Starting phenix.real_space_refine on Thu Dec 26 09:55:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8snh_40625/12_2024/8snh_40625_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8snh_40625/12_2024/8snh_40625.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8snh_40625/12_2024/8snh_40625.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8snh_40625/12_2024/8snh_40625.map" model { file = "/net/cci-nas-00/data/ceres_data/8snh_40625/12_2024/8snh_40625_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8snh_40625/12_2024/8snh_40625_trim.cif" } resolution = 2.7 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= 0.002 sd= 0.182 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: 8 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 19 7.16 5 Cu 1 5.60 5 S 140 5.16 5 C 15892 2.51 5 N 3937 2.21 5 O 4174 1.98 5 H 19392 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 43557 Number of models: 1 Model: "" Number of chains: 24 Chain: "E" Number of atoms: 3719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3719 Classifications: {'peptide': 468} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 15, 'TRANS': 452} Chain: "C" Number of atoms: 2827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 2827 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 20, 'TRANS': 169} Chain: "I" Number of atoms: 6556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 6556 Classifications: {'peptide': 403} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 379} Chain: "J" Number of atoms: 3663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 3663 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 13, 'TRANS': 218} Chain: "K" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 2585 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 173} Chain: "L" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 244 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} Chain: "Z" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 2883 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 20, 'TRANS': 173} Chain: "D" Number of atoms: 6556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 403, 6556 Classifications: {'peptide': 403} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 379} Chain: "M" Number of atoms: 3250 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 3250 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 11, 'TRANS': 192} Chain breaks: 1 Chain: "N" Number of atoms: 2585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 181, 2585 Classifications: {'peptide': 181} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 173} Chain: "O" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 244 Classifications: {'peptide': 16} Link IDs: {'PTRANS': 1, 'TRANS': 14} Chain: "F" Number of atoms: 2917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 2917 Classifications: {'peptide': 200} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 188} Unresolved non-hydrogen bonds: 78 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 2, 'ASN:plan1': 1, 'TYR:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 40 Chain: "G" Number of atoms: 4655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 4655 Classifications: {'peptide': 304} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 14, 'TRANS': 289} Chain: "E" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 89 Unusual residues: {' CA': 2, ' CU': 1, 'HEM': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 180 Unusual residues: {'HEM': 2, 'I7Y': 1, 'U10': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 11 Chain: "J" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'FES': 1, 'I7Y': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 149 Unusual residues: {'HEM': 2, 'U10': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 86 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 86 Unusual residues: {'HEC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5498 SG CYS C 124 85.925 89.842 78.269 1.00 73.85 S ATOM 5565 SG CYS C 129 82.145 90.282 77.754 1.00 84.77 S ATOM 5902 SG CYS C 152 83.432 92.560 79.326 1.00 77.21 S ATOM 21406 SG CYS Z 124 43.257 59.253 40.939 1.00 43.68 S ATOM 21811 SG CYS Z 152 46.202 59.766 39.023 1.00 46.64 S Time building chain proxies: 20.36, per 1000 atoms: 0.47 Number of scatterers: 43557 At special positions: 0 Unit cell: (115.36, 141.11, 161.71, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) Cu 1 28.99 Fe 19 26.01 Ca 2 19.99 S 140 16.00 O 4174 8.00 N 3937 7.00 C 15892 6.00 H 19392 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS J 165 " - pdb=" SG CYS J 191 " distance=2.03 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=33, symmetry=0 Number of additional bonds: simple=33, symmetry=0 Coordination: Other bonds: Time building additional restraints: 11.99 Conformation dependent library (CDL) restraints added in 3.5 seconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES C 201 " pdb="FE2 FES C 201 " - pdb=" ND1 HIS C 155 " pdb="FE2 FES C 201 " - pdb=" ND1 HIS C 126 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 152 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 124 " pdb="FE1 FES C 201 " - pdb=" SG CYS C 129 " pdb=" FES Z 201 " pdb="FE2 FES Z 201 " - pdb=" ND1 HIS Z 155 " pdb="FE2 FES Z 201 " - pdb=" ND1 HIS Z 126 " pdb="FE1 FES Z 201 " - pdb=" SG CYS Z 152 " pdb="FE1 FES Z 201 " - pdb=" SG CYS Z 124 " Number of angles added : 9 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5434 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 20 sheets defined 60.7% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.70 Creating SS restraints... Processing helix chain 'E' and resid 11 through 42 removed outlier: 4.040A pdb=" N VAL E 15 " --> pdb=" O ASN E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 43 through 47 Processing helix chain 'E' and resid 49 through 52 Processing helix chain 'E' and resid 53 through 68 Proline residue: E 59 - end of helix removed outlier: 3.778A pdb=" N ILE E 66 " --> pdb=" O THR E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 68 through 87 removed outlier: 4.165A pdb=" N GLN E 83 " --> pdb=" O TYR E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 114 Processing helix chain 'E' and resid 133 through 152 Processing helix chain 'E' and resid 159 through 180 removed outlier: 5.108A pdb=" N HIS E 176 " --> pdb=" O THR E 172 " (cutoff:3.500A) Processing helix chain 'E' and resid 195 through 211 removed outlier: 4.083A pdb=" N ASN E 209 " --> pdb=" O TRP E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 232 Proline residue: E 228 - end of helix Processing helix chain 'E' and resid 237 through 253 removed outlier: 4.409A pdb=" N ILE E 253 " --> pdb=" O ILE E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 255 through 261 removed outlier: 3.617A pdb=" N HIS E 258 " --> pdb=" O ALA E 255 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N HIS E 261 " --> pdb=" O HIS E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 266 through 294 removed outlier: 4.386A pdb=" N ALA E 282 " --> pdb=" O LEU E 278 " (cutoff:3.500A) Proline residue: E 283 - end of helix Processing helix chain 'E' and resid 298 through 304 Processing helix chain 'E' and resid 305 through 329 Proline residue: E 326 - end of helix Processing helix chain 'E' and resid 330 through 337 removed outlier: 3.919A pdb=" N LEU E 336 " --> pdb=" O THR E 332 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 352 removed outlier: 4.222A pdb=" N ILE E 344 " --> pdb=" O THR E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 354 through 371 Proline residue: E 368 - end of helix Processing helix chain 'E' and resid 378 through 413 removed outlier: 3.861A pdb=" N GLY E 392 " --> pdb=" O LEU E 388 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N LEU E 395 " --> pdb=" O ILE E 391 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N TYR E 396 " --> pdb=" O GLY E 392 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 461 Proline residue: E 433 - end of helix Processing helix chain 'E' and resid 464 through 473 removed outlier: 3.871A pdb=" N ALA E 472 " --> pdb=" O ILE E 468 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG