Starting phenix.real_space_refine on Fri Sep 11 20:59:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6hd1_0200/09_2026/6hd1_0200.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hd1_0200/09_2026/6hd1_0200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6hd1_0200/09_2026/6hd1_0200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hd1_0200/09_2026/6hd1_0200.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6hd1_0200/09_2026/6hd1_0200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hd1_0200/09_2026/6hd1_0200.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6hd1_0200/09_2026/6hd1_0200.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6hd1_0200/09_2026/6hd1_0200.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.006 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 Fe 3 7.16 5 P 18 5.49 5 S 51 5.16 5 C 7209 2.51 5 N 1800 2.21 5 O 1926 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 36 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11007 Number of models: 1 Model: "" Number of chains: 2 Chain: "C" Number of atoms: 3487 Number of conformers: 1 Conformer: "" Number of residues, atoms: 436, 3487 Classifications: {'peptide': 436} Link IDs: {'PTRANS': 20, 'TRANS': 415} Chain: "C" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 182 Unusual residues: {'44E': 1, 'FAD': 1, 'HEM': 1, 'NAG': 1, 'NAP': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: A, B Time building chain proxies: 3.18, per 1000 atoms: 0.29 Number of scatterers: 11007 At special positions: 0 Unit cell: (93.5935, 95.6505, 117.249, 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) Fe 3 26.01 S 51 16.00 P 18 15.00 O 1926 8.00 N 1800 7.00 C 7209 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=3, symmetry=0 Links applied NAG-ASN " NAG A 504 " - " ASN A 323 " " NAG B 504 " - " ASN B 323 " " NAG C 504 " - " ASN C 323 " Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.95 Conformation dependent library (CDL) restraints added in 536.6 milliseconds 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2454 Finding SS restraints... Secondary structure from input PDB file: 78 helices and 3 sheets defined 66.5% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'C' and resid 28 through 40 removed outlier: 3.559A pdb=" N SER C 33 " --> pdb=" O ASP C 29 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 66 through 71 Processing helix chain 'C' and resid 86 through 93 removed outlier: 3.596A pdb=" N THR C 90 " --> pdb=" O ASP C 87 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR C 93 " --> pdb=" O THR C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 125 Processing helix chain 'C' and resid 138 through 145 Processing helix chain 'C' and resid 159 through 171 removed outlier: 3.643A pdb=" N ARG C 165 " --> pdb=" O LYS C 161 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG C 171 " --> pdb=" O MET C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 172 through 174 No H-bonds generated for 'chain 'C' and resid 172 through 174' Processing helix chain 'C' and resid 182 through 184 No H-bonds generated for 'chain 'C' and resid 182 through 184' Processing helix chain 'C' and resid 185 through 192 removed outlier: 3.607A pdb=" N GLU C 190 " --> pdb=" O ALA C 186 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS C 191 " --> pdb=" O LYS C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 200 through 223 removed outlier: 3.561A pdb=" N PHE C 213 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE C 220 " --> pdb=" O PHE C 216 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG C 221 " --> pdb=" O TYR C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 229 Processing helix chain 'C' and resid 234 through 239 removed outlier: 4.114A pdb=" N ARG C 237 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N MET C 238 " --> pdb=" O THR C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 242 through 273 Proline residue: C 248 - end of helix removed outlier: 3.838A pdb=" N TYR C 259 " --> pdb=" O LEU C 255 " (cutoff:3.500A) Proline residue: C 261 - end of helix removed outlier: 3.595A pdb=" N LEU C 270 " --> pdb=" O ALA C 266 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 284 through 289 Processing helix chain 'C' and resid 289 through 310 removed outlier: 3.602A pdb=" N VAL C 296 " --> pdb=" O GLN C 292 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL C 310 " --> pdb=" O LEU C 306 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 313 No H-bonds generated for 'chain 'C' and resid 311 through 313' Processing helix chain 'C' and resid 314 through 331 Processing helix chain 'C' and resid 338 through 345 Processing helix chain 'C' and resid 346 through 366 removed outlier: 3.814A pdb=" N ALA C 350 " --> pdb=" O ASP C 346 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE C 359 " --> pdb=" O GLY C 355 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY C 363 " --> pdb=" O PHE C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 374 removed outlier: 3.947A pdb=" N VAL C 374 " --> pdb=" O SER C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 384 Processing helix chain 'C' and resid 384 through 406 removed outlier: 3.661A pdb=" N TYR C 388 " --> pdb=" O SER C 384 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU C 389 " --> pdb=" O LYS C 385 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR C 398 " --> pdb=" O CYS C 394 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N TYR C 401 " --> pdb=" O HIS C 397 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS C 404 " --> pdb=" O VAL C 400 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG C 405 " --> pdb=" O TYR C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 420 through 423 Processing helix chain 'C' and resid 424 through 438 removed outlier: 3.651A pdb=" N CYS C 428 " --> pdb=" O LEU C 424 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 450 removed outlier: 3.599A pdb=" N ASN C 444 " --> pdb=" O PRO C 440 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N THR C 445 " --> pdb=" O CYS C 441 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 40 removed outlier: 3.559A pdb=" N SER A 33 " --> pdb=" O ASP A 29 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 71 Processing helix chain 'A' and resid 86 through 93 removed outlier: 3.596A pdb=" N THR A 90 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR A 93 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 125 Processing helix chain 'A' and resid 138 through 145 Processing helix chain 'A' and resid 159 through 171 removed outlier: 3.643A pdb=" N ARG A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ARG A 171 " --> pdb=" O MET