Starting phenix.real_space_refine on Thu Mar 5 01:36:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6pk7_20355/03_2026/6pk7_20355.cif Found real_map, /net/cci-nas-00/data/ceres_data/6pk7_20355/03_2026/6pk7_20355.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6pk7_20355/03_2026/6pk7_20355.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6pk7_20355/03_2026/6pk7_20355.map" model { file = "/net/cci-nas-00/data/ceres_data/6pk7_20355/03_2026/6pk7_20355.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6pk7_20355/03_2026/6pk7_20355.cif" } resolution = 3.1 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= 0.041 sd= 1.139 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: 5 Type Number sf(0) Gaussians P 20 5.49 5 S 92 5.16 5 C 11312 2.51 5 N 3080 2.21 5 O 3316 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17820 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4399 Classifications: {'peptide': 557} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 527} Chain: "D" Number of atoms: 4399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4399 Classifications: {'peptide': 557} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 527} Chain: "E" Number of atoms: 4399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4399 Classifications: {'peptide': 557} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 527} Chain: "F" Number of atoms: 4399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4399 Classifications: {'peptide': 557} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 527} Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'ADP': 1, 'CTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'ADP': 1, 'CTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'ADP': 1, 'CTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'ADP': 1, 'CTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 8 residue: pdb=" N GLU A 155 " occ=0.75 ... (7 atoms not shown) pdb=" OE2 GLU A 155 " occ=0.75 residue: pdb=" N CYS A 243 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS A 243 " occ=0.75 residue: pdb=" N GLU D 155 " occ=0.75 ... (7 atoms not shown) pdb=" OE2 GLU D 155 " occ=0.75 residue: pdb=" N CYS D 243 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS D 243 " occ=0.75 residue: pdb=" N GLU E 155 " occ=0.75 ... (7 atoms not shown) pdb=" OE2 GLU E 155 " occ=0.75 residue: pdb=" N CYS E 243 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS E 243 " occ=0.75 residue: pdb=" N GLU F 155 " occ=0.75 ... (7 atoms not shown) pdb=" OE2 GLU F 155 " occ=0.75 residue: pdb=" N CYS F 243 " occ=0.75 ... (4 atoms not shown) pdb=" SG CYS F 243 " occ=0.75 Time building chain proxies: 3.56, per 1000 atoms: 0.20 Number of scatterers: 17820 At special positions: 0 Unit cell: (143.85, 89.25, 124.95, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 92 16.00 P 20 15.00 O 3316 8.00 N 3080 7.00 C 11312 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.51 Conformation dependent library (CDL) restraints added in 826.4 milliseconds 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4112 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 20 sheets defined 43.3% alpha, 13.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 15 through 29 Processing helix chain 'A' and resid 68 through 72 Processing helix chain 'A' and resid 73 through 78 Processing helix chain 'A' and resid 90 through 104 removed outlier: 3.732A pdb=" N GLN A 95 " --> pdb=" O GLY A 91 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG A 103 " --> pdb=" O ASN A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 129 Processing helix chain 'A' and resid 155 through 165 removed outlier: 3.962A pdb=" N PHE A 159 " --> pdb=" O GLU A 155 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU A 161 " --> pdb=" O MET A 157 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 170 removed outlier: 3.664A pdb=" N ALA A 170 " --> pdb=" O PHE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 194 through 208 removed outlier: 3.778A pdb=" N GLN A 198 " --> pdb=" O THR A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 234 removed outlier: 3.818A pdb=" N MET A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE A 233 " --> pdb=" O LYS A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 239 No H-bonds generated for 'chain 'A' and resid 237 through 239' Processing helix chain 'A' and resid 251 through 260 removed outlier: 4.223A pdb=" N VAL A 255 " --> pdb=" O TYR A 251 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A 259 " --> pdb=" O VAL A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 270 removed outlier: 3.616A pdb=" N TYR A 265 " --> pdb=" O SER A 261 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 294 removed outlier: 4.045A pdb=" N TRP A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ASN A 287 " --> pdb=" O PHE A 283 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ARG A 291 " --> pdb=" O ASN A 287 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU