Starting phenix.real_space_refine on Sat May 17 22:27:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cbk_16543/05_2025/8cbk_16543.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cbk_16543/05_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_16543/05_2025/8cbk_16543.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cbk_16543/05_2025/8cbk_16543.map" model { file = "/net/cci-nas-00/data/ceres_data/8cbk_16543/05_2025/8cbk_16543.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cbk_16543/05_2025/8cbk_16543.cif" } resolution = 2.76 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLN:plan1': 1, 'GLU:plan': 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: 11.50, per 1000 atoms: 0.71 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: 4.73 Conformation dependent library (CDL) restraints added in 2.0 seconds 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: 5.75 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: 5.47 Time building geometry restraints manager: 5.42 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: 6.550 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: 0.760 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 46.750 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.070 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:11.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 66.170 ------------------------------------------------------------------------------- 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 : 6.21 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.034 0.001 TRP F 66 HIS 0.008 0.001 HIS F 242 PHE 0.014 0.001 PHE E 288 TYR 0.019 0.001 TYR F 135 ARG 0.003 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.11882 ( 844) hydrogen bonds : angle 5.88195 ( 2365) metal coordination : bond 0.00588 ( 4) metal coordination : angle 3.74120 ( 3) covalent geometry : bond 0.00355 (16702) covalent geometry : angle 0.55878 (23063) *********************** 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 : 1.861 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: 0.7975 (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 283 LYS cc_start: 0.9565 (tmmt) cc_final: 0.9358 (tmmm) REVERT: E 404 PHE cc_start: 0.8009 (m-10) cc_final: 0.7580 (m-10) REVERT: E 455 TRP cc_start: 0.9342 (m100) cc_final: 0.9077 (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: 0.8274 (m100) REVERT: F 116 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8811 (mp0) 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: 1.2026 time to fit residues: 423.4116 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 : 1.619 ------------------------------------------------------------------------------- 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 160 optimal weight: 0.9990 chunk 144 optimal weight: 0.2980 chunk 79 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 97 optimal weight: 0.0970 chunk 76 optimal weight: 3.9990 chunk 148 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 90 optimal weight: 0.4980 chunk 110 optimal weight: 3.9990 chunk 172 optimal weight: 0.4980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 E 424 GLN E 447 HIS F 147 GLN F 348 ASN F 390 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.107823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.065300 restraints weight = 34628.111| |-----------------------------------------------------------------------------| r_work (start): 0.2794 rms_B_bonded: 2.79 r_work: 0.2626 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 16706 Z= 0.130 Angle : 0.646 13.727 23066 Z= 0.314 Chirality : 0.042 0.345 2708 Planarity : 0.004 0.063 2618 Dihedral : 16.099 126.036 3561 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.80 % Allowed : 9.99 % Favored : 89.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.20), residues: 1821 helix: 2.39 (0.17), residues: 916 sheet: -0.23 (0.35), residues: 234 loop : -0.04 (0.25), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP E 124 HIS 0.006 0.001 HIS F 242 PHE 0.021 0.001 PHE E 481 TYR 0.013 0.001 TYR E 365 ARG 0.004 0.000 ARG E 515 Details of bonding type rmsd hydrogen bonds : bond 0.03628 ( 844) hydrogen bonds : angle 4.75724 ( 2365) metal coordination : bond 0.00706 ( 4) metal coordination : angle 3.85493 ( 3) covalent geometry : bond 0.00283 (16702) covalent geometry : angle 0.64434 (23063) *********************** 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 316 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 304 time to evaluate : 1.757 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: 0.8871 (m-30) cc_final: 0.8541 (m-30) REVERT: B 48 GLU cc_start: 0.8353 (pm20) cc_final: 0.8143 (pm20) REVERT: B 64 ASP cc_start: 0.8133 (t0) cc_final: 0.7910 (t0) REVERT: B 68 GLU cc_start: 0.8628 (tt0) cc_final: 0.8379 (tt0) REVERT: B 70 ASP cc_start: 0.9028 (m-30) cc_final: 0.8723 (m-30) REVERT: B 160 GLU cc_start: 0.8725 (mp0) cc_final: 0.8182 (pm20) REVERT: C 70 ASP cc_start: 0.9100 (m-30) cc_final: 0.8895 (m-30) REVERT: C 211 GLU cc_start: 0.8602 (tp30) cc_final: 0.7851 (tp30) REVERT: D 48 GLU cc_start: 0.8840 (tp30) cc_final: 0.8450 (tp30) REVERT: D 70 ASP cc_start: 0.8944 (m-30) cc_final: 0.8676 (m-30) REVERT: E 148 MET cc_start: 0.8341 (mmp) cc_final: 0.8021 (mmp) REVERT: E 209 GLU cc_start: 0.8647 (tm-30) cc_final: 0.8190 (tp30) REVERT: E 248 ASN cc_start: 0.9551 (t0) cc_final: 0.9328 (OUTLIER) REVERT: E 266 LEU cc_start: 0.9502 (tm) cc_final: 0.9189 (tm) REVERT: E 285 PHE cc_start: 0.8881 (t80) cc_final: 0.8092 (t80) REVERT: E 288 PHE cc_start: 0.8602 (t80) cc_final: 0.8201 (t80) REVERT: E 312 GLN cc_start: 0.9185 (tm-30) cc_final: 0.8897 (tm-30) REVERT: E 326 TRP cc_start: 0.9518 (t-100) cc_final: 0.9242 (t-100) REVERT: E 353 LYS cc_start: 0.9187 (mmpt) cc_final: 0.8748 (mttt) REVERT: E 404 PHE cc_start: 0.8276 (m-80) cc_final: 0.7868 (m-10) REVERT: E 427 LEU cc_start: 0.9363 (pp) cc_final: 0.9124 (pp) REVERT: E 448 MET cc_start: 0.9633 (tmm) cc_final: 0.9077 (tpt) REVERT: E 455 TRP cc_start: 0.9366 (m100) cc_final: 0.8235 (m100) REVERT: E 526 LEU cc_start: 0.9015 (mm) cc_final: 0.8309 (mm) REVERT: F 100 MET cc_start: 0.9562 (mmm) cc_final: 0.8403 (mmm) REVERT: F 101 TRP cc_start: 0.9467 (m100) cc_final: 0.9093 (m100) REVERT: F 116 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8755 (mp0) REVERT: F 314 ASP cc_start: 0.9150 (p0) cc_final: 0.8788 (p0) REVERT: F 371 GLU cc_start: 0.9229 (mt-10) cc_final: 0.8796 (mt-10) outliers start: 12 outliers final: 6 residues processed: 306 average time/residue: 1.1731 time to fit residues: 399.8710 Evaluate side-chains 245 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 240 time to evaluate : 1.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 160 GLU Chi-restraints excluded: chain D residue 220 GLN Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 482 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 188 optimal weight: 40.0000 chunk 55 optimal weight: 0.9990 chunk 86 optimal weight: 3.9990 chunk 159 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 180 optimal weight: 9.9990 chunk 137 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 189 optimal weight: 30.0000 chunk 125 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 242 HIS ** 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 = 0.3628 r_free = 0.3628 target = 0.106045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.063188 restraints weight = 34001.023| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 2.75 r_work: 0.2582 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16706 Z= 0.183 Angle : 0.633 10.217 23066 Z= 0.314 Chirality : 0.042 0.295 2708 Planarity : 0.004 0.062 2618 Dihedral : 16.065 127.502 3559 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.66 % Allowed : 13.45 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.20), residues: 1821 helix: 2.26 (0.17), residues: 912 sheet: -0.24 (0.34), residues: 234 loop : -0.06 (0.25), residues: 675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.003 TRP F 66 HIS 0.010 0.001 HIS F 242 PHE 0.030 0.001 PHE E 518 TYR 0.013 0.001 TYR E 267 ARG 0.002 0.000 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.03778 ( 844) hydrogen bonds : angle 4.70815 ( 2365) metal coordination : bond 0.00991 ( 4) metal coordination : angle 4.01860 ( 3) covalent geometry : bond 0.00413 (16702) covalent geometry : angle 0.63145 (23063) *********************** 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 280 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 255 time to evaluate : 1.677 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: 0.8957 (m-30) cc_final: 0.8614 (m-30) REVERT: B 64 ASP cc_start: 0.8323 (t0) cc_final: 0.8120 (t0) REVERT: B 70 ASP cc_start: 0.9154 (m-30) cc_final: 0.8851 (m-30) REVERT: B 118 LEU cc_start: 0.9424 (OUTLIER) cc_final: 0.9185 (mp) REVERT: B 160 GLU cc_start: 0.8774 (mp0) cc_final: 0.8271 (pm20) REVERT: C 70 ASP cc_start: 0.9154 (m-30) cc_final: 0.8920 (m-30) REVERT: C 211 GLU cc_start: 0.8643 (tp30) cc_final: 0.7880 (tp30) REVERT: D 48 GLU cc_start: 0.8875 (tp30) cc_final: 0.8497 (tp30) REVERT: D 70 ASP cc_start: 0.9072 (m-30) cc_final: 0.8808 (m-30) REVERT: D 86 ASP cc_start: 0.9059 (m-30) cc_final: 0.8752 (m-30) REVERT: D 135 GLU cc_start: 0.9073 (tp30) cc_final: 0.8805 (mm-30) REVERT: E 129 GLU cc_start: 0.9402 (mp0) cc_final: 0.9201 (mp0) REVERT: E 148 MET cc_start: 0.8361 (mmp) cc_final: 0.8048 (mmp) REVERT: E 234 GLU cc_start: 0.9380 (tp30) cc_final: 0.8971 (tp30) REVERT: E 266 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9124 (tm) REVERT: E 288 PHE cc_start: 0.8768 (t80) cc_final: 0.8344 (t80) REVERT: E 353 LYS cc_start: 0.9232 (mmpt) cc_final: 0.8860 (mttt) REVERT: E 404 PHE cc_start: 0.8251 (m-80) cc_final: 0.7821 (m-10) REVERT: E 426 LEU cc_start: 0.9778 (tt) cc_final: 0.9515 (pp) REVERT: E 514 GLN cc_start: 0.9437 (tt0) cc_final: 0.8823 (mm110) REVERT: E 556 TRP cc_start: 0.9271 (m-90) cc_final: 0.9033 (m-90) REVERT: F 67 LYS cc_start: 0.9569 (mmmt) cc_final: 0.9355 (mmmt) REVERT: F 116 GLU cc_start: 0.9084 (mt-10) cc_final: 0.8822 (mp0) REVERT: F 257 GLU cc_start: 0.9067 (tp30) cc_final: 0.8713 (mm-30) REVERT: F 314 ASP cc_start: 0.9158 (p0) cc_final: 0.8752 (p0) REVERT: F 371 GLU cc_start: 0.9266 (mt-10) cc_final: 0.8855 (mt-10) outliers start: 25 outliers final: 9 residues processed: 266 average time/residue: 1.2287 time to fit residues: 364.1769 Evaluate side-chains 223 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 212 time to evaluate : 1.