Starting phenix.real_space_refine on Sun Aug 24 02:04:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cbk_16543/08_2025/8cbk_16543.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cbk_16543/08_2025/8cbk_16543.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cbk_16543/08_2025/8cbk_16543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cbk_16543/08_2025/8cbk_16543.map" model { file = "/net/cci-nas-00/data/ceres_data/8cbk_16543/08_2025/8cbk_16543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cbk_16543/08_2025/8cbk_16543.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 1.029 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 101 5.49 5 Mg 1 5.21 5 S 71 5.16 5 C 9874 2.51 5 N 2832 2.21 5 O 3341 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16221 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "B" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "C" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "D" Number of atoms: 1848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1848 Classifications: {'peptide': 255} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 241} Chain: "E" Number of atoms: 3814 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3814 Classifications: {'peptide': 470} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 17, 'TRANS': 452} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "F" Number of atoms: 2832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 343, 2832 Classifications: {'peptide': 343} Link IDs: {'PTRANS': 9, 'TRANS': 333} Chain: "T" Number of atoms: 1971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1971 Classifications: {'RNA': 93} Modifications used: {'rna2p_pur': 9, 'rna2p_pyr': 9, 'rna3p_pur': 38, 'rna3p_pyr': 37} Link IDs: {'rna2p': 18, 'rna3p': 74} Chain breaks: 4 Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 9321 SG CYS E 348 62.040 43.374 15.436 1.00196.69 S ATOM 9337 SG CYS E 351 64.801 44.405 12.797 1.00214.65 S ATOM 11179 SG CYS E 578 63.196 47.045 14.911 1.00211.34 S Time building chain proxies: 3.75, per 1000 atoms: 0.23 Number of scatterers: 16221 At special positions: 0 Unit cell: (103.016, 112.144, 166.912, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 71 16.00 P 101 15.00 Mg 1 11.99 O 3341 8.00 N 2832 7.00 C 9874 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.48 Conformation dependent library (CDL) restraints added in 751.8 milliseconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN E 601 " pdb="ZN ZN E 601 " - pdb=" NE2 HIS E 557 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 578 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 351 " pdb="ZN ZN E 601 " - pdb=" SG CYS E 348 " Number of angles added : 3 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3352 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 11 sheets defined 56.5% alpha, 8.7% beta 33 base pairs and 43 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 20 through 33 Processing helix chain 'A' and resid 42 through 45 Processing helix chain 'A' and resid 46 through 55 removed outlier: 4.031A pdb=" N GLN A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 83 Processing helix chain 'A' and resid 110 through 137 removed outlier: 3.559A pdb=" N PHE A 114 " --> pdb=" O THR A 110 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N MET A 123 " --> pdb=" O ASP A 119 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLY A 124 " --> pdb=" O VAL A 120 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLY A 134 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLU A 135 " --> pdb=" O LEU A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 159 Processing helix chain 'A' and resid 165 through 187 removed outlier: 4.384A pdb=" N LEU A 180 " --> pdb=" O VAL A 176 " (cutoff:3.500A) Proline residue: A 181 - end of helix Processing helix chain 'A' and resid 203 through 209 removed outlier: 3.839A pdb=" N SER A 208 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 220 Processing helix chain 'A' and resid 229 through 243 removed outlier: 3.546A pdb=" N TYR A 233 " --> pdb=" O ASP A 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 32 Processing helix chain 'B' and resid 42 through 45 Processing helix chain 'B' and resid 46 through 55 removed outlier: 4.144A pdb=" N GLN B 50 " --> pdb=" O GLY B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 83 Processing helix chain 'B' and resid 110 through 122 removed outlier: 3.595A pdb=" N PHE B 114 " --> pdb=" O THR B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 137 removed outlier: 3.792A pdb=" N GLY B 134 " --> pdb=" O ARG B 130 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLU B 135 " --> pdb=" O LEU B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 159 Processing helix chain 'B' and resid 165 through 187 removed outlier: 4.362A pdb=" N LEU B 180 " --> pdb=" O VAL B 176 " (cutoff:3.500A) Proline residue: B 181 - end of helix Processing helix chain 'B' and resid 203 through 208 removed outlier: 3.841A pdb=" N THR B 207 " --> pdb=" O THR B 203 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N SER B 208 " --> pdb=" O PRO B 204 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 203 through 208' Processing helix chain 'B' and resid 210 through 221 Processing helix chain 'B' and resid 229 through 243 Processing helix chain 'C' and resid 20 through 33 Processing helix chain 'C' and resid 46 through 54 removed outlier: 3.899A pdb=" N GLN C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 83 Processing helix chain 'C' and resid 110 through 122 removed outlier: 3.615A pdb=" N PHE C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 137 Processing helix chain 'C' and resid 156 through 161 Processing helix chain 'C' and resid 165 through 187 removed outlier: 4.333A pdb=" N LEU C 180 " --> pdb=" O VAL C 176 " (cutoff:3.500A) Proline residue: C 181 - end of helix Processing helix chain 'C' and resid 203 through 208 removed outlier: 3.767A pdb=" N SER C 208 " --> pdb=" O PRO C 204 " (cutoff:3.500A) Processing helix chain 'C' and resid 210 through 221 Processing helix chain 'C' and resid 229 through 243 removed outlier: 3.523A pdb=" N TYR C 233 " --> pdb=" O ASP C 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 34 Processing helix chain 'D' and resid 42 through 45 Processing helix chain 'D' and resid 46 through 55 removed outlier: 3.658A pdb=" N GLN D 50 " --> pdb=" O GLY D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 83 Processing helix chain 'D' and resid 110 through 122 removed outlier: 3.659A pdb=" N PHE D 114 " --> pdb=" O THR D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 137 Processing helix chain 'D' and resid 155 through 159 Processing helix chain 'D' and resid 165 through 186 removed outlier: 4.407A pdb=" N LEU D 180 " --> pdb=" O VAL D 176 " (cutoff:3.500A) Proline residue: D 181 - end of helix Processing helix chain 'D' and resid 203 through 208 removed outlier: 3.615A pdb=" N SER D 208 " --> pdb=" O PRO D 204 " (cutoff:3.500A) Processing helix chain 'D' and resid 210 through 221 Processing helix chain 'D' and resid 229 through 243 removed outlier: 3.541A pdb=" N TYR D 233 " --> pdb=" O ASP D 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 129 removed outlier: 3.988A pdb=" N TRP E 124 " --> pdb=" O ASN E 120 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ASP E 125 " --> pdb=" O SER E 121 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N LYS E 126 " --> pdb=" O GLU E 122 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU E 129 " --> pdb=" O ASP E 125 " (cutoff:3.500A) Processing helix chain 'E' and resid 143 through 148 Processing helix chain 'E' and resid 153 through 169 