Starting phenix.real_space_refine on Tue Apr 7 03:48:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9y9l_72707/04_2026/9y9l_72707.cif Found real_map, /net/cci-nas-00/data/ceres_data/9y9l_72707/04_2026/9y9l_72707.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.06 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9y9l_72707/04_2026/9y9l_72707.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9y9l_72707/04_2026/9y9l_72707.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9y9l_72707/04_2026/9y9l_72707.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9y9l_72707/04_2026/9y9l_72707.map" } resolution = 3.06 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 131 5.16 5 C 15114 2.51 5 N 4025 2.21 5 O 4632 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23917 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2839 Classifications: {'peptide': 362} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 19, 'TRANS': 342} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "Y" Number of atoms: 2183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2183 Classifications: {'peptide': 269} Link IDs: {'PTRANS': 10, 'TRANS': 258} Chain: "Z" Number of atoms: 2131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 2131 Classifications: {'peptide': 270} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 260} Chain: "a" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1317 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "b" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1317 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "c" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1317 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "d" Number of atoms: 1317 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1317 Classifications: {'peptide': 166} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 160} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.75, per 1000 atoms: 0.24 Number of scatterers: 23917 At special positions: 0 Unit cell: (117.18, 120.42, 219.78, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 131 16.00 P 10 15.00 Mg 5 11.99 O 4632 8.00 N 4025 7.00 C 15114 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.79 Conformation dependent library (CDL) restraints added in 1.1 seconds 5932 Ramachandran restraints generated. 2966 Oldfield, 0 Emsley, 2966 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5644 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 36 sheets defined 46.9% alpha, 23.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.97 Creating SS restraints... Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.726A pdb=" N SER A 60 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LYS A 61 " --> pdb=" O ALA A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 92 Processing helix chain 'A' and resid 97 through 101 removed outlier: 3.777A pdb=" N HIS A 101 " --> pdb=" O PRO A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 Processing helix chain 'A' and resid 137 through 145 removed outlier: 3.678A pdb=" N SER A 145 " --> pdb=" O SER A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.768A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 197 removed outlier: 3.957A pdb=" N GLU A 195 " --> pdb=" O LYS A 191 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ARG A 196 " --> pdb=" O ILE A 192 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY A 197 " --> pdb=" O LEU A 193 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.679A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 Processing helix chain 'A' and resid 251 through 256 removed outlier: 3.707A pdb=" N ARG A 254 " --> pdb=" O GLY A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.676A pdb=" N THR A 260 " --> pdb=" O CYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.517A pdb=" N PHE A 266 " --> pdb=" O GLN A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 273 through 284 Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 removed outlier: 4.155A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 306 removed outlier: 4.215A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 321 removed outlier: 3.546A pdb=" N ARG A 312 " --> pdb=" O GLY A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 349 through 356 removed outlier: 3.815A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N TRP A 356 " --> pdb=" O GLN A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 369 through 374 Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.734A pdb=" N SER B 60 " --> pdb=" O GLU B 57 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LYS B 61 " --> pdb=" O ALA B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 91 Processing helix chain 'B' and resid 97 through 101 removed outlier: 3.713A pdb=" N HIS B 101 " --> pdb=" O PRO B 98 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 Processing helix chain 'B' and resid 137 through 145 removed outlier: 3.566A pdb=" N SER B 145 " --> pdb=" O SER B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 197 removed outlier: 4.016A pdb=" N GLU B 195 " --> pdb=" O LYS B 191 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ARG B 196 " --> pdb=" O ILE B 192 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLY B 197 " --> pdb=" O LEU B 193 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.644A pdb=" N CYS B 217 " --> pdb=" O LYS B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 231 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.616A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 258 through 262 Processing helix chain 'B' and resid 263 through 267 removed outlier: 3.516A pdb=" N PHE B 266 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 284 Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 removed outlier: 4.031A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 306 removed outlier: 4.196A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 321 Processing helix chain 'B' and resid 337 through 347 Processing helix chain 'B' and resid 349 through 356 removed outlier: 3.571A pdb=" N PHE B 352 " --> pdb=" O LEU B 349 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 4.810A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TRP B 356 " --> pdb=" O GLN B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 369 through 374 Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.737A pdb=" N SER C 60 " --> pdb=" O GLU C 57 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS C 61 " --> pdb=" O ALA C 58 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 92 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.787A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 126 Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 181 through 197 removed outlier: 3.937A pdb=" N GLU C 195 " --> pdb=" O LYS C 191 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG C 196 " --> pdb=" O ILE C 192 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N GLY C 197 " --> pdb=" O LEU C 193 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.714A pdb=" N CYS C 217 " --> pdb=" O LYS C 213 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 231 Processing helix chain 'C' and resid 251 through 256 removed outlier: 3.651A pdb=" N ARG C 254 " --> pdb=" O GLY C 251 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 262 removed outlier: 3.689A pdb=" N THR C 260 " --> pdb=" O CYS C 257 " (cutoff:3.500A) Processing helix chain 'C' and resid 263 through 267 Processing helix chain 'C' and resid 273 through 284 Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 removed outlier: 4.143A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 302 through 306 removed outlier: 4.157A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 321 removed outlier: 3.512A pdb=" N ARG C 312 " --> pdb=" O GLY C 308 " (cutoff:3.500A) Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 347 Processing helix chain 'C' and resid 352 through 356 removed outlier: 3.637A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 369 through 374 Processing helix chain 'D' and resid 55 through 61 Processing helix chain 'D' and resid 78 through 93 removed outlier: 3.598A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLU D 93 " --> pdb=" O