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain D residue 220 GLN Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 486 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 129 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 96 optimal weight: 0.9980 chunk 116 optimal weight: 0.9990 chunk 59 optimal weight: 0.0980 chunk 41 optimal weight: 0.8980 chunk 66 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 454 GLN ** E 540 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 = 0.3660 r_free = 0.3660 target = 0.107800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.065101 restraints weight = 34088.615| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.77 r_work: 0.2638 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 16706 Z= 0.125 Angle : 0.635 14.168 23066 Z= 0.309 Chirality : 0.041 0.275 2708 Planarity : 0.004 0.059 2618 Dihedral : 15.952 126.932 3559 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.73 % Allowed : 15.11 % Favored : 83.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.20), residues: 1821 helix: 2.28 (0.17), residues: 911 sheet: -0.20 (0.33), residues: 239 loop : -0.04 (0.25), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.048 0.003 TRP F 66 HIS 0.008 0.001 HIS E 152 PHE 0.029 0.001 PHE E 481 TYR 0.024 0.001 TYR E 484 ARG 0.003 0.000 ARG E 421 Details of bonding type rmsd hydrogen bonds : bond 0.03398 ( 844) hydrogen bonds : angle 4.56545 ( 2365) metal coordination : bond 0.00833 ( 4) metal coordination : angle 3.55387 ( 3) covalent geometry : bond 0.00276 (16702) covalent geometry : angle 0.63384 (23063) *********************** 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 270 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 244 time to evaluate : 1.730 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: 0.8936 (m-30) cc_final: 0.8714 (m-30) REVERT: B 70 ASP cc_start: 0.9134 (m-30) cc_final: 0.8829 (m-30) REVERT: B 160 GLU cc_start: 0.8744 (mp0) cc_final: 0.8303 (pm20) REVERT: C 70 ASP cc_start: 0.9155 (m-30) cc_final: 0.8881 (m-30) REVERT: C 211 GLU cc_start: 0.8582 (tp30) cc_final: 0.7783 (tp30) REVERT: D 70 ASP cc_start: 0.9064 (m-30) cc_final: 0.8792 (m-30) REVERT: D 86 ASP cc_start: 0.9074 (m-30) cc_final: 0.8783 (m-30) REVERT: E 148 MET cc_start: 0.8365 (mmp) cc_final: 0.7980 (mmp) REVERT: E 266 LEU cc_start: 0.9458 (OUTLIER) cc_final: 0.9197 (tm) REVERT: E 269 GLU cc_start: 0.9270 (OUTLIER) cc_final: 0.9061 (pm20) REVERT: E 288 PHE cc_start: 0.8661 (t80) cc_final: 0.8209 (t80) REVERT: E 353 LYS cc_start: 0.9214 (mmpt) cc_final: 0.8845 (mttt) REVERT: E 404 PHE cc_start: 0.8191 (m-80) cc_final: 0.7760 (m-10) REVERT: E 426 LEU cc_start: 0.9758 (tt) cc_final: 0.9480 (pp) REVERT: E 427 LEU cc_start: 0.9424 (pp) cc_final: 0.9057 (pp) REVERT: E 448 MET cc_start: 0.9430 (tmm) cc_final: 0.9173 (tpt) REVERT: E 521 GLN cc_start: 0.9675 (tm-30) cc_final: 0.9285 (tm-30) REVERT: F 66 TRP cc_start: 0.8053 (OUTLIER) cc_final: 0.7802 (p90) REVERT: F 116 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8787 (mp0) REVERT: F 257 GLU cc_start: 0.9020 (tp30) cc_final: 0.8669 (mm-30) REVERT: F 314 ASP cc_start: 0.9171 (p0) cc_final: 0.8687 (p0) REVERT: F 371 GLU cc_start: 0.9243 (mt-10) cc_final: 0.8855 (mt-10) outliers start: 26 outliers final: 10 residues processed: 257 average time/residue: 1.1830 time to fit residues: 338.3314 Evaluate side-chains 236 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 223 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 483 LEU Chi-restraints excluded: chain F residue 66 TRP 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 186 optimal weight: 9.9990 chunk 128 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 7 optimal weight: 0.0470 chunk 36 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 129 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- 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 540 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.107088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.064218 restraints weight = 34395.187| |-----------------------------------------------------------------------------| r_work (start): 0.2777 rms_B_bonded: 2.84 r_work: 0.2608 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2610 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= 0.147 Angle : 0.650 18.988 23066 Z= 0.315 Chirality : 0.042 0.292 2708 Planarity : 0.004 0.056 2618 Dihedral : 15.875 127.379 3559 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.73 % Allowed : 16.38 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.20), residues: 1821 helix: 2.21 (0.17), residues: 912 sheet: -0.25 (0.33), residues: 227 loop : -0.08 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP F 66 HIS 0.008 0.001 HIS E 152 PHE 0.027 0.001 PHE E 518 TYR 0.017 0.001 TYR E 314 ARG 0.007 0.000 ARG E 227 Details of bonding type rmsd hydrogen bonds : bond 0.03467 ( 844) hydrogen bonds : angle 4.56556 ( 2365) metal coordination : bond 0.01039 ( 4) metal coordination : angle 3.80108 ( 3) covalent geometry : bond 0.00331 (16702) covalent geometry : angle 0.64860 (23063) *********************** 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 273 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 247 time to evaluate : 1.626 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: B 41 ASP cc_start: 0.8938 (t0) cc_final: 0.8718 (t70) REVERT: B 70 ASP cc_start: 0.9159 (m-30) cc_final: 0.8850 (m-30) REVERT: B 118 LEU cc_start: 0.9432 (OUTLIER) cc_final: 0.9172 (mp) REVERT: B 160 GLU cc_start: 0.8781 (mp0) cc_final: 0.8315 (pm20) REVERT: C 70 ASP cc_start: 0.9175 (m-30) cc_final: 0.8891 (m-30) REVERT: C 211 GLU cc_start: 0.8585 (tp30) cc_final: 0.7800 (tp30) REVERT: D 70 ASP cc_start: 0.9053 (m-30) cc_final: 0.8788 (m-30) REVERT: D 86 ASP cc_start: 0.9057 (m-30) cc_final: 0.8737 (m-30) REVERT: D 135 GLU cc_start: 0.9088 (tp30) cc_final: 0.8861 (mm-30) REVERT: E 148 MET cc_start: 0.8372 (mmp) cc_final: 0.7894 (mmp) REVERT: E 234 GLU cc_start: 0.9339 (tp30) cc_final: 0.8810 (tp30) REVERT: E 266 LEU cc_start: 0.9469 (OUTLIER) cc_final: 0.9223 (tm) REVERT: E 288 PHE cc_start: 0.8697 (t80) cc_final: 0.8095 (t80) REVERT: E 307 TYR cc_start: 0.9380 (t80) cc_final: 0.9003 (t80) REVERT: E 353 LYS cc_start: 0.9231 (mmpt) cc_final: 0.8878 (mttt) REVERT: E 404 PHE cc_start: 0.8205 (m-80) cc_final: 0.7850 (m-10) REVERT: E 426 LEU cc_start: 0.9757 (tt) cc_final: 0.9502 (pp) REVERT: E 427 LEU cc_start: 0.9425 (pp) cc_final: 0.9070 (pp) REVERT: E 521 GLN cc_start: 0.9698 (tm-30) cc_final: 0.9467 (tm-30) REVERT: F 107 GLU cc_start: 0.8735 (mm-30) cc_final: 0.8522 (mm-30) REVERT: F 116 GLU cc_start: 0.9058 (mt-10) cc_final: 0.8782 (mp0) REVERT: F 257 GLU cc_start: 0.9059 (tp30) cc_final: 0.8702 (mm-30) REVERT: F 314 ASP cc_start: 0.9164 (p0) cc_final: 0.8721 (p0) REVERT: F 371 GLU cc_start: 0.9255 (mt-10) cc_final: 0.8862 (mt-10) outliers start: 26 outliers final: 14 residues processed: 258 average time/residue: 1.1907 time to fit residues: 342.8244 Evaluate side-chains 237 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 221 time to evaluate : 1.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain E residue 248 ASN Chi-restraints excluded: chain E residue 264 TRP Chi-restraints excluded: chain E residue 266 LEU Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 415 LYS Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 483 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 29 optimal weight: 0.9990 chunk 187 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 100 optimal weight: 9.9990 chunk 169 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 111 optimal weight: 0.9990 chunk 152 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 173 optimal weight: 2.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 260 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.105380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.062545 restraints weight = 34329.361| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 2.81 r_work: 0.2567 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.2701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16706 Z= 0.214 Angle : 0.688 18.749 23066 Z= 0.336 Chirality : 0.043 0.298 2708 Planarity : 0.004 0.055 2618 Dihedral : 15.920 129.387 3559 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.40 % Allowed : 17.24 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.20), residues: 1821 helix: 2.13 (0.17), residues: 908 sheet: -0.14 (0.33), residues: 225 loop : -0.15 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.004 TRP F 66 HIS 0.008 0.001 HIS E 152 PHE 0.025 0.001 PHE E 481 TYR 0.020 0.001 TYR E 213 ARG 0.005 0.000 ARG E 227 Details of bonding type rmsd hydrogen bonds : bond 0.03755 ( 844) hydrogen bonds : angle 4.71944 ( 2365) metal coordination : bond 0.01306 ( 4) metal coordination : angle 4.21053 ( 3) covalent geometry : bond 0.00482 (16702) covalent geometry : angle 0.68654 (23063) *********************** 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 258 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 222 time to evaluate : 1.596 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: 0.8865 (m-30) cc_final: 0.8617 (m-30) REVERT: B 70 ASP cc_start: 0.9180 (m-30) cc_final: 0.8883 (m-30) REVERT: B 118 LEU cc_start: 0.9442 (OUTLIER) cc_final: 0.9187 (mp) REVERT: B 160 GLU cc_start: 0.8821 (mp0) cc_final: 0.8327 (pm20) REVERT: C 70 ASP cc_start: 0.9190 (m-30) cc_final: 0.8913 (m-30) REVERT: C 86 ASP cc_start: 0.9046 (m-30) cc_final: 0.8788 (m-30) REVERT: C 211 GLU cc_start: 0.8587 (tp30) cc_final: 0.7821 (tp30) REVERT: D 70 ASP cc_start: 0.9096 (m-30) cc_final: 0.8823 (m-30) REVERT: D 86 ASP cc_start: 0.9084 (m-30) cc_final: 0.8789 (m-30) REVERT: D 135 GLU cc_start: 0.9094 (tp30) cc_final: 0.8810 (mm-30) REVERT: E 148 MET cc_start: 0.8575 (mmp) cc_final: 0.8200 (mmp) REVERT: E 307 TYR cc_start: 0.9377 (t80) cc_final: 0.8980 (t80) REVERT: E 353 LYS cc_start: 0.9275 (mmpt) cc_final: 0.8918 (mttt) REVERT: E 404 PHE cc_start: 0.8253 (m-80) cc_final: 0.7861 (m-10) REVERT: E 426 LEU cc_start: 0.9760 (tt) cc_final: 0.9522 (pp) REVERT: E 427 LEU cc_start: 0.9416 (OUTLIER) cc_final: 0.9068 (pp) REVERT: E 446 LYS cc_start: 0.9784 (mttt) cc_final: 0.9495 (mmmt) REVERT: E 448 MET cc_start: 0.9428 (tpt) cc_final: 0.8909 (tpt) REVERT: E 473 ASP cc_start: 0.9072 (p0) cc_final: 0.8714 (p0) REVERT: E 514 GLN cc_start: 0.9441 (tt0) cc_final: 0.9158 (mt0) REVERT: E 521 GLN cc_start: 0.9713 (tm-30) cc_final: 0.9497 (tm-30) REVERT: E 564 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9091 (mm) REVERT: F 102 ARG cc_start: 0.9210 (OUTLIER) cc_final: 0.8797 (mmm160) REVERT: F 254 LEU cc_start: 0.9612 (OUTLIER) cc_final: 