E 473 " --> pdb=" O LEU E 469 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 36 Proline residue: C 32 - end of helix Processing helix chain 'C' and resid 40 through 47 Processing helix chain 'C' and resid 78 through 85 removed outlier: 3.582A pdb=" N LEU C 82 " --> pdb=" O THR C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 92 removed outlier: 4.621A pdb=" N GLU C 89 " --> pdb=" O PRO C 86 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLY C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LEU C 92 " --> pdb=" O GLU C 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 12 removed outlier: 3.612A pdb=" N ARG I 11 " --> pdb=" O TRP I 7 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 22 Processing helix chain 'I' and resid 32 through 35 Processing helix chain 'I' and resid 36 through 57 Processing helix chain 'I' and resid 65 through 76 Processing helix chain 'I' and resid 79 through 108 Processing helix chain 'I' and resid 115 through 139 removed outlier: 3.542A pdb=" N LEU I 138 " --> pdb=" O PHE I 134 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LEU I 139 " --> pdb=" O MET I 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 142 through 156 removed outlier: 4.007A pdb=" N PHE I 156 " --> pdb=" O ILE I 152 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 159 No H-bonds generated for 'chain 'I' and resid 157 through 159' Processing helix chain 'I' and resid 162 through 172 Processing helix chain 'I' and resid 177 through 190 Processing helix chain 'I' and resid 190 through 211 Processing helix chain 'I' and resid 219 through 223 Processing helix chain 'I' and resid 236 through 262 removed outlier: 6.681A pdb=" N THR I 241 " --> pdb=" O HIS I 237 " (cutoff:3.500A) Processing helix chain 'I' and resid 271 through 276 Processing helix chain 'I' and resid 290 through 292 No H-bonds generated for 'chain 'I' and resid 290 through 292' Processing helix chain 'I' and resid 293 through 303 Processing helix chain 'I' and resid 305 through 327 removed outlier: 3.633A pdb=" N ILE I 317 " --> pdb=" O MET I 313 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LEU I 320 " --> pdb=" O ALA I 316 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N PHE I 321 " --> pdb=" O ILE I 317 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N VAL I 322 " --> pdb=" O ALA I 318 " (cutoff:3.500A) Proline residue: I 324 - end of helix Processing helix chain 'I' and resid 338 through 360 Processing helix chain 'I' and resid 364 through 384 removed outlier: 3.925A pdb=" N PHE I 382 " --> pdb=" O TYR I 378 " (cutoff:3.500A) Processing helix chain 'I' and resid 384 through 392 removed outlier: 4.289A pdb=" N ARG I 390 " --> pdb=" O PRO I 386 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLU I 392 " --> pdb=" O TYR I 388 " (cutoff:3.500A) Processing helix chain 'J' and resid 36 through 51 Processing helix chain 'J' and resid 62 through 70 Processing helix chain 'J' and resid 72 through 80 Processing helix chain 'J' and resid 96 through 105 Processing helix chain 'J' and resid 113 through 119 Processing helix chain 'J' and resid 119 through 127 Processing helix chain 'J' and resid 154 through 159 Processing helix chain 'J' and resid 204 through 224 Processing helix chain 'J' and resid 226 through 254 Processing helix chain 'K' and resid 23 through 31 removed outlier: 3.977A pdb=" N ALA K 29 " --> pdb=" O ALA K 25 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 39 Processing helix chain 'K' and resid 56 through 69 Processing helix chain 'K' and resid 74 through 78 Processing helix chain 'K' and resid 85 through 98 Processing helix chain 'K' and resid 107 through 121 removed outlier: 4.573A pdb=" N ALA K 112 " --> pdb=" O PRO K 108 " (cutoff:3.500A) removed outlier: 5.665A pdb=" N GLN K 113 " --> pdb=" O ASN K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 166 Processing helix chain 'K' and resid 176 through 184 removed outlier: 3.879A pdb=" N LYS K 184 " --> pdb=" O SER K 180 " (cutoff:3.500A) Processing helix chain 'K' and resid 186 through 199 removed outlier: 3.541A pdb=" N GLY K 199 " --> pdb=" O SER K 195 " (cutoff:3.500A) Processing helix chain 'L' and resid 25 through 29 Processing helix chain 'Z' and resid 9 through 36 Proline residue: Z 32 - end of helix Processing helix chain 'Z' and resid 42 through 46 removed outlier: 3.539A pdb=" N ALA Z 45 " --> pdb=" O LYS Z 42 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N ALA Z 46 " --> pdb=" O ALA Z 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 42 through 46' Processing helix chain 'Z' and resid 78 through 85 Processing helix chain 'Z' and resid 86 through 92 removed outlier: 4.813A pdb=" N GLY Z 90 " --> pdb=" O SER Z 87 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU Z 92 " --> pdb=" O GLU Z 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 12 removed outlier: 3.629A pdb=" N ARG D 11 " --> pdb=" O TRP D 7 " (cutoff:3.500A) Processing helix chain 'D' and resid 13 through 22 Processing helix chain 'D' and resid 32 through 35 Processing helix chain 'D' and resid 36 through 57 Processing helix chain 'D' and resid 65 through 76 Processing helix chain 'D' and resid 79 through 109 Processing helix chain 'D' and resid 115 through 139 Processing helix chain 'D' and resid 142 through 156 removed outlier: 4.033A pdb=" N PHE D 156 " --> pdb=" O ILE D 152 " (cutoff:3.500A) Processing helix chain 'D' and resid 157 through 159 No H-bonds generated for 'chain 'D' and resid 157 through 159' Processing helix chain 'D' and resid 162 through 172 Processing helix chain 'D' and resid 177 through 190 Processing helix chain 'D' and resid 190 through 211 Processing helix chain 'D' and resid 219 through 223 Processing helix chain 'D' and resid 236 through 262 removed outlier: 6.734A pdb=" N THR D 241 " --> pdb=" O HIS D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 271 through 276 Processing helix chain 'D' and resid 290 through 292 No H-bonds generated for 'chain 'D' and resid 290 through 292' Processing helix chain 'D' and resid 293 through 303 Processing helix chain 'D' and resid 305 through 327 removed outlier: 4.527A pdb=" N LEU D 320 " --> pdb=" O ALA D 316 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N PHE D 321 " --> pdb=" O ILE D 317 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL D 322 " --> pdb=" O ALA D 318 " (cutoff:3.500A) Proline residue: D 324 - end of helix Processing helix chain 'D' and resid 333 through 337 Processing helix chain 'D' and resid 338 through 359 Processing helix chain 'D' and resid 364 through 384 removed outlier: 3.885A pdb=" N PHE D 382 " --> pdb=" O TYR D 378 " (cutoff:3.500A) Processing helix chain 'D' and resid 384 through 392 removed outlier: 4.388A pdb=" N ARG D 390 " --> pdb=" O PRO D 386 " (cutoff:3.500A) Processing helix chain 'M' and resid 36 through 51 Processing helix chain 'M' and resid 62 through 70 Processing helix chain 'M' and resid 72 through 80 Processing helix chain 'M' and resid 96 through 105 Processing helix chain 'M' and resid 113 through 118 Processing helix chain 'M' and resid 119 through 128 removed outlier: 3.547A pdb=" N ARG M 128 " --> pdb=" O TYR M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 159 Processing helix chain 'M' and resid 204 through 224 Processing helix chain 'M' and resid 226 through 256 removed outlier: 3.606A pdb=" N TYR M 236 " --> pdb=" O ARG M 232 " (cutoff:3.500A) Processing helix chain 'N' and resid 23 through 31 removed outlier: 3.837A pdb=" N ALA N 29 " --> pdb=" O ALA N 25 " (cutoff:3.500A) Processing helix chain 'N' and resid 34 through 39 Processing helix chain 'N' and resid 56 through 69 Processing helix chain 'N' and resid 74 through 78 Processing helix chain 'N' and resid 85 through 99 removed outlier: 3.630A pdb=" N GLN N 99 " --> pdb=" O TYR N 95 " (cutoff:3.500A) Processing helix chain 'N' and resid 107 through 121 removed outlier: 4.665A pdb=" N ALA N 112 " --> pdb=" O PRO N 108 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N GLN N 113 " --> pdb=" O ASN N 109 " (cutoff:3.500A) Processing helix chain 'N' and resid 153 through 166 Processing helix chain 'N' and resid 176 through 183 