THR D 89 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 126 removed outlier: 3.695A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N THR D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 146 Processing helix chain 'D' and resid 181 through 195 removed outlier: 3.962A pdb=" N GLU D 195 " --> pdb=" O LYS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 217 removed outlier: 3.952A pdb=" N CYS D 217 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 231 Processing helix chain 'D' and resid 251 through 256 removed outlier: 3.645A pdb=" N ARG D 254 " --> pdb=" O GLY D 251 " (cutoff:3.500A) Processing helix chain 'D' and resid 257 through 262 removed outlier: 3.639A pdb=" N THR D 260 " --> pdb=" O CYS D 257 " (cutoff:3.500A) Processing helix chain 'D' and resid 263 through 267 Processing helix chain 'D' and resid 273 through 284 Processing helix chain 'D' and resid 286 through 294 removed outlier: 4.339A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 302 through 306 removed outlier: 4.305A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 321 removed outlier: 3.504A pdb=" N ARG D 312 " --> pdb=" O GLY D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 349 removed outlier: 3.595A pdb=" N ILE D 345 " --> pdb=" O ILE D 341 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N LEU D 346 " --> pdb=" O GLY D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 353 removed outlier: 3.882A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 350 through 353' Processing helix chain 'D' and resid 358 through 366 removed outlier: 3.808A pdb=" N TYR D 362 " --> pdb=" O THR D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 374 removed outlier: 4.004A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N CYS D 374 " --> pdb=" O VAL D 370 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.544A pdb=" N LEU E 65 " --> pdb=" O ARG E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.601A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.728A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 112 through 126 removed outlier: 3.670A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 181 through 194 Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.815A pdb=" N CYS E 217 " --> pdb=" O LYS E 213 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 231 Processing helix chain 'E' and resid 251 through 256 removed outlier: 3.691A pdb=" N ARG E 254 " --> pdb=" O GLY E 251 " (cutoff:3.500A) Processing helix chain 'E' and resid 257 through 262 removed outlier: 3.813A pdb=" N THR E 260 " --> pdb=" O CYS E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 267 Processing helix chain 'E' and resid 273 through 284 Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 removed outlier: 3.951A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 305 removed outlier: 3.680A pdb=" N THR E 304 " --> pdb=" O GLY E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 319 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 358 through 366 Processing helix chain 'E' and resid 369 through 374 Processing helix chain 'Y' and resid 9 through 23 removed outlier: 3.696A pdb=" N HIS Y 23 " --> pdb=" O LYS Y 19 " (cutoff:3.500A) Processing helix chain 'Y' and resid 28 through 41 removed outlier: 3.685A pdb=" N VAL Y 32 " --> pdb=" O GLU Y 28 " (cutoff:3.500A) Processing helix chain 'Y' and resid 43 through 48 Processing helix chain 'Y' and resid 50 through 61 Processing helix chain 'Y' and resid 117 through 136 removed outlier: 4.369A pdb=" N ALA Y 127 " --> pdb=" O SER Y 123 " (cutoff:3.500A) Processing helix chain 'Y' and resid 147 through 151 removed outlier: 4.246A pdb=" N GLY Y 150 " --> pdb=" O THR Y 147 " (cutoff:3.500A) Processing helix chain 'Y' and resid 165 through 167 No H-bonds generated for 'chain 'Y' and resid 165 through 167' Processing helix chain 'Y' and resid 220 through 254 removed outlier: 5.047A pdb=" N SER Y 251 " --> pdb=" O TYR Y 247 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N ASP Y 252 " --> pdb=" O GLN Y 248 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR Y 253 " --> pdb=" O THR Y 249 " (cutoff:3.500A) Processing helix chain 'Y' and resid 270 through 276 removed outlier: 3.885A pdb=" N ILE Y 274 " --> pdb=" O ASP Y 270 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER Y 276 " --> pdb=" O ASN Y 272 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3 through 14 Processing helix chain 'Z' and resid 20 through 30 removed outlier: 4.052A pdb=" N ASP Z 30 " --> pdb=" O SER Z 26 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 43 removed outlier: 3.663A pdb=" N LEU Z 40 " --> pdb=" O CYS Z 36 " (cutoff:3.500A) Processing helix chain 'Z' and resid 90 through 111 removed outlier: 3.854A pdb=" N ASP Z 105 " --> pdb=" O ASN Z 101 " (cutoff:3.500A) Processing helix chain 'Z' and resid 208 through 244 removed outlier: 3.625A pdb=" N ASN Z 212 " --> pdb=" O PRO Z 208 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N TYR Z 232 " --> pdb=" O LEU Z 228 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N PHE Z 233 " --> pdb=" O ASN Z 229 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG Z 244 " --> pdb=" O VAL Z 240 " (cutoff:3.500A) Processing helix chain 'Z' and resid 253 through 270 Processing helix chain 'a' and resid 8 through 20 removed outlier: 3.819A pdb=" N ILE a 12 " --> pdb=" O ASN a 8 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL a 20 " --> pdb=" O ASN a 16 " (cutoff:3.500A) Processing helix chain 'a' and resid 25 through 31 Processing helix chain 'a' and resid 58 through 60 No H-bonds generated for 'chain 'a' and resid 58 through 60' Processing helix chain 'a' and resid 66 through 74 Processing helix chain 'a' and resid 110 through 128 removed outlier: 5.224A pdb=" N ASP a 122 " --> pdb=" O ALA a 118 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N ALA a 123 " --> pdb=" O SER a 119 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE a 124 " --> pdb=" O SER a 120 " (cutoff:3.500A) Processing helix chain 'a' and resid 139 through 143 removed outlier: 3.564A pdb=" N ASP a 142 " --> pdb=" O GLY a 139 " (cutoff:3.500A) Processing helix chain 'a' and resid 146 through 153 Processing helix chain 'a' and resid 154 through 156 No H-bonds generated for 'chain 'a' and resid 154 through 156' Processing helix chain 'b' and resid 8 through 20 removed outlier: 3.800A pdb=" N ILE b 12 " --> pdb=" O ASN b 8 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL b 20 " --> pdb=" O ASN b 16 " (cutoff:3.500A) Processing helix chain 'b' and resid 25 through 31 Processing helix chain 'b' and resid 58 through 60 No H-bonds generated for 'chain 'b' and resid 58 through 60' Processing helix chain 'b' and resid 66 through 74 Processing helix chain 'b' and resid 110 through 120 Processing helix chain 'b' and resid 120 through 128 removed outlier: 3.964A pdb=" N ILE b 124 " --> pdb=" O SER b 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 139 through 143 removed outlier: 3.567A pdb=" N ASP b 142 " --> pdb=" O GLY b 139 " (cutoff:3.500A) Processing helix chain 'b' and resid 145 through 153 removed outlier: 4.226A pdb=" N LEU b 149 " --> pdb=" O ASP b 145 " (cutoff:3.500A) Processing helix chain 'b' and resid 154 through 156 No H-bonds generated for 'chain 'b' and resid 154 through 156' Processing helix chain 'c' and resid 8 through 20 removed outlier: 3.769A pdb=" N ILE c 12 " --> pdb=" O ASN c 8 " (cutoff:3.500A) Processing helix chain 'c' and resid 25 through 31 Processing helix chain 'c' and resid 58 through 60 No H-bonds generated for 'chain 'c' and resid 58 through 60' Processing helix chain 'c' and resid 66 through 74 Processing helix chain 'c' and resid 110 through 128 removed outlier: 5.184A pdb=" N ASP c 122 " --> pdb=" O ALA c 118 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ALA c 123 " --> pdb=" O SER c 119 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N ILE c 124 " --> pdb=" O SER c 120 " (cutoff:3.500A) Processing helix chain 'c' and resid 139 through 143 Processing helix chain 'c' and resid 145 through 153 removed outlier: 4.204A pdb=" N LEU c 149 " --> pdb=" O ASP c 145 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 19 Processing