removed outlier: 3.876A pdb=" N VAL E 157 " --> pdb=" O SER E 153 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N SER E 160 " --> pdb=" O ASP E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 188 Processing helix chain 'E' and resid 190 through 205 Processing helix chain 'E' and resid 211 through 221 Processing helix chain 'E' and resid 225 through 240 removed outlier: 4.033A pdb=" N VAL E 239 " --> pdb=" O ASP E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 257 Processing helix chain 'E' and resid 259 through 274 Processing helix chain 'E' and resid 278 through 290 removed outlier: 3.679A pdb=" N LEU E 282 " --> pdb=" O MET E 278 " (cutoff:3.500A) Processing helix chain 'E' and resid 294 through 312 Processing helix chain 'E' and resid 316 through 330 Processing helix chain 'E' and resid 361 through 377 Processing helix chain 'E' and resid 379 through 386 Processing helix chain 'E' and resid 387 through 401 Processing helix chain 'E' and resid 421 through 435 Processing helix chain 'E' and resid 445 through 450 removed outlier: 3.996A pdb=" N ARG E 450 " --> pdb=" O LYS E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 467 Processing helix chain 'E' and resid 477 through 490 removed outlier: 4.121A pdb=" N PHE E 481 " --> pdb=" O GLU E 477 " (cutoff:3.500A) Processing helix chain 'E' and resid 501 through 506 Processing helix chain 'E' and resid 510 through 523 Processing helix chain 'F' and resid 62 through 82 Processing helix chain 'F' and resid 89 through 105 removed outlier: 3.863A pdb=" N ALA F 93 " --> pdb=" O ASP F 89 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N GLU F 96 " --> pdb=" O ALA F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 113 through 122 Processing helix chain 'F' and resid 125 through 168 removed outlier: 3.865A pdb=" N GLU F 167 " --> pdb=" O ILE F 163 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N THR F 168 " --> pdb=" O LYS F 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 172 through 176 Processing helix chain 'F' and resid 182 through 202 removed outlier: 3.620A pdb=" N GLN F 200 " --> pdb=" O ALA F 196 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 215 Processing helix chain 'F' and resid 216 through 236 Processing helix chain 'F' and resid 252 through 263 Processing helix chain 'F' and resid 264 through 269 removed outlier: 3.565A pdb=" N ASP F 267 " --> pdb=" O GLU F 264 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU F 269 " --> pdb=" O TRP F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 277 through 281 Processing helix chain 'F' and resid 283 through 285 No H-bonds generated for 'chain 'F' and resid 283 through 285' Processing helix chain 'F' and resid 320 through 330 Processing helix chain 'F' and resid 337 through 342 Processing helix chain 'F' and resid 352 through 365 Processing helix chain 'F' and resid 368 through 373 Processing helix chain 'F' and resid 374 through 376 No H-bonds generated for 'chain 'F' and resid 374 through 376' Processing helix chain 'F' and resid 388 through 403 Processing sheet with id=AA1, first strand: chain 'A' and resid 58 through 62 removed outlier: 6.442A pdb=" N ALA A 37 " --> pdb=" O VAL A 59 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ALA A 61 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU A 39 " --> pdb=" O ALA A 61 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ALA A 88 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N THR A 153 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N ASN A 90 " --> pdb=" O THR A 153 " (cutoff:3.500A) removed outlier: 9.016A pdb=" N ILE A 251 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR A 195 " --> pdb=" O ILE A 251 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 62 removed outlier: 6.350A pdb=" N ALA B 37 " --> pdb=" O VAL B 59 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N ALA B 61 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N LEU B 39 " --> pdb=" O ALA B 61 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N ILE B 251 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N THR B 195 " --> pdb=" O ILE B 251 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA5, first strand: chain 'C' and resid 58 through 62 removed outlier: 6.398A pdb=" N ALA C 37 " --> pdb=" O VAL C 59 " (cutoff:3.500A) removed outlier: 7.495A pdb=" N ALA C 61 " --> pdb=" O ALA C 37 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU C 39 " --> pdb=" O ALA C 61 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL C 12 " --> pdb=" O VAL C 87 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N VAL C 89 " --> pdb=" O VAL C 12 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL C 14 " --> pdb=" O VAL C 89 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'D' and resid 58 through 62 removed outlier: 6.455A pdb=" N ALA D 37 " --> pdb=" O VAL D 59 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N ALA D 61 " --> pdb=" O ALA D 37 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N LEU D 39 " --> pdb=" O ALA D 61 " (cutoff:3.500A) removed outlier: 8.958A pdb=" N ILE D 251 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N THR D 195 " --> pdb=" O ILE D 251 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AA9, first strand: chain 'E' and resid 336 through 341 Processing sheet with id=AB1, first strand: chain 'E' and resid 469 through 470 removed outlier: 8.742A pdb=" N PHE E 470 " --> pdb=" O LEU E 440 " (cutoff:3.500A) removed outlier: 7.109A pdb=" N VAL E 442 " --> pdb=" O PHE E 470 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL E 407 " --> pdb=" O ILE E 496 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 272 through 273 removed outlier: 8.575A pdb=" N ILE F 309 " --> pdb=" O PRO F 204 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL F 206 " --> pdb=" O ILE F 309 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N GLY F 310 " --> pdb=" O LEU F 290 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N ALA F 332 " --> pdb=" O ILE F 287 " (cutoff:3.500A) 765 hydrogen bonds defined for protein. 2211 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 79 hydrogen bonds 154 hydrogen bond angles 0 basepair planarities 33 basepair parallelities 43 stacking parallelities Total time for adding SS restraints: 2.96 Time building geometry restraints manager: 1.89 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: 2857 1.33 - 1.45: 4443 1.45 - 1.57: 9092 1.57 - 1.69: 197 1.69 - 1.81: 113 Bond restraints: 16702 Sorted by residual: bond pdb=" O3 NAD A 301 " pdb=" PA NAD A 301 " ideal model delta sigma weight residual 1.653 1.578 0.075 2.00e-02 2.50e+03 1.40e+01 bond pdb=" O3 NAD B 301 " pdb=" PA NAD B 301 " ideal model delta sigma weight residual 1.653 1.579 0.074 2.00e-02 2.50e+03 1.36e+01 bond pdb=" O3 NAD C 301 " pdb=" PA NAD C 301 " ideal model delta sigma weight residual 1.653 1.581 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" O3 NAD D 301 " pdb=" PA NAD D 301 " ideal model delta sigma weight residual 1.653 1.581 0.072 2.00e-02 2.50e+03 1.28e+01 bond pdb=" C2N NAD D 301 " pdb=" C3N NAD D 301 " ideal model delta sigma weight residual 1.381 1.311 0.070 2.00e-02 2.50e+03 1.22e+01 ... (remaining 16697 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 22409 1.41 - 2.81: 480 2.81 - 4.22: 140 4.22 - 5.62: 24 5.62 - 7.03: 10 Bond angle restraints: 23063 Sorted by residual: angle pdb=" N HIS E 447 " pdb=" CA HIS E 447 " pdb=" C HIS E 447 " ideal model delta sigma weight residual 111.07 105.85 5.22 1.07e+00 8.73e-01 2.38e+01 angle pdb=" C GLU E 280 " pdb=" N THR E 281 " pdb=" CA THR E 281 " ideal model delta sigma weight residual 120.65 114.47 6.18 1.32e+00 5.74e-01 