Processing helix chain 'N' and resid 186 through 199 Processing helix chain 'O' and resid 25 through 29 Processing helix chain 'F' and resid 3 through 10 removed outlier: 4.240A pdb=" N LEU F 7 " --> pdb=" O ASN F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 30 removed outlier: 4.056A pdb=" N GLY F 25 " --> pdb=" O ALA F 21 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY F 26 " --> pdb=" O VAL F 22 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N THR F 28 " --> pdb=" O ILE F 24 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN F 29 " --> pdb=" O GLY F 25 " (cutoff:3.500A) Processing helix chain 'F' and resid 31 through 34 Processing helix chain 'F' and resid 50 through 63 Processing helix chain 'F' and resid 64 through 68 removed outlier: 3.658A pdb=" N GLY F 67 " --> pdb=" O GLY F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 84 Processing helix chain 'F' and resid 88 through 93 removed outlier: 3.562A pdb=" N VAL F 93 " --> pdb=" O GLY F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 125 removed outlier: 4.442A pdb=" N ALA F 123 " --> pdb=" O ASP F 119 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 132 removed outlier: 4.098A pdb=" N VAL F 131 " --> pdb=" O ASN F 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 152 through 163 Processing helix chain 'F' and resid 168 through 179 removed outlier: 4.727A pdb=" N ARG F 176 " --> pdb=" O ILE F 172 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N GLU F 177 " --> pdb=" O ALA F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 194 Processing helix chain 'G' and resid 2 through 28 removed outlier: 4.151A pdb=" N THR G 13 " --> pdb=" O ILE G 9 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ARG G 28 " --> pdb=" O VAL G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 55 through 66 Processing helix chain 'G' and resid 71 through 76 Processing helix chain 'G' and resid 94 through 110 Processing helix chain 'G' and resid 110 through 120 removed outlier: 3.776A pdb=" N PHE G 114 " --> pdb=" O TYR G 110 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA G 115 " --> pdb=" O GLY G 111 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS G 116 " --> pdb=" O PRO G 112 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N TYR G 117 " --> pdb=" O ILE G 113 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N MET G 120 " --> pdb=" O LYS G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 127 Processing helix chain 'G' and resid 128 through 143 Processing helix chain 'G' and resid 172 through 181 removed outlier: 4.561A pdb=" N ILE G 178 " --> pdb=" O ILE G 174 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY G 181 " --> pdb=" O THR G 177 " (cutoff:3.500A) Processing helix chain 'G' and resid 196 through 200 Processing helix chain 'G' and resid 201 through 206 Processing helix chain 'G' and resid 221 through 233 removed outlier: 3.754A pdb=" N VAL G 231 " --> pdb=" O GLN G 227 " (cutoff:3.500A) Processing helix chain 'G' and resid 266 through 273 Processing helix chain 'G' and resid 289 through 298 removed outlier: 3.697A pdb=" N ILE G 293 " --> pdb=" O GLU G 289 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU G 294 " --> pdb=" O LYS G 290 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA G 296 " --> pdb=" O HIS G 292 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N ILE G 298 " --> pdb=" O LEU G 294 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 182 through 186 removed outlier: 6.828A pdb=" N LYS E 189 " --> pdb=" O VAL E 185 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 50 through 53 removed outlier: 6.719A pdb=" N VAL C 187 " --> pdb=" O ASP C 183 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 62 through 67 Processing sheet with id=AA4, first strand: chain 'C' and resid 132 through 134 Processing sheet with id=AA5, first strand: chain 'I' and resid 26 through 28 Processing sheet with id=AA6, first strand: chain 'J' and resid 57 through 61 removed outlier: 6.451A pdb=" N GLN J 60 " --> pdb=" O MET J 91 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'J' and resid 130 through 132 Processing sheet with id=AA8, first strand: chain 'J' and resid 161 through 169 removed outlier: 6.235A pdb=" N VAL J 162 " --> pdb=" O LEU J 194 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N LEU J 194 " --> pdb=" O VAL J 162 " (cutoff:3.500A) removed outlier: 5.878A pdb=" N GLY J 164 " --> pdb=" O ASP J 192 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 171 through 172 Processing sheet with id=AB1, first strand: chain 'K' and resid 200 through 201 Processing sheet with id=AB2, first strand: chain 'Z' and resid 50 through 53 removed outlier: 6.757A pdb=" N THR Z 189 " --> pdb=" O PHE Z 182 " (cutoff:3.500A) removed outlier: 5.678A pdb=" N PHE Z 182 " --> pdb=" O THR Z 189 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'Z' and resid 61 through 67 removed outlier: 3.873A pdb=" N GLN Z 61 " --> pdb=" O HIS Z 76 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Z' and resid 132 through 134 Processing sheet with id=AB5, first strand: chain 'D' and resid 26 through 28 Processing sheet with id=AB6, first strand: chain 'M' and resid 57 through 61 removed outlier: 3.896A pdb=" N MET M 91 " --> pdb=" O ALA M 57 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 130 through 132 Processing sheet with id=AB8, first strand: chain 'M' and resid 161 through 162 Processing sheet with id=AB9, first strand: chain 'N' and resid 200 through 201 Processing sheet with id=AC1, first strand: chain 'G' and resid 39 through 43 removed outlier: 6.743A pdb=" N GLU G 49 " --> pdb=" O MET G 40 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 182 through 183 1264 hydrogen bonds defined for protein. 3639 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 19.10 Time building geometry restraints manager: 14.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.11: 19379 1.11 - 1.38: 9774 1.38 - 1.66: 14878 1.66 - 1.93: 242 1.93 - 2.21: 68 Bond restraints: 44341 Sorted by residual: bond pdb=" C07 I7Y Z 202 " pdb=" C08 I7Y Z 202 " ideal model delta sigma weight residual 1.542 1.253 0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C07 I7Y I 501 " pdb=" C08 I7Y I 501 " ideal model delta sigma weight residual 1.542 1.253 0.289 2.00e-02 2.50e+03 2.09e+02 bond pdb=" C07 I7Y I 501 " pdb=" C15 I7Y I 501 " ideal model delta sigma weight residual 1.526 1.775 -0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C07 I7Y Z 202 " pdb=" C15 I7Y Z 202 " ideal model delta sigma weight residual 1.526 1.775 -0.249 2.00e-02 2.50e+03 1.55e+02 bond pdb=" C02 I7Y I 501 " pdb=" C10 I7Y I 501 " ideal model delta sigma weight residual 1.526 1.295 0.231 2.00e-02 2.50e+03 1.33e+02 ... (remaining 44336 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.76: 78291 6.76 - 13.53: 36 13.53 - 20.29: 1 20.29 - 27.05: 0 27.05 - 33.82: 9 Bond angle restraints: 78337 Sorted by residual: angle pdb=" C74 I7Y I 501 " pdb=" C73 I7Y I 501 " pdb=" C76 I7Y I 501 " ideal model delta sigma weight residual 114.35 148.17 -33.82 3.00e+00 1.11e-01 1.27e+02 angle pdb=" C74 I7Y Z 202 " pdb=" C73 I7Y Z 202 " pdb=" C76 I7Y Z 202 " ideal model delta sigma weight residual 114.35 148.16 -33.81 3.00e+00 1.11e-01 1.27e+02 angle pdb=" CD ARG F 77 " pdb=" CG ARG F 77 " pdb=" HG3 ARG F 77 " ideal model delta sigma weight residual 108.00 78.09 29.91 3.00e+00 1.11e-01 9.94e+01 angle pdb=" CD ARG F 77 " pdb=" CG ARG F 77 " pdb=" HG2 ARG F 77 " ideal model delta sigma weight residual 108.00 78.34 29.66 3.00e+00 1.11e-01 9.77e+01 angle pdb=" C74 I7Y I 501 " pdb=" C73 I7Y I 501 " pdb=" O80 I7Y I 501 " ideal model delta sigma weight residual 107.63 79.89 27.74 3.00e+00 1.11e-01 8.55e+01 ... (remaining 78332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.23: 19508 24.23 - 48.47: 1357 48.47 - 72.70: 321 72.70 - 96.94: 66 96.94 - 121.17: 14 Dihedral angle restraints: 21266 sinusoidal: 11146 harmonic: 10120 Sorted by residual: dihedral pdb=" C2B HEC G 401 " pdb=" C3B HEC G 401 " pdb=" CAB HEC G 401 " pdb=" CBB HEC G 401 " ideal model delta sinusoidal sigma weight residual 60.00 133.66 -73.66 2 1.00e+01 1.00e-02 4.42e+01 dihedral