helix chain 'd' and resid 25 through 30 Processing helix chain 'd' and resid 58 through 60 No H-bonds generated for 'chain 'd' and resid 58 through 60' Processing helix chain 'd' and resid 66 through 74 removed outlier: 3.612A pdb=" N SER d 70 " --> pdb=" O ASP d 66 " (cutoff:3.500A) Processing helix chain 'd' and resid 110 through 128 removed outlier: 5.117A pdb=" N ASP d 122 " --> pdb=" O ALA d 118 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N ALA d 123 " --> pdb=" O SER d 119 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ILE d 124 " --> pdb=" O SER d 120 " (cutoff:3.500A) Processing helix chain 'd' and resid 139 through 143 Processing helix chain 'd' and resid 146 through 153 Processing helix chain 'd' and resid 154 through 156 No H-bonds generated for 'chain 'd' and resid 154 through 156' Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 31 removed outlier: 3.710A pdb=" N THR A 106 " --> pdb=" O CYS A 10 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N ASN A 12 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N TYR A 133 " --> pdb=" O THR A 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 Processing sheet with id=AA3, first strand: chain 'A' and resid 169 through 170 Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 removed outlier: 6.252A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA6, first strand: chain 'B' and resid 29 through 32 removed outlier: 3.715A pdb=" N THR B 106 " --> pdb=" O CYS B 10 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N ASN B 12 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N TYR B 133 " --> pdb=" O THR B 103 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 53 through 54 Processing sheet with id=AA8, first strand: chain 'B' and resid 169 through 170 Processing sheet with id=AA9, first strand: chain 'B' and resid 169 through 170 removed outlier: 6.265A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB2, first strand: chain 'C' and resid 29 through 32 removed outlier: 3.779A pdb=" N THR C 106 " --> pdb=" O CYS C 10 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N ASN C 12 " --> pdb=" O THR C 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB4, first strand: chain 'C' and resid 169 through 170 Processing sheet with id=AB5, first strand: chain 'C' and resid 169 through 170 removed outlier: 6.286A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 32 removed outlier: 3.757A pdb=" N THR D 106 " --> pdb=" O CYS D 10 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N ASN D 12 " --> pdb=" O THR D 106 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AB9, first strand: chain 'D' and resid 176 through 178 removed outlier: 6.063A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ASN D 297 " --> pdb=" O ILE D 330 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC2, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.754A pdb=" N THR E 106 " --> pdb=" O CYS E 10 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASN E 12 " --> pdb=" O THR E 106 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 53 through 54 Processing sheet with id=AC4, first strand: chain 'E' and resid 160 through 166 removed outlier: 7.791A pdb=" N VAL E 298 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AC6, first strand: chain 'Y' and resid 64 through 65 Processing sheet with id=AC7, first strand: chain 'Y' and resid 86 through 89 removed outlier: 3.752A pdb=" N LYS Y 97 " --> pdb=" O ASP Y 107 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ASP Y 107 " --> pdb=" O LYS Y 97 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N ASP Y 99 " --> pdb=" O ALA Y 105 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ALA Y 105 " --> pdb=" O ASP Y 99 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'Y' and resid 139 through 146 removed outlier: 3.680A pdb=" N GLY Y 171 " --> pdb=" O GLN Y 162 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N THR Y 180 " --> pdb=" O GLN Y 187 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N GLN Y 187 " --> pdb=" O THR Y 180 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LYS Z 145 " --> pdb=" O GLN Z 178 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'Z' and resid 48 through 52 removed outlier: 4.356A pdb=" N LYS Z 48 " --> pdb=" O LEU Z 61 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'Z' and resid 66 through 67 removed outlier: 3.698A pdb=" N SER Z 70 " --> pdb=" O ASP Z 67 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR Z 71 " --> pdb=" O ASP Z 80 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASP Z 80 " --> pdb=" O TYR Z 71 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'a' and resid 6 through 7 removed outlier: 7.628A pdb=" N THR a 6 " --> pdb=" O ILE a 47 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N VAL a 49 " --> pdb=" O THR a 6 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL a 49 " --> pdb=" O LEU a 40 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N LEU a 40 " --> pdb=" O VAL a 49 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N GLU a 51 " --> pdb=" O PHE a 38 " (cutoff:3.500A) removed outlier: 10.807A pdb=" N PHE a 38 " --> pdb=" O GLU a 51 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N LYS a 53 " --> pdb=" O VAL a 36 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N VAL a 36 " --> pdb=" O LYS a 53 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE a 55 " --> pdb=" O LYS a 34 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LYS a 34 " --> pdb=" O ASP a 86 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N HIS a 133 " --> pdb=" O LEU a 99 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'a' and resid 6 through 7 removed outlier: 7.628A pdb=" N THR a 6 " --> pdb=" O ILE a 47 " (cutoff:3.500A) removed outlier: 9.617A pdb=" N VAL a 49 " --> pdb=" O THR a 6 " (cutoff:3.500A) removed outlier: 7.224A pdb=" N VAL a 49 " --> pdb=" O LEU a 40 " (cutoff:3.500A) removed outlier: 7.898A pdb=" N LEU a 40 " --> pdb=" O VAL a 49 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N GLU a 51 " --> pdb=" O PHE a 38 " (cutoff:3.500A) removed outlier: 10.807A pdb=" N PHE a 38 " --> pdb=" O GLU a 51 " (cutoff:3.500A) removed outlier: 8.507A pdb=" N LYS a 53 " --> pdb=" O VAL a 36 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N VAL a 36 " --> pdb=" O LYS a 53 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ILE a 55 " --> pdb=" O LYS a 34 " (cutoff:3.500A) removed outlier: 7.006A pdb=" N LYS a 34 " --> pdb=" O ASP a 86 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'b' and resid 6 through 7 removed outlier: 7.534A pdb=" N THR b 6 " --> pdb=" O ILE b 47 " (cutoff:3.500A) removed outlier: 9.478A pdb=" N VAL b 49 " --> pdb=" O THR b 6 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LEU b 37 " --> pdb=" O GLU b 50 " (cutoff:3.500A) removed outlier: 9.212A pdb=" N ALA b 52 " --> pdb=" O ALA b 35 " (cutoff:3.500A) removed outlier: 11.022A pdb=" N ALA b 35 " --> pdb=" O ALA b 52 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N GLN b 54 " --> pdb=" O LYS b 33 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N LYS b 33 " --> pdb=" O GLN b 54 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LYS b 34 " --> pdb=" O ASP b 86 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N HIS b 133 " --> pdb=" O LEU b 99 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'b' and resid 6 through 7 removed outlier: 7.534A pdb=" N THR b 6 " --> pdb=" O ILE b 47 " (cutoff:3.500A) removed outlier: 9.478A pdb=" N VAL b 49 " --> pdb=" O THR b 6 " (cutoff:3.500A) removed outlier: 5.280A pdb=" N LEU b 37 " --> pdb=" O GLU b 50 " (cutoff:3.500A) removed outlier: 9.212A pdb=" N ALA b 52 " --> pdb=" O ALA b 35 " (cutoff:3.500A) removed outlier: 11.022A pdb=" N ALA b 35 " --> pdb=" O ALA b 52 " (cutoff:3.500A) removed outlier: 9.912A pdb=" N GLN b 54 " --> pdb=" O LYS b 33 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N LYS b 33 " --> pdb=" O GLN b 54 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LYS b 34 " --> pdb=" O ASP b 86 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'c' and resid 6 through 7 removed outlier: 7.594A pdb=" N THR c 6 " --> pdb=" O ILE c 47 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N