A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 174 No H-bonds generated for 'chain 'A' and resid 172 through 174' Processing helix chain 'A' and resid 182 through 184 No H-bonds generated for 'chain 'A' and resid 182 through 184' Processing helix chain 'A' and resid 185 through 192 removed outlier: 3.607A pdb=" N GLU A 190 " --> pdb=" O ALA A 186 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS A 191 " --> pdb=" O LYS A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 200 through 223 removed outlier: 3.560A pdb=" N PHE A 213 " --> pdb=" O VAL A 209 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE A 220 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG A 221 " --> pdb=" O TYR A 217 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 234 through 239 removed outlier: 4.113A pdb=" N ARG A 237 " --> pdb=" O ASN A 234 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N MET A 238 " --> pdb=" O THR A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 273 Proline residue: A 248 - end of helix removed outlier: 3.838A pdb=" N TYR A 259 " --> pdb=" O LEU A 255 " (cutoff:3.500A) Proline residue: A 261 - end of helix removed outlier: 3.596A pdb=" N LEU A 270 " --> pdb=" O ALA A 266 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG A 272 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 289 Processing helix chain 'A' and resid 289 through 310 removed outlier: 3.604A pdb=" N VAL A 296 " --> pdb=" O GLN A 292 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL A 310 " --> pdb=" O LEU A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 313 No H-bonds generated for 'chain 'A' and resid 311 through 313' Processing helix chain 'A' and resid 314 through 331 Processing helix chain 'A' and resid 338 through 345 Processing helix chain 'A' and resid 346 through 366 removed outlier: 3.815A pdb=" N ALA A 350 " --> pdb=" O ASP A 346 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N GLY A 363 " --> pdb=" O PHE A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 374 removed outlier: 3.948A pdb=" N VAL A 374 " --> pdb=" O SER A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 384 Processing helix chain 'A' and resid 384 through 406 removed outlier: 3.661A pdb=" N TYR A 388 " --> pdb=" O SER A 384 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU A 389 " --> pdb=" O LYS A 385 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR A 398 " --> pdb=" O CYS A 394 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N TYR A 401 " --> pdb=" O HIS A 397 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS A 404 " --> pdb=" O VAL A 400 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ARG A 405 " --> pdb=" O TYR A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 423 Processing helix chain 'A' and resid 424 through 438 removed outlier: 3.652A pdb=" N CYS A 428 " --> pdb=" O LEU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 439 through 450 removed outlier: 3.600A pdb=" N ASN A 444 " --> pdb=" O PRO A 440 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N THR A 445 " --> pdb=" O CYS A 441 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 40 removed outlier: 3.559A pdb=" N SER B 33 " --> pdb=" O ASP B 29 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLN B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 71 Processing helix chain 'B' and resid 86 through 93 removed outlier: 3.597A pdb=" N THR B 90 " --> pdb=" O ASP B 87 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N THR B 93 " --> pdb=" O THR B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 116 through 125 Processing helix chain 'B' and resid 138 through 145 Processing helix chain 'B' and resid 159 through 171 removed outlier: 3.644A pdb=" N ARG B 165 " --> pdb=" O LYS B 161 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ARG B 171 " --> pdb=" O MET B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 174 No H-bonds generated for 'chain 'B' and resid 172 through 174' Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 185 through 192 removed outlier: 3.608A pdb=" N GLU B 190 " --> pdb=" O ALA B 186 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYS B 191 " --> pdb=" O LYS B 187 " (cutoff:3.500A) Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 200 through 223 removed outlier: 3.561A pdb=" N PHE B 213 " --> pdb=" O VAL B 209 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ILE B 220 " --> pdb=" O PHE B 216 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ARG B 221 " --> pdb=" O TYR B 217 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 229 Processing helix chain 'B' and resid 234 through 239 removed outlier: 4.115A pdb=" N ARG B 237 " --> pdb=" O ASN B 234 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N MET B 238 " --> pdb=" O THR B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 273 Proline residue: B 248 - end of helix removed outlier: 3.838A pdb=" N TYR B 259 " --> pdb=" O LEU B 255 " (cutoff:3.500A) Proline residue: B 261 - end of helix removed outlier: 3.595A pdb=" N LEU B 270 " --> pdb=" O ALA B 266 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N ARG B 272 " --> pdb=" O LEU B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 284 through 289 Processing helix chain 'B' and resid 289 through 310 removed outlier: 3.604A pdb=" N VAL B 296 " --> pdb=" O GLN B 292 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N VAL B 310 " --> pdb=" O LEU B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 313 No H-bonds generated for 'chain 'B' and resid 311 through 313' Processing helix chain 'B' and resid 314 through 331 Processing helix chain 'B' and resid 338 through 345 Processing helix chain 'B' and resid 346 through 366 removed outlier: 3.815A pdb=" N ALA B 350 " --> pdb=" O ASP B 346 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE B 359 " --> pdb=" O GLY B 355 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY B 363 " --> pdb=" O PHE B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 374 removed outlier: 3.947A pdb=" N VAL B 374 " --> pdb=" O SER B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 384 Processing helix chain 'B' and resid 384 through 406 removed outlier: 3.663A pdb=" N TYR B 388 " --> pdb=" O SER B 384 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N LEU B 389 " --> pdb=" O LYS B 385 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N THR B 398 " --> pdb=" O CYS B 394 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N TYR B 401 " --> pdb=" O HIS B 397 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS B 404 " --> pdb=" O VAL B 400 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARG B 405 " --> pdb=" O TYR