2.19e+01 angle pdb=" C TYR F 135 " pdb=" CA TYR F 135 " pdb=" CB TYR F 135 " ideal model delta sigma weight residual 110.90 104.36 6.54 1.58e+00 4.01e-01 1.72e+01 angle pdb=" CA THR F 127 " pdb=" CB THR F 127 " pdb=" OG1 THR F 127 " ideal model delta sigma weight residual 109.60 103.86 5.74 1.50e+00 4.44e-01 1.46e+01 angle pdb=" C PHE E 339 " pdb=" N THR E 340 " pdb=" CA THR E 340 " ideal model delta sigma weight residual 122.82 116.49 6.33 1.68e+00 3.54e-01 1.42e+01 ... (remaining 23058 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.50: 9593 26.50 - 52.99: 515 52.99 - 79.49: 150 79.49 - 105.98: 11 105.98 - 132.48: 4 Dihedral angle restraints: 10273 sinusoidal: 5057 harmonic: 5216 Sorted by residual: dihedral pdb=" CA LEU F 385 " pdb=" C LEU F 385 " pdb=" N GLU F 386 " pdb=" CA GLU F 386 " ideal model delta harmonic sigma weight residual 180.00 -161.64 -18.36 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" C4' G T 31 " pdb=" C3' G T 31 " pdb=" O3' G T 31 " pdb=" P U T 32 " ideal model delta sinusoidal sigma weight residual -110.00 22.48 -132.48 1 3.50e+01 8.16e-04 1.31e+01 dihedral pdb=" C TYR F 135 " pdb=" N TYR F 135 " pdb=" CA TYR F 135 " pdb=" CB TYR F 135 " ideal model delta harmonic sigma weight residual -122.60 -113.89 -8.71 0 2.50e+00 1.60e-01 1.21e+01 ... (remaining 10270 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2301 0.047 - 0.094: 274 0.094 - 0.141: 120 0.141 - 0.188: 10 0.188 - 0.235: 3 Chirality restraints: 2708 Sorted by residual: chirality pdb=" CA TYR F 135 " pdb=" N TYR F 135 " pdb=" C TYR F 135 " pdb=" CB TYR F 135 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CA THR E 281 " pdb=" N THR E 281 " pdb=" C THR E 281 " pdb=" CB THR E 281 " both_signs ideal model delta sigma weight residual False 2.53 2.74 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" C2' SAH F 501 " pdb=" C1' SAH F 501 " pdb=" C3' SAH F 501 " pdb=" O2' SAH F 501 " both_signs ideal model delta sigma weight residual False -2.53 -2.72 0.19 2.00e-01 2.50e+01 9.04e-01 ... (remaining 2705 not shown) Planarity restraints: 2618 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD D 301 " 0.044 2.00e-02 2.50e+03 2.70e-02 1.45e+01 pdb=" C2N NAD D 301 " -0.035 2.00e-02 2.50e+03 pdb=" C3N NAD D 301 " -0.005 2.00e-02 2.50e+03 pdb=" C4N NAD D 301 " 0.009 2.00e-02 2.50e+03 pdb=" C5N NAD D 301 " 0.005 2.00e-02 2.50e+03 pdb=" C6N NAD D 301 " 0.003 2.00e-02 2.50e+03 pdb=" C7N NAD D 301 " 0.022 2.00e-02 2.50e+03 pdb=" N1N NAD D 301 " -0.045 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG E 211 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.58e+00 pdb=" C ARG E 211 " -0.044 2.00e-02 2.50e+03 pdb=" O ARG E 211 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY E 212 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU E 209 " 0.041 5.00e-02 4.00e+02 6.17e-02 6.09e+00 pdb=" N PRO E 210 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO E 210 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO E 210 " 0.034 5.00e-02 4.00e+02 ... (remaining 2615 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 119 2.51 - 3.10: 12851 3.10 - 3.70: 26962 3.70 - 4.30: 38438 4.30 - 4.90: 61122 Nonbonded interactions: 139492 Sorted by model distance: nonbonded pdb=" OP1 G T 1 " pdb="MG MG T 201 " model vdw 1.908 2.170 nonbonded pdb=" O2' A T 19 " pdb=" OP1 A T 20 " model vdw 2.035 3.040 nonbonded pdb=" OG SER E 361 " pdb=" OE1 GLU E 363 " model vdw 2.226 3.040 nonbonded pdb=" OD1 ASN F 162 " pdb=" N ILE F 163 " model vdw 2.245 3.120 nonbonded pdb=" O ASP E 510 " pdb=" OG1 THR E 513 " model vdw 2.249 3.040 ... (remaining 139487 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' selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 10.390 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: 0.350 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 18.660 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 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 0.075 16706 Z= 0.187 Angle : 0.560 7.028 23066 Z= 0.297 Chirality : 0.039 0.235 2708 Planarity : 0.003 0.062 2618 Dihedral : 16.814 132.477 6921 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 3.95 % Favored : 95.99 % Rotamer: Outliers : 0.13 % Allowed : 0.40 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.72 (0.21), residues: 1821 helix: 2.53 (0.18), residues: 911 sheet: -0.21 (0.40), residues: 186 loop : -0.28 (0.23), residues: 724 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 95 TYR 0.019 0.001 TYR F 135 PHE 0.014 0.001 PHE E 288 TRP 0.034 0.001 TRP F 66 HIS 0.008 0.001 HIS F 242 Details of bonding type rmsd covalent geometry : bond 0.00355 (16702) covalent geometry : angle 0.55878 (23063) hydrogen bonds : bond 0.11882 ( 844) hydrogen bonds : angle 5.88195 ( 2365) metal coordination : bond 0.00588 ( 4) metal coordination : angle 3.74120 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 314 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8989 (m-30) cc_final: 0.8659 (m-30) REVERT: A 160 GLU cc_start: 0.7944 (pt0) cc_final: 0.7705 (pt0) REVERT: B 48 GLU cc_start: 0.8300 (pm20) cc_final: 0.8068 (pm20) REVERT: B 68 GLU cc_start: 0.8707 (tt0) cc_final: 0.8460 (tt0) REVERT: B 70 ASP cc_start: 0.9200 (m-30) cc_final: 0.8960 (m-30) REVERT: C 211 GLU cc_start: 0.8720 (tp30) cc_final: 0.8006 (tp30) REVERT: D 48 GLU cc_start: 0.8842 (tp30) cc_final: 0.8586 (tp30) REVERT: D 70 ASP cc_start: 0.9080 (m-30) cc_final: 0.8804 (m-30) REVERT: E 148 MET cc_start: 0.8413 (mmp) cc_final: 0.8136 (mmp) REVERT: E 161 LEU cc_start: 0.9632 (mm) cc_final: 0.9391 (mm) REVERT: E 178 LEU cc_start: 0.9194 (tp) cc_final: 0.8925 (tp) REVERT: E 182 LEU cc_start: 0.9791 (mt) cc_final: 0.9577 (mt) REVERT: E 269 GLU cc_start: 0.9175 (tp30) cc_final: 0.8631 (tp30) REVERT: E 404 PHE cc_start: 0.8009 (m-10) cc_final: 0.7580 (m-10) REVERT: E 427 LEU cc_start: 0.9571 (tt) cc_final: 0.9355 (pp) REVERT: E 428 ASN cc_start: 0.9597 (m-40) cc_final: 0.9358 (m110) REVERT: E 455 TRP cc_start: 0.9342 (m100) cc_final: 0.9067 (m100) REVERT: E 505 LYS cc_start: 0.9333 (pptt) cc_final: 0.9083 (pptt) REVERT: E 556 TRP cc_start: 0.8839 (m100) cc_final: 0.8145 (m100) REVERT: F 209 MET cc_start: 0.9014 (mpp) cc_final: 0.8286 (mpt) REVERT: F 314 ASP cc_start: 0.8926 (p0) cc_final: 0.8427 (p0) REVERT: F 371 GLU cc_start: 0.9104 (mt-10) cc_final: 0.8712 (mt-10) outliers start: 2 outliers final: 1 residues processed: 316 average time/residue: 0.5320 time to fit residues: 186.2200 Evaluate side-chains 252 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 251 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 447 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 4.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 149 optimal weight: 0.0170 overall best weight: 1.0022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 90 ASN A 152 ASN C 260 GLN E 258 GLN E 273 HIS F 147 GLN F 348 ASN F 390 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.106687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.064109 restraints weight = 34579.893| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 2.78 r_work: 0.2598 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16706 Z= 0.149 Angle : 0.637 12.632 23066 Z= 0.312 Chirality : 0.042 0.340 2708 Planarity : 0.004 0.061 2618 Dihedral : 16.141 127.094 3561 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.00 % Allowed : 10.19 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.20), residues: 1821 helix: 2.40 (0.17), residues: 916 sheet: -0.23 (0.34), residues: 234 loop : -0.06 (0.25), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 227 TYR 0.014 0.001 TYR E 365 PHE 0.021 0.001 PHE E 481 TRP 0.029 0.002 TRP E 124 HIS 0.008 0.001 HIS F 242 Details of bonding type rmsd covalent geometry : bond 0.00332 (16702) covalent geometry : angle 0.63552 (23063) hydrogen bonds : bond 0.03800 ( 844) hydrogen bonds : angle 4.79921 ( 2365) metal coordination : bond 0.00776 ( 4) metal coordination : angle 4.07658 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 273 time to evaluate : 0.