Starting phenix.real_space_refine on Thu Jun 4 07:47:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6hd1_0200/06_2026/6hd1_0200.cif Found real_map, /net/cci-nas-00/data/ceres_data/6hd1_0200/06_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_0200/06_2026/6hd1_0200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6hd1_0200/06_2026/6hd1_0200.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6hd1_0200/06_2026/6hd1_0200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6hd1_0200/06_2026/6hd1_0200.map" } 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-dev-6079/lib/python3.9/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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Restraints were copied for chains: A, B Time building chain proxies: 2.84, per 1000 atoms: 0.26 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: 0.97 Conformation dependent library (CDL) restraints added in 518.6 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: 0.25 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: 1.59 Time building geometry restraints manager: 1.25 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: 6567 35.61 - 71.21: 206 71.21 - 106.82: 37 106.82 - 142.42: 0 142.42 - 178.03: 3 Dihedral angle restraints: 6813 sinusoidal: 2988 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 6810 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: 0.880 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 10.680 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 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 : 17.195 178.025 4359 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 : 0.371 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: 0.0922 time to fit residues: 36.3551 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 : 0.316 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3150 r_free = 0.3150 target = 0.076520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.057342 restraints weight = 31196.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.059601 restraints weight = 14956.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.060938 restraints weight = 10015.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.061834 restraints weight = 8079.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.062412 restraints weight = 7098.719| |-----------------------------------------------------------------------------| r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.328 11331 Z= 0.148 Angle : 0.752 15.906 15507 Z= 0.337 Chirality : 0.045 0.147 1743 Planarity : 0.005 0.039 1839 Dihedral : 18.160 172.187 1948 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.73 % Allowed : 12.23 % Favored : 85.05 % 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: -2.44 (0.22), residues: 1302 helix: -1.03 (0.17), residues: 786 sheet: -1.68 (0.47), residues: 102 loop : -2.51 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 450 TYR 0.016 0.001 TYR A 67 PHE 0.025 0.001 PHE C 202 TRP 0.019 0.002 TRP B 286 HIS 0.004 0.001 HIS C 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (11325) covalent geometry : angle 0.74800 / 0.34 (15498) hydrogen bonds : bond 0.04920 / 3.37 ( 504) hydrogen bonds : angle 4.74264 / 3.24 ( 1458) Misc. bond : bond 0.32293 / 16.18 ( 3) link_NAG-ASN : bond 0.00683 / 0.34 ( 3) link_NAG-ASN : angle 3.10300 / 2.00 ( 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 212 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 181 time to evaluate : 0.458 Fit side-chains REVERT: C 38 MET cc_start: 0.8967 (mtp) cc_final: 0.8542 (mtp) REVERT: C 77 ILE cc_start: 0.9382 (mt) cc_final: 0.9136 (tp) REVERT: C 150 SER cc_start: 0.9223 (p) cc_final: 0.9004 (p) REVERT: C 268 LEU cc_start: 0.9436 (tp) cc_final: 0.9133 (tt) REVERT: C 380 ARG cc_start: 0.8817 (ttp-170) cc_final: 0.8500 (ttt90) REVERT: A 77 ILE cc_start: 0.9270 (mt) cc_final: 0.9042 (tp) REVERT: A 268 LEU cc_start: 0.9410 (OUTLIER) cc_final: 0.9191 (tt) REVERT: A 378 GLU cc_start: 0.8518 (mt-10) cc_final: 0.8220 (mt-10) REVERT: A 391 LEU cc_start: 0.9687 (OUTLIER) cc_final: 0.9446 (tm) REVERT: B 92 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.8999 (pp) REVERT: B 147 LEU cc_start: 0.8643 (OUTLIER) cc_final: 0.8286 (pp) REVERT: B 184 MET cc_start: 0.8137 (mmp) cc_final: 0.7801 (tmm) REVERT: B 202 PHE cc_start: 0.8258 (t80) cc_final: 0.7948 (t80) outliers start: 31 outliers final: 9 residues processed: 200 average time/residue: 0.0752 time to fit residues: 23.9407 Evaluate side-chains 