B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 423 Processing helix chain 'B' and resid 424 through 438 removed outlier: 3.651A pdb=" N CYS B 428 " --> pdb=" O LEU B 424 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 450 removed outlier: 3.599A pdb=" N ASN B 444 " --> pdb=" O PRO B 440 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N THR B 445 " --> pdb=" O CYS B 441 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 64 through 65 removed outlier: 7.795A pdb=" N LEU C 65 " --> pdb=" O VAL C 45 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N PHE C 47 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL C 22 " --> pdb=" O VAL C 46 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLY C 48 " --> pdb=" O VAL C 22 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE C 24 " --> pdb=" O GLY C 48 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE C 76 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL C 153 " --> pdb=" O MET C 178 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 65 removed outlier: 7.795A pdb=" N LEU A 65 " --> pdb=" O VAL A 45 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N PHE A 47 " --> pdb=" O LEU A 65 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N VAL A 22 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N GLY A 48 " --> pdb=" O VAL A 22 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE A 24 " --> pdb=" O GLY A 48 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N ILE A 76 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 5.962A pdb=" N VAL A 153 " --> pdb=" O MET A 178 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 64 through 65 removed outlier: 7.796A pdb=" N LEU B 65 " --> pdb=" O VAL B 45 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N PHE B 47 " --> pdb=" O LEU B 65 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL B 22 " --> pdb=" O VAL B 46 " (cutoff:3.500A) removed outlier: 7.742A pdb=" N GLY B 48 " --> pdb=" O VAL B 22 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILE B 24 " --> pdb=" O GLY B 48 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N ILE B 76 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N VAL B 153 " --> pdb=" O MET B 178 " (cutoff:3.500A) 504 hydrogen bonds defined for protein. 1458 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: 1.60 Time building geometry restraints manager: 1.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.36: 3426 1.36 - 1.54: 7678 1.54 - 1.72: 134 1.72 - 1.90: 78 1.90 - 2.07: 9 Bond restraints: 11325 Sorted by residual: bond pdb=" C1D NAP C 501 " pdb=" C2D NAP C 501 " ideal model delta sigma weight residual 1.533 1.296 0.237 2.00e-02 2.50e+03 1.40e+02 bond pdb=" C1D NAP A 501 " pdb=" C2D NAP A 501 " ideal model delta sigma weight residual 1.533 1.297 0.236 2.00e-02 2.50e+03 1.39e+02 bond pdb=" C1D NAP B 501 " pdb=" C2D NAP B 501 " ideal model delta sigma weight residual 1.533 1.298 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C1D NAP C 501 " pdb=" O4D NAP C 501 " ideal model delta sigma weight residual 1.375 1.609 -0.234 2.00e-02 2.50e+03 1.36e+02 bond pdb=" C1D NAP A 501 " pdb=" O4D NAP A 501 " ideal model delta sigma weight residual 1.375 1.608 -0.233 2.00e-02 2.50e+03 1.36e+02 ... (remaining 11320 not shown) Histogram of bond angle deviations from ideal: 0.00 - 10.95: 15474 10.95 - 21.90: 21 21.90 - 32.84: 0 32.84 - 43.79: 0 43.79 - 54.74: 3 Bond angle restraints: 15498 Sorted by residual: angle pdb=" O13 44E B 505 " pdb=" P 44E B 505 " pdb=" O14 44E B 505 " ideal model delta sigma weight residual 54.79 109.53 -54.74 3.00e+00 1.11e-01 3.33e+02 angle pdb=" O13 44E C 505 " pdb=" P 44E C 505 " pdb=" O14 44E C 505 " ideal model delta sigma weight residual 54.79 109.51 -54.72 3.00e+00 1.11e-01 3.33e+02 angle pdb=" O13 44E A 505 " pdb=" P 44E A 505 " pdb=" O14 44E A 505 " ideal model delta sigma weight residual 54.79 109.49 -54.70 3.00e+00 1.11e-01 3.32e+02 angle pdb=" O12 44E B 505 " pdb=" P 44E B 505 " pdb=" O14 44E B 505 " ideal model delta sigma weight residual 127.76 109.81 17.95 3.00e+00 1.11e-01 3.58e+01 angle pdb=" O12 44E A 505 " pdb=" P 44E A 505 " pdb=" O14 44E A 505 " ideal model delta sigma weight residual 127.76 109.82 17.94 3.00e+00 1.11e-01 3.58e+01 ... (remaining 15493 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.61: 6357 35.61 - 71.21: 98 71.21 - 106.82: 25 106.82 - 142.42: 0 142.42 - 178.03: 3 Dihedral angle restraints: 6483 sinusoidal: 2658 harmonic: 3825 Sorted by residual: dihedral pdb=" C2C HEM A 502 " pdb=" C3C HEM A 502 " pdb=" CAC HEM A 502 " pdb=" CBC HEM A 502 " ideal model delta sinusoidal sigma weight residual 0.00 -79.75 79.75 2 1.00e+01 1.00e-02 4.65e+01 dihedral pdb=" C2C HEM B 502 " pdb=" C3C HEM B 502 " pdb=" CAC HEM B 502 " pdb=" CBC HEM B 502 " ideal model delta sinusoidal sigma weight residual -0.00 -79.74 79.74 2 1.00e+01 1.00e-02 4.65e+01 dihedral pdb=" C2C HEM C 502 " pdb=" C3C HEM C 502 " pdb=" CAC HEM C 502 " pdb=" CBC HEM C 502 " ideal model delta sinusoidal sigma weight residual -0.00 -79.68 79.68 2 1.00e+01 1.00e-02 4.65e+01 ... (remaining 6480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 1427 0.075 - 0.151: 287 0.151 - 0.226: 20 0.226 - 0.301: 6 0.301 - 0.377: 3 Chirality restraints: 1743 Sorted by residual: chirality pdb=" C2B NAP C 501 " pdb=" C1B NAP C 501 " pdb=" C3B NAP C 501 " pdb=" O2B NAP C 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.38 -0.38 2.00e-01 2.50e+01 3.55e+00 chirality pdb=" C2B NAP B 501 " pdb=" C1B NAP B 501 " pdb=" C3B NAP B 501 " pdb=" O2B NAP B 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.38 -0.38 2.00e-01 2.50e+01 3.53e+00 chirality pdb=" C2B NAP A 501 " pdb=" C1B NAP A 501 " pdb=" C3B NAP A 501 " pdb=" O2B NAP A 501 " both_signs ideal model delta sigma weight residual False -2.75 -2.38 -0.37 2.00e-01 2.50e+01 3.45e+00 ... (remaining 1740 not shown) Planarity restraints: 1842 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 286 " -0.017 2.00e-02 2.50e+03 1.53e-02 5.85e+00 pdb=" CG TRP C 286 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP C 286 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP C 286 " -0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP C 286 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP C 286 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP C 286 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 286 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 286 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP C 286 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 286 " -0.017 2.00e-02 2.50e+03 1.53e-02 5.83e+00 pdb=" CG TRP B 286 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP B 286 