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8890 (m-30) cc_final: 0.8560 (m-30) REVERT: A 119 ASP cc_start: 0.8946 (m-30) cc_final: 0.8743 (m-30) REVERT: B 48 GLU cc_start: 0.8358 (pm20) cc_final: 0.8144 (pm20) REVERT: B 68 GLU cc_start: 0.8654 (tt0) cc_final: 0.8430 (tt0) REVERT: B 70 ASP cc_start: 0.9057 (m-30) cc_final: 0.8754 (m-30) REVERT: B 160 GLU cc_start: 0.8755 (mp0) cc_final: 0.8208 (pm20) REVERT: C 211 GLU cc_start: 0.8618 (tp30) cc_final: 0.7957 (tp30) REVERT: D 48 GLU cc_start: 0.8871 (tp30) cc_final: 0.8474 (tp30) REVERT: D 70 ASP cc_start: 0.8968 (m-30) cc_final: 0.8700 (m-30) REVERT: E 148 MET cc_start: 0.8369 (mmp) cc_final: 0.8069 (mmp) REVERT: E 178 LEU cc_start: 0.9281 (tp) cc_final: 0.9079 (tp) REVERT: E 209 GLU cc_start: 0.8665 (tm-30) cc_final: 0.8320 (tp30) REVERT: E 285 PHE cc_start: 0.8894 (t80) cc_final: 0.8122 (t80) REVERT: E 288 PHE cc_start: 0.8611 (t80) cc_final: 0.8227 (t80) REVERT: E 312 GLN cc_start: 0.9178 (tm-30) cc_final: 0.8897 (tm-30) REVERT: E 353 LYS cc_start: 0.9188 (mmpt) cc_final: 0.8902 (mmmm) REVERT: E 404 PHE cc_start: 0.8303 (m-80) cc_final: 0.7876 (m-10) REVERT: E 426 LEU cc_start: 0.9771 (tt) cc_final: 0.9516 (pp) REVERT: E 427 LEU cc_start: 0.9610 (tt) cc_final: 0.9222 (pp) REVERT: E 428 ASN cc_start: 0.9651 (m-40) cc_final: 0.9416 (m110) REVERT: E 448 MET cc_start: 0.9500 (tmm) cc_final: 0.9261 (tpt) REVERT: E 455 TRP cc_start: 0.9301 (m100) cc_final: 0.8693 (m100) REVERT: F 95 ARG cc_start: 0.8938 (mtt180) cc_final: 0.8724 (mmt180) REVERT: F 100 MET cc_start: 0.9570 (mmm) cc_final: 0.9145 (mmm) REVERT: F 101 TRP cc_start: 0.9451 (m100) cc_final: 0.9134 (m100) REVERT: F 116 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8820 (mp0) REVERT: F 314 ASP cc_start: 0.9164 (p0) cc_final: 0.8799 (p0) REVERT: F 371 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8799 (mt-10) outliers start: 15 outliers final: 8 residues processed: 279 average time/residue: 0.5518 time to fit residues: 170.0569 Evaluate side-chains 235 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 227 time to evaluate : 0.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain D residue 220 GLN Chi-restraints excluded: chain E residue 248 ASN Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain F residue 184 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 162 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 166 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 83 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 70 optimal weight: 0.3980 chunk 137 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 260 GLN E 396 ASN E 514 GLN E 540 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.106082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.063181 restraints weight = 34583.883| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 2.79 r_work: 0.2582 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8660 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16706 Z= 0.170 Angle : 0.622 11.919 23066 Z= 0.309 Chirality : 0.041 0.299 2708 Planarity : 0.004 0.060 2618 Dihedral : 16.062 127.749 3559 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.66 % Allowed : 13.18 % Favored : 85.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.63 (0.20), residues: 1821 helix: 2.30 (0.17), residues: 911 sheet: -0.33 (0.34), residues: 221 loop : -0.04 (0.24), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 227 TYR 0.020 0.001 TYR E 484 PHE 0.020 0.001 PHE F 97 TRP 0.048 0.003 TRP F 66 HIS 0.009 0.001 HIS F 242 Details of bonding type rmsd covalent geometry : bond 0.00383 (16702) covalent geometry : angle 0.62060 (23063) hydrogen bonds : bond 0.03669 ( 844) hydrogen bonds : angle 4.67827 ( 2365) metal coordination : bond 0.00938 ( 4) metal coordination : angle 3.93686 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 243 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8953 (m-30) cc_final: 0.8607 (m-30) REVERT: A 119 ASP cc_start: 0.8996 (m-30) cc_final: 0.8754 (m-30) REVERT: B 68 GLU cc_start: 0.8698 (tt0) cc_final: 0.8422 (tt0) REVERT: B 70 ASP cc_start: 0.9154 (m-30) cc_final: 0.8837 (m-30) REVERT: B 160 GLU cc_start: 0.8796 (mp0) cc_final: 0.8292 (pm20) REVERT: C 70 ASP cc_start: 0.9166 (m-30) cc_final: 0.8965 (m-30) REVERT: C 211 GLU cc_start: 0.8634 (tp30) cc_final: 0.7869 (tp30) REVERT: D 48 GLU cc_start: 0.8877 (tp30) cc_final: 0.8499 (tp30) REVERT: D 70 ASP cc_start: 0.9076 (m-30) cc_final: 0.8812 (m-30) REVERT: D 86 ASP cc_start: 0.9032 (m-30) cc_final: 0.8752 (m-30) REVERT: D 135 GLU cc_start: 0.9072 (tp30) cc_final: 0.8815 (mm-30) REVERT: E 129 GLU cc_start: 0.9374 (mp0) cc_final: 0.9160 (mp0) REVERT: E 148 MET cc_start: 0.8341 (mmp) cc_final: 0.8028 (mmp) REVERT: E 269 GLU cc_start: 0.9426 (tp30) cc_final: 0.8863 (tp30) REVERT: E 283 LYS cc_start: 0.9327 (ptmm) cc_final: 0.9057 (tmmm) REVERT: E 288 PHE cc_start: 0.8730 (t80) cc_final: 0.8313 (t80) REVERT: E 353 LYS cc_start: 0.9223 (mmpt) cc_final: 0.8887 (mmtm) REVERT: E 365 TYR cc_start: 0.8464 (OUTLIER) cc_final: 0.8048 (t80) REVERT: E 404 PHE cc_start: 0.8229 (m-80) cc_final: 0.7795 (m-10) REVERT: E 426 LEU cc_start: 0.9763 (tt) cc_final: 0.9437 (pp) REVERT: E 427 LEU cc_start: 0.9576 (tt) cc_final: 0.9147 (pp) REVERT: E 428 ASN cc_start: 0.9616 (m-40) cc_final: 0.9348 (m110) REVERT: E 556 TRP cc_start: 0.9207 (m-90) cc_final: 0.8966 (m-90) REVERT: F 100 MET cc_start: 0.9624 (mmm) cc_final: 0.9371 (mmm) REVERT: F 166 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8117 (pp) REVERT: F 257 GLU cc_start: 0.9102 (tp30) cc_final: 0.8735 (mm-30) REVERT: F 314 ASP cc_start: 0.9152 (p0) cc_final: 0.8742 (p0) REVERT: F 371 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8861 (mt-10) outliers start: 25 outliers final: 12 residues processed: 254 average time/residue: 0.5025 time to fit residues: 142.8100 Evaluate side-chains 227 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 213 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain D residue 220 GLN Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 177 LEU Chi-restraints excluded: chain E residue 248 ASN Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 365 TYR Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 415 LYS Chi-restraints excluded: chain E residue 425 LEU Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 486 THR Chi-restraints excluded: chain F residue 166 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 67 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 110 optimal weight: 8.9990 chunk 81 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 157 optimal weight: 0.0030 chunk 156 optimal weight: 4.9990 chunk 107 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 13 optimal weight: 0.0470 chunk 140 optimal weight: 4.9990 overall best weight: 0.5288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 260 GLN E 424 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.108009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.065248 restraints weight = 34360.174| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.80 r_work: 0.2641 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16706 Z= 0.119 Angle : 0.618 13.324 23066 Z= 0.301 Chirality : 0.041 0.277 2708 Planarity : 0.004 0.068 2618 Dihedral : 15.934 126.773 3559 