VAL c 49 " --> pdb=" O THR c 6 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL c 49 " --> pdb=" O LEU c 40 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LEU c 40 " --> pdb=" O VAL c 49 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N GLU c 51 " --> pdb=" O PHE c 38 " (cutoff:3.500A) removed outlier: 10.891A pdb=" N PHE c 38 " --> pdb=" O GLU c 51 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N LYS c 53 " --> pdb=" O VAL c 36 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N VAL c 36 " --> pdb=" O LYS c 53 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE c 55 " --> pdb=" O LYS c 34 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LYS c 34 " --> pdb=" O ASP c 86 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N HIS c 133 " --> pdb=" O LEU c 99 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'c' and resid 6 through 7 removed outlier: 7.594A pdb=" N THR c 6 " --> pdb=" O ILE c 47 " (cutoff:3.500A) removed outlier: 9.553A pdb=" N VAL c 49 " --> pdb=" O THR c 6 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL c 49 " --> pdb=" O LEU c 40 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N LEU c 40 " --> pdb=" O VAL c 49 " (cutoff:3.500A) removed outlier: 9.250A pdb=" N GLU c 51 " --> pdb=" O PHE c 38 " (cutoff:3.500A) removed outlier: 10.891A pdb=" N PHE c 38 " --> pdb=" O GLU c 51 " (cutoff:3.500A) removed outlier: 8.619A pdb=" N LYS c 53 " --> pdb=" O VAL c 36 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N VAL c 36 " --> pdb=" O LYS c 53 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE c 55 " --> pdb=" O LYS c 34 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N LYS c 34 " --> pdb=" O ASP c 86 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'd' and resid 6 through 7 removed outlier: 7.237A pdb=" N THR d 6 " --> pdb=" O ILE d 47 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N VAL d 49 " --> pdb=" O THR d 6 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU d 37 " --> pdb=" O GLU d 50 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N ALA d 52 " --> pdb=" O ALA d 35 " (cutoff:3.500A) removed outlier: 11.204A pdb=" N ALA d 35 " --> pdb=" O ALA d 52 " (cutoff:3.500A) removed outlier: 9.707A pdb=" N GLN d 54 " --> pdb=" O LYS d 33 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N LYS d 33 " --> pdb=" O GLN d 54 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS d 34 " --> pdb=" O ASP d 86 " (cutoff:3.500A) removed outlier: 10.083A pdb=" N HIS d 133 " --> pdb=" O GLU d 97 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N LEU d 99 " --> pdb=" O HIS d 133 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N TRP d 135 " --> pdb=" O LEU d 99 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N PHE d 101 " --> pdb=" O TRP d 135 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'd' and resid 6 through 7 removed outlier: 7.237A pdb=" N THR d 6 " --> pdb=" O ILE d 47 " (cutoff:3.500A) removed outlier: 9.338A pdb=" N VAL d 49 " --> pdb=" O THR d 6 " (cutoff:3.500A) removed outlier: 5.380A pdb=" N LEU d 37 " --> pdb=" O GLU d 50 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N ALA d 52 " --> pdb=" O ALA d 35 " (cutoff:3.500A) removed outlier: 11.204A pdb=" N ALA d 35 " --> pdb=" O ALA d 52 " (cutoff:3.500A) removed outlier: 9.707A pdb=" N GLN d 54 " --> pdb=" O LYS d 33 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N LYS d 33 " --> pdb=" O GLN d 54 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N LYS d 34 " --> pdb=" O ASP d 86 " (cutoff:3.500A) 1192 hydrogen bonds defined for protein. 3237 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: 4.63 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4562 1.33 - 1.45: 5885 1.45 - 1.58: 13705 1.58 - 1.70: 18 1.70 - 1.83: 221 Bond restraints: 24391 Sorted by residual: bond pdb=" CA ILE Y 181 " pdb=" CB ILE Y 181 " ideal model delta sigma weight residual 1.530 1.559 -0.029 1.05e-02 9.07e+03 7.42e+00 bond pdb=" CB ASP Z 105 " pdb=" CG ASP Z 105 " ideal model delta sigma weight residual 1.516 1.583 -0.067 2.50e-02 1.60e+03 7.20e+00 bond pdb=" N THR b 63 " pdb=" CA THR b 63 " ideal model delta sigma weight residual 1.457 1.491 -0.033 1.29e-02 6.01e+03 6.73e+00 bond pdb=" CA TYR Y 70 " pdb=" CB TYR Y 70 " ideal model delta sigma weight residual 1.527 1.563 -0.036 1.49e-02 4.50e+03 5.84e+00 bond pdb=" CA THR b 63 " pdb=" C THR b 63 " ideal model delta sigma weight residual 1.523 1.554 -0.031 1.34e-02 5.57e+03 5.27e+00 ... (remaining 24386 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 32153 3.13 - 6.25: 756 6.25 - 9.38: 85 9.38 - 12.50: 13 12.50 - 15.63: 5 Bond angle restraints: 33012 Sorted by residual: angle pdb=" CA LYS Z 142 " pdb=" CB LYS Z 142 " pdb=" CG LYS Z 142 " ideal model delta sigma weight residual 114.10 127.28 -13.18 2.00e+00 2.50e-01 4.34e+01 angle pdb=" N GLU Z 264 " pdb=" CA GLU Z 264 " pdb=" CB GLU Z 264 " ideal model delta sigma weight residual 110.40 120.47 -10.07 1.63e+00 3.76e-01 3.82e+01 angle pdb=" C GLY Y 116 " pdb=" N LEU Y 117 " pdb=" CA LEU Y 117 " ideal model delta sigma weight residual 120.38 129.24 -8.86 1.46e+00 4.69e-01 3.68e+01 angle pdb=" C ILE Y 148 " pdb=" N ASP Y 149 " pdb=" CA ASP Y 149 " ideal model delta sigma weight residual 121.54 132.84 -11.30 1.91e+00 2.74e-01 3.50e+01 angle pdb=" C CYS Z 36 " pdb=" N GLU Z 37 " pdb=" CA GLU Z 37 " ideal model delta sigma weight residual 120.54 128.50 -7.96 1.35e+00 5.49e-01 3.48e+01 ... (remaining 33007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 13552 17.87 - 35.74: 1005 35.74 - 53.61: 199 53.61 - 71.48: 34 71.48 - 89.35: 23 Dihedral angle restraints: 14813 sinusoidal: 6054 harmonic: 8759 Sorted by residual: dihedral pdb=" CA PRO Y 183 " pdb=" C PRO Y 183 " pdb=" N PRO Y 184 " pdb=" CA PRO Y 184 " ideal model delta harmonic sigma weight residual -180.00 -108.16 -71.84 0 5.00e+00 4.00e-02 2.06e+02 dihedral pdb=" CA CYS Y 124 " pdb=" C CYS Y 124 " pdb=" N ASP Y 125 " pdb=" CA ASP Y 125 " ideal model delta harmonic sigma weight residual -180.00 -150.66 -29.34 0 5.00e+00 4.00e-02 3.44e+01 dihedral pdb=" CA LEU Y 117 " pdb=" C LEU Y 117 " pdb=" N LYS Y 118 " pdb=" CA LYS Y 118 " ideal model delta harmonic sigma weight residual -180.00 -152.73 -27.27 0 5.00e+00 4.00e-02 2.98e+01 ... (remaining 14810 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 3486 0.121 - 0.243: 179 0.243 - 0.364: 16 0.364 - 0.486: 0 0.486 - 0.607: 1 Chirality restraints: 3682 Sorted by residual: chirality pdb=" CB ILE Y 181 " pdb=" CA ILE Y 181 " pdb=" CG1 ILE Y 181 " pdb=" CG2 ILE Y 181 " both_signs ideal model delta sigma weight residual False 2.64 2.04 0.61 2.00e-01 2.50e+01 9.21e+00 chirality pdb=" CA ASN Y 84 " pdb=" N ASN Y 84 " pdb=" C ASN Y 84 " pdb=" CB ASN Y 84 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" CB VAL Y 8 " pdb=" CA VAL Y 8 " pdb=" CG1 VAL Y 8 " pdb=" CG2 VAL Y 8 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.18e+00 ... (remaining 3679 not shown) Planarity restraints: 4218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO Y 183 " -0.068 5.00e-02 4.00e+02 1.04e-01 1.72e+01 pdb=" N PRO Y 184 " 0.179 5.00e-02 4.00e+02 pdb=" CA PRO Y 184 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO Y 184 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN d 16 " 0.020 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" CG ASN d 16 " -0.071 2.00e-02 2.50e+03 pdb=" OD1 ASN d 16 " 0.027 2.00e-02 2.50e+03 pdb=" ND2 ASN d 16 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 206 " 0.293 9.50e-02 1.11e+02 1.32e-01 1.19e+01 pdb=" NE ARG D 206 " -0.024 2.00e-02 2.50e+03 pdb=" CZ ARG D 206 " 0.017 2.00e-02 2.50e+03 pdb=" NH1 ARG D 206 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG D 206 " 0.004 2.00e-02 2.50e+03 ... (remaining 4215 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 120 2.68 - 3.24: 20770 3.24 - 3.79: 35790 3.79 - 4.35: 49835 4.35 - 4.90: 81786 Nonbonded interactions: 188301 Sorted by model distance: nonbonded pdb=" O1B ADP A 400 " pdb="MG MG A 401 " model vdw 2.131 2.170 nonbonded pdb=" O1B ADP C 400 " pdb="MG MG C 401 " model vdw 2.136 2.170 nonbonded pdb=" O1B ADP B 400 " pdb="MG MG B 401 " model vdw 2.138 2.170 nonbonded pdb=" O1B ADP D 400 " pdb="MG MG D 401 " model vdw 2.140 2.170 nonbonded pdb=" O1B ADP E 400 " pdb="MG MG E 401 " model vdw 2.143 2.170 ... (remaining 188296 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 24.