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 286 " -0.006 2.00e-02 2.50e+03 pdb=" NE1 TRP B 286 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP B 286 " -0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP B 286 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 286 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 286 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 286 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 286 " 0.017 2.00e-02 2.50e+03 1.51e-02 5.69e+00 pdb=" CG TRP A 286 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP A 286 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP A 286 " 0.007 2.00e-02 2.50e+03 pdb=" NE1 TRP A 286 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 286 " 0.008 2.00e-02 2.50e+03 pdb=" CE3 TRP A 286 " 0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 286 " -0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 286 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP A 286 " -0.002 2.00e-02 2.50e+03 ... (remaining 1839 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 50 2.56 - 3.14: 8619 3.14 - 3.73: 16749 3.73 - 4.31: 23815 4.31 - 4.90: 38541 Nonbonded interactions: 87774 Sorted by model distance: nonbonded pdb=" NE2 HIS C 397 " pdb="FE HEM C 502 " model vdw 1.971 3.080 nonbonded pdb=" NE2 HIS B 397 " pdb="FE HEM B 502 " model vdw 1.972 3.080 nonbonded pdb=" NE2 HIS A 397 " pdb="FE HEM A 502 " model vdw 1.972 3.080 nonbonded pdb=" OD2 ASP A 148 " pdb=" N3 FAD B 503 " model vdw 2.246 3.120 nonbonded pdb=" O3' FAD C 503 " pdb=" O5' FAD C 503 " model vdw 2.271 3.040 ... (remaining 87769 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: 0.03 Found NCS groups: ncs_group { reference = chain 'C' selection = chain 'A' selection = chain 'B' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.060 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: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.000 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 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 : 0.016 0.241 11331 Z= 0.712 Angle : 1.519 54.739 15507 Z= 0.655 Chirality : 0.062 0.377 1743 Planarity : 0.008 0.059 1839 Dihedral : 14.408 178.025 4029 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 0.79 % Allowed : 4.22 % Favored : 94.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -5.57 (0.16), residues: 1302 helix: -3.74 (0.10), residues: 816 sheet: -1.81 (0.46), residues: 102 loop : -3.53 (0.28), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 314 TYR 0.024 0.002 TYR B 271 PHE 0.027 0.003 PHE C 359 TRP 0.042 0.003 TRP C 286 HIS 0.012 0.002 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.01550 / 0.71 (11325) covalent geometry : angle 1.51590 / 0.65 (15498) hydrogen bonds : bond 0.27182 / 17.93 ( 504) hydrogen bonds : angle 9.28052 / 6.30 ( 1458) Misc. bond : bond 0.20393 / 10.22 ( 3) link_NAG-ASN : bond 0.00797 / 0.40 ( 3) link_NAG-ASN : angle 4.21003 / 2.76 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 260 time to evaluate : 0.471 Fit side-chains revert: symmetry clash REVERT: C 77 ILE cc_start: 0.9468 (mt) cc_final: 0.9260 (tp) REVERT: C 222 ASP cc_start: 0.8490 (m-30) cc_final: 0.8270 (m-30) REVERT: C 268 LEU cc_start: 0.9458 (tp) cc_final: 0.9212 (tp) REVERT: C 347 SER cc_start: 0.9419 (t) cc_final: 0.9062 (m) REVERT: C 366 SER cc_start: 0.9284 (m) cc_final: 0.9074 (p) REVERT: C 443 ASP cc_start: 0.9204 (t70) cc_final: 0.8972 (p0) REVERT: A 77 ILE cc_start: 0.9398 (mt) cc_final: 0.9183 (tp) REVERT: A 184 MET cc_start: 0.8214 (mmp) cc_final: 0.7967 (tmm) REVERT: A 202 PHE cc_start: 0.8417 (t80) cc_final: 0.8087 (t80) REVERT: A 222 ASP cc_start: 0.8487 (m-30) cc_final: 0.8094 (m-30) REVERT: A 259 TYR cc_start: 0.9125 (m-80) cc_final: 0.8841 (m-10) REVERT: A 282 TRP cc_start: 0.9279 (p-90) cc_final: 0.8935 (p-90) REVERT: A 347 SER cc_start: 0.9536 (t) cc_final: 0.9179 (m) REVERT: A 378 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8074 (mp0) REVERT: B 33 SER cc_start: 0.9468 (m) cc_final: 0.9185 (p) REVERT: B 92 LEU cc_start: 0.9371 (OUTLIER) cc_final: 0.9028 (pp) REVERT: B 147 LEU cc_start: 0.8719 (OUTLIER) cc_final: 0.8440 (pp) REVERT: B 168 ASP cc_start: 0.8122 (m-30) cc_final: 0.7786 (m-30) REVERT: B 184 MET cc_start: 0.8212 (mmp) cc_final: 0.7974 (tmm) REVERT: B 202 PHE cc_start: 0.8434 (t80) cc_final: 0.8202 (t80) REVERT: B 347 SER cc_start: 0.9455 (t) cc_final: 0.9084 (m) REVERT: B 447 THR cc_start: 0.9305 (m) cc_final: 0.9073 (p) outliers start: 9 outliers final: 0 residues processed: 268 average time/residue: 0.0929 time to fit residues: 37.0222 Evaluate side-chains 133 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 147 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 2.9990 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 19 GLN C 234 ASN ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 234 ASN ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 234 ASN B 285 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.076704 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.057330 restraints weight = 31016.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.059593 restraints weight = 14900.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.060971 restraints weight = 9976.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.061643 restraints weight = 8035.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.062201 restraints weight = 7196.625| |-----------------------------------------------------------------------------| r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.313 11331 Z= 0.142 Angle : 0.738 15.933 15507 Z= 0.333 Chirality : 0.044 0.155 1743 Planarity : 0.005 0.038 1839 Dihedral : 15.097 174.249 1618 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.90 % Allowed : 11.79 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -2.40 (0.22), residues: 1302 helix: -1.01 (0.17), residues: 786 sheet: -1.65 (0.48), residues: 102 loop : -2.47 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 450 TYR 0.018 0.001 TYR A 67 PHE 0.027 0.001 PHE C 202 TRP 0.018 0.002 TRP B 286 HIS 0.004 0.001 HIS C 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (11325) covalent geometry : angle 0.73481 / 0.33 (15498) hydrogen bonds : bond 0.04458 / 3.06 ( 504) hydrogen bonds : angle 4.66050 / 3.18 ( 1458) Misc. bond : bond 0.30661 / 15.37 ( 3) link_NAG-ASN : bond 0.00703 / 0.35 ( 3) link_NAG-ASN : angle 2.74005 / 1.78 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 189 time to evaluate : 0.400 Fit side-chains REVERT: C 38 MET cc_start: 0.8998 (mtp) cc_final: 0.8459 (mtp) REVERT: C 77 ILE cc_start: 0.9376 (mt) cc_final: 0.9126 (tp) REVERT: C 150 SER cc_start: 