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 1.53 % Allowed : 15.51 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.20), residues: 1821 helix: 2.29 (0.17), residues: 910 sheet: -0.24 (0.34), residues: 227 loop : -0.01 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 227 TYR 0.020 0.001 TYR E 314 PHE 0.028 0.001 PHE E 481 TRP 0.049 0.003 TRP F 66 HIS 0.008 0.001 HIS E 152 Details of bonding type rmsd covalent geometry : bond 0.00262 (16702) covalent geometry : angle 0.61662 (23063) hydrogen bonds : bond 0.03262 ( 844) hydrogen bonds : angle 4.51154 ( 2365) metal coordination : bond 0.00770 ( 4) metal coordination : angle 3.39780 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 251 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8931 (m-30) cc_final: 0.8722 (m-30) REVERT: B 68 GLU cc_start: 0.8676 (tt0) cc_final: 0.8406 (tt0) REVERT: B 70 ASP cc_start: 0.9130 (m-30) cc_final: 0.8824 (m-30) REVERT: B 115 GLN cc_start: 0.8794 (tt0) cc_final: 0.8535 (tt0) REVERT: B 160 GLU cc_start: 0.8768 (mp0) cc_final: 0.8324 (pm20) REVERT: B 232 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8540 (mt-10) REVERT: B 260 GLN cc_start: 0.9147 (mm110) cc_final: 0.6643 (pt0) REVERT: C 70 ASP cc_start: 0.9160 (m-30) cc_final: 0.8913 (m-30) REVERT: C 211 GLU cc_start: 0.8584 (tp30) cc_final: 0.7820 (tp30) REVERT: D 70 ASP cc_start: 0.9039 (m-30) cc_final: 0.8770 (m-30) REVERT: D 86 ASP cc_start: 0.9060 (m-30) cc_final: 0.8762 (m-30) REVERT: E 148 MET cc_start: 0.8348 (mmp) cc_final: 0.8059 (mmp) REVERT: E 269 GLU cc_start: 0.9428 (tp30) cc_final: 0.8965 (tp30) REVERT: E 288 PHE cc_start: 0.8647 (t80) cc_final: 0.8228 (t80) REVERT: E 307 TYR cc_start: 0.9365 (t80) cc_final: 0.9061 (t80) REVERT: E 312 GLN cc_start: 0.9347 (pp30) cc_final: 0.8989 (tm-30) REVERT: E 353 LYS cc_start: 0.9199 (mmpt) cc_final: 0.8833 (mttt) REVERT: E 404 PHE cc_start: 0.8191 (m-80) cc_final: 0.7790 (m-10) REVERT: E 426 LEU cc_start: 0.9762 (tt) cc_final: 0.9447 (pp) REVERT: E 427 LEU cc_start: 0.9593 (tt) cc_final: 0.9171 (pp) REVERT: E 428 ASN cc_start: 0.9574 (m-40) cc_final: 0.9318 (m110) REVERT: E 521 GLN cc_start: 0.9650 (tm-30) cc_final: 0.9152 (tm-30) REVERT: F 95 ARG cc_start: 0.8861 (mtt180) cc_final: 0.8555 (mtt180) REVERT: F 166 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8079 (pp) REVERT: F 257 GLU cc_start: 0.9060 (tp30) cc_final: 0.8700 (mm-30) REVERT: F 314 ASP cc_start: 0.9160 (p0) cc_final: 0.8674 (p0) REVERT: F 371 GLU cc_start: 0.9237 (mt-10) cc_final: 0.8852 (mt-10) outliers start: 23 outliers final: 8 residues processed: 262 average time/residue: 0.5813 time to fit residues: 171.4808 Evaluate side-chains 239 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 230 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain F residue 166 LEU Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 220 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 136 optimal weight: 3.9990 chunk 128 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 4 optimal weight: 1.9990 chunk 157 optimal weight: 9.9990 chunk 81 optimal weight: 0.9980 chunk 123 optimal weight: 6.9990 chunk 88 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 155 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 115 GLN C 260 GLN ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 550 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 = 0.3600 r_free = 0.3600 target = 0.104133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2797 r_free = 0.2797 target = 0.061067 restraints weight = 34428.290| |-----------------------------------------------------------------------------| r_work (start): 0.2711 rms_B_bonded: 2.79 r_work: 0.2540 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 16706 Z= 0.266 Angle : 0.680 18.670 23066 Z= 0.335 Chirality : 0.043 0.288 2708 Planarity : 0.004 0.060 2618 Dihedral : 15.988 130.255 3559 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.26 % Allowed : 16.05 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.36 (0.20), residues: 1821 helix: 2.08 (0.17), residues: 916 sheet: -0.24 (0.33), residues: 225 loop : -0.26 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG F 217 TYR 0.015 0.001 TYR E 365 PHE 0.020 0.001 PHE F 97 TRP 0.052 0.003 TRP F 66 HIS 0.009 0.001 HIS F 242 Details of bonding type rmsd covalent geometry : bond 0.00596 (16702) covalent geometry : angle 0.67816 (23063) hydrogen bonds : bond 0.03957 ( 844) hydrogen bonds : angle 4.75001 ( 2365) metal coordination : bond 0.01399 ( 4) metal coordination : angle 4.54077 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 232 time to evaluate : 0.642 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8983 (m-30) cc_final: 0.8633 (m-30) REVERT: B 68 GLU cc_start: 0.8719 (tt0) cc_final: 0.8489 (tt0) REVERT: B 70 ASP cc_start: 0.9182 (m-30) cc_final: 0.8884 (m-30) REVERT: B 160 GLU cc_start: 0.8848 (mp0) cc_final: 0.8334 (pm20) REVERT: C 70 ASP cc_start: 0.9186 (m-30) cc_final: 0.8950 (m-30) REVERT: C 211 GLU cc_start: 0.8624 (tp30) cc_final: 0.7854 (tp30) REVERT: C 229 ASP cc_start: 0.9049 (t0) cc_final: 0.8839 (t0) REVERT: D 70 ASP cc_start: 0.9100 (m-30) cc_final: 0.8806 (m-30) REVERT: D 86 ASP cc_start: 0.9073 (m-30) cc_final: 0.8785 (m-30) REVERT: D 135 GLU cc_start: 0.9112 (tp30) cc_final: 0.8809 (mm-30) REVERT: E 129 GLU cc_start: 0.9365 (mp0) cc_final: 0.9081 (pm20) REVERT: E 148 MET cc_start: 0.8416 (mmp) cc_final: 0.8125 (mmp) REVERT: E 269 GLU cc_start: 0.9473 (tp30) cc_final: 0.8909 (tp30) REVERT: E 283 LYS cc_start: 0.9277 (OUTLIER) cc_final: 0.9027 (tmmm) REVERT: E 307 TYR cc_start: 0.9486 (t80) cc_final: 0.9088 (t80) REVERT: E 353 LYS cc_start: 0.9269 (mmpt) cc_final: 0.8898 (mttt) REVERT: E 404 PHE cc_start: 0.8237 (m-80) cc_final: 0.7883 (m-10) REVERT: E 415 LYS cc_start: 0.9098 (ptmt) cc_final: 0.8854 (pttp) REVERT: E 426 LEU cc_start: 0.9781 (tt) cc_final: 0.9497 (pp) REVERT: E 427 LEU cc_start: 0.9616 (tt) cc_final: 0.9220 (pp) REVERT: E 428 ASN cc_start: 0.9571 (m-40) cc_final: 0.9292 (m110) REVERT: E 446 LYS cc_start: 0.9798 (mttt) cc_final: 0.9506 (mmmt) REVERT: E 448 MET cc_start: 0.9508 (tpt) cc_final: 0.9211 (tpt) REVERT: E 473 ASP cc_start: 0.9127 (p0) cc_final: 0.8771 (p0) REVERT: E 521 GLN cc_start: 0.9686 (tm-30) cc_final: 0.9383 (tm-30) REVERT: E 556 TRP cc_start: 0.9261 (m-90) cc_final: 0.9006 (m-90) REVERT: E 564 LEU cc_start: 0.9318 (OUTLIER) cc_final: 0.9103 (mm) REVERT: F 257 GLU cc_start: 0.9118 (tp30) cc_final: 0.8755 (mm-30) REVERT: F 314 ASP cc_start: 0.9148 (p0) cc_final: 0.8708 (p0) REVERT: F 371 GLU cc_start: 0.9278 (mt-10) cc_final: 0.8891 (mt-10) outliers start: 34 outliers final: 13 residues processed: 255 average time/residue: 0.5466 time to fit residues: 154.9396 Evaluate side-chains 228 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 213 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 248 ASN Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 283 LYS Chi-restraints excluded: chain E residue 326 TRP Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 422 GLU Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain E residue 564 LEU Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain F residue 184 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 77 optimal weight: 1.9990 chunk 164 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 54 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 171 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 GLN C 260 GLN ** E 248 ASN ** 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 = 0.3641 r_free = 0.3641 target = 0.106964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.064132 restraints weight = 34187.126| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 2.82 r_work: 0.2611 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2611 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16706 Z= 0.133 Angle : 0.655 19.084 23066 Z= 0.321 Chirality : 0.042 0.304 2708 Planarity : 0.004 0.055 2618 Dihedral : 15.892 128.871 3559 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.80 % Allowed : 17.84 % Favored : 80.