139 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 126 time to evaluate : 0.497 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 84 optimal weight: 5.9990 chunk 61 optimal weight: 0.9990 chunk 43 optimal weight: 10.0000 chunk 98 optimal weight: 8.9990 chunk 128 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 85 HIS A 19 GLN A 40 GLN A 85 HIS ** A 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 85 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.075341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2687 r_free = 0.2687 target = 0.056119 restraints weight = 31629.896| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.058360 restraints weight = 15251.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2772 r_free = 0.2772 target = 0.059674 restraints weight = 10228.993| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.060409 restraints weight = 8282.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.060969 restraints weight = 7405.901| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.3196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.328 11331 Z= 0.188 Angle : 0.741 17.318 15507 Z= 0.321 Chirality : 0.046 0.227 1743 Planarity : 0.004 0.033 1839 Dihedral : 16.334 171.176 1948 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 3.43 % Allowed : 14.51 % Favored : 82.06 % 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: -1.21 (0.23), residues: 1302 helix: 0.13 (0.18), residues: 801 sheet: -1.55 (0.49), residues: 102 loop : -2.43 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 278 TYR 0.014 0.001 TYR B 259 PHE 0.022 0.002 PHE C 359 TRP 0.019 0.002 TRP C 286 HIS 0.004 0.001 HIS C 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.18 (11325) covalent geometry : angle 0.73914 / 0.32 (15498) hydrogen bonds : bond 0.03730 / 2.55 ( 504) hydrogen bonds : angle 4.15796 / 2.83 ( 1458) Misc. bond : bond 0.32604 / 16.35 ( 3) link_NAG-ASN : bond 0.00723 / 0.36 ( 3) link_NAG-ASN : angle 2.29836 / 1.60 ( 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 176 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 0.423 Fit side-chains REVERT: C 77 ILE cc_start: 0.9346 (mt) cc_final: 0.9122 (tp) REVERT: C 268 LEU cc_start: 0.9437 (tp) cc_final: 0.9170 (tt) REVERT: C 380 ARG cc_start: 0.8815 (ttp-170) cc_final: 0.8523 (ttt90) REVERT: C 438 ILE cc_start: 0.9227 (OUTLIER) cc_final: 0.8985 (tp) REVERT: A 38 MET cc_start: 0.8733 (mtp) cc_final: 0.8525 (mtp) REVERT: A 39 LEU cc_start: 0.9353 (OUTLIER) cc_final: 0.9074 (mt) REVERT: A 77 ILE cc_start: 0.9306 (mt) cc_final: 0.9040 (tp) REVERT: A 268 LEU cc_start: 0.9415 (OUTLIER) cc_final: 0.9138 (tt) REVERT: A 378 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8340 (mt-10) REVERT: A 391 LEU cc_start: 0.9669 (OUTLIER) cc_final: 0.9395 (tm) REVERT: A 438 ILE cc_start: 0.9212 (mm) cc_final: 0.8983 (tp) REVERT: B 147 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8313 (pp) outliers start: 39 outliers final: 20 residues processed: 164 average time/residue: 0.0748 time to fit residues: 20.0151 Evaluate side-chains 140 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 115 time to evaluate : 0.482 ------------------------------------------------------------------------------- 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 438 ILE 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: 7.9990 chunk 44 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 16 optimal weight: 0.3980 chunk 53 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 30 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3150 r_free = 0.3150 target = 0.076481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.057324 restraints weight = 31635.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.059579 restraints weight = 15169.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.061011 restraints weight = 10222.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.061663 restraints weight = 8199.