0.9215 (p) cc_final: 0.8995 (p) REVERT: C 268 LEU cc_start: 0.9432 (tp) cc_final: 0.9224 (tt) REVERT: C 380 ARG cc_start: 0.8807 (ttp-170) cc_final: 0.8482 (ttt90) REVERT: A 77 ILE cc_start: 0.9296 (mt) cc_final: 0.9038 (tp) REVERT: A 268 LEU cc_start: 0.9422 (OUTLIER) cc_final: 0.9190 (tt) REVERT: A 378 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8211 (mt-10) REVERT: A 391 LEU cc_start: 0.9686 (OUTLIER) cc_final: 0.9441 (tm) REVERT: B 92 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9006 (pp) REVERT: B 147 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8273 (pp) REVERT: B 184 MET cc_start: 0.8162 (mmp) cc_final: 0.7820 (tmm) REVERT: B 202 PHE cc_start: 0.8252 (t80) cc_final: 0.7913 (t80) outliers start: 33 outliers final: 11 residues processed: 207 average time/residue: 0.0726 time to fit residues: 24.2662 Evaluate side-chains 132 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 117 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 92 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 391 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 84 optimal weight: 7.9990 chunk 61 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 128 optimal weight: 2.9990 chunk 75 optimal weight: 1.9990 chunk 68 optimal weight: 8.9990 chunk 26 optimal weight: 0.8980 chunk 99 optimal weight: 8.9990 chunk 88 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 19 GLN A 40 GLN ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.075551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.057619 restraints weight = 31498.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2768 r_free = 0.2768 target = 0.059821 restraints weight = 14638.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.061178 restraints weight = 9542.960| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.061902 restraints weight = 7558.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.062381 restraints weight = 6671.208| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.330 11331 Z= 0.184 Angle : 0.727 17.356 15507 Z= 0.316 Chirality : 0.045 0.200 1743 Planarity : 0.004 0.034 1839 Dihedral : 14.578 169.769 1618 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 3.43 % Allowed : 14.86 % Favored : 81.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.26 (0.23), residues: 1302 helix: 0.10 (0.18), residues: 798 sheet: -1.55 (0.49), residues: 102 loop : -2.43 (0.32), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 290 TYR 0.013 0.001 TYR B 259 PHE 0.022 0.002 PHE B 359 TRP 0.018 0.002 TRP C 286 HIS 0.003 0.001 HIS C 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.18 (11325) covalent geometry : angle 0.72532 / 0.32 (15498) hydrogen bonds : bond 0.03774 / 2.57 ( 504) hydrogen bonds : angle 4.16282 / 2.84 ( 1458) Misc. bond : bond 0.32693 / 16.39 ( 3) link_NAG-ASN : bond 0.00690 / 0.34 ( 3) link_NAG-ASN : angle 2.10339 / 1.51 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 132 time to evaluate : 0.455 Fit side-chains REVERT: C 77 ILE cc_start: 0.9342 (mt) cc_final: 0.9116 (tp) REVERT: C 268 LEU cc_start: 0.9440 (tp) cc_final: 0.9165 (tt) REVERT: C 380 ARG cc_start: 0.8808 (ttp-170) cc_final: 0.8494 (ttt90) REVERT: A 39 LEU cc_start: 0.9351 (OUTLIER) cc_final: 0.9069 (mt) REVERT: A 77 ILE cc_start: 0.9316 (mt) cc_final: 0.9097 (tp) REVERT: A 268 LEU cc_start: 0.9420 (OUTLIER) cc_final: 0.9134 (tt) REVERT: A 378 GLU cc_start: 0.8620 (mt-10) cc_final: 0.8325 (mt-10) REVERT: A 391 LEU cc_start: 0.9669 (OUTLIER) cc_final: 0.9403 (tm) REVERT: B 147 LEU cc_start: 0.8584 (OUTLIER) cc_final: 0.8308 (pp) outliers start: 39 outliers final: 22 residues processed: 159 average time/residue: 0.0743 time to fit residues: 19.3795 Evaluate side-chains 136 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 110 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 428 CYS Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 390 THR Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 390 THR Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 447 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 107 optimal weight: 0.0050 chunk 44 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 82 optimal weight: 7.9990 chunk 16 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.8598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.076268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2717 r_free = 0.2717 target = 0.057345 restraints weight = 31520.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.059605 restraints weight = 15003.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.061009 restraints weight = 10018.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.061786 restraints weight = 8024.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.062027 restraints weight = 7128.796| |-----------------------------------------------------------------------------| r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.229 11331 Z= 0.117 Angle : 0.658 14.162 15507 Z= 0.285 Chirality : 0.043 0.187 1743 Planarity : 0.004 0.033 1839 Dihedral : 14.181 170.773 1616 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 2.90 % Allowed : 16.36 % Favored : 80.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.69 (0.24), residues: 1302 helix: 0.64 (0.19), residues: 801 sheet: -1.42 (0.48), residues: 102 loop : -2.42 (0.31), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 290 TYR 0.012 0.001 TYR C 348 PHE 0.023 0.001 PHE B 202 TRP 0.016 0.001 TRP A 286 HIS 0.003 0.001 HIS B 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.11 (11325) covalent geometry : angle 0.65665 / 0.28 (15498) hydrogen bonds : bond 0.03212 / 2.19 ( 504) hydrogen bonds : angle 3.88056 / 2.64 ( 1458) Misc. bond : bond 0.22621 / 11.34 ( 3) link_NAG-ASN : bond 0.00770 / 0.39 ( 3) link_NAG-ASN : angle 1.91193 / 1.34 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 140 time to evaluate : 0.449 Fit side-chains REVERT: C 38 MET cc_start: 0.8925 (mtp) cc_final: 0.8518 (mtp) REVERT: C 77 ILE cc_start: 0.9243 (mt) cc_final: 0.8994 (tp) REVERT: C 150 SER cc_start: 0.9206 (p) cc_final: 0.8948 (p) REVERT: C 268 LEU cc_start: 0.9383 (tp) cc_final: 0.9001 (tt) REVERT: C 380 ARG cc_start: 0.8804 (ttp-170) cc_final: 0.8493 (ttt90) REVERT: A 38 MET cc_start: 0.8668 (mtp) cc_final: 0.8415 (mtp) REVERT: A 77 ILE cc_start: 0.9273 (mt) cc_final: 0.9036 (tp) REVERT: A 268 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9082 (tt) REVERT: A 378 GLU cc_start: 0.8606 (mt-10) cc_final: 0.8342 (mt-10) REVERT: A 391 LEU cc_start: 0.9658 (OUTLIER) cc_final: 0.9358 (tm) REVERT: B 147 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8248 (pp) REVERT: B 380 ARG cc_start: 0.8816 (ttp-170) cc_final: 0.8497 (ttt90) outliers start: 33 outliers final: 21 residues processed: 161 average time/residue: 0.0753 time to fit residues: 19.6511 Evaluate side-chains 146 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 255 LEU Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 424 LEU Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 391 LEU Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 391 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 61 optimal weight: 0.4980 chunk 54 optimal weight: 0.9990 chunk 9 optimal weight: 6.9990 chunk 79 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 102 optimal weight: 9.9990 chunk 89 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 328 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.076342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.058022 restraints weight = 31439.