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.41 (0.20), residues: 1821 helix: 2.09 (0.17), residues: 912 sheet: -0.18 (0.33), residues: 223 loop : -0.21 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 146 TYR 0.013 0.001 TYR E 484 PHE 0.025 0.001 PHE E 481 TRP 0.057 0.003 TRP F 66 HIS 0.008 0.001 HIS E 152 Details of bonding type rmsd covalent geometry : bond 0.00297 (16702) covalent geometry : angle 0.65432 (23063) hydrogen bonds : bond 0.03389 ( 844) hydrogen bonds : angle 4.53766 ( 2365) metal coordination : bond 0.00619 ( 4) metal coordination : angle 3.24579 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 238 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 68 GLU cc_start: 0.8672 (tt0) cc_final: 0.8398 (tt0) REVERT: B 70 ASP cc_start: 0.9124 (m-30) cc_final: 0.8820 (m-30) REVERT: B 118 LEU cc_start: 0.9435 (OUTLIER) cc_final: 0.9182 (mp) REVERT: B 160 GLU cc_start: 0.8787 (mp0) cc_final: 0.8290 (pm20) REVERT: C 70 ASP cc_start: 0.9162 (m-30) cc_final: 0.8905 (m-30) REVERT: C 211 GLU cc_start: 0.8556 (tp30) cc_final: 0.7790 (tp30) REVERT: D 70 ASP cc_start: 0.9069 (m-30) cc_final: 0.8809 (m-30) REVERT: D 86 ASP cc_start: 0.9073 (m-30) cc_final: 0.8796 (m-30) REVERT: D 135 GLU cc_start: 0.9068 (tp30) cc_final: 0.8839 (mm-30) REVERT: E 148 MET cc_start: 0.8290 (mmp) cc_final: 0.8055 (mmp) REVERT: E 164 TRP cc_start: 0.8647 (p-90) cc_final: 0.8445 (p-90) REVERT: E 269 GLU cc_start: 0.9461 (tp30) cc_final: 0.8514 (tp30) REVERT: E 273 HIS cc_start: 0.8857 (m90) cc_final: 0.7264 (m-70) REVERT: E 288 PHE cc_start: 0.8695 (t80) cc_final: 0.8141 (t80) REVERT: E 307 TYR cc_start: 0.9386 (t80) cc_final: 0.9058 (t80) REVERT: E 327 PHE cc_start: 0.9121 (OUTLIER) cc_final: 0.8880 (t80) REVERT: E 353 LYS cc_start: 0.9244 (mmpt) cc_final: 0.8859 (mttt) REVERT: E 404 PHE cc_start: 0.8166 (m-80) cc_final: 0.7792 (m-10) REVERT: E 415 LYS cc_start: 0.8987 (ptmt) cc_final: 0.8754 (ptpp) REVERT: E 426 LEU cc_start: 0.9788 (tt) cc_final: 0.9511 (pp) REVERT: E 427 LEU cc_start: 0.9611 (tt) cc_final: 0.9224 (pp) REVERT: E 428 ASN cc_start: 0.9532 (m-40) cc_final: 0.9250 (m110) REVERT: E 448 MET cc_start: 0.9533 (tpt) cc_final: 0.9200 (tpt) REVERT: E 514 GLN cc_start: 0.9443 (tt0) cc_final: 0.9173 (mt0) REVERT: E 521 GLN cc_start: 0.9667 (tm-30) cc_final: 0.9421 (tm-30) REVERT: E 556 TRP cc_start: 0.9205 (m-90) cc_final: 0.8975 (m-90) REVERT: F 95 ARG cc_start: 0.8814 (mmt180) cc_final: 0.8539 (mmt180) REVERT: F 102 ARG cc_start: 0.9208 (OUTLIER) cc_final: 0.8753 (mmm160) REVERT: F 254 LEU cc_start: 0.9596 (OUTLIER) cc_final: 0.9332 (tt) REVERT: F 257 GLU cc_start: 0.9088 (tp30) cc_final: 0.8724 (mm-30) REVERT: F 314 ASP cc_start: 0.9158 (p0) cc_final: 0.8721 (p0) REVERT: F 371 GLU cc_start: 0.9239 (mt-10) cc_final: 0.8832 (mt-10) outliers start: 27 outliers final: 8 residues processed: 254 average time/residue: 0.6056 time to fit residues: 170.5813 Evaluate side-chains 231 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 219 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain F residue 102 ARG Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 254 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 99 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 178 optimal weight: 0.0670 chunk 123 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 85 optimal weight: 0.8980 chunk 183 optimal weight: 6.9990 chunk 0 optimal weight: 5.9990 chunk 91 optimal weight: 0.6980 chunk 104 optimal weight: 9.9990 overall best weight: 0.9320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 437 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.107123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.064371 restraints weight = 34112.041| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 2.83 r_work: 0.2602 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 16706 Z= 0.139 Angle : 0.667 17.644 23066 Z= 0.327 Chirality : 0.042 0.331 2708 Planarity : 0.004 0.054 2618 Dihedral : 15.829 128.631 3559 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.46 % Allowed : 19.51 % Favored : 79.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.20), residues: 1821 helix: 2.09 (0.17), residues: 913 sheet: -0.17 (0.33), residues: 223 loop : -0.25 (0.24), residues: 685 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 217 TYR 0.026 0.001 TYR E 213 PHE 0.016 0.001 PHE F 97 TRP 0.062 0.003 TRP F 66 HIS 0.008 0.001 HIS E 152 Details of bonding type rmsd covalent geometry : bond 0.00313 (16702) covalent geometry : angle 0.66582 (23063) hydrogen bonds : bond 0.03379 ( 844) hydrogen bonds : angle 4.51975 ( 2365) metal coordination : bond 0.00717 ( 4) metal coordination : angle 3.49850 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 237 time to evaluate : 0.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8859 (m-30) cc_final: 0.8608 (m-30) REVERT: B 41 ASP cc_start: 0.8946 (t0) cc_final: 0.8674 (t70) REVERT: B 68 GLU cc_start: 0.8684 (tt0) cc_final: 0.8462 (tt0) REVERT: B 70 ASP cc_start: 0.9139 (m-30) cc_final: 0.8836 (m-30) REVERT: B 160 GLU cc_start: 0.8804 (mp0) cc_final: 0.8309 (pm20) REVERT: C 70 ASP cc_start: 0.9164 (m-30) cc_final: 0.8909 (m-30) REVERT: C 211 GLU cc_start: 0.8552 (tp30) cc_final: 0.7787 (tp30) REVERT: D 70 ASP cc_start: 0.9061 (m-30) cc_final: 0.8798 (m-30) REVERT: D 86 ASP cc_start: 0.9058 (m-30) cc_final: 0.8780 (m-30) REVERT: D 135 GLU cc_start: 0.9064 (tp30) cc_final: 0.8841 (mm-30) REVERT: E 148 MET cc_start: 0.8197 (mmp) cc_final: 0.7963 (mmp) REVERT: E 269 GLU cc_start: 0.9470 (tp30) cc_final: 0.8909 (tp30) REVERT: E 288 PHE cc_start: 0.8684 (t80) cc_final: 0.8108 (t80) REVERT: E 307 TYR cc_start: 0.9380 (t80) cc_final: 0.9050 (t80) REVERT: E 327 PHE cc_start: 0.9069 (OUTLIER) cc_final: 0.8799 (t80) REVERT: E 353 LYS cc_start: 0.9266 (mmpt) cc_final: 0.8912 (mttt) REVERT: E 390 GLU cc_start: 0.9562 (OUTLIER) cc_final: 0.9314 (mp0) REVERT: E 404 PHE cc_start: 0.8146 (m-80) cc_final: 0.7796 (m-10) REVERT: E 415 LYS cc_start: 0.8945 (ptmt) cc_final: 0.8711 (ptpp) REVERT: E 426 LEU cc_start: 0.9786 (tt) cc_final: 0.9501 (pp) REVERT: E 427 LEU cc_start: 0.9605 (tt) cc_final: 0.9211 (pp) REVERT: E 428 ASN cc_start: 0.9518 (m-40) cc_final: 0.9210 (m110) REVERT: E 448 MET cc_start: 0.9572 (tpt) cc_final: 0.9351 (tpt) REVERT: E 514 GLN cc_start: 0.9439 (tt0) cc_final: 0.9143 (mt0) REVERT: E 521 GLN cc_start: 0.9657 (tm-30) cc_final: 0.9410 (tm-30) REVERT: E 556 TRP cc_start: 0.9216 (m-90) cc_final: 0.9011 (m-90) REVERT: F 95 ARG cc_start: 0.8808 (mmt180) cc_final: 0.8486 (mmt180) REVERT: F 254 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9347 (tt) REVERT: F 257 GLU cc_start: 0.9090 (tp30) cc_final: 0.8716 (mm-30) REVERT: F 314 ASP cc_start: 0.9168 (p0) cc_final: 0.8694 (p0) REVERT: F 371 GLU cc_start: 0.9241 (mt-10) cc_final: 0.8859 (mt-10) outliers start: 22 outliers final: 11 residues processed: 252 average time/residue: 0.5463 time to fit residues: 152.9970 Evaluate side-chains 233 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 219 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 291 ASP Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 390 GLU Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 254 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 