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.061822 restraints weight = 7372.596| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.213 11331 Z= 0.117 Angle : 0.654 13.574 15507 Z= 0.285 Chirality : 0.044 0.175 1743 Planarity : 0.004 0.032 1839 Dihedral : 15.386 169.418 1946 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.37 % Allowed : 16.71 % Favored : 80.91 % 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: -0.81 (0.24), residues: 1302 helix: 0.56 (0.19), residues: 828 sheet: -1.28 (0.42), residues: 123 loop : -2.85 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 290 TYR 0.012 0.001 TYR C 348 PHE 0.025 0.001 PHE B 202 TRP 0.015 0.001 TRP C 286 HIS 0.003 0.000 HIS B 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.11 (11325) covalent geometry : angle 0.65162 / 0.28 (15498) hydrogen bonds : bond 0.03182 / 2.17 ( 504) hydrogen bonds : angle 3.86519 / 2.63 ( 1458) Misc. bond : bond 0.21063 / 10.56 ( 3) link_NAG-ASN : bond 0.00744 / 0.37 ( 3) link_NAG-ASN : angle 2.35971 / 1.61 ( 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 172 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 145 time to evaluate : 0.388 Fit side-chains REVERT: C 38 MET cc_start: 0.8934 (mtp) cc_final: 0.8545 (mtp) REVERT: C 77 ILE cc_start: 0.9290 (mt) cc_final: 0.9070 (tp) REVERT: C 268 LEU cc_start: 0.9369 (tp) cc_final: 0.8973 (tt) REVERT: C 380 ARG cc_start: 0.8821 (ttp-170) cc_final: 0.8488 (ttt90) REVERT: A 77 ILE cc_start: 0.9280 (mt) cc_final: 0.9023 (tp) REVERT: A 268 LEU cc_start: 0.9355 (tp) cc_final: 0.9019 (tt) REVERT: A 378 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8356 (mt-10) REVERT: A 391 LEU cc_start: 0.9657 (OUTLIER) cc_final: 0.9351 (tm) REVERT: A 438 ILE cc_start: 0.9223 (mm) cc_final: 0.8736 (tp) REVERT: B 147 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8259 (pp) REVERT: B 380 ARG cc_start: 0.8815 (ttp-170) cc_final: 0.8510 (ttt90) outliers start: 27 outliers final: 16 residues processed: 165 average time/residue: 0.0756 time to fit residues: 20.0814 Evaluate side-chains 151 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.443 ------------------------------------------------------------------------------- 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 255 LEU Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 424 LEU 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 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: 6.9990 chunk 60 optimal weight: 2.9990 chunk 29 optimal weight: 0.0980 chunk 61 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 9 optimal weight: 8.9990 chunk 79 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 98 optimal weight: 10.0000 chunk 102 optimal weight: 8.9990 chunk 89 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3139 r_free = 0.3139 target = 0.075867 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2696 r_free = 0.2696 target = 0.056468 restraints weight = 31842.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.058733 restraints weight = 15140.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.060165 restraints weight = 10131.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.060862 restraints weight = 8138.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.061407 restraints weight = 7292.746| |-----------------------------------------------------------------------------| r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.3737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.231 11331 Z= 0.141 Angle : 0.677 15.218 15507 Z= 0.290 Chirality : 0.044 0.216 1743 Planarity : 0.003 0.031 1839 Dihedral : 14.788 167.466 1946 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 2.99 % Allowed : 17.41 % Favored : 79.60 % 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: 0.92 (0.19), residues: 801 sheet: -1.13 (0.43), residues: 123 loop : -2.46 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 290 TYR 0.012 0.001 TYR C 348 PHE 0.022 0.001 PHE C 202 TRP 0.014 0.001 TRP A 286 HIS 0.003 0.001 HIS B 129 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.14 (11325) covalent geometry : angle 0.67529 / 0.29 (15498) hydrogen bonds : bond 0.03071 / 2.10 ( 504) hydrogen bonds : angle 3.83710 / 2.62 ( 1458) Misc. bond : bond 0.22352 / 11.18 ( 3) link_NAG-ASN : bond 0.00687 / 0.34 ( 3) link_NAG-ASN : angle 2.11286 / 1.45 ( 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 167 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 133 time to evaluate : 0.412 Fit side-chains REVERT: C 38 MET cc_start: 0.8935 (mtp) cc_final: 0.8494 (mtp) REVERT: C 77 ILE cc_start: 0.9289 (mt) cc_final: 0.9030 (tp) REVERT: C 268 LEU cc_start: 0.9369 (tp) cc_final: 0.8966 (tt) REVERT: C 380 ARG cc_start: 0.8861 (ttp-170) cc_final: 0.8499 (ttt90) REVERT: A 77 ILE cc_start: 0.9236 (mt) cc_final: 0.8928 (tp) REVERT: A 391 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9344 (tm) REVERT: A 438 ILE cc_start: 0.9202 (mm) cc_final: 0.8909 (tp) REVERT: A 443 ASP cc_start: 0.8771 (m-30) cc_final: 0.8428 (m-30) REVERT: B 147 LEU