pdb=" C2B HEC J 500 " pdb=" C3B HEC J 500 " pdb=" CAB HEC J 500 " pdb=" CBB HEC J 500 " ideal model delta sinusoidal sigma weight residual 60.00 129.52 -69.52 2 1.00e+01 1.00e-02 4.21e+01 dihedral pdb=" C2C HEC N 501 " pdb=" C3C HEC N 501 " pdb=" CAC HEC N 501 " pdb=" CBC HEC N 501 " ideal model delta sinusoidal sigma weight residual 60.00 117.18 -57.18 2 1.00e+01 1.00e-02 3.39e+01 ... (remaining 21263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.282: 3576 0.282 - 0.565: 5 0.565 - 0.847: 2 0.847 - 1.130: 0 1.130 - 1.412: 2 Chirality restraints: 3585 Sorted by residual: chirality pdb=" C74 I7Y I 501 " pdb=" C03 I7Y I 501 " pdb=" C73 I7Y I 501 " pdb=" C75 I7Y I 501 " both_signs ideal model delta sigma weight residual False -2.55 -1.14 -1.41 2.00e-01 2.50e+01 4.99e+01 chirality pdb=" C74 I7Y Z 202 " pdb=" C03 I7Y Z 202 " pdb=" C73 I7Y Z 202 " pdb=" C75 I7Y Z 202 " both_signs ideal model delta sigma weight residual False -2.55 -1.14 -1.41 2.00e-01 2.50e+01 4.98e+01 chirality pdb=" C02 I7Y I 501 " pdb=" C03 I7Y I 501 " pdb=" C06 I7Y I 501 " pdb=" C10 I7Y I 501 " both_signs ideal model delta sigma weight residual False 2.93 2.25 0.68 2.00e-01 2.50e+01 1.14e+01 ... (remaining 3582 not shown) Planarity restraints: 6605 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1C HEC N 501 " -0.025 2.00e-02 2.50e+03 6.25e-02 8.80e+01 pdb=" C2C HEC N 501 " 0.171 2.00e-02 2.50e+03 pdb=" C3C HEC N 501 " -0.015 2.00e-02 2.50e+03 pdb=" C4C HEC N 501 " -0.007 2.00e-02 2.50e+03 pdb=" CAC HEC N 501 " -0.040 2.00e-02 2.50e+03 pdb=" CHC HEC N 501 " -0.030 2.00e-02 2.50e+03 pdb=" CHD HEC N 501 " 0.006 2.00e-02 2.50e+03 pdb=" CMC HEC N 501 " -0.048 2.00e-02 2.50e+03 pdb=" NC HEC N 501 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC K 501 " -0.018 2.00e-02 2.50e+03 5.67e-02 7.23e+01 pdb=" C2C HEC K 501 " 0.155 2.00e-02 2.50e+03 pdb=" C3C HEC K 501 " -0.037 2.00e-02 2.50e+03 pdb=" C4C HEC K 501 " -0.004 2.00e-02 2.50e+03 pdb=" CAC HEC K 501 " -0.021 2.00e-02 2.50e+03 pdb=" CHC HEC K 501 " -0.027 2.00e-02 2.50e+03 pdb=" CHD HEC K 501 " 0.002 2.00e-02 2.50e+03 pdb=" CMC HEC K 501 " -0.046 2.00e-02 2.50e+03 pdb=" NC HEC K 501 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1C HEC F 301 " -0.013 2.00e-02 2.50e+03 3.10e-02 2.16e+01 pdb=" C2C HEC F 301 " 0.083 2.00e-02 2.50e+03 pdb=" C3C HEC F 301 " 0.005 2.00e-02 2.50e+03 pdb=" C4C HEC F 301 " -0.004 2.00e-02 2.50e+03 pdb=" CAC HEC F 301 " -0.027 2.00e-02 2.50e+03 pdb=" CHC HEC F 301 " -0.017 2.00e-02 2.50e+03 pdb=" CHD HEC F 301 " 0.002 2.00e-02 2.50e+03 pdb=" CMC HEC F 301 " -0.024 2.00e-02 2.50e+03 pdb=" NC HEC F 301 " -0.006 2.00e-02 2.50e+03 ... (remaining 6602 not shown) Histogram of nonbonded interaction distances: 1.33 - 1.98: 431 1.98 - 2.64: 51962 2.64 - 3.29: 130455 3.29 - 3.95: 173374 3.95 - 4.60: 267224 Nonbonded interactions: 623446 Sorted by model distance: nonbonded pdb=" OD2 ASP E 417 " pdb="HH21 ARG G 137 " model vdw 1.331 2.450 nonbonded pdb=" OE1 GLU Z 104 " pdb=" H GLU Z 104 " model vdw 1.400 2.450 nonbonded pdb=" H CYS Z 124 " pdb=" O CYS Z 129 " model vdw 1.490 2.450 nonbonded pdb=" HH TYR J 240 " pdb=" O VAL Z 21 " model vdw 1.519 2.450 nonbonded pdb=" O TRP D 291 " pdb=" HG1 THR D 294 " model vdw 1.535 2.450 ... (remaining 623441 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 'C' and resid 6 through 195) selection = (chain 'Z' and ((resid 6 and (name N or name CA or name C or name O or name CB o \ r name CG1 or name CG2 or name HA or name HB or name HG11 or name HG12 or name H \ G13 or name HG21 or name HG22 or name HG23)) or resid 7 through 128 or (resid 12 \ 9 and (name N or name CA or name C or name O or name CB or name SG or name H or \ name HA or name HB2 or name HB3)) or resid 130 through 195)) } ncs_group { reference = (chain 'D' and (resid 1 through 403 or resid 502)) selection = (chain 'I' and (resid 1 through 403 or resid 502)) } ncs_group { reference = (chain 'J' and (resid 26 through 163 or (resid 193 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name OE1 or name NE2 or name H \ A or name HB2 or name HB3 or name HG2 or name HG3 or name HE21 or name HE22)) or \ resid 194 through 257 or resid 500)) selection = (chain 'M' and ((resid 26 and (name N or name CA or name C or name O or name CB \ or name CG or name CD or name OE1 or name NE2 or name HA or name HB2 or name HB3 \ or name HG2 or name HG3 or name HE21 or name HE22)) or resid 27 through 257 or \ resid 500)) } ncs_group { reference = chain 'K' selection = chain 'N' } ncs_group { reference = chain 'L' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.900 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: 0.780 Extract box with map and model: 1.650 Check model and map are aligned: 0.340 Set scattering table: 0.430 Process input model: 109.150 Find NCS groups from input model: 1.280 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:14.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 130.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 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 : 0.007 0.289 24949 Z= 0.507 Angle : 0.824 33.817 34152 Z= 0.375 Chirality : 0.057 1.412 3585 Planarity : 0.004 0.063 4245 Dihedral : 18.277 121.174 8908 Min Nonbonded Distance : 1.908 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.10 % Allowed : 2.90 % Favored : 97.00 % Rotamer: Outliers : 1.04 % Allowed : 19.96 % Favored : 79.00 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.16), residues: 2964 helix: 0.80 (0.13), residues: 1624 sheet: -2.00 (0.63), residues: 56 loop : -0.00 (0.17), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 54 HIS 0.006 0.001 HIS I 188 PHE 0.025 0.001 PHE G 68 TYR 0.044 0.002 TYR G 264 ARG 0.013 0.000 ARG J 253 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue TYR 126 is missing expected H atoms. Skipping. Residue THR 153 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Evaluate side-chains 439 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 414 time to evaluate : 3.436 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: E 261 HIS cc_start: 0.7902 (OUTLIER) cc_final: 0.7411 (t-90) REVERT: E 410 MET cc_start: 0.8113 (mmm) cc_final: 0.7715 (mtm) REVERT: D 3 LYS cc_start: 0.8143 (mmtp) cc_final: 0.7809 (mppt) outliers start: 25 outliers final: 15 residues processed: 434 average time/residue: 2.6150 time to fit residues: 1319.3334 Evaluate side-chains 403 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 387 time to evaluate : 3.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 182 SER Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 473 ARG Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 212 SER Chi-restraints excluded: chain J residue 170 VAL Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain G residue 35 THR Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 301 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 249 optimal weight: 0.7980 chunk 223 optimal weight: 0.9990 chunk 124 optimal weight: 1.9990 chunk 76 optimal weight: 0.9990 chunk 150 optimal weight: 0.3980 chunk 119 optimal weight: 2.9990 chunk 231 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 chunk 140 optimal weight: 1.9990 chunk 172 optimal weight: 0.9990 chunk 267 optimal weight: 6.