183 optimal weight: 6.9990 chunk 122 optimal weight: 8.9990 chunk 9 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 109 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 0.0970 chunk 188 optimal weight: 40.0000 chunk 156 optimal weight: 8.9990 chunk 48 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 242 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.106742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.064186 restraints weight = 34150.913| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 2.80 r_work: 0.2603 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16706 Z= 0.152 Angle : 0.686 16.650 23066 Z= 0.339 Chirality : 0.043 0.329 2708 Planarity : 0.004 0.053 2618 Dihedral : 15.804 128.755 3559 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.46 % Allowed : 20.31 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.32 (0.20), residues: 1821 helix: 2.02 (0.17), residues: 912 sheet: -0.00 (0.33), residues: 238 loop : -0.34 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 217 TYR 0.013 0.001 TYR E 484 PHE 0.022 0.001 PHE E 481 TRP 0.065 0.004 TRP F 66 HIS 0.008 0.001 HIS E 152 Details of bonding type rmsd covalent geometry : bond 0.00342 (16702) covalent geometry : angle 0.68454 (23063) hydrogen bonds : bond 0.03473 ( 844) hydrogen bonds : angle 4.54250 ( 2365) metal coordination : bond 0.00877 ( 4) metal coordination : angle 3.58793 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 232 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8867 (m-30) cc_final: 0.8605 (m-30) REVERT: B 41 ASP cc_start: 0.8935 (t0) cc_final: 0.8668 (t70) REVERT: B 68 GLU cc_start: 0.8682 (tt0) cc_final: 0.8467 (tt0) REVERT: B 70 ASP cc_start: 0.9141 (m-30) cc_final: 0.8836 (m-30) REVERT: B 160 GLU cc_start: 0.8793 (mp0) cc_final: 0.8307 (pm20) REVERT: B 232 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8330 (mt-10) REVERT: C 70 ASP cc_start: 0.9181 (m-30) cc_final: 0.8915 (m-30) REVERT: C 211 GLU cc_start: 0.8571 (tp30) cc_final: 0.7807 (tp30) REVERT: D 70 ASP cc_start: 0.9074 (m-30) cc_final: 0.8809 (m-30) REVERT: D 86 ASP cc_start: 0.9087 (m-30) cc_final: 0.8811 (m-30) REVERT: D 135 GLU cc_start: 0.9066 (tp30) cc_final: 0.8831 (mm-30) REVERT: E 148 MET cc_start: 0.8198 (mmp) cc_final: 0.7976 (mmp) REVERT: E 234 GLU cc_start: 0.9327 (tp30) cc_final: 0.8785 (tp30) REVERT: E 269 GLU cc_start: 0.9473 (tp30) cc_final: 0.9007 (tp30) REVERT: E 288 PHE cc_start: 0.8667 (t80) cc_final: 0.8167 (t80) REVERT: E 307 TYR cc_start: 0.9407 (t80) cc_final: 0.9089 (t80) REVERT: E 327 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.8813 (t80) REVERT: E 353 LYS cc_start: 0.9258 (mmpt) cc_final: 0.8915 (mttt) REVERT: E 390 GLU cc_start: 0.9565 (OUTLIER) cc_final: 0.9268 (mp0) REVERT: E 404 PHE cc_start: 0.8185 (m-80) cc_final: 0.7824 (m-10) REVERT: E 426 LEU cc_start: 0.9787 (tt) cc_final: 0.9505 (pp) REVERT: E 427 LEU cc_start: 0.9602 (tt) cc_final: 0.9208 (pp) REVERT: E 428 ASN cc_start: 0.9513 (m-40) cc_final: 0.9206 (m110) REVERT: E 446 LYS cc_start: 0.9805 (mttt) cc_final: 0.9497 (mmmt) REVERT: E 473 ASP cc_start: 0.9050 (p0) cc_final: 0.8759 (p0) REVERT: E 514 GLN cc_start: 0.9438 (tt0) cc_final: 0.9149 (mt0) REVERT: E 521 GLN cc_start: 0.9637 (tm-30) cc_final: 0.9319 (tm-30) REVERT: E 556 TRP cc_start: 0.9244 (m-90) cc_final: 0.9028 (m-90) REVERT: E 564 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.9117 (mm) REVERT: F 211 TYR cc_start: 0.8958 (m-80) cc_final: 0.8751 (m-80) REVERT: F 254 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9360 (tt) REVERT: F 257 GLU cc_start: 0.9097 (tp30) cc_final: 0.8726 (mm-30) REVERT: F 314 ASP cc_start: 0.9161 (p0) cc_final: 0.8707 (p0) REVERT: F 371 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8858 (mt-10) outliers start: 22 outliers final: 10 residues processed: 246 average time/residue: 0.4811 time to fit residues: 131.6772 Evaluate side-chains 226 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 212 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 390 GLU Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 564 LEU Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain F residue 102 ARG Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 254 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 31 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 77 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 54 optimal weight: 6.9990 chunk 154 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 91 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 260 GLN ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 310 ASN E 428 ASN ** E 550 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 = 0.3617 r_free = 0.3617 target = 0.105317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.062705 restraints weight = 34113.213| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 2.81 r_work: 0.2574 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 16706 Z= 0.197 Angle : 0.729 15.782 23066 Z= 0.358 Chirality : 0.044 0.312 2708 Planarity : 0.004 0.051 2618 Dihedral : 15.856 130.115 3559 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 1.26 % Allowed : 20.91 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.20 (0.20), residues: 1821 helix: 1.92 (0.17), residues: 916 sheet: -0.07 (0.33), residues: 231 loop : -0.40 (0.24), residues: 674 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 217 TYR 0.016 0.001 TYR E 365 PHE 0.016 0.001 PHE F 97 TRP 0.069 0.004 TRP F 66 HIS 0.008 0.001 HIS E 152 Details of bonding type rmsd covalent geometry : bond 0.00446 (16702) covalent geometry : angle 0.72786 (23063) hydrogen bonds : bond 0.03696 ( 844) hydrogen bonds : angle 4.65310 ( 2365) metal coordination : bond 0.01061 ( 4) metal coordination : angle 3.85048 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 233 time to evaluate : 0.649 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8887 (m-30) cc_final: 0.8618 (m-30) REVERT: B 68 GLU cc_start: 0.8699 (tt0) cc_final: 0.8401 (tt0) REVERT: B 70 ASP cc_start: 0.9164 (m-30) cc_final: 0.8861 (m-30) REVERT: B 160 GLU cc_start: 0.8809 (mp0) cc_final: 0.8302 (pm20) REVERT: C 70 ASP cc_start: 0.9202 (m-30) cc_final: 0.8963 (m-30) REVERT: C 86 ASP cc_start: 0.9065 (m-30) cc_final: 0.8778 (m-30) REVERT: C 211 GLU cc_start: 0.8593 (tp30) cc_final: 0.7822 (tp30) REVERT: D 70 ASP cc_start: 0.9100 (m-30) cc_final: 0.8831 (m-30) REVERT: D 86 ASP cc_start: 0.9094 (m-30) cc_final: 0.8806 (m-30) REVERT: D 135 GLU cc_start: 0.9108 (tp30) cc_final: 0.8827 (mm-30) REVERT: E 122 GLU cc_start: 0.9163 (tp30) cc_final: 0.8849 (pp20) REVERT: E 148 MET cc_start: 0.8186 (mmp) cc_final: 0.7978 (mmp) REVERT: E 234 GLU cc_start: 0.9321 (tp30) cc_final: 0.8810 (tp30) REVERT: E 269 GLU cc_start: 0.9437 (tp30) cc_final: 0.8965 (tp30) REVERT: E 307 TYR cc_start: 0.9430 (t80) cc_final: 0.9079 (t80) REVERT: E 327 PHE cc_start: 0.9043 (OUTLIER) cc_final: 0.8806 (t80) REVERT: E 353 LYS cc_start: 0.9270 (mmpt) cc_final: 0.8950 (mttt) REVERT: E 390 GLU cc_start: 0.9576 (OUTLIER) cc_final: 0.9277 (mp0) REVERT: E 404 PHE cc_start: 0.8214 (m-80) cc_final: 0.7849 (m-10) REVERT: E 415 LYS cc_start: 0.8982 (ptmt) cc_final: 0.8735 (pttp) REVERT: E 426 LEU cc_start: 0.9781 (tt) cc_final: 0.9512 (pp) REVERT: E 427 LEU cc_start: 0.9596 (tt) cc_final: 0.9215 (pp) REVERT: E 428 ASN cc_start: 0.9521 (m110) cc_final: 0.9216 (m110) REVERT: E 446 LYS cc_start: 0.9795 (mttt) cc_final: 0.9503 (mmmt) REVERT: E 448 MET cc_start: 0.9560 (tpt) cc_final: 0.9092 (tpt) REVERT: E 473 ASP cc_start: 0.9014 (p0) cc_final: 0.8708 (p0) REVERT: E 514 GLN cc_start: 0.9459 (tt0) cc_final: 0.9171 (mt0) REVERT: E 521 GLN cc_start: 0.9620 (tm-30) cc_final: 0.9324 (tm-30) REVERT: E 556 TRP cc_start: 0.9230 (m-90) cc_final: 0.8981 (m-90) REVERT: E 564 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9111 (mm) REVERT: F 102 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.8987 (mtp85) REVERT: F 254 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9363 (tt) REVERT: F 257 GLU cc_start: 0.9128 (tp30) cc_final: 0.8757 (mm-30) REVERT: F 314 ASP cc_start: 0.9157 (p0) cc_final: 0.8708 (p0) REVERT: F 371 GLU cc_start: 0.9246 (mt-10) cc_final: 0.8847 (mt-10) outliers start: 19 outliers final: 10 residues processed: 247 average time/residue: 0.6214 time to fit residues: 170.0388 Evaluate side-chains 232 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 217 time to evaluate : 0.