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.060220 restraints weight = 14579.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.061609 restraints weight = 9620.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.062373 restraints weight = 7657.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.062823 restraints weight = 6760.956| |-----------------------------------------------------------------------------| r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.3636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.192 11331 Z= 0.111 Angle : 0.645 13.706 15507 Z= 0.277 Chirality : 0.043 0.204 1743 Planarity : 0.003 0.031 1839 Dihedral : 13.725 171.006 1616 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.90 % Allowed : 16.80 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.27 (0.24), residues: 1302 helix: 0.97 (0.19), residues: 804 sheet: -1.20 (0.49), residues: 102 loop : -2.31 (0.31), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 278 TYR 0.011 0.001 TYR C 348 PHE 0.022 0.001 PHE B 202 TRP 0.017 0.001 TRP A 286 HIS 0.002 0.001 HIS C 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.11 (11325) covalent geometry : angle 0.64400 / 0.28 (15498) hydrogen bonds : bond 0.02970 / 2.03 ( 504) hydrogen bonds : angle 3.73577 / 2.54 ( 1458) Misc. bond : bond 0.18801 / 9.42 ( 3) link_NAG-ASN : bond 0.00668 / 0.33 ( 3) link_NAG-ASN : angle 1.87820 / 1.32 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 137 time to evaluate : 0.337 Fit side-chains REVERT: C 38 MET cc_start: 0.8873 (mtp) cc_final: 0.8448 (mtp) REVERT: C 77 ILE cc_start: 0.9121 (mt) cc_final: 0.8872 (tp) REVERT: C 268 LEU cc_start: 0.9370 (tp) cc_final: 0.8968 (tt) REVERT: C 347 SER cc_start: 0.9402 (m) cc_final: 0.9173 (p) REVERT: C 380 ARG cc_start: 0.8817 (ttp-170) cc_final: 0.8488 (ttt90) REVERT: A 77 ILE cc_start: 0.9233 (mt) cc_final: 0.8947 (tp) REVERT: A 268 LEU cc_start: 0.9354 (OUTLIER) cc_final: 0.9009 (tt) REVERT: A 378 GLU cc_start: 0.8594 (mt-10) cc_final: 0.8365 (mt-10) REVERT: B 147 LEU cc_start: 0.8488 (OUTLIER) cc_final: 0.8232 (pp) REVERT: B 380 ARG cc_start: 0.8833 (ttp-170) cc_final: 0.8524 (ttt90) outliers start: 33 outliers final: 21 residues processed: 159 average time/residue: 0.0731 time to fit residues: 18.9981 Evaluate side-chains 149 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 126 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 218 CYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 441 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 54 optimal weight: 0.8980 chunk 69 optimal weight: 0.6980 chunk 125 optimal weight: 0.0770 chunk 85 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 78 optimal weight: 0.9990 chunk 6 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 285 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.077564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.059446 restraints weight = 31335.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.061676 restraints weight = 14546.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.063010 restraints weight = 9519.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.063948 restraints weight = 7586.609| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.064338 restraints weight = 6604.581| |-----------------------------------------------------------------------------| r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.149 11331 Z= 0.102 Angle : 0.640 13.028 15507 Z= 0.275 Chirality : 0.043 0.141 1743 Planarity : 0.003 0.031 1839 Dihedral : 13.253 171.734 1616 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.02 % Allowed : 18.82 % Favored : 79.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.36 (0.24), residues: 1302 helix: 0.83 (0.19), residues: 840 sheet: -0.93 (0.50), residues: 102 loop : -2.58 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 278 TYR 0.014 0.001 TYR A 348 PHE 0.023 0.001 PHE B 202 TRP 0.017 0.001 TRP A 286 HIS 0.004 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.10 (11325) covalent geometry : angle 0.63835 / 0.28 (15498) hydrogen bonds : bond 0.02836 / 1.92 ( 504) hydrogen bonds : angle 3.64094 / 2.48 ( 1458) Misc. bond : bond 0.14714 / 7.38 ( 3) link_NAG-ASN : bond 0.00680 / 0.34 ( 3) link_NAG-ASN : angle 1.79822 / 1.21 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 0.429 Fit side-chains revert: symmetry clash REVERT: C 38 MET cc_start: 0.8863 (mtp) cc_final: 0.8461 (mtp) REVERT: C 268 LEU cc_start: 0.9332 (tp) cc_final: 0.8950 (tt) REVERT: C 347 SER cc_start: 0.9373 (m) cc_final: 0.9161 (p) REVERT: C 380 ARG cc_start: 0.8838 (ttp-170) cc_final: 0.8491 (ttt90) REVERT: A 77 ILE cc_start: 0.9209 (mt) cc_final: 0.8929 (tp) REVERT: A 438 ILE cc_start: 0.9158 (mm) cc_final: 0.8839 (tp) REVERT: B 147 LEU cc_start: 0.8490 (OUTLIER) cc_final: 0.8261 (pp) REVERT: B 380 ARG cc_start: 0.8832 (ttp-170) cc_final: 0.8531 (ttt90) outliers start: 23 outliers final: 16 residues processed: 151 average time/residue: 0.0739 time to fit residues: 18.2629 Evaluate side-chains 138 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 121 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.7980 chunk 51 optimal weight: 8.9990 chunk 87 optimal weight: 5.9990 chunk 91 optimal weight: 0.0050 chunk 103 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 100 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 46 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.076270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.057030 restraints weight = 31459.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.059244 restraints weight = 14883.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2800 r_free = 0.2800 target = 0.060661 restraints weight = 10008.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.061360 restraints weight = 8037.