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 208 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS E 407 GLN E 432 HIS J 90 HIS Z 3 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.0724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 24949 Z= 0.240 Angle : 0.653 14.876 34152 Z= 0.304 Chirality : 0.041 0.209 3585 Planarity : 0.004 0.054 4245 Dihedral : 11.905 133.442 3690 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 10.59 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.14 % Favored : 96.79 % Rotamer: Outliers : 2.17 % Allowed : 17.88 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.15), residues: 2964 helix: 0.91 (0.13), residues: 1645 sheet: -2.57 (0.57), residues: 52 loop : 0.03 (0.17), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 204 HIS 0.008 0.001 HIS I 87 PHE 0.022 0.001 PHE M 243 TYR 0.017 0.002 TYR J 240 ARG 0.005 0.000 ARG J 253 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue TYR 126 is missing expected H atoms. Skipping. Residue THR 153 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Evaluate side-chains 456 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 404 time to evaluate : 3.649 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: E 238 TYR cc_start: 0.6465 (t80) cc_final: 0.6207 (t80) REVERT: E 279 ILE cc_start: 0.7852 (OUTLIER) cc_final: 0.7515 (mp) REVERT: E 410 MET cc_start: 0.8293 (mmm) cc_final: 0.7972 (mtt) REVERT: E 426 GLU cc_start: 0.7759 (mt-10) cc_final: 0.7545 (mt-10) REVERT: K 23 ASP cc_start: 0.8268 (t0) cc_final: 0.8000 (t70) REVERT: D 3 LYS cc_start: 0.8139 (mmtp) cc_final: 0.7826 (mppt) REVERT: D 308 MET cc_start: 0.8270 (tpp) cc_final: 0.8043 (tpt) REVERT: M 231 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: F 81 GLU cc_start: 0.8220 (OUTLIER) cc_final: 0.7579 (mp0) REVERT: F 158 GLU cc_start: 0.7281 (OUTLIER) cc_final: 0.7054 (mt-10) REVERT: F 172 ILE cc_start: 0.8668 (OUTLIER) cc_final: 0.8456 (mp) REVERT: F 185 MET cc_start: 0.8689 (tpp) cc_final: 0.8402 (tpp) REVERT: G 72 TYR cc_start: 0.4927 (OUTLIER) cc_final: 0.3832 (t80) outliers start: 52 outliers final: 21 residues processed: 435 average time/residue: 2.6366 time to fit residues: 1334.5732 Evaluate side-chains 413 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 386 time to evaluate : 3.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 181 MET Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain I residue 110 SER Chi-restraints excluded: chain I residue 212 SER Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 72 TYR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 101 ARG Chi-restraints excluded: chain G residue 134 MET Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 230 SER Chi-restraints excluded: chain G residue 279 MET Chi-restraints excluded: chain G residue 301 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 148 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 222 optimal weight: 1.9990 chunk 182 optimal weight: 0.6980 chunk 73 optimal weight: 0.9990 chunk 268 optimal weight: 9.9990 chunk 289 optimal weight: 6.9990 chunk 239 optimal weight: 2.9990 chunk 266 optimal weight: 4.9990 chunk 91 optimal weight: 0.3980 chunk 215 optimal weight: 1.9990 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS E 407 GLN I 280 GLN Z 3 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.0943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 24949 Z= 0.251 Angle : 0.635 13.998 34152 Z= 0.293 Chirality : 0.041 0.198 3585 Planarity : 0.004 0.054 4245 Dihedral : 11.216 132.306 3678 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.04 % Favored : 96.93 % Rotamer: Outliers : 2.08 % Allowed : 18.00 % Favored : 79.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.15), residues: 2964 helix: 0.97 (0.13), residues: 1653 sheet: -2.53 (0.56), residues: 51 loop : 0.06 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 204 HIS 0.008 0.001 HIS I 87 PHE 0.018 0.001 PHE M 243 TYR 0.016 0.002 TYR D 388 ARG 0.003 0.000 ARG J 253 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue TYR 126 is missing expected H atoms. Skipping. Residue THR 153 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Evaluate side-chains 460 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 410 time to evaluate : 4.052 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: symmetry clash REVERT: E 238 TYR cc_start: 0.6726 (t80) cc_final: 0.6428 (t80) REVERT: E 239 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.7618 (mtp85) REVERT: E 261 HIS cc_start: 0.8141 (OUTLIER) cc_final: 0.7709 (m-70) REVERT: E 279 ILE cc_start: 0.8110 (OUTLIER) cc_final: 0.7849 (mp) REVERT: E 410 MET cc_start: 0.8419 (mmm) cc_final: 0.8019 (mtt) REVERT: E 412 ARG cc_start: 0.8031 (ttm-80) cc_final: 0.7777 (ttm170) REVERT: J 255 TYR cc_start: 0.7191 (OUTLIER) cc_final: 0.6621 (t80) REVERT: D 3 LYS cc_start: 0.8126 (mmtp) cc_final: 0.7816 (mppt) REVERT: D 308 MET cc_start: 0.8267 (tpp) cc_final: 0.8052 (tpt) REVERT: M 231 GLU cc_start: 0.8275 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: F 172 ILE cc_start: 0.8687 (OUTLIER) cc_final: 0.8461 (mp) REVERT: F 185 MET cc_start: 0.8656 (tpp) cc_final: 0.8375 (tpp) REVERT: G 28 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7330 (ppp-140) REVERT: G 72 TYR cc_start: 0.4947 (OUTLIER) cc_final: 0.3923 (t80) REVERT: G 166 ARG cc_start: 0.8425 (OUTLIER) cc_final: 0.7270 (ptp90) REVERT: G 288 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.8030 (tmmm) outliers start: 50 outliers final: 23 residues processed: 438 average time/residue: 2.6881 time to fit residues: 1366.6351 Evaluate side-chains 421 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 388 time to evaluate : 3.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 239 ARG Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 279 ILE Chi-restraints excluded: chain E residue 357 MET Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 452 MET Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain I residue 287 ILE Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain G residue 28 ARG Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 72 TYR Chi-restraints excluded: chain G residue 101 ARG Chi-restraints excluded: chain G residue 137 ARG Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 279 MET Chi-restraints excluded: chain G residue 288 LYS Chi-restraints excluded: chain G residue 301 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 265 optimal weight: 3.9990 chunk 201 optimal weight: 1.9990 chunk 139 optimal weight: 0.5980 chunk 29 optimal weight: 0.0670 chunk 128 optimal weight: 5.9990 chunk 180 optimal weight: 0.7980 chunk 269 optimal weight: 3.9990 chunk 285 optimal weight: 5.9990 chunk 140 optimal weight: 0.6980 chunk 255 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS Z 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 24949 Z= 0.199 Angle : 0.601 13.027 34152 Z= 0.278 Chirality : 0.040 0.176 3585 Planarity : 0.004 0.053 4245 Dihedral : 10.804 130.938 3673 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.48 % Favored : 96.49 % Rotamer: Outliers : 2.12 % Allowed : 18.08 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.16), residues: 2964 helix: 1.14 (0.13), residues: 1649 sheet: -2.74 (0.54), residues: 50 loop : 0.09 (0.18), residues: 1265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 54 HIS 0.006 0.001 HIS I 87 PHE 0.017 0.001 PHE M 243 TYR 0.018 0.001 TYR D 388 ARG 0.003 0.000 ARG K 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue TYR 126 is missing expected H atoms. Skipping. Residue THR 153 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Evaluate side-chains 461 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 410 time to evaluate : 3.456 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: E 238 TYR cc_start: 0.6696 (t80) cc_final: 0.6385 (t80) REVERT: E 261 HIS cc_start: 0.8026 (OUTLIER) cc_final: 0.7772 (m-70) REVERT: E 371 TYR cc_start: 0.7591 (m-80) cc_final: 0.7221 (m-80) REVERT: E 375 LYS cc_start: 0.8194 (ttpp) cc_final: 0.7949 (ptmt) REVERT: E 410 MET cc_start: 0.8446 (mmm) cc_final: 0.8106 (mtt) REVERT: E 412 ARG cc_start: 0.8007 (ttm-80) cc_final: 0.7775 (ttm170) REVERT: E 462 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.6834 (pt0) REVERT: J 255 TYR cc_start: 0.7121 (OUTLIER) cc_final: 0.6567 (t80) REVERT: D 3 LYS cc_start: 0.8090 (mmtp) cc_final: 0.7803 (mppt) REVERT: D 308 MET cc_start: 0.8247 (tpp) cc_final: 0.8044 (tpt) REVERT: M 231 GLU cc_start: 0.8271 (OUTLIER) cc_final: 0.7704 (mp0) REVERT: F 172 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8441 (mp) REVERT: F 185 MET cc_start: 0.8674 (tpp) cc_final: 0.8379 (tpp) REVERT: G 28 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7298 (ppp-140) REVERT: G 120 MET cc_start: 0.6301 (mpp) cc_final: 0.5849 (mpp) REVERT: G 288 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8055 (tmmm) outliers start: 51 outliers final: 18 residues processed: 436 average time/residue: 2.6867 time to fit residues: 1358.0682 Evaluate side-chains 417 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 392 time to evaluate : 3.