A 293 " --> pdb=" O ALA A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 329 removed outlier: 3.709A pdb=" N ALA A 327 " --> pdb=" O HIS A 323 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 342 No H-bonds generated for 'chain 'A' and resid 340 through 342' Processing helix chain 'A' and resid 343 through 350 removed outlier: 3.905A pdb=" N GLU A 347 " --> pdb=" O GLU A 343 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR A 348 " --> pdb=" O LYS A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 364 removed outlier: 3.717A pdb=" N ALA A 357 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS A 360 " --> pdb=" O GLU A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 390 removed outlier: 4.076A pdb=" N LYS A 381 " --> pdb=" O GLY A 377 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN A 383 " --> pdb=" O LEU A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 413 Processing helix chain 'A' and resid 464 through 469 Processing helix chain 'A' and resid 486 through 493 removed outlier: 3.583A pdb=" N ILE A 489 " --> pdb=" O PRO A 486 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LYS A 490 " --> pdb=" O ASN A 487 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN A 491 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU A 493 " --> pdb=" O LYS A 490 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 531 removed outlier: 3.807A pdb=" N SER A 530 " --> pdb=" O PRO A 527 " (cutoff:3.500A) Processing helix chain 'A' and resid 537 through 546 Processing helix chain 'A' and resid 550 through 555 removed outlier: 3.847A pdb=" N LEU A 555 " --> pdb=" O LEU A 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 29 Processing helix chain 'D' and resid 68 through 72 Processing helix chain 'D' and resid 73 through 78 Processing helix chain 'D' and resid 90 through 104 removed outlier: 3.732A pdb=" N GLN D 95 " --> pdb=" O GLY D 91 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG D 103 " --> pdb=" O ASN D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 129 Processing helix chain 'D' and resid 155 through 165 removed outlier: 3.962A pdb=" N PHE D 159 " --> pdb=" O GLU D 155 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU D 161 " --> pdb=" O MET D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 170 removed outlier: 3.664A pdb=" N ALA D 170 " --> pdb=" O PHE D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 171 through 173 No H-bonds generated for 'chain 'D' and resid 171 through 173' Processing helix chain 'D' and resid 194 through 208 removed outlier: 3.778A pdb=" N GLN D 198 " --> pdb=" O THR D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 225 through 234 removed outlier: 3.819A pdb=" N MET D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE D 233 " --> pdb=" O LYS D 229 " (cutoff:3.500A) Processing helix chain 'D' and resid 237 through 239 No H-bonds generated for 'chain 'D' and resid 237 through 239' Processing helix chain 'D' and resid 251 through 260 removed outlier: 4.223A pdb=" N VAL D 255 " --> pdb=" O TYR D 251 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU D 259 " --> pdb=" O VAL D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 261 through 270 removed outlier: 3.616A pdb=" N TYR D 265 " --> pdb=" O SER D 261 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU D 268 " --> pdb=" O LYS D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 294 removed outlier: 4.046A pdb=" N TRP D 285 " --> pdb=" O LEU D 281 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ASN D 287 " --> pdb=" O PHE D 283 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG D 291 " --> pdb=" O ASN D 287 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU D 293 " --> pdb=" O ALA D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 314 through 329 removed outlier: 3.709A pdb=" N ALA D 327 " --> pdb=" O HIS D 323 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 342 No H-bonds generated for 'chain 'D' and resid 340 through 342' Processing helix chain 'D' and resid 343 through 350 removed outlier: 3.905A pdb=" N GLU D 347 " --> pdb=" O GLU D 343 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR D 348 " --> pdb=" O LYS D 344 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 364 removed outlier: 3.716A pdb=" N ALA D 357 " --> pdb=" O LYS D 353 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS D 360 " --> pdb=" O GLU D 356 " (cutoff:3.500A) Processing helix chain 'D' and resid 377 through 390 removed outlier: 4.075A pdb=" N LYS D 381 " --> pdb=" O GLY D 377 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN D 383 " --> pdb=" O LEU D 379 " (cutoff:3.500A) Processing helix chain 'D' and resid 400 through 413 Processing helix chain 'D' and resid 464 through 469 Processing helix chain 'D' and resid 486 through 493 removed outlier: 3.584A pdb=" N ILE D 489 " --> pdb=" O PRO D 486 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LYS D 490 " --> pdb=" O