cc_start: 0.8520 (OUTLIER) cc_final: 0.8273 (pp) REVERT: B 298 LEU cc_start: 0.9387 (tp) cc_final: 0.8884 (tt) REVERT: B 380 ARG cc_start: 0.8846 (ttp-170) cc_final: 0.8521 (ttt90) outliers start: 34 outliers final: 23 residues processed: 156 average time/residue: 0.0708 time to fit residues: 17.8570 Evaluate side-chains 145 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.435 ------------------------------------------------------------------------------- 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 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 271 TYR 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 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 54 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 125 optimal weight: 0.0870 chunk 85 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 0.6980 chunk 112 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 73 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3158 r_free = 0.3158 target = 0.076737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.057535 restraints weight = 31551.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.059804 restraints weight = 15241.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.061187 restraints weight = 10240.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.061867 restraints weight = 8305.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.062165 restraints weight = 7466.263| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.3920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.163 11331 Z= 0.106 Angle : 0.640 13.199 15507 Z= 0.278 Chirality : 0.043 0.170 1743 Planarity : 0.003 0.031 1839 Dihedral : 14.229 166.416 1946 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.37 % Allowed : 18.29 % Favored : 79.33 % 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: -0.28 (0.24), residues: 1302 helix: 0.97 (0.19), residues: 825 sheet: -0.90 (0.44), residues: 123 loop : -2.70 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 377 TYR 0.011 0.001 TYR C 348 PHE 0.023 0.001 PHE B 202 TRP 0.014 0.001 TRP B 286 HIS 0.003 0.000 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.10 (11325) covalent geometry : angle 0.63825 / 0.28 (15498) hydrogen bonds : bond 0.02875 / 1.96 ( 504) hydrogen bonds : angle 3.71113 / 2.54 ( 1458) Misc. bond : bond 0.16157 / 8.10 ( 3) link_NAG-ASN : bond 0.00646 / 0.32 ( 3) link_NAG-ASN : angle 2.13963 / 1.48 ( 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 159 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.427 Fit side-chains REVERT: C 38 MET cc_start: 0.8873 (mtp) cc_final: 0.8466 (mtp) REVERT: C 77 ILE cc_start: 0.9174 (mt) cc_final: 0.8942 (tp) REVERT: C 347 SER cc_start: 0.9378 (m) cc_final: 0.9167 (p) REVERT: C 380 ARG cc_start: 0.8826 (ttp-170) cc_final: 0.8479 (ttt90) REVERT: A 77 ILE cc_start: 0.9220 (mt) cc_final: 0.8929 (tp) REVERT: A 287 MET cc_start: 0.8792 (mmm) cc_final: 0.8534 (mmm) REVERT: A 438 ILE cc_start: 0.9160 (mm) cc_final: 0.8863 (tp) REVERT: B 147 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8307 (pp) REVERT: B 380 ARG cc_start: 0.8827 (ttp-170) cc_final: 0.8547 (ttt90) outliers start: 27 outliers final: 18 residues processed: 151 average time/residue: 0.0740 time to fit residues: 18.1241 Evaluate side-chains 139 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 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 130 VAL Chi-restraints excluded: chain C residue 218 CYS 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 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 399 LEU Chi-restraints excluded: chain A residue 428 CYS 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 271 TYR Chi-restraints excluded: chain B residue 391 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 4.9990 chunk 51 optimal weight: 8.9990 chunk 87 optimal weight: 10.0000 chunk 91 optimal weight: 0.0470 chunk 103 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 46 optimal weight: 20.0000 chunk 6 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 overall best weight: 1.3080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3139 r_free = 0.3139 target = 0.075834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.056475 restraints weight = 31570.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.058713 restraints weight = 15060.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.060112 restraints weight = 10158.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.060810 restraints weight = 8215.