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 261 HIS Chi-restraints excluded: chain E residue 395 LEU Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain G residue 28 ARG Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 101 ARG Chi-restraints excluded: chain G residue 137 ARG Chi-restraints excluded: chain G residue 207 THR Chi-restraints excluded: chain G residue 279 MET Chi-restraints excluded: chain G residue 288 LYS Chi-restraints excluded: chain G residue 301 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 237 optimal weight: 1.9990 chunk 161 optimal weight: 4.9990 chunk 4 optimal weight: 0.7980 chunk 212 optimal weight: 0.7980 chunk 117 optimal weight: 0.0870 chunk 243 optimal weight: 2.9990 chunk 197 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 145 optimal weight: 1.9990 chunk 255 optimal weight: 2.9990 chunk 71 optimal weight: 0.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 244 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 300 HIS I 227 ASN Z 3 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 24949 Z= 0.241 Angle : 0.621 13.676 34152 Z= 0.285 Chirality : 0.040 0.175 3585 Planarity : 0.004 0.053 4245 Dihedral : 10.678 124.434 3673 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.31 % Favored : 96.66 % Rotamer: Outliers : 2.38 % Allowed : 18.50 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.15), residues: 2964 helix: 1.18 (0.13), residues: 1647 sheet: -2.72 (0.56), residues: 50 loop : 0.09 (0.18), residues: 1267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 54 HIS 0.008 0.001 HIS I 87 PHE 0.016 0.001 PHE I 95 TYR 0.017 0.002 TYR D 388 ARG 0.004 0.000 ARG J 253 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue TYR 126 is missing expected H atoms. Skipping. Residue THR 153 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Evaluate side-chains 458 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 401 time to evaluate : 3.911 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 238 TYR cc_start: 0.6872 (t80) cc_final: 0.6572 (t80) REVERT: E 357 MET cc_start: 0.8718 (OUTLIER) cc_final: 0.8392 (mmt) REVERT: E 371 TYR cc_start: 0.7678 (m-80) cc_final: 0.7227 (m-80) REVERT: E 375 LYS cc_start: 0.8306 (ttpp) cc_final: 0.8087 (ptmm) REVERT: E 410 MET cc_start: 0.8529 (mmm) cc_final: 0.8226 (mtt) REVERT: E 412 ARG cc_start: 0.8046 (ttm-80) cc_final: 0.7783 (ttm170) REVERT: E 426 GLU cc_start: 0.7870 (mt-10) cc_final: 0.7613 (mt-10) REVERT: E 462 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.6897 (pt0) REVERT: J 255 TYR cc_start: 0.7229 (OUTLIER) cc_final: 0.6763 (t80) REVERT: Z 12 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7826 (ttm-80) REVERT: M 231 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7716 (mp0) REVERT: F 81 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.7577 (mp0) REVERT: F 158 GLU cc_start: 0.7332 (OUTLIER) cc_final: 0.7108 (mt-10) REVERT: F 172 ILE cc_start: 0.8679 (OUTLIER) cc_final: 0.8451 (mp) REVERT: F 185 MET cc_start: 0.8647 (tpp) cc_final: 0.8386 (tpp) REVERT: G 28 ARG cc_start: 0.7673 (OUTLIER) cc_final: 0.7309 (ppp-140) REVERT: G 166 ARG cc_start: 0.8450 (OUTLIER) cc_final: 0.7379 (ptp90) REVERT: G 288 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8057 (tmmm) outliers start: 57 outliers final: 25 residues processed: 435 average time/residue: 2.6350 time to fit residues: 1329.6965 Evaluate side-chains 415 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 379 time to evaluate : 3.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 94 THR Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 168 PHE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 222 MET Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 357 MET Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain Z residue 12 ARG Chi-restraints excluded: chain Z residue 109 LYS Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 28 ARG Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 101 ARG Chi-restraints excluded: chain G residue 137 ARG Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 279 MET Chi-restraints excluded: chain G residue 288 LYS Chi-restraints excluded: chain G residue 301 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 95 optimal weight: 1.9990 chunk 256 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 167 optimal weight: 0.0670 chunk 70 optimal weight: 0.9990 chunk 285 optimal weight: 3.9990 chunk 236 optimal weight: 0.0980 chunk 132 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 149 optimal weight: 3.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 280 GLN Z 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 24949 Z= 0.198 Angle : 0.598 12.974 34152 Z= 0.275 Chirality : 0.040 0.144 3585 Planarity : 0.004 0.053 4245 Dihedral : 10.229 116.833 3670 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.31 % Favored : 96.66 % Rotamer: Outliers : 1.62 % Allowed : 19.00 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 1.01 (0.16), residues: 2964 helix: 1.28 (0.13), residues: 1645 sheet: -2.71 (0.56), residues: 50 loop : 0.13 (0.18), residues: 1269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 54 HIS 0.009 0.001 HIS E 244 PHE 0.017 0.001 PHE G 68 TYR 0.024 0.001 TYR G 264 ARG 0.004 0.000 ARG J 253 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue TYR 126 is missing expected H atoms. Skipping. Residue THR 153 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Evaluate side-chains 434 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 395 time to evaluate : 3.436 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: symmetry clash revert: symmetry clash REVERT: E 238 TYR cc_start: 0.6843 (t80) cc_final: 0.6545 (t80) REVERT: E 357 MET cc_start: 0.8740 (OUTLIER) cc_final: 0.8475 (mmt) REVERT: E 371 TYR cc_start: 0.7695 (m-80) cc_final: 0.7222 (m-80) REVERT: E 410 MET cc_start: 0.8567 (mmm) cc_final: 0.8311 (mtt) REVERT: E 412 ARG cc_start: 0.8059 (ttm-80) cc_final: 0.7753 (ttm170) REVERT: E 462 GLN cc_start: 0.7143 (OUTLIER) cc_final: 0.6853 (pt0) REVERT: I 361 GLN cc_start: 0.7908 (mt0) cc_final: 0.7692 (pt0) REVERT: J 255 TYR cc_start: 0.7105 (OUTLIER) cc_final: 0.6642 (t80) REVERT: Z 12 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7835 (ttm-80) REVERT: D 74 MET cc_start: 0.8982 (mmm) cc_final: 0.8777 (mmm) REVERT: M 231 GLU cc_start: 0.8343 (OUTLIER) cc_final: 0.7804 (mp0) REVERT: F 158 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7119 (mt-10) REVERT: F 172 ILE cc_start: 0.8684 (OUTLIER) cc_final: 0.8444 (mp) REVERT: F 185 MET cc_start: 0.8645 (tpp) cc_final: 0.8376 (tpp) REVERT: G 28 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7342 (ppp-140) REVERT: G 166 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7399 (ptp90) REVERT: G 288 LYS cc_start: 0.8378 (OUTLIER) cc_final: 0.8066 (tmmm) outliers start: 39 outliers final: 17 residues processed: 418 average time/residue: 2.7955 time to fit residues: 1355.0667 Evaluate side-chains 407 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 380 time to evaluate : 3.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 357 MET Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain Z residue 12 ARG Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 28 ARG Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 101 ARG Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 279 MET Chi-restraints excluded: chain G residue 288 LYS Chi-restraints excluded: chain G residue 301 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 275 optimal weight: 6.9990 chunk 32 optimal weight: 7.9990 chunk 162 optimal weight: 0.7980 chunk 208 optimal weight: 2.9990 chunk 161 optimal weight: 0.9990 chunk 240 optimal weight: 1.9990 chunk 159 optimal weight: 0.6980 chunk 284 optimal weight: 10.0000 chunk 177 optimal weight: 1.9990 chunk 173 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 227 ASN I 280 GLN Z 3 ASN Z 61 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 24949 Z= 0.291 Angle : 0.642 14.146 34152 Z= 0.296 Chirality : 0.041 0.141 3585 Planarity : 0.004 0.055 4245 Dihedral : 10.048 124.416 3669 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.17 % Favored : 96.79 % Rotamer: Outliers : 2.04 % Allowed : 18.67 % Favored : 79.