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 22.390 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 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 : 0.006 0.073 24391 Z= 0.289 Angle : 1.124 15.631 33012 Z= 0.616 Chirality : 0.062 0.607 3682 Planarity : 0.010 0.132 4218 Dihedral : 13.740 89.354 9169 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 1.32 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.37 % Favored : 96.59 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.99 (0.14), residues: 2966 helix: -2.25 (0.11), residues: 1111 sheet: -0.11 (0.21), residues: 613 loop : -0.81 (0.17), residues: 1242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.002 ARG D 206 TYR 0.027 0.002 TYR D 362 PHE 0.039 0.003 PHE B 90 TRP 0.056 0.003 TRP Y 271 HIS 0.012 0.002 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00560 (24391) covalent geometry : angle 1.12384 (33012) hydrogen bonds : bond 0.17062 ( 1158) hydrogen bonds : angle 7.44324 ( 3237) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5932 Ramachandran restraints generated. 2966 Oldfield, 0 Emsley, 2966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5932 Ramachandran restraints generated. 2966 Oldfield, 0 Emsley, 2966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 177 time to evaluate : 1.062 Fit side-chains REVERT: A 299 MET cc_start: 0.9090 (mmm) cc_final: 0.8873 (mtm) REVERT: B 246 GLN cc_start: 0.8908 (mt0) cc_final: 0.8118 (mp10) REVERT: B 353 GLN cc_start: 0.9048 (mm-40) cc_final: 0.8690 (mp10) REVERT: C 82 MET cc_start: 0.8891 (tpt) cc_final: 0.8668 (mmm) REVERT: C 246 GLN cc_start: 0.9140 (mt0) cc_final: 0.8788 (mt0) REVERT: C 283 MET cc_start: 0.9251 (mmt) cc_final: 0.8912 (mpp) REVERT: E 121 GLN cc_start: 0.9461 (tt0) cc_final: 0.9226 (mm-40) REVERT: E 283 MET cc_start: 0.9229 (mmt) cc_final: 0.8890 (tpp) REVERT: Y 57 TYR cc_start: 0.8799 (t80) cc_final: 0.8494 (t80) REVERT: Y 59 MET cc_start: 0.8949 (mtm) cc_final: 0.8397 (ttm) REVERT: Z 36 CYS cc_start: 0.9050 (t) cc_final: 0.8618 (p) REVERT: b 115 MET cc_start: 0.9231 (tpt) cc_final: 0.8634 (tpp) REVERT: c 26 GLN cc_start: 0.9312 (mp10) cc_final: 0.9085 (mp10) REVERT: d 45 ARG cc_start: 0.8856 (mmm-85) cc_final: 0.8456 (mmm-85) REVERT: d 80 CYS cc_start: 0.9322 (m) cc_final: 0.9081 (m) REVERT: d 115 MET cc_start: 0.9295 (tpt) cc_final: 0.9037 (tpt) REVERT: d 146 ARG cc_start: 0.8275 (ptt90) cc_final: 0.8040 (ptm160) outliers start: 0 outliers final: 0 residues processed: 177 average time/residue: 0.1626 time to fit residues: 46.9422 Evaluate side-chains 155 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 197 optimal weight: 9.9990 chunk 215 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.4980 chunk 207 optimal weight: 0.1980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 overall best weight: 2.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 HIS B 101 HIS C 101 HIS E 162 ASN E 360 GLN Y 223 GLN Z 19 GLN Z 178 GLN Z 188 ASN b 78 ASN d 138 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.047418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.034306 restraints weight = 114991.018| |-----------------------------------------------------------------------------| r_work (start): 0.2747 rms_B_bonded: 3.74 r_work: 0.2592 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 24391 Z= 0.184 Angle : 0.603 7.794 33012 Z= 0.313 Chirality : 0.045 0.203 3682 Planarity : 0.005 0.077 4218 Dihedral : 5.508 62.277 3321 Min Nonbonded Distance : 1.849 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.34 % Favored : 96.59 % Rotamer: Outliers : 0.27 % Allowed : 3.07 % Favored : 96.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.15), residues: 2966 helix: -0.03 (0.15), residues: 1130 sheet: -0.16 (0.20), residues: 672 loop : -0.42 (0.18), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG b 45 TYR 0.017 0.001 TYR Y 239 PHE 0.020 0.001 PHE Y 228 TRP 0.029 0.002 TRP Y 120 HIS 0.004 0.001 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00415 (24391) covalent geometry : angle 0.60312 (33012) hydrogen bonds : bond 0.04275 ( 1158) hydrogen bonds : angle 4.99244 ( 3237) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5932 Ramachandran restraints generated. 2966 Oldfield, 0 Emsley, 2966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5932 Ramachandran restraints generated. 2966 Oldfield, 0 Emsley, 2966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 158 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 353 GLN cc_start: 0.8094 (mp10) cc_final: 0.7879 (mp10) REVERT: B 292 ASP cc_start: 0.9030 (m-30) cc_final: 0.8792 (t0) REVERT: B 353 GLN cc_start: 0.9106 (mm-40) cc_final: 0.8737 (mp10) REVERT: C 82 MET cc_start: 0.9034 (tpt) cc_final: 0.8809 (mmm) REVERT: C 246 GLN cc_start: 0.9064 (mt0) cc_final: 0.8848 (mt0) REVERT: D 325 MET cc_start: 0.9109 (mmm) cc_final: 0.8841 (mmm) REVERT: E 132 MET cc_start: 0.8998 (ptt) cc_final: 0.8526 (ppp) REVERT: Y 59 MET cc_start: 0.9084 (mtm) cc_final: 0.8728 (mtm) REVERT: c 26 GLN cc_start: 0.9314 (mp10) cc_final: 0.9081 (mp10) REVERT: d 80 CYS cc_start: 0.9383 (m) cc_final: 0.8953 (m) outliers start: 7 outliers final: 3 residues processed: 164 average time/residue: 0.1572 time to fit residues: 41.9454 Evaluate side-chains 148 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 145 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain Z residue 264 GLU Chi-restraints excluded: chain c residue 78 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 66 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 151 optimal weight: 3.9990 chunk 295 optimal weight: 10.0000 chunk 161 optimal weight: 5.9990 chunk 63 optimal weight: 0.0870 chunk 71 optimal weight: 7.9990 chunk 139 optimal weight: 2.9990 chunk 294 optimal weight: 10.0000 chunk 116 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 overall best weight: 3.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 19 GLN Z 229 ASN c 133 HIS d 46 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.046360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.033317 restraints weight = 115690.559| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 3.69 r_work: 0.2549 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8824 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 24391 Z= 0.232 Angle : 0.595 6.474 33012 Z= 0.307 Chirality : 0.046 0.182 3682 Planarity : 0.004 0.078 4218 Dihedral : 5.409 68.915 3321 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 3.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.57 % Favored : 96.36 % Rotamer: Outliers : 0.69 % Allowed : 3.99 % Favored : 95.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.16), residues: 2966 helix: 0.87 (0.16), residues: 1129 sheet: -0.15 (0.20), residues: 666 loop : -0.20 (0.18), residues: 1171 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG d 45 TYR 0.018 0.001 TYR Y 239 PHE 0.018 0.002 PHE Y 228 TRP 0.023 0.002 TRP Y 173 HIS 0.005 0.001 HIS D 371 Details of bonding type rmsd covalent geometry : bond 0.00532 (24391) covalent geometry : angle 0.59537 (33012) hydrogen bonds : bond 0.04384 ( 1158) hydrogen bonds : angle 4.72688 ( 3237) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5932 Ramachandran restraints generated. 2966 Oldfield, 0 Emsley, 2966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5932 Ramachandran restraints generated. 