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.061811 restraints weight = 7177.675| |-----------------------------------------------------------------------------| r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.184 11331 Z= 0.126 Angle : 0.663 14.952 15507 Z= 0.281 Chirality : 0.043 0.197 1743 Planarity : 0.003 0.029 1839 Dihedral : 12.657 171.863 1616 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 2.90 % Allowed : 18.65 % Favored : 78.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.14 (0.25), residues: 1302 helix: 0.98 (0.19), residues: 840 sheet: -0.77 (0.51), residues: 102 loop : -2.44 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 377 TYR 0.011 0.001 TYR C 348 PHE 0.023 0.001 PHE B 202 TRP 0.022 0.001 TRP A 286 HIS 0.002 0.001 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.12 (11325) covalent geometry : angle 0.66182 / 0.28 (15498) hydrogen bonds : bond 0.02882 / 1.96 ( 504) hydrogen bonds : angle 3.65906 / 2.50 ( 1458) Misc. bond : bond 0.18042 / 9.05 ( 3) link_NAG-ASN : bond 0.00560 / 0.28 ( 3) link_NAG-ASN : angle 1.84701 / 1.33 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 121 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: C 38 MET cc_start: 0.8837 (mtp) cc_final: 0.8434 (mtp) REVERT: C 268 LEU cc_start: 0.9329 (tp) cc_final: 0.8934 (tt) REVERT: C 380 ARG cc_start: 0.8820 (ttp-170) cc_final: 0.8484 (ttt90) REVERT: C 438 ILE cc_start: 0.9170 (OUTLIER) cc_final: 0.8931 (tp) REVERT: A 77 ILE cc_start: 0.9247 (mt) cc_final: 0.8952 (tp) REVERT: A 147 LEU cc_start: 0.8827 (OUTLIER) cc_final: 0.8602 (pp) REVERT: B 38 MET cc_start: 0.8727 (mtp) cc_final: 0.8478 (mtp) REVERT: B 380 ARG cc_start: 0.8794 (ttp-170) cc_final: 0.8503 (ttt90) outliers start: 33 outliers final: 25 residues processed: 142 average time/residue: 0.0772 time to fit residues: 17.8354 Evaluate side-chains 145 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 130 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 390 THR Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 391 LEU Chi-restraints excluded: chain B residue 399 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 77 optimal weight: 0.7980 chunk 3 optimal weight: 0.2980 chunk 125 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 81 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.077212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.058962 restraints weight = 31171.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.061156 restraints weight = 14660.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.062513 restraints weight = 9695.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.063402 restraints weight = 7734.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.063791 restraints weight = 6737.454| |-----------------------------------------------------------------------------| r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.4048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 11331 Z= 0.106 Angle : 0.661 13.924 15507 Z= 0.280 Chirality : 0.043 0.246 1743 Planarity : 0.003 0.030 1839 Dihedral : 12.157 171.572 1614 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.93 % Allowed : 19.53 % Favored : 78.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.06 (0.25), residues: 1302 helix: 1.09 (0.19), residues: 843 sheet: -0.57 (0.52), residues: 102 loop : -2.33 (0.33), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 151 TYR 0.014 0.001 TYR C 348 PHE 0.024 0.001 PHE B 202 TRP 0.022 0.001 TRP A 286 HIS 0.002 0.000 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.10 (11325) covalent geometry : angle 0.66028 / 0.28 (15498) hydrogen bonds : bond 0.02761 / 1.85 ( 504) hydrogen bonds : angle 3.59025 / 2.45 ( 1458) Misc. bond : bond 0.13850 / 6.94 ( 3) link_NAG-ASN : bond 0.00628 / 0.31 ( 3) link_NAG-ASN : angle 1.70500 / 1.20 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 132 time to evaluate : 0.421 Fit side-chains REVERT: C 38 MET cc_start: 0.8888 (mtp) cc_final: 0.8502 (mtp) REVERT: C 268 LEU cc_start: 0.9305 (tp) cc_final: 0.8900 (tt) REVERT: C 380 ARG cc_start: 0.8822 (ttp-170) cc_final: 0.8435 (ttt90) REVERT: A 77 ILE cc_start: 0.9235 (mt) cc_final: 0.8941 (tp) REVERT: A 147 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8538 (pp) REVERT: A 380 ARG cc_start: 0.8837 (ttp-170) cc_final: 0.8553 (ttt90) REVERT: A 438 ILE cc_start: 0.9145 (OUTLIER) cc_final: 0.8803 (tp) REVERT: B 38 MET cc_start: 0.8757 (mtp) cc_final: 0.8473 (mtp) REVERT: B 244 ASN cc_start: 0.9423 (t0) cc_final: 0.9051 (t0) REVERT: B 380 ARG cc_start: 0.8822 (ttp-170) cc_final: 0.8509 (ttt90) outliers start: 22 outliers final: 16 residues processed: 146 average time/residue: 0.0813 time to fit residues: 18.8114 Evaluate side-chains 143 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 125 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 391 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 83 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 chunk 17 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 103 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 70 optimal weight: 0.8980 chunk 10 optimal weight: 0.0070 chunk 80 optimal weight: 0.8980 chunk 110 optimal weight: 0.9990 overall best weight: 0.7398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.077123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.059029 restraints weight = 31169.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.061210 restraints weight = 14721.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.062523 restraints weight = 9740.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.063438 restraints weight = 7794.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.063883 restraints weight = 6805.149| |-----------------------------------------------------------------------------| r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.4132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 11331 Z= 0.107 Angle : 0.658 13.273 15507 Z= 0.280 Chirality : 0.043 0.264 1743 Planarity : 0.003 0.029 1839 Dihedral : 11.852 172.105 1614 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.11 % Allowed : 19.61 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.14 (0.25), residues: 1302 helix: 1.14 (0.19), residues: 840 sheet: -0.34 (0.52), residues: 102 loop : -2.29 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 272 TYR 0.011 0.001 TYR C 348 PHE 0.027 0.001 PHE C 202 TRP 0.020 0.001 TRP A 286 HIS 0.002 0.000 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.11 (11325) covalent geometry : angle 0.65717 / 0.28 (15498) hydrogen bonds : bond 0.02712 / 1.83 ( 504) hydrogen bonds : angle 3.58861 / 