0.9365 (tt) REVERT: F 257 GLU cc_start: 0.9101 (tp30) cc_final: 0.8735 (mm-30) REVERT: F 314 ASP cc_start: 0.9170 (p0) cc_final: 0.8752 (p0) REVERT: F 371 GLU cc_start: 0.9260 (mt-10) cc_final: 0.8865 (mt-10) outliers start: 36 outliers final: 18 residues processed: 243 average time/residue: 1.1455 time to fit residues: 311.3613 Evaluate side-chains 228 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 205 time to evaluate : 1.642 ------------------------------------------------------------------------------- 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 145 ILE 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 387 THR Chi-restraints excluded: chain E residue 390 GLU Chi-restraints excluded: chain E residue 407 VAL Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 415 LYS Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 482 LEU Chi-restraints excluded: chain E residue 486 THR Chi-restraints excluded: chain E residue 564 LEU Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain F residue 70 MET 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 186 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 152 optimal weight: 0.2980 chunk 82 optimal weight: 1.9990 chunk 114 optimal weight: 8.9990 chunk 107 optimal weight: 5.9990 chunk 159 optimal weight: 0.7980 chunk 145 optimal weight: 8.9990 chunk 86 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 164 optimal weight: 3.9990 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN C 260 GLN E 310 ASN ** E 389 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 = 0.3634 r_free = 0.3634 target = 0.106571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.063894 restraints weight = 34265.112| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 2.80 r_work: 0.2593 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16706 Z= 0.157 Angle : 0.678 18.778 23066 Z= 0.331 Chirality : 0.042 0.391 2708 Planarity : 0.004 0.056 2618 Dihedral : 15.873 129.015 3559 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.13 % Allowed : 17.91 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.20), residues: 1821 helix: 2.07 (0.17), residues: 908 sheet: -0.11 (0.33), residues: 223 loop : -0.20 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.003 TRP F 66 HIS 0.009 0.001 HIS E 152 PHE 0.016 0.001 PHE E 288 TYR 0.013 0.001 TYR E 484 ARG 0.005 0.000 ARG E 227 Details of bonding type rmsd hydrogen bonds : bond 0.03499 ( 844) hydrogen bonds : angle 4.64838 ( 2365) metal coordination : bond 0.00785 ( 4) metal coordination : angle 3.36386 ( 3) covalent geometry : bond 0.00353 (16702) covalent geometry : angle 0.67742 (23063) *********************** 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 254 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 222 time to evaluate : 1.877 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8860 (m-30) cc_final: 0.8597 (m-30) REVERT: B 70 ASP cc_start: 0.9134 (m-30) cc_final: 0.8844 (m-30) REVERT: B 160 GLU cc_start: 0.8801 (mp0) cc_final: 0.8306 (pm20) REVERT: C 70 ASP cc_start: 0.9192 (m-30) cc_final: 0.8903 (m-30) REVERT: C 86 ASP cc_start: 0.9052 (m-30) cc_final: 0.8784 (m-30) REVERT: C 211 GLU cc_start: 0.8575 (tp30) cc_final: 0.7788 (tp30) REVERT: D 70 ASP cc_start: 0.9075 (m-30) cc_final: 0.8814 (m-30) REVERT: D 86 ASP cc_start: 0.9065 (m-30) cc_final: 0.8763 (m-30) REVERT: D 135 GLU cc_start: 0.9093 (tp30) cc_final: 0.8866 (mm-30) REVERT: E 148 MET cc_start: 0.8465 (mmp) cc_final: 0.8151 (mmp) REVERT: E 234 GLU cc_start: 0.9326 (tp30) cc_final: 0.8790 (tp30) REVERT: E 269 GLU cc_start: 0.9270 (OUTLIER) cc_final: 0.8941 (pp20) REVERT: E 270 LEU cc_start: 0.9712 (OUTLIER) cc_final: 0.9375 (tm) REVERT: E 288 PHE cc_start: 0.8715 (t80) cc_final: 0.8147 (t80) REVERT: E 307 TYR cc_start: 0.9364 (t80) cc_final: 0.8977 (t80) REVERT: E 353 LYS cc_start: 0.9275 (mmpt) cc_final: 0.8925 (mttt) REVERT: E 404 PHE cc_start: 0.8243 (m-80) cc_final: 0.7843 (m-10) REVERT: E 426 LEU cc_start: 0.9758 (tt) cc_final: 0.9514 (pp) REVERT: E 427 LEU cc_start: 0.9407 (OUTLIER) cc_final: 0.9054 (pp) REVERT: E 446 LYS cc_start: 0.9784 (mttt) cc_final: 0.9525 (mmmt) REVERT: E 448 MET cc_start: 0.9491 (tpt) cc_final: 0.8993 (tpt) REVERT: E 473 ASP cc_start: 0.9044 (p0) cc_final: 0.8713 (p0) REVERT: E 514 GLN cc_start: 0.9407 (tt0) cc_final: 0.9157 (mt0) REVERT: E 521 GLN cc_start: 0.9698 (tm-30) cc_final: 0.9427 (tm-30) REVERT: E 564 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9098 (mm) REVERT: F 95 ARG cc_start: 0.8730 (mmt180) cc_final: 0.8487 (mmt180) REVERT: F 102 ARG cc_start: 0.9200 (OUTLIER) cc_final: 0.8795 (mmm160) REVERT: F 116 GLU cc_start: 0.9072 (mt-10) cc_final: 0.8781 (mp0) REVERT: F 254 LEU cc_start: 0.9602 (OUTLIER) cc_final: 0.9337 (tt) REVERT: F 257 GLU cc_start: 0.9079 (tp30) cc_final: 0.8713 (mm-30) REVERT: F 314 ASP cc_start: 0.9179 (p0) cc_final: 0.8728 (p0) REVERT: F 371 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8843 (mt-10) outliers start: 32 outliers final: 16 residues processed: 240 average time/residue: 1.1894 time to fit residues: 318.7354 Evaluate side-chains 232 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 210 time to evaluate : 1.752 ------------------------------------------------------------------------------- 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 248 ASN Chi-restraints excluded: chain E residue 269 GLU Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 390 GLU Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 415 LYS Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 483 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 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 55 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 108 optimal weight: 0.8980 chunk 51 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 chunk 163 optimal weight: 3.9990 chunk 142 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 28 optimal weight: 0.6980 chunk 156 optimal weight: 9.