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 390 GLU Chi-restraints excluded: chain E residue 422 GLU Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 564 LEU Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain F residue 102 ARG Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 184 ASP Chi-restraints excluded: chain F residue 254 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 171 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 142 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 177 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 58 optimal weight: 5.9990 chunk 47 optimal weight: 0.2980 chunk 78 optimal weight: 0.6980 chunk 30 optimal weight: 0.7980 chunk 133 optimal weight: 9.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 GLN C 260 GLN ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 428 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.108026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.065541 restraints weight = 34316.702| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 2.84 r_work: 0.2633 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16706 Z= 0.132 Angle : 0.723 16.095 23066 Z= 0.353 Chirality : 0.043 0.339 2708 Planarity : 0.004 0.056 2618 Dihedral : 15.747 128.580 3559 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.26 % Allowed : 21.11 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.19 (0.20), residues: 1821 helix: 1.86 (0.17), residues: 924 sheet: -0.07 (0.33), residues: 231 loop : -0.38 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 217 TYR 0.016 0.001 TYR F 211 PHE 0.019 0.001 PHE E 481 TRP 0.081 0.004 TRP F 66 HIS 0.008 0.001 HIS E 152 Details of bonding type rmsd covalent geometry : bond 0.00297 (16702) covalent geometry : angle 0.72276 (23063) hydrogen bonds : bond 0.03300 ( 844) hydrogen bonds : angle 4.51583 ( 2365) metal coordination : bond 0.00534 ( 4) metal coordination : angle 2.89056 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3642 Ramachandran restraints generated. 1821 Oldfield, 0 Emsley, 1821 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 230 time to evaluate : 0.651 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8860 (m-30) cc_final: 0.8587 (m-30) REVERT: A 142 ASP cc_start: 0.8880 (t0) cc_final: 0.8556 (t0) REVERT: B 68 GLU cc_start: 0.8662 (tt0) cc_final: 0.8381 (tt0) REVERT: B 70 ASP cc_start: 0.9130 (m-30) cc_final: 0.8827 (m-30) REVERT: B 115 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8416 (mm-40) REVERT: B 160 GLU cc_start: 0.8726 (mp0) cc_final: 0.8245 (pm20) REVERT: C 70 ASP cc_start: 0.9160 (m-30) cc_final: 0.8905 (m-30) REVERT: C 211 GLU cc_start: 0.8511 (tp30) cc_final: 0.7753 (tp30) REVERT: D 70 ASP cc_start: 0.9056 (m-30) cc_final: 0.8792 (m-30) REVERT: D 86 ASP cc_start: 0.9058 (m-30) cc_final: 0.8788 (m-30) REVERT: D 135 GLU cc_start: 0.9062 (tp30) cc_final: 0.8845 (mm-30) REVERT: E 122 GLU cc_start: 0.9150 (tp30) cc_final: 0.8820 (pp20) REVERT: E 148 MET cc_start: 0.8201 (mmp) cc_final: 0.7975 (mmp) REVERT: E 234 GLU cc_start: 0.9295 (tp30) cc_final: 0.8771 (tp30) REVERT: E 269 GLU cc_start: 0.9452 (tp30) cc_final: 0.8981 (tp30) REVERT: E 288 PHE cc_start: 0.8678 (t80) cc_final: 0.8303 (t80) REVERT: E 307 TYR cc_start: 0.9428 (t80) cc_final: 0.9097 (t80) REVERT: E 327 PHE cc_start: 0.9042 (OUTLIER) cc_final: 0.8808 (t80) REVERT: E 353 LYS cc_start: 0.9279 (mmpt) cc_final: 0.8970 (mttt) REVERT: E 390 GLU cc_start: 0.9553 (OUTLIER) cc_final: 0.9286 (mp0) REVERT: E 404 PHE cc_start: 0.8200 (m-80) cc_final: 0.7832 (m-10) REVERT: E 426 LEU cc_start: 0.9785 (tt) cc_final: 0.9492 (pp) REVERT: E 427 LEU cc_start: 0.9599 (tt) cc_final: 0.9193 (pp) REVERT: E 428 ASN cc_start: 0.9515 (m-40) cc_final: 0.9214 (m110) REVERT: E 448 MET cc_start: 0.9590 (tpt) cc_final: 0.9256 (tpt) REVERT: E 514 GLN cc_start: 0.9450 (tt0) cc_final: 0.9162 (mt0) REVERT: E 521 GLN cc_start: 0.9612 (tm-30) cc_final: 0.9289 (tm-30) REVERT: E 564 LEU cc_start: 0.9360 (OUTLIER) cc_final: 0.9143 (mm) REVERT: F 97 PHE cc_start: 0.9490 (t80) cc_final: 0.9149 (t80) REVERT: F 100 MET cc_start: 0.9323 (mpm) cc_final: 0.9106 (pp-130) REVERT: F 107 GLU cc_start: 0.8572 (mm-30) cc_final: 0.8082 (tp30) REVERT: F 211 TYR cc_start: 0.8895 (m-80) cc_final: 0.8692 (m-80) REVERT: F 254 LEU cc_start: 0.9610 (OUTLIER) cc_final: 0.9355 (tt) REVERT: F 257 GLU cc_start: 0.9087 (tp30) cc_final: 0.8714 (mm-30) REVERT: F 314 ASP cc_start: 0.9176 (p0) cc_final: 0.8693 (p0) REVERT: F 371 GLU cc_start: 0.9218 (mt-10) cc_final: 0.8816 (mt-10) outliers start: 19 outliers final: 9 residues processed: 244 average time/residue: 0.5687 time to fit residues: 155.0128 Evaluate side-chains 236 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 222 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 115 GLN Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 281 THR Chi-restraints excluded: chain E residue 327 PHE Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 390 GLU Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 564 LEU Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain F residue 102 ARG Chi-restraints excluded: chain F residue 108 VAL Chi-restraints excluded: chain F residue 254 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 92 optimal weight: 0.9980 chunk 171 optimal weight: 3.9990 chunk 112 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 187 optimal weight: 8.9990 chunk 176 optimal weight: 0.7980 chunk 141 optimal weight: 10.0000 chunk 96 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 172 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 GLN C 260 GLN D 152 ASN ** E 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 265 ASN E 447 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.107383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.064963 restraints weight = 34137.547| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 2.83 r_work: 0.2622 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 16706 Z= 0.143 Angle : 0.718 15.807 23066 Z= 0.353 Chirality : 0.043 0.329 2708 Planarity : 0.005 0.057 2618 Dihedral : 15.715 128.458 3559 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.20 % Allowed : 21.50 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.18 (0.20), residues: 1821 helix: 1.87 (0.17), residues: 924 sheet: -0.10 (0.33), residues: 231 loop : -0.39 (0.24), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 146 TYR 0.021 0.001 TYR F 135 PHE 0.021 0.001 PHE B 114 TRP 0.085 0.004 TRP F 66 HIS 0.008 0.001 HIS E 152 Details of bonding type rmsd covalent geometry : bond 0.00325 (16702) covalent geometry : angle 0.71755 (23063) hydrogen bonds : bond 0.03395 ( 844) hydrogen bonds : angle 4.51987 ( 2365) metal coordination : bond 0.00648 ( 4) metal coordination : angle 3.22760 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5780.35 seconds wall clock time: 99 minutes 23.78 seconds (5963.78 seconds total)