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.16), residues: 2964 helix: 1.19 (0.13), residues: 1652 sheet: -2.53 (0.53), residues: 62 loop : 0.16 (0.18), residues: 1250 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 54 HIS 0.009 0.001 HIS E 244 PHE 0.018 0.002 PHE I 95 TYR 0.028 0.002 TYR G 264 ARG 0.006 0.000 ARG I 84 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue TYR 126 is missing expected H atoms. Skipping. Residue THR 153 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Evaluate side-chains 434 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 385 time to evaluate : 3.795 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: symmetry clash revert: symmetry clash REVERT: E 238 TYR cc_start: 0.7020 (t80) cc_final: 0.6748 (t80) REVERT: E 357 MET cc_start: 0.8823 (OUTLIER) cc_final: 0.8546 (mmt) REVERT: E 371 TYR cc_start: 0.7833 (m-80) cc_final: 0.7322 (m-80) REVERT: E 410 MET cc_start: 0.8654 (mmm) cc_final: 0.8448 (mtt) REVERT: E 412 ARG cc_start: 0.8085 (ttm-80) cc_final: 0.7781 (ttm170) REVERT: E 462 GLN cc_start: 0.7110 (OUTLIER) cc_final: 0.6821 (pt0) REVERT: J 255 TYR cc_start: 0.7402 (OUTLIER) cc_final: 0.7092 (t80) REVERT: Z 12 ARG cc_start: 0.8117 (OUTLIER) cc_final: 0.7839 (ttm-80) REVERT: M 231 GLU cc_start: 0.8301 (OUTLIER) cc_final: 0.7713 (mp0) REVERT: F 81 GLU cc_start: 0.8389 (OUTLIER) cc_final: 0.7622 (mp0) REVERT: F 158 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7160 (mt-10) REVERT: F 172 ILE cc_start: 0.8692 (OUTLIER) cc_final: 0.8476 (mp) REVERT: F 185 MET cc_start: 0.8663 (tpp) cc_final: 0.8368 (tpp) REVERT: G 28 ARG cc_start: 0.7702 (OUTLIER) cc_final: 0.7342 (ppp-140) REVERT: G 166 ARG cc_start: 0.8418 (OUTLIER) cc_final: 0.7378 (ptp90) REVERT: G 240 GLU cc_start: 0.6913 (mp0) cc_final: 0.6577 (mp0) REVERT: G 288 LYS cc_start: 0.8546 (OUTLIER) cc_final: 0.8241 (tmmm) outliers start: 49 outliers final: 24 residues processed: 412 average time/residue: 2.7111 time to fit residues: 1292.7181 Evaluate side-chains 405 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 370 time to evaluate : 3.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 168 PHE Chi-restraints excluded: chain E residue 181 MET Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 243 VAL Chi-restraints excluded: chain E residue 252 TYR Chi-restraints excluded: chain E residue 357 MET Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain C residue 130 SER Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain Z residue 12 ARG Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 28 ARG Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 101 ARG Chi-restraints excluded: chain G residue 166 ARG Chi-restraints excluded: chain G residue 279 MET Chi-restraints excluded: chain G residue 288 LYS Chi-restraints excluded: chain G residue 301 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 175 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 169 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 180 optimal weight: 1.9990 chunk 193 optimal weight: 0.6980 chunk 140 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 223 optimal weight: 0.0970 chunk 258 optimal weight: 0.7980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 3 ASN Z 61 GLN Z 169 GLN G 282 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24949 Z= 0.209 Angle : 0.598 13.302 34152 Z= 0.278 Chirality : 0.040 0.143 3585 Planarity : 0.004 0.054 4245 Dihedral : 9.781 132.116 3669 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.34 % Favored : 96.63 % Rotamer: Outliers : 1.54 % Allowed : 19.08 % Favored : 79.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % 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: 1.03 (0.16), residues: 2964 helix: 1.27 (0.13), residues: 1652 sheet: -2.52 (0.58), residues: 56 loop : 0.19 (0.18), residues: 1256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 54 HIS 0.009 0.001 HIS E 244 PHE 0.016 0.001 PHE J 247 TYR 0.023 0.001 TYR G 264 ARG 0.007 0.000 ARG J 253 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue TYR 126 is missing expected H atoms. Skipping. Residue THR 153 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Evaluate side-chains 433 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 396 time to evaluate : 3.545 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 238 TYR cc_start: 0.6927 (t80) cc_final: 0.6679 (t80) REVERT: E 357 MET cc_start: 0.8856 (OUTLIER) cc_final: 0.8584 (mmt) REVERT: E 371 TYR cc_start: 0.7807 (m-80) cc_final: 0.7327 (m-80) REVERT: E 400 LEU cc_start: 0.8188 (mt) cc_final: 0.7894 (mt) REVERT: E 412 ARG cc_start: 0.8021 (ttm-80) cc_final: 0.7730 (ttm170) REVERT: E 436 ILE cc_start: 0.8625 (OUTLIER) cc_final: 0.8306 (mt) REVERT: E 462 GLN cc_start: 0.7098 (OUTLIER) cc_final: 0.6812 (pt0) REVERT: I 361 GLN cc_start: 0.7967 (mt0) cc_final: 0.7709 (pt0) REVERT: J 255 TYR cc_start: 0.7152 (OUTLIER) cc_final: 0.6790 (t80) REVERT: Z 12 ARG cc_start: 0.8109 (OUTLIER) cc_final: 0.7849 (ttm-80) REVERT: M 231 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7708 (mp0) REVERT: F 81 GLU cc_start: 0.8383 (OUTLIER) cc_final: 0.7614 (mp0) REVERT: F 158 GLU cc_start: 0.7386 (OUTLIER) cc_final: 0.7152 (mt-10) REVERT: F 172 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8470 (mp) REVERT: F 185 MET cc_start: 0.8618 (tpp) cc_final: 0.8327 (tpp) REVERT: G 28 ARG cc_start: 0.7692 (OUTLIER) cc_final: 0.7421 (ppp-140) REVERT: G 288 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8274 (tmmm) outliers start: 37 outliers final: 16 residues processed: 417 average time/residue: 2.8406 time to fit residues: 1374.6340 Evaluate side-chains 410 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 383 time to evaluate : 3.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 168 PHE Chi-restraints excluded: chain E residue 357 MET Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain Z residue 12 ARG Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain F residue 50 THR Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain F residue 172 ILE Chi-restraints excluded: chain F residue 197 THR Chi-restraints excluded: chain G residue 28 ARG Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 101 ARG Chi-restraints excluded: chain G residue 279 MET Chi-restraints excluded: chain G residue 288 LYS Chi-restraints excluded: chain G residue 301 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 272 optimal weight: 4.9990 chunk 248 optimal weight: 3.9990 chunk 264 optimal weight: 3.9990 chunk 159 optimal weight: 0.7980 chunk 115 optimal weight: 1.9990 chunk 208 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 239 optimal weight: 2.9990 chunk 250 optimal weight: 3.9990 chunk 173 optimal weight: 1.9990 chunk 280 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 227 ASN I 280 GLN Z 3 ASN Z 61 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.089 24949 Z= 0.406 Angle : 0.702 14.656 34152 Z= 0.327 Chirality : 0.043 0.147 3585 Planarity : 0.005 0.057 4245 Dihedral : 10.332 123.194 3669 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.07 % Favored : 96.90 % Rotamer: Outliers : 1.71 % Allowed : 19.33 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.15), residues: 2964 helix: 1.04 (0.13), residues: 1649 sheet: -2.48 (0.55), residues: 62 loop : 0.12 (0.18), residues: 1253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 54 HIS 0.011 0.001 HIS I 101 PHE 0.020 0.002 PHE I 95 TYR 0.020 0.002 TYR D 240 ARG 0.009 0.001 ARG I 84 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue TYR 126 is missing expected H atoms. Skipping. Residue THR 153 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Evaluate side-chains 422 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 381 time to evaluate : 4.003 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 238 TYR cc_start: 0.7247 (t80) cc_final: 0.6978 (t80) REVERT: E 357 MET cc_start: 0.8886 (OUTLIER) cc_final: 0.8585 (mmp) REVERT: E 371 TYR cc_start: 0.8002 (m-80) cc_final: 0.7420 (m-80) REVERT: E 400 LEU cc_start: 0.8351 (mt) cc_final: 0.8106 (mt) REVERT: E 412 ARG cc_start: 0.8092 (ttm-80) cc_final: 0.7854 (ttm170) REVERT: E 436 ILE cc_start: 0.8661 (OUTLIER) cc_final: 0.8365 (mt) REVERT: E 462 GLN cc_start: 0.7198 (OUTLIER) cc_final: 0.6912 (pt0) REVERT: J 255 TYR cc_start: 0.7565 (OUTLIER) cc_final: 0.6864 (t80) REVERT: Z 12 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7818 (ttm-80) REVERT: Z 114 LYS cc_start: 0.8274 (mttt) cc_final: 0.8043 (ptpt) REVERT: M 231 GLU cc_start: 0.8385 (OUTLIER) cc_final: 0.7759 (mp0) REVERT: F 81 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7661 (mp0) REVERT: F 158 GLU cc_start: 0.7378 (OUTLIER) cc_final: 0.7155 (mt-10) REVERT: F 185 MET cc_start: 0.8664 (tpp) cc_final: 0.8333 (tpp) REVERT: G 28 ARG cc_start: 0.7842 (OUTLIER) cc_final: 0.7554 (ppp-140) REVERT: G 160 LEU cc_start: 0.8373 (OUTLIER) cc_final: 0.8048 (pp) REVERT: G 288 LYS cc_start: 0.8579 (OUTLIER) cc_final: 0.8318 (tmmm) outliers start: 41 outliers final: 16 residues processed: 403 average time/residue: 2.7363 time to fit residues: 1276.2700 Evaluate side-chains 401 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 374 time to evaluate : 3.