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 260 GLN ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.107498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.064495 restraints weight = 33954.823| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 2.83 r_work: 0.2608 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 16706 Z= 0.138 Angle : 0.692 18.369 23066 Z= 0.337 Chirality : 0.042 0.352 2708 Planarity : 0.004 0.057 2618 Dihedral : 15.805 128.408 3559 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 1.80 % Allowed : 19.11 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.20), residues: 1821 helix: 2.06 (0.17), residues: 910 sheet: -0.08 (0.33), residues: 223 loop : -0.21 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.004 TRP F 66 HIS 0.009 0.001 HIS E 152 PHE 0.021 0.001 PHE E 481 TYR 0.013 0.001 TYR F 211 ARG 0.005 0.000 ARG E 227 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 844) hydrogen bonds : angle 4.57547 ( 2365) metal coordination : bond 0.00700 ( 4) metal coordination : angle 3.42825 ( 3) covalent geometry : bond 0.00315 (16702) covalent geometry : angle 0.69050 (23063) *********************** 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 256 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 229 time to evaluate : 1.646 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8843 (m-30) cc_final: 0.8572 (m-30) REVERT: B 41 ASP cc_start: 0.8967 (t0) cc_final: 0.8663 (t70) REVERT: B 70 ASP cc_start: 0.9110 (m-30) cc_final: 0.8821 (m-30) REVERT: B 160 GLU cc_start: 0.8799 (mp0) cc_final: 0.8295 (pm20) REVERT: B 259 MET cc_start: 0.9471 (mmm) cc_final: 0.9235 (mmm) REVERT: C 68 GLU cc_start: 0.8730 (tt0) cc_final: 0.8520 (tt0) REVERT: C 70 ASP cc_start: 0.9171 (m-30) cc_final: 0.8878 (m-30) REVERT: C 86 ASP cc_start: 0.9045 (m-30) cc_final: 0.8717 (m-30) REVERT: C 211 GLU cc_start: 0.8545 (tp30) cc_final: 0.7759 (tp30) REVERT: D 70 ASP cc_start: 0.9067 (m-30) cc_final: 0.8809 (m-30) REVERT: D 86 ASP cc_start: 0.9073 (m-30) cc_final: 0.8785 (m-30) REVERT: D 135 GLU cc_start: 0.9067 (tp30) cc_final: 0.8842 (mm-30) REVERT: E 148 MET cc_start: 0.8443 (mmp) cc_final: 0.8141 (mmp) REVERT: E 234 GLU cc_start: 0.9298 (tp30) cc_final: 0.8760 (tp30) REVERT: E 269 GLU cc_start: 0.9224 (OUTLIER) cc_final: 0.8933 (pp20) REVERT: E 270 LEU cc_start: 0.9674 (OUTLIER) cc_final: 0.9312 (tm) REVERT: E 288 PHE cc_start: 0.8676 (t80) cc_final: 0.8125 (t80) REVERT: E 307 TYR cc_start: 0.9352 (t80) cc_final: 0.8939 (t80) REVERT: E 353 LYS cc_start: 0.9275 (mmpt) cc_final: 0.8949 (mttt) REVERT: E 404 PHE cc_start: 0.8210 (m-80) cc_final: 0.7803 (m-10) REVERT: E 426 LEU cc_start: 0.9746 (tt) cc_final: 0.9505 (pp) REVERT: E 427 LEU cc_start: 0.9398 (OUTLIER) cc_final: 0.9043 (pp) REVERT: E 446 LYS cc_start: 0.9785 (mttt) cc_final: 0.9556 (mmmt) REVERT: E 448 MET cc_start: 0.9507 (tpt) cc_final: 0.8991 (tpt) REVERT: E 473 ASP cc_start: 0.9001 (p0) cc_final: 0.8740 (p0) REVERT: E 514 GLN cc_start: 0.9402 (tt0) cc_final: 0.9164 (mt0) REVERT: E 521 GLN cc_start: 0.9677 (tm-30) cc_final: 0.9381 (tm-30) REVERT: E 564 LEU cc_start: 0.9332 (OUTLIER) cc_final: 0.9115 (mm) REVERT: F 102 ARG cc_start: 0.9197 (OUTLIER) cc_final: 0.8765 (mmm160) REVERT: F 107 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8278 (mm-30) REVERT: F 254 LEU cc_start: 0.9598 (OUTLIER) cc_final: 0.9356 (tt) REVERT: F 257 GLU cc_start: 0.9069 (tp30) cc_final: 0.8696 (mm-30) REVERT: F 314 ASP cc_start: 0.9179 (p0) cc_final: 0.8738 (p0) REVERT: F 371 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8839 (mt-10) outliers start: 27 outliers final: 15 residues processed: 246 average time/residue: 1.2081 time to fit residues: 330.5358 Evaluate side-chains 232 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 211 time to evaluate : 1.823 ------------------------------------------------------------------------------- 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 269 GLU Chi-restraints excluded: chain E residue 270 LEU Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 390 GLU Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 415 LYS Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 442 VAL Chi-restraints excluded: chain E residue 483 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 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 72 optimal weight: 0.0000 chunk 56 optimal weight: 0.9990 chunk 135 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 67 optimal weight: 1.9990 chunk 113 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 116 optimal weight: 0.0870 chunk 55 optimal weight: 0.9980 chunk 183 optimal weight: 5.9990 overall