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.061171 restraints weight = 7375.236| |-----------------------------------------------------------------------------| r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.4005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.194 11331 Z= 0.136 Angle : 0.672 14.931 15507 Z= 0.287 Chirality : 0.044 0.162 1743 Planarity : 0.003 0.029 1839 Dihedral : 13.717 166.097 1946 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.81 % Allowed : 18.38 % Favored : 78.80 % 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: -0.10 (0.25), residues: 1302 helix: 1.10 (0.19), residues: 828 sheet: -0.78 (0.44), residues: 123 loop : -2.63 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 272 TYR 0.013 0.001 TYR A 348 PHE 0.024 0.001 PHE B 202 TRP 0.014 0.001 TRP A 286 HIS 0.002 0.000 HIS B 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00352 / 0.13 (11325) covalent geometry : angle 0.67028 / 0.29 (15498) hydrogen bonds : bond 0.02915 / 1.99 ( 504) hydrogen bonds : angle 3.70643 / 2.53 ( 1458) Misc. bond : bond 0.19189 / 9.62 ( 3) link_NAG-ASN : bond 0.00588 / 0.29 ( 3) link_NAG-ASN : angle 2.07216 / 1.46 ( 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 158 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 126 time to evaluate : 0.427 Fit side-chains REVERT: C 38 MET cc_start: 0.8864 (mtp) cc_final: 0.8461 (mtp) REVERT: C 77 ILE cc_start: 0.9184 (mt) cc_final: 0.8957 (tp) REVERT: C 380 ARG cc_start: 0.8824 (ttp-170) cc_final: 0.8489 (ttt90) REVERT: A 77 ILE cc_start: 0.9235 (mt) cc_final: 0.8926 (tp) REVERT: A 287 MET cc_start: 0.8750 (mmm) cc_final: 0.8506 (mmm) REVERT: A 380 ARG cc_start: 0.8817 (ttp-170) cc_final: 0.8562 (ttt90) REVERT: A 443 ASP cc_start: 0.8730 (m-30) cc_final: 0.8277 (m-30) REVERT: B 380 ARG cc_start: 0.8796 (ttp-170) cc_final: 0.8492 (ttt90) outliers start: 32 outliers final: 24 residues processed: 147 average time/residue: 0.0811 time to fit residues: 18.9709 Evaluate side-chains 142 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 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 130 VAL Chi-restraints excluded: chain C residue 209 VAL Chi-restraints excluded: chain C residue 218 CYS Chi-restraints excluded: chain C residue 223 VAL 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 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 268 LEU Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 209 VAL Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 271 TYR Chi-restraints excluded: chain B residue 391 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.9980 chunk 13 optimal weight: 3.9990 chunk 77 optimal weight: 0.3980 chunk 3 optimal weight: 0.0570 chunk 125 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.6898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.3161 r_free = 0.3161 target = 0.076866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.057716 restraints weight = 31391.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.059946 restraints weight = 15278.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.061350 restraints weight = 10369.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2833 r_free = 0.2833 target = 0.061968 restraints weight = 8375.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.062524 restraints weight = 7550.464| |-----------------------------------------------------------------------------| r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.4154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.139 11331 Z= 0.106 Angle : 0.661 13.409 15507 Z= 0.283 Chirality : 0.043 0.196 1743 Planarity : 0.003 0.028 1839 Dihedral : 13.340 164.812 1944 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.29 % Allowed : 19.26 % 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: 0.03 (0.25), residues: 1302 helix: 1.16 (0.19), residues: 828 sheet: -0.66 (0.45), residues: 123 loop : -2.51 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 151 TYR 0.014 0.001 TYR C 348 PHE 0.024 0.001 PHE B 202 TRP 0.012 0.001 TRP B 286 HIS 0.002 0.000 HIS C 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 (11325) covalent geometry : angle 0.65939 / 0.28 (15498) hydrogen bonds : bond 0.02768 / 1.87 ( 504) hydrogen bonds : angle 3.61666 / 2.46 ( 1458) Misc. bond : bond 0.13804 / 6.92 ( 3) link_NAG-ASN : bond 0.00605 / 0.30 ( 3) link_NAG-ASN : angle 2.06185 / 1.42 ( 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 162 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 