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 LEU Chi-restraints excluded: chain E residue 53 SER Chi-restraints excluded: chain E residue 167 SER Chi-restraints excluded: chain E residue 181 MET Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 357 MET Chi-restraints excluded: chain E residue 366 LEU Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain Z residue 12 ARG Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain F residue 81 GLU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain G residue 28 ARG Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 101 ARG Chi-restraints excluded: chain G residue 160 LEU Chi-restraints excluded: chain G residue 279 MET Chi-restraints excluded: chain G residue 288 LYS Chi-restraints excluded: chain G residue 301 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 171 optimal weight: 0.9990 chunk 132 optimal weight: 0.9980 chunk 194 optimal weight: 0.8980 chunk 293 optimal weight: 2.9990 chunk 270 optimal weight: 0.9980 chunk 234 optimal weight: 0.0980 chunk 24 optimal weight: 0.0970 chunk 180 optimal weight: 0.5980 chunk 143 optimal weight: 0.7980 chunk 185 optimal weight: 0.9990 chunk 249 optimal weight: 0.7980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 HIS ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 3 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 24949 Z= 0.203 Angle : 0.612 13.715 34152 Z= 0.286 Chirality : 0.040 0.145 3585 Planarity : 0.004 0.055 4245 Dihedral : 9.787 122.965 3669 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.24 % Favored : 96.73 % Rotamer: Outliers : 1.12 % Allowed : 19.96 % Favored : 78.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.16), residues: 2964 helix: 1.20 (0.13), residues: 1655 sheet: -2.36 (0.57), residues: 62 loop : 0.21 (0.18), residues: 1247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 147 HIS 0.006 0.001 HIS E 244 PHE 0.018 0.001 PHE J 247 TYR 0.019 0.001 TYR D 388 ARG 0.004 0.000 ARG J 253 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5928 Ramachandran restraints generated. 2964 Oldfield, 0 Emsley, 2964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue MET 1 is missing expected H atoms. Skipping. Residue LYS 2 is missing expected H atoms. Skipping. Residue ILE 16 is missing expected H atoms. Skipping. Residue VAL 19 is missing expected H atoms. Skipping. Residue VAL 73 is missing expected H atoms. Skipping. Residue SER 102 is missing expected H atoms. Skipping. Residue TYR 126 is missing expected H atoms. Skipping. Residue THR 153 is missing expected H atoms. Skipping. Residue THR 155 is missing expected H atoms. Skipping. Residue MET 157 is missing expected H atoms. Skipping. Residue LEU 160 is missing expected H atoms. Skipping. Residue LYS 162 is missing expected H atoms. Skipping. Residue VAL 179 is missing expected H atoms. Skipping. Residue LEU 188 is missing expected H atoms. Skipping. Residue TYR 8 is missing expected H atoms. Skipping. Evaluate side-chains 426 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 399 time to evaluate : 4.317 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: symmetry clash revert: symmetry clash REVERT: E 238 TYR cc_start: 0.6931 (t80) cc_final: 0.6710 (t80) REVERT: E 357 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8652 (mmt) REVERT: E 371 TYR cc_start: 0.7897 (m-80) cc_final: 0.7385 (m-80) REVERT: E 412 ARG cc_start: 0.8003 (ttm-80) cc_final: 0.7679 (ttm170) REVERT: E 436 ILE cc_start: 0.8601 (OUTLIER) cc_final: 0.8349 (mt) REVERT: E 462 GLN cc_start: 0.7146 (OUTLIER) cc_final: 0.6868 (pt0) REVERT: I 361 GLN cc_start: 0.7973 (mt0) cc_final: 0.7736 (pt0) REVERT: J 255 TYR cc_start: 0.7191 (OUTLIER) cc_final: 0.6926 (t80) REVERT: Z 12 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7806 (ttm-80) REVERT: M 231 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7732 (mp0) REVERT: F 158 GLU cc_start: 0.7377 (OUTLIER) cc_final: 0.7164 (mt-10) REVERT: F 185 MET cc_start: 0.8632 (tpp) cc_final: 0.8291 (tpp) REVERT: G 28 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7525 (ppp-140) REVERT: G 40 MET cc_start: 0.7395 (mmm) cc_final: 0.7056 (mmm) REVERT: G 200 ASN cc_start: 0.8043 (m-40) cc_final: 0.7788 (t0) outliers start: 27 outliers final: 14 residues processed: 415 average time/residue: 2.7647 time to fit residues: 1336.2169 Evaluate side-chains 408 residues out of total 2420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 386 time to evaluate : 3.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 357 MET Chi-restraints excluded: chain E residue 436 ILE Chi-restraints excluded: chain E residue 462 GLN Chi-restraints excluded: chain J residue 255 TYR Chi-restraints excluded: chain Z residue 12 ARG Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 192 VAL Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain D residue 287 ILE Chi-restraints excluded: chain D residue 364 SER Chi-restraints excluded: chain M residue 195 THR Chi-restraints excluded: chain M residue 231 GLU Chi-restraints excluded: chain F residue 87 SER Chi-restraints excluded: chain F residue 149 ASP Chi-restraints excluded: chain F residue 158 GLU Chi-restraints excluded: chain G residue 28 ARG Chi-restraints excluded: chain G residue 94 THR Chi-restraints excluded: chain G residue 101 ARG Chi-restraints excluded: chain G residue 279 MET Chi-restraints excluded: chain G residue 288 LYS Chi-restraints excluded: chain G residue 301 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 295 random chunks: chunk 71 optimal weight: 0.4980 chunk 215 optimal weight: 1.9990 chunk 34 optimal weight: 10.0000 chunk 65 optimal weight: 0.5980 chunk 234 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 chunk 205 optimal weight: 2.9990 chunk 13 optimal weight: 5.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 176 HIS ** E 203 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 227 ASN I 280 GLN Z 3 ASN Z 61 GLN G 95 GLN G 282 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.141812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.098884 restraints weight = 69057.151| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 2.07 r_work: 0.2634 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2506 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 24949 Z= 0.309 Angle : 0.657 14.487 34152 Z= 0.306 Chirality : 0.041 0.169 3585 Planarity : 0.004 0.055 4245 Dihedral : 10.000 120.451 3669 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.21 % Favored : 96.76 % Rotamer: Outliers : 1.29 % Allowed : 20.00 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.01 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.15), residues: 2964 helix: 1.13 (0.13), residues: 1657 sheet: -2.28 (0.58), residues: 62 loop : 0.17 (0.18), residues: 1245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 54 HIS 0.008 0.001 HIS I 101 PHE 0.018 0.002 PHE I 95 TYR 0.018 0.002 TYR J 221 ARG 0.006 0.000 ARG I 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 18075.09 seconds wall clock time: 323 minutes 40.83 seconds (19420.83 seconds total)