2966 Oldfield, 0 Emsley, 2966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 353 GLN cc_start: 0.9106 (mm-40) cc_final: 0.8721 (mp10) REVERT: C 82 MET cc_start: 0.9045 (tpt) cc_final: 0.8815 (mmm) REVERT: C 353 GLN cc_start: 0.9145 (mp10) cc_final: 0.8749 (mp10) REVERT: D 283 MET cc_start: 0.9364 (tpp) cc_final: 0.9111 (tpp) REVERT: D 325 MET cc_start: 0.9134 (mmm) cc_final: 0.8838 (mmm) REVERT: E 132 MET cc_start: 0.9221 (ptt) cc_final: 0.8845 (ppp) REVERT: E 176 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8188 (mtm) REVERT: Y 59 MET cc_start: 0.9150 (mtm) cc_final: 0.8823 (mtm) REVERT: Z 36 CYS cc_start: 0.9080 (t) cc_final: 0.8563 (p) REVERT: c 26 GLN cc_start: 0.9338 (mp10) cc_final: 0.9132 (mp10) REVERT: d 54 GLN cc_start: 0.8610 (mp10) cc_final: 0.8291 (mp10) REVERT: d 80 CYS cc_start: 0.9434 (m) cc_final: 0.8932 (m) outliers start: 18 outliers final: 9 residues processed: 156 average time/residue: 0.1575 time to fit residues: 40.7868 Evaluate side-chains 153 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 143 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 132 MET Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain a residue 25 THR Chi-restraints excluded: chain c residue 78 ASN Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain d residue 6 THR Chi-restraints excluded: chain d residue 26 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 2 optimal weight: 0.0030 chunk 216 optimal weight: 0.9980 chunk 121 optimal weight: 6.9990 chunk 104 optimal weight: 3.9990 chunk 195 optimal weight: 9.9990 chunk 250 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 213 optimal weight: 9.9990 chunk 239 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 overall best weight: 0.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN A 162 ASN Y 197 HIS Z 19 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.047520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.034466 restraints weight = 114460.189| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 3.72 r_work: 0.2597 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 24391 Z= 0.091 Angle : 0.506 7.545 33012 Z= 0.257 Chirality : 0.042 0.190 3682 Planarity : 0.004 0.073 4218 Dihedral : 5.016 57.927 3321 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.14 % Favored : 96.83 % Rotamer: Outliers : 0.50 % Allowed : 5.07 % Favored : 94.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.16), residues: 2966 helix: 1.24 (0.16), residues: 1155 sheet: -0.07 (0.21), residues: 676 loop : 0.07 (0.19), residues: 1135 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG d 45 TYR 0.012 0.001 TYR Y 239 PHE 0.016 0.001 PHE Y 228 TRP 0.017 0.001 TRP Y 173 HIS 0.006 0.001 HIS E 275 Details of bonding type rmsd covalent geometry : bond 0.00195 (24391) covalent geometry : angle 0.50635 (33012) hydrogen bonds : bond 0.03114 ( 1158) hydrogen bonds : angle 4.37104 ( 3237) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5932 Ramachandran restraints generated. 2966 Oldfield, 0 Emsley, 2966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5932 Ramachandran restraints generated. 2966 Oldfield, 0 Emsley, 2966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 0.986 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 132 MET cc_start: 0.8901 (ptm) cc_final: 0.8691 (ttp) REVERT: B 353 GLN cc_start: 0.9076 (mm-40) cc_final: 0.8719 (mp10) REVERT: C 82 MET cc_start: 0.9002 (tpt) cc_final: 0.8778 (mmm) REVERT: C 305 MET cc_start: 0.9211 (mmt) cc_final: 0.8852 (mmt) REVERT: C 353 GLN cc_start: 0.9138 (mp10) cc_final: 0.8934 (mp10) REVERT: D 283 MET cc_start: 0.9391 (tpp) cc_final: 0.9088 (tpp) REVERT: D 325 MET cc_start: 0.9110 (mmm) cc_final: 0.8870 (mmm) REVERT: E 132 MET cc_start: 0.9158 (ptt) cc_final: 0.8864 (ppp) REVERT: Y 59 MET cc_start: 0.9112 (mtm) cc_final: 0.8774 (mtm) REVERT: c 26 GLN cc_start: 0.9327 (mp10) cc_final: 0.9118 (mp10) REVERT: d 45 ARG cc_start: 0.9231 (ttm110) cc_final: 0.8437 (mmm-85) REVERT: d 54 GLN cc_start: 0.8636 (mp10) cc_final: 0.8250 (mp10) REVERT: d 80 CYS cc_start: 0.9380 (m) cc_final: 0.8906 (m) outliers start: 13 outliers final: 6 residues processed: 152 average time/residue: 0.1624 time to fit residues: 40.4845 Evaluate side-chains 147 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain Z residue 88 MET Chi-restraints excluded: chain c residue 78 ASN Chi-restraints excluded: chain c residue 111 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 284 optimal weight: 5.9990 chunk 85 optimal weight: 7.9990 chunk 6 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 241 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 232 optimal weight: 8.9990 chunk 171 optimal weight: 3.9990 chunk 180 optimal weight: 9.9990 chunk 266 optimal weight: 0.9990 chunk 235 optimal weight: 9.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Y 223 GLN Z 19 GLN Z 101 ASN Z 255 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.046252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.033256 restraints weight = 115639.381| |-----------------------------------------------------------------------------| r_work (start): 0.2701 rms_B_bonded: 3.72 r_work: 0.2544 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 24391 Z= 0.233 Angle : 0.578 8.690 33012 Z= 0.294 Chirality : 0.045 0.184 3682 Planarity : 0.004 0.074 4218 Dihedral : 5.172 66.475 3321 Min Nonbonded Distance : 1.875 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.91 % Favored : 96.06 % Rotamer: Outliers : 0.69 % Allowed : 5.68 % Favored : 93.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.16), residues: 2966 helix: 1.40 (0.16), residues: 1136 sheet: -0.01 (0.21), residues: 669 loop : 0.05 (0.18), residues: 1161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 45 TYR 0.016 0.001 TYR b 89 PHE 0.017 0.001 PHE Y 228 TRP 0.016 0.002 TRP Y 173 HIS 0.004 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00538 (24391) covalent geometry : angle 0.57800 (33012) hydrogen bonds : bond 0.03962 ( 1158) hydrogen bonds : angle 4.50117 ( 3237) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5932 Ramachandran restraints generated. 2966 Oldfield, 0 Emsley, 2966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5932 Ramachandran restraints generated. 2966 Oldfield, 0 Emsley, 2966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 143 time to evaluate : 1.039 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 314 GLN cc_start: 0.9003 (OUTLIER) cc_final: 0.8608 (tt0) REVERT: B 353 GLN cc_start: 0.9096 (mm-40) cc_final: 0.8859 (mp10) REVERT: C 82 MET cc_start: 0.9032 (tpt) cc_final: 0.8800 (mmm) REVERT: C 353 GLN cc_start: 0.9139 (mp10) cc_final: 0.8923 (mp10) REVERT: D 283 MET cc_start: 0.9352 (tpp) cc_final: 0.9035 (tpp) REVERT: D 325 MET cc_start: 0.9133 (mmm) cc_final: 0.8882 (mmm) REVERT: E 132 MET cc_start: 0.9236 (ptt) cc_final: 0.8794 (ppp) REVERT: Y 59 MET cc_start: 0.9143 (mtm) cc_final: 0.8802 (mtm) REVERT: Z 36 CYS cc_start: 0.9001 (t) cc_final: 0.8437 (p) REVERT: d 54 GLN cc_start: 0.8604 (mp10) cc_final: 0.8375 (mp10) REVERT: d 80 CYS cc_start: 0.9438 (m) cc_final: 0.8872 (m) outliers start: 18 outliers final: 13 residues processed: 157 average time/residue: 0.1592 time to fit residues: 41.3240 Evaluate side-chains 156 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 314 GLN Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain Z residue 8 CYS Chi-restraints excluded: chain Z residue 88 MET Chi-restraints excluded: chain Z residue 179 THR Chi-restraints excluded: chain a residue 25 THR Chi-restraints excluded: chain c residue 78 ASN Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain d residue 6 THR Chi-restraints excluded: chain d residue 26 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 288 optimal weight: 2.9990 chunk 294 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 chunk 125 optimal weight: 0.9980 chunk 189 optimal weight: 0.0070 chunk 197 optimal weight: 0.0470 chunk 67 optimal weight: 4.9990 chunk 251 optimal weight: 7.9990 chunk 184 optimal weight: 9.9990 chunk 214 optimal weight: 20.0000 overall best weight: 1.0100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 128 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.047220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.034271 restraints weight = 114753.006| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 3.71 r_work: 0.2585 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 24391 Z= 0.098 Angle : 0.512 8.797 33012 Z= 0.258 Chirality : 0.042 0.189 3682 Planarity : 0.004 0.072 4218 Dihedral : 4.903 57.351 3321 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 2.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.14 % Favored : 96.83 % Rotamer: Outliers : 0.54 % Allowed : 6.34 % Favored : 93.