136 time to evaluate : 0.404 Fit side-chains REVERT: C 38 MET cc_start: 0.8893 (mtp) cc_final: 0.8508 (mtp) REVERT: C 77 ILE cc_start: 0.9112 (mt) cc_final: 0.8906 (tp) REVERT: C 380 ARG cc_start: 0.8816 (ttp-170) cc_final: 0.8442 (ttt90) REVERT: A 77 ILE cc_start: 0.9195 (mt) cc_final: 0.8885 (tp) REVERT: A 287 MET cc_start: 0.8680 (mmm) cc_final: 0.8463 (mmm) REVERT: A 380 ARG cc_start: 0.8855 (ttp-170) cc_final: 0.8552 (ttt90) REVERT: A 438 ILE cc_start: 0.9036 (mm) cc_final: 0.8732 (tp) REVERT: B 244 ASN cc_start: 0.9419 (t0) cc_final: 0.9047 (t0) REVERT: B 380 ARG cc_start: 0.8813 (ttp-170) cc_final: 0.8507 (ttt90) outliers start: 26 outliers final: 21 residues processed: 154 average time/residue: 0.0818 time to fit residues: 19.8272 Evaluate side-chains 143 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 223 VAL Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 399 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 271 TYR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 428 CYS Chi-restraints excluded: chain B residue 218 CYS Chi-restraints excluded: chain B residue 271 TYR 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: 3.9990 chunk 100 optimal weight: 0.6980 chunk 17 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 103 optimal weight: 0.9980 chunk 78 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 10 optimal weight: 6.9990 chunk 80 optimal weight: 0.8980 chunk 110 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.077075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.058739 restraints weight = 31308.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.060951 restraints weight = 14841.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.062153 restraints weight = 9847.164| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.063147 restraints weight = 8018.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.063465 restraints weight = 6964.011| |-----------------------------------------------------------------------------| r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.146 11331 Z= 0.111 Angle : 0.677 13.488 15507 Z= 0.288 Chirality : 0.043 0.210 1743 Planarity : 0.003 0.028 1839 Dihedral : 13.114 165.865 1944 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 2.02 % Allowed : 20.05 % Favored : 77.92 % 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: 0.12 (0.25), residues: 1302 helix: 1.21 (0.19), residues: 828 sheet: -0.51 (0.45), residues: 123 loop : -2.46 (0.33), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 290 TYR 0.011 0.001 TYR C 348 PHE 0.028 0.001 PHE C 202 TRP 0.013 0.001 TRP B 286 HIS 0.002 0.000 HIS B 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.11 (11325) covalent geometry : angle 0.67595 / 0.29 (15498) hydrogen bonds : bond 0.02778 / 1.88 ( 504) hydrogen bonds : angle 3.62501 / 2.47 ( 1458) Misc. bond : bond 0.13977 / 7.00 ( 3) link_NAG-ASN : bond 0.00587 / 0.29 ( 3) link_NAG-ASN : angle 1.99373 / 1.39 ( 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 155 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.421 Fit side-chains REVERT: C 38 MET cc_start: 0.8878 (mtp) cc_final: 0.8492 (mtp) REVERT: C 380 ARG cc_start: 0.8832 (ttp-170) cc_final: 0.8453 (ttt90) REVERT: A 77 ILE cc_start: 0.9193 (mt) cc_final: 0.8883 (tp) REVERT: A 380 ARG cc_start: 0.8864 (ttp-170) cc_final: 0.8508 (ttt90) REVERT: A 438 ILE cc_start: 0.9033 (mm) cc_final: 0.8707 (tp) REVERT: A 443 ASP cc_start: 0.8650 (m-30) cc_final: 0.8138 (m-30) REVERT: B 244 ASN cc_start: 0.9423 (t0) cc_final: 0.9010 (t0) REVERT: B 380 ARG cc_start: 0.8843 (ttp-170) cc_final: 0.8500 (ttt90) outliers start: 23 outliers final: 22 residues processed: 146 average time/residue: 0.0799 time to fit residues: 18.5158 Evaluate side-chains 145 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 223 VAL Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 360 VAL Chi-restraints excluded: chain C residue 399 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 218 CYS Chi-restraints excluded: chain A residue 268 LEU Chi-restraints excluded: chain A residue 271 TYR Chi-restraints excluded: chain A residue 399 LEU Chi-restraints excluded: chain A residue 428 CYS 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 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: 0.3980 chunk 112 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 98 optimal weight: 0.6980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.076118 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.057625 restraints weight = 31573.