_start: 0.9014 (OUTLIER) cc_final: 0.8658 (mmm) REVERT: G 190 LYS cc_start: 0.8500 (mtpp) cc_final: 0.8068 (mppt) REVERT: G 225 GLN cc_start: 0.8333 (mm-40) cc_final: 0.8035 (mm-40) REVERT: M 92 MET cc_start: 0.7380 (mtm) cc_final: 0.6824 (mpp) outliers start: 30 outliers final: 19 residues processed: 188 average time/residue: 1.4390 time to fit residues: 304.3059 Evaluate side-chains 184 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 3.023 ------------------------------------------------------------------------------- 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 A residue 263 ARG Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 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 12 optimal weight: 0.4980 chunk 96 optimal weight: 3.9990 chunk 151 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 chunk 117 optimal weight: 0.8980 chunk 188 optimal weight: 0.2980 chunk 219 optimal weight: 10.0000 chunk 145 optimal weight: 3.9990 chunk 178 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.3610 r_free = 0.3610 target = 0.096458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.072139 restraints weight = 41676.014| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 1.94 r_work: 0.3007 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.1916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 20546 Z= 0.134 Angle : 0.562 12.028 28377 Z= 0.289 Chirality : 0.042 0.212 3211 Planarity : 0.004 0.043 3297 Dihedral : 19.492 177.592 3961 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 1.52 % Allowed : 15.62 % Favored : 82.86 % 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: 0.44 (0.18), residues: 2271 helix: 1.58 (0.20), residues: 762 sheet: 0.18 (0.26), residues: 385 loop : -0.54 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 255 HIS 0.005 0.001 HIS F 49 PHE 0.013 0.001 PHE E 38 TYR 0.017 0.001 TYR G 141 ARG 0.013 0.000 ARG E 88 Details of bonding type rmsd hydrogen bonds : bond 0.03318 ( 840) hydrogen bonds : angle 5.29017 ( 2287) metal coordination : bond 0.00544 ( 4) metal coordination : angle 4.13308 ( 6) covalent geometry : bond 0.00301 (20542) covalent geometry : angle 0.55862 (28371) ********************** 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 189 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 161 time to evaluate : 2.462 Fit side-chains revert: symmetry clash REVERT: A 263 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7886 (mtm-85) REVERT: B 214 THR cc_start: 0.8530 (m) cc_final: 0.8260 (p) REVERT: C 1 MET cc_start: 0.8705 (tpp) cc_final: 0.8500 (tpt) REVERT: C 202 GLN cc_start: 0.7727 (tp40) cc_final: 0.7385 (tp-100) REVERT: C 302 LEU cc_start: 0.8604 (tm) cc_final: 0.8372 (tp) REVERT: D 1 MET cc_start: 0.8580 (tmm) cc_final: 0.8294 (tpt) REVERT: E 1 MET cc_start: 0.7569 (pmm) cc_final: 0.5928 (pmm) REVERT: E 30 ASN cc_start: 0.7905 (m110) cc_final: 0.7478 (m110) REVERT: E 88 ARG cc_start: 0.8006 (ptp-110) cc_final: 0.7706 (ptp-110) REVERT: E 145 MET cc_start: 0.7280 (mtt) cc_final: 0.6612 (mtt) REVERT: E 154 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7875 (mp10) REVERT: E 332 MET cc_start: 0.7440 (ppp) cc_final: 0.5856 (ptt) REVERT: F 1 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.6946 (pmm) REVERT: F 61 SER cc_start: 0.9047 (t) cc_final: 0.8780 (p) REVERT: G 190 LYS cc_start: 0.8485 (mtpp) cc_final: 0.8078 (mppt) REVERT: G 225 GLN cc_start: 0.8329 (mm-40) cc_final: 0.8029 (mm-40) REVERT: M 92 MET cc_start: 0.7334 (mtm) cc_final: 0.6777 (mpp) outliers start: 28 outliers final: 20 residues processed: 178 average time/residue: 1.5065 time to fit residues: 302.4588 Evaluate side-chains 181 residues out of total 1844 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 158 time to evaluate : 2.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ILE Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 114 VAL Chi-restraints excluded: chain A residue 146 VAL Chi-restraints excluded: chain A residue 165 ILE Chi-restraints excluded: chain A residue 261 VAL Chi-restraints excluded: chain A residue 263 ARG Chi-restraints excluded: chain B residue 26 ASP Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 261 VAL Chi-restraints excluded: chain C residue 56 VAL Chi-restraints excluded: chain C residue 211 LEU Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain E residue 154 GLN Chi-restraints excluded: chain E residue 179 THR Chi-restraints excluded: chain E residue 243 PHE Chi-restraints excluded: chain F residue 1 MET Chi-restraints excluded: chain F residue 199 MET Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 193 LEU Chi-restraints excluded: chain M residue 197 VAL 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: 0.6980 chunk 211 optimal weight: 1.9990 chunk 147 optimal weight: 7.9990 chunk 192 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 54 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 194 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.3602 r_free = 0.3602 target = 0.096038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.071630 restraints weight = 41806.550| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.94 r_work: 0.2995 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 20546 Z= 0.154 Angle : 0.566 12.977 28377 Z= 0.291 Chirality : 0.042 0.214 3211 Planarity : 0.004 0.043 3297 Dihedral : 19.474 178.154 3961 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.57 % Allowed : 15.62 % Favored : 82.81 % 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: 0.42 (0.18), residues: 2271 helix: 1.57 (0.20), residues: 762 sheet: 0.16 (0.25), residues: 385 loop : -0.54 (0.18), residues: 1124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 255 HIS 0.006 0.001 HIS F 49 PHE 0.011 0.001 PHE B 133 TYR 0.017 0.001 TYR G 141 ARG 0.012 0.000 ARG E 88 Details of bonding type rmsd hydrogen bonds : bond 0.03351 ( 840) hydrogen bonds : angle 5.30527 ( 2287) metal coordination : bond 0.00542 ( 4) metal coordination : angle 4.14324 ( 6) covalent geometry : bond 0.00356 (20542) covalent geometry : angle 0.56284 (28371) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13773.90 seconds wall clock time: 235 minutes 54.24 seconds (14154.24 seconds total)