2.45 ( 1458) Misc. bond : bond 0.13456 / 6.74 ( 3) link_NAG-ASN : bond 0.00578 / 0.29 ( 3) link_NAG-ASN : angle 1.70649 / 1.18 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 130 time to evaluate : 0.467 Fit side-chains REVERT: C 38 MET cc_start: 0.8871 (mtp) cc_final: 0.8489 (mtp) REVERT: C 77 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8800 (tp) REVERT: C 380 ARG cc_start: 0.8827 (ttp-170) cc_final: 0.8461 (ttt90) REVERT: C 438 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8914 (tp) REVERT: A 77 ILE cc_start: 0.9204 (mt) cc_final: 0.8933 (tp) REVERT: A 380 ARG cc_start: 0.8871 (ttp-170) cc_final: 0.8555 (ttt90) REVERT: A 438 ILE cc_start: 0.9135 (OUTLIER) cc_final: 0.8918 (tp) REVERT: B 38 MET cc_start: 0.8749 (mtp) cc_final: 0.8472 (mtp) REVERT: B 244 ASN cc_start: 0.9421 (t0) cc_final: 0.9043 (t0) REVERT: B 380 ARG cc_start: 0.8828 (ttp-170) cc_final: 0.8514 (ttt90) outliers start: 24 outliers final: 18 residues processed: 144 average time/residue: 0.0826 time to fit residues: 19.0136 Evaluate side-chains 142 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 121 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 438 ILE Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 86 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 58 optimal weight: 0.0030 chunk 101 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 102 optimal weight: 0.9990 chunk 107 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 overall best weight: 0.7594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.077408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.058300 restraints weight = 31377.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.060521 restraints weight = 15135.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.061868 restraints weight = 10177.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.062684 restraints weight = 8209.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.063316 restraints weight = 7286.423| |-----------------------------------------------------------------------------| r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.4212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.133 11331 Z= 0.109 Angle : 0.658 13.256 15507 Z= 0.282 Chirality : 0.044 0.257 1743 Planarity : 0.003 0.029 1839 Dihedral : 11.697 172.292 1614 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.76 % Allowed : 20.49 % Favored : 77.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.22 (0.25), residues: 1302 helix: 1.26 (0.19), residues: 822 sheet: -0.28 (0.52), residues: 102 loop : -2.26 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 278 TYR 0.011 0.001 TYR C 348 PHE 0.026 0.001 PHE A 202 TRP 0.020 0.001 TRP A 286 HIS 0.002 0.000 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.11 (11325) covalent geometry : angle 0.65713 / 0.28 (15498) hydrogen bonds : bond 0.02702 / 1.83 ( 504) hydrogen bonds : angle 3.57028 / 2.44 ( 1458) Misc. bond : bond 0.12963 / 6.50 ( 3) link_NAG-ASN : bond 0.00555 / 0.28 ( 3) link_NAG-ASN : angle 1.73162 / 1.18 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2604 Ramachandran restraints generated. 1302 Oldfield, 0 Emsley, 1302 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.302 Fit side-chains REVERT: C 38 MET cc_start: 0.8910 (mtp) cc_final: 0.8635 (mtp) REVERT: C 77 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8813 (tp) REVERT: C 287 MET cc_start: 0.8635 (mmm) cc_final: 0.8406 (mtp) REVERT: C 380 ARG cc_start: 0.8813 (ttp-170) cc_final: 0.8443 (ttt90) REVERT: A 77 ILE cc_start: 0.9192 (mt) cc_final: 0.8920 (tp) REVERT: A 380 ARG cc_start: 0.8881 (ttp-170) cc_final: 0.8508 (ttt90) REVERT: A 438 ILE cc_start: 0.9144 (OUTLIER) cc_final: 0.8921 (tp) REVERT: B 38 MET cc_start: 0.8800 (mtp) cc_final: 0.8517 (mtp) REVERT: B 244 ASN cc_start: 0.9417 (t0) cc_final: 0.9042 (t0) REVERT: B 380 ARG cc_start: 0.8846 (ttp-170) cc_final: 0.8503 (ttt90) outliers start: 20 outliers final: 17 residues processed: 137 average time/residue: 0.0747 time to fit residues: 16.3882 Evaluate side-chains 141 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 122 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 34 LEU Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 223 VAL Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 344 LEU Chi-restraints excluded: chain C residue 399 LEU Chi-restraints excluded: chain C residue 449 ILE Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 209 VAL Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain A residue 344 LEU Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 438 ILE Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 268 LEU Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 324 LEU Chi-restraints excluded: chain B residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 39 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 chunk 100 optimal weight: 0.8980 chunk 126 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 85 optimal weight: 0.6980 chunk 32 optimal weight: 6.9990 chunk 110 optimal weight: 4.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.077403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.058302 restraints weight = 31358.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.060517 restraints weight = 15104.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.061751 restraints weight = 10165.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.062727 restraints weight = 8309.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.063053 restraints weight = 7285.555| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.4268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.141 11331 Z= 0.111 Angle : 0.669 13.432 15507 Z= 0.285 Chirality : 0.043 0.258 1743 Planarity : 0.003 0.028 1839 Dihedral : 11.561 172.662 1614 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 1.85 % Allowed : 20.76 % Favored : 77.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.27 (0.25), residues: 1302 helix: 1.28 (0.19), residues: 822 sheet: -0.22 (0.53), residues: 102 loop : -2.21 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 278 TYR 0.011 0.001 TYR C 348 PHE 0.028 0.001 PHE B 202 TRP 0.021 0.001 TRP A 286 HIS 0.002 0.000 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00291 / 0.11 (11325) covalent geometry : angle 0.66777 / 0.28 (15498) hydrogen bonds : bond 0.02692 / 1.82 ( 504) hydrogen bonds : angle 3.56671 / 2.45 ( 1458) Misc. bond : bond 0.13374 / 6.69 ( 3) link_NAG-ASN : bond 0.00539 / 0.27 ( 3) link_NAG-ASN : angle 1.72564 / 1.18 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1683.90 seconds wall clock time: 30 minutes 3.48 seconds (1803.48 seconds total)