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.059820 restraints weight = 14939.182| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.061225 restraints weight = 9936.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.061933 restraints weight = 7932.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.062411 restraints weight = 7060.327| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.172 11331 Z= 0.139 Angle : 0.696 14.925 15507 Z= 0.296 Chirality : 0.044 0.258 1743 Planarity : 0.003 0.029 1839 Dihedral : 13.004 165.753 1944 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.55 % Allowed : 19.61 % Favored : 77.84 % 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: 0.16 (0.25), residues: 1302 helix: 1.22 (0.19), residues: 828 sheet: -0.43 (0.45), residues: 123 loop : -2.43 (0.33), residues: 351 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 0.026 0.001 PHE C 202 TRP 0.015 0.001 TRP A 286 HIS 0.001 0.000 HIS A 85 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.14 (11325) covalent geometry : angle 0.69431 / 0.30 (15498) hydrogen bonds : bond 0.02853 / 1.93 ( 504) hydrogen bonds : angle 3.69279 / 2.52 ( 1458) Misc. bond : bond 0.17190 / 8.62 ( 3) link_NAG-ASN : bond 0.00573 / 0.29 ( 3) link_NAG-ASN : angle 1.96535 / 1.35 ( 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 150 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.411 Fit side-chains REVERT: C 38 MET cc_start: 0.8902 (mtp) cc_final: 0.8603 (mtp) REVERT: C 380 ARG cc_start: 0.8838 (ttp-170) cc_final: 0.8453 (ttt90) REVERT: A 77 ILE cc_start: 0.9184 (mt) cc_final: 0.8896 (tp) REVERT: A 380 ARG cc_start: 0.8875 (ttp-170) cc_final: 0.8495 (ttt90) REVERT: B 380 ARG cc_start: 0.8847 (ttp-170) cc_final: 0.8500 (ttt90) outliers start: 29 outliers final: 25 residues processed: 138 average time/residue: 0.0798 time to fit residues: 17.4316 Evaluate side-chains 143 residues out of total 1137 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 118 time to evaluate : 0.429 ------------------------------------------------------------------------------- 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 223 VAL Chi-restraints excluded: chain C residue 240 ILE Chi-restraints excluded: chain C residue 268 LEU Chi-restraints excluded: chain C residue 271 TYR Chi-restraints excluded: chain C residue 360 VAL 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 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 399 LEU Chi-restraints excluded: chain A residue 428 CYS 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 39 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 100 optimal weight: 0.5980 chunk 126 optimal weight: 0.6980 chunk 72 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 83 optimal weight: 2.9990 chunk 18 optimal weight: 0.0040 chunk 85 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.077772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.059430 restraints weight = 31265.792| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.061661 restraints weight = 14785.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.063030 restraints weight = 9807.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.063901 restraints weight = 7811.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.064539 restraints weight = 6848.898| |-----------------------------------------------------------------------------| r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.118 11331 Z= 0.104 Angle : 0.673 12.605 15507 Z= 0.289 Chirality : 0.044 0.267 1743 Planarity : 0.003 0.028 1839 Dihedral : 12.814 164.682 1944 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.02 % Allowed : 20.40 % Favored : 77.57 % 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: 0.23 (0.25), residues: 1302 helix: 1.26 (0.19), residues: 828 sheet: -0.36 (0.46), residues: 123 loop : -2.37 (0.33), residues: 351 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 C 202 TRP 0.014 0.001 TRP A 286 HIS 0.002 0.000 HIS C 397 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.10 (11325) covalent geometry : angle 0.67114 / 0.29 (15498) hydrogen bonds : bond 0.02673 / 1.81 ( 504) hydrogen bonds : angle 3.61650 / 2.46 ( 1458) Misc. bond : bond 0.11579 / 5.80 ( 3) link_NAG-ASN : bond 0.00571 / 0.29 ( 3) link_NAG-ASN : angle 1.93086 / 1.30 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1691.89 seconds wall clock time: 30 minutes 9.50 seconds (1809.50 seconds total)