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.16), residues: 2966 helix: 1.52 (0.16), residues: 1155 sheet: 0.10 (0.21), residues: 669 loop : 0.17 (0.19), residues: 1142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG b 45 TYR 0.011 0.001 TYR Y 239 PHE 0.014 0.001 PHE Y 228 TRP 0.015 0.001 TRP Y 173 HIS 0.003 0.000 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00217 (24391) covalent geometry : angle 0.51198 (33012) hydrogen bonds : bond 0.02991 ( 1158) hydrogen bonds : angle 4.22274 ( 3237) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5932 Ramachandran restraints generated. 2966 Oldfield, 0 Emsley, 2966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5932 Ramachandran restraints generated. 2966 Oldfield, 0 Emsley, 2966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 MET cc_start: 0.8900 (ptm) cc_final: 0.8668 (ttp) REVERT: B 353 GLN cc_start: 0.9068 (mm-40) cc_final: 0.8768 (mp10) REVERT: C 82 MET cc_start: 0.8975 (tpt) cc_final: 0.8728 (mmm) REVERT: C 353 GLN cc_start: 0.9136 (mp10) cc_final: 0.8919 (mp10) REVERT: D 283 MET cc_start: 0.9331 (tpp) cc_final: 0.9085 (tpp) REVERT: D 325 MET cc_start: 0.9101 (mmm) cc_final: 0.8887 (mmm) REVERT: E 132 MET cc_start: 0.9186 (ptt) cc_final: 0.8844 (ppp) REVERT: Y 59 MET cc_start: 0.9132 (mtm) cc_final: 0.8793 (mtm) REVERT: Z 13 MET cc_start: 0.9347 (tpt) cc_final: 0.9091 (tpt) REVERT: Z 36 CYS cc_start: 0.9010 (t) cc_final: 0.8494 (p) REVERT: d 45 ARG cc_start: 0.9222 (ttm110) cc_final: 0.8530 (mmm-85) REVERT: d 54 GLN cc_start: 0.8645 (mp10) cc_final: 0.8247 (mp10) REVERT: d 80 CYS cc_start: 0.9421 (m) cc_final: 0.8871 (m) outliers start: 14 outliers final: 9 residues processed: 155 average time/residue: 0.1590 time to fit residues: 40.4585 Evaluate side-chains 150 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 1.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain Z residue 35 LEU Chi-restraints excluded: chain Z residue 88 MET Chi-restraints excluded: chain Z residue 179 THR Chi-restraints excluded: chain c residue 78 ASN Chi-restraints excluded: chain c residue 111 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 2 optimal weight: 0.0980 chunk 98 optimal weight: 4.9990 chunk 227 optimal weight: 10.0000 chunk 17 optimal weight: 0.9990 chunk 94 optimal weight: 10.0000 chunk 123 optimal weight: 1.9990 chunk 56 optimal weight: 0.0000 chunk 293 optimal weight: 0.9980 chunk 46 optimal weight: 0.9980 chunk 294 optimal weight: 8.9990 chunk 236 optimal weight: 7.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 19 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.047673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.034676 restraints weight = 114709.347| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.72 r_work: 0.2607 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 24391 Z= 0.087 Angle : 0.495 7.890 33012 Z= 0.248 Chirality : 0.042 0.187 3682 Planarity : 0.003 0.071 4218 Dihedral : 4.642 48.844 3321 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 2.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.27 % Favored : 96.70 % Rotamer: Outliers : 0.50 % Allowed : 6.68 % Favored : 92.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.16), residues: 2966 helix: 1.69 (0.16), residues: 1155 sheet: 0.28 (0.21), residues: 654 loop : 0.20 (0.19), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG b 45 TYR 0.011 0.001 TYR Y 239 PHE 0.013 0.001 PHE Y 228 TRP 0.014 0.001 TRP Y 173 HIS 0.002 0.000 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00188 (24391) covalent geometry : angle 0.49470 (33012) hydrogen bonds : bond 0.02733 ( 1158) hydrogen bonds : angle 4.05070 ( 3237) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5932 Ramachandran restraints generated. 2966 Oldfield, 0 Emsley, 2966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5932 Ramachandran restraints generated. 2966 Oldfield, 0 Emsley, 2966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 132 MET cc_start: 0.8884 (ptm) cc_final: 0.8657 (ttp) REVERT: B 353 GLN cc_start: 0.9024 (mm-40) cc_final: 0.8809 (mp10) REVERT: C 82 MET cc_start: 0.8994 (tpt) cc_final: 0.8751 (mmm) REVERT: C 305 MET cc_start: 0.9122 (mmt) cc_final: 0.8742 (mmt) REVERT: C 353 GLN cc_start: 0.9133 (mp10) cc_final: 0.8928 (mp10) REVERT: D 283 MET cc_start: 0.9322 (tpp) cc_final: 0.9104 (tpp) REVERT: E 132 MET cc_start: 0.9172 (ptt) cc_final: 0.8875 (ppp) REVERT: E 190 MET cc_start: 0.8900 (mmt) cc_final: 0.8685 (mmt) REVERT: Y 59 MET cc_start: 0.9143 (mtm) cc_final: 0.8803 (mtm) REVERT: d 54 GLN cc_start: 0.8618 (mp10) cc_final: 0.8174 (mp10) REVERT: d 80 CYS cc_start: 0.9390 (m) cc_final: 0.8814 (m) outliers start: 13 outliers final: 11 residues processed: 152 average time/residue: 0.1563 time to fit residues: 39.4769 Evaluate side-chains 153 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain Z residue 35 LEU Chi-restraints excluded: chain Z residue 88 MET Chi-restraints excluded: chain Z residue 179 THR Chi-restraints excluded: chain a residue 25 THR Chi-restraints excluded: chain c residue 78 ASN Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain d residue 129 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 56 optimal weight: 0.0070 chunk 243 optimal weight: 6.9990 chunk 138 optimal weight: 6.9990 chunk 218 optimal weight: 8.9990 chunk 268 optimal weight: 6.9990 chunk 223 optimal weight: 7.9990 chunk 177 optimal weight: 9.9990 chunk 262 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 295 optimal weight: 9.9990 chunk 161 optimal weight: 7.9990 overall best weight: 4.1604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 353 GLN Y 92 ASN Z 19 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.046070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.033137 restraints weight = 115388.529| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 3.66 r_work: 0.2542 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 24391 Z= 0.249 Angle : 0.593 11.053 33012 Z= 0.299 Chirality : 0.045 0.173 3682 Planarity : 0.004 0.066 4218 Dihedral : 5.057 64.514 3321 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.88 % Favored : 96.09 % Rotamer: Outliers : 0.54 % Allowed : 6.91 % Favored : 92.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.75 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.16), residues: 2966 helix: 1.44 (0.16), residues: 1180 sheet: 0.11 (0.21), residues: 669 loop : 0.14 (0.19), residues: 1117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG b 45 TYR 0.020 0.001 TYR b 89 PHE 0.013 0.001 PHE Y 228 TRP 0.013 0.002 TRP A 79 HIS 0.005 0.001 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00573 (24391) covalent geometry : angle 0.59344 (33012) hydrogen bonds : bond 0.03994 ( 1158) hydrogen bonds : angle 4.39022 ( 3237) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5932 Ramachandran restraints generated. 2966 Oldfield, 0 Emsley, 2966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5932 Ramachandran restraints generated. 2966 Oldfield, 0 Emsley, 2966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 GLU cc_start: 0.8948 (OUTLIER) cc_final: 0.8607 (mp0) REVERT: B 132 MET cc_start: 0.9048 (ptm) cc_final: 0.8833 (ttp) REVERT: B 353 GLN cc_start: 0.9083 (mm-40) cc_final: 0.8753 (mp10) REVERT: C 82 MET cc_start: 0.9032 (tpt) cc_final: 0.8791 (mmm) REVERT: C 353 GLN cc_start: 0.9139 (mp10) cc_final: 0.8926 (mp10) REVERT: D 283 MET cc_start: 0.9308 (tpp) cc_final: 0.9068 (tpp) REVERT: E 132 MET cc_start: 0.9264 (ptt) cc_final: 0.8784 (ppp) REVERT: Y 59 MET cc_start: 0.9173 (mtm) cc_final: 0.8709 (mtm) REVERT: Z 36 CYS cc_start: 0.8953 (t) cc_final: 0.8413 (p) REVERT: d 45 ARG cc_start: 0.9206 (ttm110) cc_final: 0.8499 (mmm-85) REVERT: d 54 GLN cc_start: 0.8611 (mp10) cc_final: 0.8358 (mp10) REVERT: d 80 CYS cc_start: 0.9450 (m) cc_final: 0.8825 (m) outliers start: 14 outliers final: 12 residues processed: 153 average time/residue: 0.1565 time to fit residues: 39.5215 Evaluate side-chains 152 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain B residue 318 THR Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain Z residue 35 LEU Chi-restraints excluded: chain Z residue 88 MET Chi-restraints excluded: chain Z residue 179 THR Chi-restraints excluded: chain a residue 25 THR Chi-restraints excluded: chain c residue 78 ASN Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain d residue 129 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 223 optimal weight: 10.0000 chunk 194 optimal weight: 20.0000 chunk 263 optimal weight: 7.9990 chunk 45 optimal weight: 0.4980 chunk 229 optimal weight: 0.9980 chunk 182 optimal weight: 0.6980 chunk 4 optimal weight: 6.9990 chunk 204 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 73 optimal weight: 4.9990 chunk 292 optimal weight: 8.9990 overall best weight: 1.