best weight: 0.5564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN C 260 GLN D 152 ASN ** E 389 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 = 0.3657 r_free = 0.3657 target = 0.108331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.065784 restraints weight = 34136.235| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.86 r_work: 0.2635 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8611 moved from start: 0.3156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16706 Z= 0.125 Angle : 0.691 18.109 23066 Z= 0.337 Chirality : 0.043 0.339 2708 Planarity : 0.004 0.059 2618 Dihedral : 15.727 127.429 3559 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.53 % Allowed : 19.97 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.20), residues: 1821 helix: 2.05 (0.17), residues: 910 sheet: 0.00 (0.33), residues: 231 loop : -0.29 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.004 TRP F 66 HIS 0.009 0.001 HIS E 152 PHE 0.014 0.001 PHE E 288 TYR 0.013 0.001 TYR E 484 ARG 0.005 0.000 ARG E 227 Details of bonding type rmsd hydrogen bonds : bond 0.03270 ( 844) hydrogen bonds : angle 4.53580 ( 2365) metal coordination : bond 0.00612 ( 4) metal coordination : angle 3.14849 ( 3) covalent geometry : bond 0.00279 (16702) covalent geometry : angle 0.69037 (23063) *********************** 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 254 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 231 time to evaluate : 1.619 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8853 (m-30) cc_final: 0.8577 (m-30) REVERT: B 41 ASP cc_start: 0.8961 (t0) cc_final: 0.8627 (t70) REVERT: B 70 ASP cc_start: 0.9094 (m-30) cc_final: 0.8810 (m-30) REVERT: B 115 GLN cc_start: 0.8744 (tt0) cc_final: 0.8542 (mt0) REVERT: B 160 GLU cc_start: 0.8770 (mp0) cc_final: 0.8277 (pm20) REVERT: B 232 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8612 (mt-10) REVERT: B 259 MET cc_start: 0.9452 (mmm) cc_final: 0.9182 (mmm) REVERT: B 260 GLN cc_start: 0.9120 (mm110) cc_final: 0.6601 (pt0) REVERT: C 70 ASP cc_start: 0.9158 (m-30) cc_final: 0.8856 (m-30) REVERT: C 86 ASP cc_start: 0.9037 (m-30) cc_final: 0.8812 (m-30) REVERT: C 211 GLU cc_start: 0.8522 (tp30) cc_final: 0.7891 (tp30) REVERT: D 70 ASP cc_start: 0.9052 (m-30) cc_final: 0.8789 (m-30) REVERT: D 86 ASP cc_start: 0.9054 (m-30) cc_final: 0.8782 (m-30) REVERT: E 148 MET cc_start: 0.8383 (mmp) cc_final: 0.8088 (mmp) REVERT: E 234 GLU cc_start: 0.9267 (tp30) cc_final: 0.8716 (tp30) REVERT: E 288 PHE cc_start: 0.8627 (t80) cc_final: 0.8192 (t80) REVERT: E 307 TYR cc_start: 0.9340 (t80) cc_final: 0.9134 (t80) REVERT: E 353 LYS cc_start: 0.9261 (mmpt) cc_final: 0.8948 (mttt) REVERT: E 404 PHE cc_start: 0.8182 (m-80) cc_final: 0.7793 (m-10) REVERT: E 426 LEU cc_start: 0.9744 (tt) cc_final: 0.9493 (pp) REVERT: E 427 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9031 (pp) REVERT: E 446 LYS cc_start: 0.9779 (mttt) cc_final: 0.9568 (mmmt) REVERT: E 448 MET cc_start: 0.9517 (tpt) cc_final: 0.9050 (tpt) REVERT: E 473 ASP cc_start: 0.8966 (p0) cc_final: 0.8698 (p0) REVERT: E 514 GLN cc_start: 0.9400 (tt0) cc_final: 0.9157 (mt0) REVERT: E 521 GLN cc_start: 0.9663 (tm-30) cc_final: 0.9426 (tm-30) REVERT: E 564 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9128 (mm) REVERT: F 102 ARG cc_start: 0.9092 (OUTLIER) cc_final: 0.8698 (mmm160) REVERT: F 107 GLU cc_start: 0.8503 (mm-30) cc_final: 0.8275 (mm-30) REVERT: F 116 GLU cc_start: 0.9217 (mt-10) cc_final: 0.8982 (mp0) REVERT: F 257 GLU cc_start: 0.9050 (tp30) cc_final: 0.8678 (mm-30) REVERT: F 314 ASP cc_start: 0.9188 (p0) cc_final: 0.8680 (p0) REVERT: F 371 GLU cc_start: 0.9231 (mt-10) cc_final: 0.8827 (mt-10) outliers start: 23 outliers final: 13 residues processed: 245 average time/residue: 1.1762 time to fit residues: 320.3998 Evaluate side-chains 237 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 221 time to evaluate : 1.631 ------------------------------------------------------------------------------- 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 276 VAL Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 390 GLU Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 415 LYS Chi-restraints excluded: chain E residue 427 LEU 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 184 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 29 optimal weight: 6.9990 chunk 125 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 116 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 chunk 147 optimal weight: 0.6980 chunk 101 optimal weight: 0.2980 chunk 49 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 260 GLN ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 447 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.108565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.065924 restraints weight = 34524.035| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.86 r_work: 0.2646 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 16706 Z= 0.132 Angle : 0.714 18.922 23066 Z= 0.347 Chirality : 0.043 0.393 2708 Planarity : 0.004 0.058 2618 Dihedral : 15.662 126.761 3559 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.13 % Allowed : 20.84 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.20), residues: 1821 helix: 2.00 (0.17), residues: 914 sheet: -0.00 (0.33), residues: 