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.046879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2756 r_free = 0.2756 target = 0.033900 restraints weight = 115415.262| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 3.72 r_work: 0.2570 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24391 Z= 0.119 Angle : 0.523 10.396 33012 Z= 0.262 Chirality : 0.043 0.170 3682 Planarity : 0.003 0.062 4218 Dihedral : 4.859 60.275 3321 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.17 % Favored : 96.80 % Rotamer: Outliers : 0.50 % Allowed : 6.91 % Favored : 92.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.16), residues: 2966 helix: 1.59 (0.16), residues: 1185 sheet: 0.16 (0.21), residues: 668 loop : 0.23 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG b 45 TYR 0.011 0.001 TYR Y 239 PHE 0.012 0.001 PHE Y 228 TRP 0.014 0.001 TRP Y 173 HIS 0.003 0.000 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00271 (24391) covalent geometry : angle 0.52326 (33012) hydrogen bonds : bond 0.03105 ( 1158) hydrogen bonds : angle 4.17495 ( 3237) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5932 Ramachandran restraints generated. 2966 Oldfield, 0 Emsley, 2966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5932 Ramachandran restraints generated. 2966 Oldfield, 0 Emsley, 2966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.820 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 GLU cc_start: 0.8952 (OUTLIER) cc_final: 0.8607 (mp0) REVERT: C 82 MET cc_start: 0.8997 (tpt) cc_final: 0.8750 (mmm) REVERT: C 353 GLN cc_start: 0.9138 (mp10) cc_final: 0.8926 (mp10) REVERT: E 190 MET cc_start: 0.8909 (mmt) cc_final: 0.8664 (mmt) REVERT: Y 59 MET cc_start: 0.9165 (mtm) cc_final: 0.8785 (ttm) REVERT: Z 36 CYS cc_start: 0.8954 (t) cc_final: 0.8435 (p) REVERT: d 45 ARG cc_start: 0.9211 (ttm110) cc_final: 0.8506 (mmm-85) REVERT: d 54 GLN cc_start: 0.8652 (mp10) cc_final: 0.8253 (mp10) REVERT: d 80 CYS cc_start: 0.9451 (m) cc_final: 0.8861 (m) outliers start: 13 outliers final: 10 residues processed: 152 average time/residue: 0.1580 time to fit residues: 39.8055 Evaluate side-chains 152 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 141 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain Z residue 35 LEU Chi-restraints excluded: chain Z residue 88 MET Chi-restraints excluded: chain Z residue 179 THR Chi-restraints excluded: chain a residue 25 THR Chi-restraints excluded: chain c residue 78 ASN Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain d residue 129 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 95 optimal weight: 6.9990 chunk 80 optimal weight: 0.0980 chunk 232 optimal weight: 7.9990 chunk 4 optimal weight: 0.4980 chunk 117 optimal weight: 3.9990 chunk 141 optimal weight: 0.8980 chunk 98 optimal weight: 3.9990 chunk 258 optimal weight: 4.9990 chunk 153 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 170 optimal weight: 5.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.046792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.033847 restraints weight = 115719.381| |-----------------------------------------------------------------------------| r_work (start): 0.2725 rms_B_bonded: 3.71 r_work: 0.2568 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 24391 Z= 0.132 Angle : 0.530 10.057 33012 Z= 0.266 Chirality : 0.043 0.164 3682 Planarity : 0.003 0.061 4218 Dihedral : 4.825 58.559 3321 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 3.19 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.61 % Favored : 96.36 % Rotamer: Outliers : 0.46 % Allowed : 7.03 % Favored : 92.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.16), residues: 2966 helix: 1.61 (0.16), residues: 1185 sheet: 0.19 (0.21), residues: 668 loop : 0.26 (0.19), residues: 1113 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG d 45 TYR 0.014 0.001 TYR D 279 PHE 0.012 0.001 PHE Y 228 TRP 0.014 0.001 TRP Y 173 HIS 0.003 0.000 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00303 (24391) covalent geometry : angle 0.53021 (33012) hydrogen bonds : bond 0.03201 ( 1158) hydrogen bonds : angle 4.16370 ( 3237) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5932 Ramachandran restraints generated. 2966 Oldfield, 0 Emsley, 2966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5932 Ramachandran restraints generated. 2966 Oldfield, 0 Emsley, 2966 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 140 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 364 GLU cc_start: 0.8947 (OUTLIER) cc_final: 0.8607 (mp0) REVERT: C 82 MET cc_start: 0.9001 (tpt) cc_final: 0.8754 (mmm) REVERT: C 353 GLN cc_start: 0.9146 (mp10) cc_final: 0.8931 (mp10) REVERT: E 190 MET cc_start: 0.8904 (mmt) cc_final: 0.8662 (mmt) REVERT: Y 59 MET cc_start: 0.9166 (mtm) cc_final: 0.8703 (mtm) REVERT: Z 36 CYS cc_start: 0.8968 (t) cc_final: 0.8454 (p) REVERT: d 54 GLN cc_start: 0.8641 (mp10) cc_final: 0.8386 (mp10) REVERT: d 80 CYS cc_start: 0.9452 (m) cc_final: 0.8833 (m) outliers start: 12 outliers final: 11 residues processed: 149 average time/residue: 0.1582 time to fit residues: 39.1208 Evaluate side-chains 151 residues out of total 2604 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain C residue 364 GLU Chi-restraints excluded: chain D residue 132 MET Chi-restraints excluded: chain D residue 364 GLU Chi-restraints excluded: chain E residue 203 THR Chi-restraints excluded: chain Z residue 35 LEU Chi-restraints excluded: chain Z residue 88 MET Chi-restraints excluded: chain Z residue 179 THR Chi-restraints excluded: chain a residue 25 THR Chi-restraints excluded: chain c residue 78 ASN Chi-restraints excluded: chain c residue 111 LEU Chi-restraints excluded: chain d residue 129 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 297 random chunks: chunk 158 optimal weight: 10.0000 chunk 87 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 74 optimal weight: 0.8980 chunk 54 optimal weight: 7.9990 chunk 58 optimal weight: 7.9990 chunk 188 optimal weight: 0.0270 chunk 90 optimal weight: 7.9990 chunk 1 optimal weight: 5.9990 chunk 213 optimal weight: 10.0000 chunk 281 optimal weight: 0.6980 overall best weight: 1.3242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 19 GLN d 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.047095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.034198 restraints weight = 114528.984| |-----------------------------------------------------------------------------| r_work (start): 0.2740 rms_B_bonded: 3.71 r_work: 0.2584 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8787 moved from start: 0.2650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 24391 Z= 0.107 Angle : 0.516 10.102 33012 Z= 0.258 Chirality : 0.043 0.163 3682 Planarity : 0.003 0.057 4218 Dihedral : 4.709 55.065 3321 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.24 % Favored : 96.73 % Rotamer: Outliers : 0.54 % Allowed : 7.03 % Favored : 92.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.75 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.16), residues: 2966 helix: 1.76 (0.16), residues: 1155 sheet: 0.17 (0.21), residues: 673 loop : 0.32 (0.19), residues: 1138 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG d 45 TYR 0.028 0.001 TYR D 279 PHE 0.012 0.001 PHE Y 228 TRP 0.014 0.001 TRP Y 173 HIS 0.003 0.000 HIS C 173 Details of bonding type rmsd covalent geometry : bond 0.00242 (24391) covalent geometry : angle 0.51611 (33012) hydrogen bonds : bond 0.02949 ( 1158) hydrogen bonds : angle 4.08092 ( 3237) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7143.69 seconds wall clock time: 123 minutes 6.84 seconds (7386.84 seconds total)