238 loop : -0.32 (0.24), residues: 669 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.003 TRP F 66 HIS 0.009 0.001 HIS E 152 PHE 0.021 0.001 PHE E 481 TYR 0.016 0.001 TYR F 211 ARG 0.013 0.000 ARG F 146 Details of bonding type rmsd hydrogen bonds : bond 0.03360 ( 844) hydrogen bonds : angle 4.52847 ( 2365) metal coordination : bond 0.00609 ( 4) metal coordination : angle 3.13940 ( 3) covalent geometry : bond 0.00297 (16702) covalent geometry : angle 0.71345 (23063) ********************** 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 245 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 228 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 ASP cc_start: 0.8870 (m-30) cc_final: 0.8596 (m-30) REVERT: B 41 ASP cc_start: 0.8953 (t0) cc_final: 0.8596 (t70) REVERT: B 70 ASP cc_start: 0.9101 (m-30) cc_final: 0.8821 (m-30) REVERT: B 160 GLU cc_start: 0.8729 (mp0) cc_final: 0.8245 (pm20) REVERT: B 232 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8561 (mt-10) REVERT: B 260 GLN cc_start: 0.9140 (mm110) cc_final: 0.6619 (pt0) REVERT: C 70 ASP cc_start: 0.9160 (m-30) cc_final: 0.8864 (m-30) REVERT: C 86 ASP cc_start: 0.9026 (m-30) cc_final: 0.8813 (m-30) REVERT: C 211 GLU cc_start: 0.8515 (tp30) cc_final: 0.7810 (tp30) REVERT: D 70 ASP cc_start: 0.9062 (m-30) cc_final: 0.8825 (m-30) REVERT: D 86 ASP cc_start: 0.9075 (m-30) cc_final: 0.8797 (m-30) REVERT: E 148 MET cc_start: 0.8309 (mmp) cc_final: 0.8025 (mmp) REVERT: E 234 GLU cc_start: 0.9254 (tp30) cc_final: 0.8699 (tp30) REVERT: E 307 TYR cc_start: 0.9328 (t80) cc_final: 0.9120 (t80) REVERT: E 353 LYS cc_start: 0.9261 (mmpt) cc_final: 0.8955 (mttt) REVERT: E 404 PHE cc_start: 0.8205 (m-80) cc_final: 0.7811 (m-10) REVERT: E 426 LEU cc_start: 0.9743 (tt) cc_final: 0.9494 (pp) REVERT: E 427 LEU cc_start: 0.9372 (OUTLIER) cc_final: 0.9014 (pp) REVERT: E 446 LYS cc_start: 0.9771 (mttt) cc_final: 0.9488 (mmmt) REVERT: E 448 MET cc_start: 0.9554 (tpt) cc_final: 0.9086 (tpt) REVERT: E 473 ASP cc_start: 0.8945 (p0) cc_final: 0.8720 (p0) REVERT: E 481 PHE cc_start: 0.9398 (m-80) cc_final: 0.9165 (m-80) REVERT: E 521 GLN cc_start: 0.9662 (tm-30) cc_final: 0.9427 (tm-30) REVERT: F 63 LEU cc_start: 0.9530 (mm) cc_final: 0.9285 (pt) REVERT: F 257 GLU cc_start: 0.9070 (tp30) cc_final: 0.8700 (mm-30) REVERT: F 314 ASP cc_start: 0.9169 (p0) cc_final: 0.8632 (p0) REVERT: F 371 GLU cc_start: 0.9230 (mt-10) cc_final: 0.8825 (mt-10) outliers start: 17 outliers final: 13 residues processed: 239 average time/residue: 1.2125 time to fit residues: 322.3462 Evaluate side-chains 228 residues out of total 1508 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 214 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 206 LEU Chi-restraints excluded: chain D residue 178 MET Chi-restraints excluded: chain E residue 146 SER Chi-restraints excluded: chain E residue 248 ASN Chi-restraints excluded: chain E residue 276 VAL Chi-restraints excluded: chain E residue 279 LEU Chi-restraints excluded: chain E residue 387 THR Chi-restraints excluded: chain E residue 413 VAL Chi-restraints excluded: chain E residue 427 LEU Chi-restraints excluded: chain E residue 440 LEU Chi-restraints excluded: chain E residue 447 HIS Chi-restraints excluded: chain E residue 549 VAL Chi-restraints excluded: chain E residue 577 LEU Chi-restraints excluded: chain F residue 184 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 190 random chunks: chunk 185 optimal weight: 6.9990 chunk 138 optimal weight: 7.9990 chunk 21 optimal weight: 0.7980 chunk 119 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 87 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 chunk 122 optimal weight: 0.0870 chunk 55 optimal weight: 0.0670 chunk 95 optimal weight: 1.9990 chunk 112 optimal weight: 0.1980 overall best weight: 0.6298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 260 GLN D 152 ASN ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 447 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.108745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.066089 restraints weight = 34305.356| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 2.86 r_work: 0.2652 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.3359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 16706 Z= 0.130 Angle : 0.714 17.682 23066 Z= 0.346 Chirality : 0.044 0.432 2708 Planarity : 0.004 0.059 2618 Dihedral : 15.634 126.393 3559 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.93 % Allowed : 21.04 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.13 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.20), residues: 1821 helix: 1.96 (0.17), residues: 920 sheet: -0.04 (0.33), residues: 231 loop : -0.34 (0.24), residues: 670 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.088 0.004 TRP F 66 HIS 0.009 0.001 HIS E 152 PHE 0.023 0.001 PHE E 481 TYR 0.013 0.001 TYR F 135 ARG 0.008 0.000 ARG E 445 Details of bonding type rmsd hydrogen bonds : bond 0.03314 ( 844) hydrogen bonds : angle 4.51979 ( 2365) metal coordination : bond 0.00610 ( 4) metal coordination : angle 3.06370 ( 3) covalent geometry : bond 0.00290 (16702) covalent geometry : angle 0.71293 (23063) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11850.06 seconds wall clock time: 204 minutes 57.81 seconds (12297.81 seconds total)