ASN D 487 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN D 491 " --> pdb=" O LEU D 488 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLU D 493 " --> pdb=" O LYS D 490 " (cutoff:3.500A) Processing helix chain 'D' and resid 527 through 531 removed outlier: 3.807A pdb=" N SER D 530 " --> pdb=" O PRO D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 537 through 546 Processing helix chain 'D' and resid 550 through 555 removed outlier: 3.847A pdb=" N LEU D 555 " --> pdb=" O LEU D 551 " (cutoff:3.500A) Processing helix chain 'E' and resid 15 through 29 Processing helix chain 'E' and resid 68 through 72 Processing helix chain 'E' and resid 73 through 78 Processing helix chain 'E' and resid 90 through 104 removed outlier: 3.732A pdb=" N GLN E 95 " --> pdb=" O GLY E 91 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG E 103 " --> pdb=" O ASN E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 117 through 129 Processing helix chain 'E' and resid 155 through 165 removed outlier: 3.962A pdb=" N PHE E 159 " --> pdb=" O GLU E 155 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU E 161 " --> pdb=" O MET E 157 " (cutoff:3.500A) Processing helix chain 'E' and resid 165 through 170 removed outlier: 3.663A pdb=" N ALA E 170 " --> pdb=" O PHE E 166 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 173 No H-bonds generated for 'chain 'E' and resid 171 through 173' Processing helix chain 'E' and resid 194 through 208 removed outlier: 3.778A pdb=" N GLN E 198 " --> pdb=" O THR E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 225 through 234 removed outlier: 3.819A pdb=" N MET E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE E 233 " --> pdb=" O LYS E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 237 through 239 No H-bonds generated for 'chain 'E' and resid 237 through 239' Processing helix chain 'E' and resid 251 through 260 removed outlier: 4.224A pdb=" N VAL E 255 " --> pdb=" O TYR E 251 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU E 259 " --> pdb=" O VAL E 255 " (cutoff:3.500A) Processing helix chain 'E' and resid 261 through 270 removed outlier: 3.616A pdb=" N TYR E 265 " --> pdb=" O SER E 261 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU E 268 " --> pdb=" O LYS E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 294 removed outlier: 4.046A pdb=" N TRP E 285 " --> pdb=" O LEU E 281 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASN E 287 " --> pdb=" O PHE E 283 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG E 291 " --> pdb=" O ASN E 287 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLU E 293 " --> pdb=" O ALA E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 314 through 329 removed outlier: 3.709A pdb=" N ALA E 327 " --> pdb=" O HIS E 323 " (cutoff:3.500A) Processing helix chain 'E' and resid 340 through 342 No H-bonds generated for 'chain 'E' and resid 340 through 342' Processing helix chain 'E' and resid 343 through 350 removed outlier: 3.905A pdb=" N GLU E 347 " --> pdb=" O GLU E 343 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N THR E 348 " --> pdb=" O LYS E 344 " (cutoff:3.500A) Processing helix chain 'E' and resid 350 through 364 removed outlier: 3.717A pdb=" N ALA E 357 " --> pdb=" O LYS E 353 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS E 360 " --> pdb=" O GLU E 356 " (cutoff:3.500A) Processing helix chain 'E' and resid 377 through 390 removed outlier: 4.076A pdb=" N LYS E 381 " --> pdb=" O GLY E 377 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN E 383 " --> pdb=" O LEU E 379 " (cutoff:3.500A) Processing helix chain 'E' and resid 400 through 413 Processing helix chain 'E' and resid 464 through 469 Processing helix chain 'E' and resid 486 through 493 removed outlier: 3.584A pdb=" N ILE E 489 " --> pdb=" O PRO E 486 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LYS E 490 " --> pdb=" O ASN E 487 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN E 491 " --> pdb=" O LEU E 488 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU E 493 " --> pdb=" O LYS E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 527 through 531 removed outlier: 3.807A pdb=" N SER E 530 " --> pdb=" O PRO E 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 546 Processing helix chain 'E' and resid 550 through 555 removed outlier: 3.846A pdb=" N LEU E 555 " --> pdb=" O LEU E 551 " (cutoff:3.500A) Processing helix chain 'F' and resid 15 through 29 Processing helix chain 'F' and resid 68 through 72 Processing helix chain 'F' and resid 73 through 78 Processing helix chain 'F' and resid 90 through 104 removed outlier: 3.732A pdb=" N GLN F 95 " --> pdb=" O GLY F 91 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ARG F 103 " --> pdb=" O ASN F 99 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 129 Processing helix chain 'F' and resid 155 through 165 removed outlier: 3.962A pdb=" N PHE F 159 " --> pdb=" O GLU F 155 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU F 161 " --> pdb=" O MET F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 165 through 170 removed outlier: 3.664A pdb=" N ALA F 170 " --> pdb=" O PHE F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 173 No H-bonds generated for 'chain 'F' and resid 171 through 173' Processing helix chain 'F' and resid 194 through 208 removed outlier: 3.778A pdb=" N GLN F 198 " --> pdb=" O THR F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 225 through 234 removed outlier: 3.818A pdb=" N MET F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N PHE F 233 " --> pdb=" O LYS F 229 " (cutoff:3.500A) Processing helix chain 'F' and resid 237 through 239 No H-bonds generated for 'chain 'F' and resid 237 through 239' Processing helix chain 'F' and resid 251 through 260 removed outlier: 4.223A pdb=" N VAL F 255 " --> pdb=" O TYR F 251 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU F 259 " --> pdb=" O VAL F 255 " (cutoff:3.500A) Processing helix chain 'F' and resid 261 through 270 removed outlier: 3.616A pdb=" N TYR F 265 " --> pdb=" O SER F 261 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU F 268 " --> pdb=" O LYS F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 294 removed outlier: 4.045A pdb=" N TRP F 285 " --> pdb=" O LEU F 281 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ASN F 287 " --> pdb=" O PHE F 283 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ARG F 291 " --> pdb=" O ASN F 287 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLU F 293 " --> pdb=" O ALA F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 314 through 329 removed outlier: 3.708A pdb=" N ALA F 327 " --> pdb=" O HIS F 323 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 342 No H-bonds generated for 'chain 'F' and resid 340 through 342' Processing helix chain 'F' and resid 343 through 350 removed outlier: 3.905A pdb=" N GLU F 347 " --> pdb=" O GLU F 343 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR F 348 " --> pdb=" O LYS F 344 " (cutoff:3.500A) Processing helix chain 'F' and resid 350 through 364 removed outlier: 3.717A pdb=" N ALA F 357 " --> pdb=" O LYS F 353 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LYS F 360 " --> pdb=" O GLU F 356 " (cutoff:3.500A) Processing helix chain 'F' and resid 377 through 390 removed outlier: 4.077A pdb=" N LYS F 381 " --> pdb=" O GLY F 377 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN F 383 " --> pdb=" O LEU F 379 " (cutoff:3.500A) Processing helix chain 'F' and resid 400 through 413 Processing helix chain 'F' and resid 464 through 469 Processing helix chain 'F' and resid 486 through 493 removed outlier: 3.583A pdb=" N ILE F 489 " --> pdb=" O PRO F 486 " (cutoff:3.500A) removed outlier: 4.820A pdb=" N LYS F 490 " --> pdb=" O ASN F 487 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN F 491 " --> pdb=" O LEU F 488 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU F 493 " --> pdb=" O LYS F 490 " (cutoff:3.500A) Processing helix chain 'F' and resid 527 through 531 removed outlier: 3.807A pdb=" N SER F 530 " --> pdb=" O PRO F 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 537 through 546 Processing helix chain 'F' and resid 550 through 555 removed outlier: 3.847A pdb=" N LEU F 555 " --> pdb=" O LEU F 551 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.370A pdb=" N ILE A 4 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU A 147 " --> pdb=" O ILE A 4 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL A 6 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N TYR A 3 " --> pdb=" O CYS A 176 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE A 178 " --> pdb=" O TYR A 3 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N LEU A 5 " --> pdb=" O ILE A 178 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL A 180 " --> pdb=" O LEU A 5 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR A 7 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N LEU A 182 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N LEU A 213 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN A 177 " --> pdb=" O LEU A 213 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL A 215 " --> pdb=" O ASN A 177 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N HIS A 179 " --> pdb=" O VAL A 215 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ARG A 217 " --> pdb=" O HIS A 179 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER A 181 " --> pdb=" O ARG A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 59 through 60 Processing sheet with id=AA3, first strand: chain 'A' and resid 335 through 338 removed outlier: 6.668A pdb=" N ALA A 302 " --> pdb=" O LEU A 368 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE A 367 " --> pdb=" O LEU A 396 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N VAL A 398 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N VAL A 369 " --> pdb=" O VAL A 398 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE A 395 " --> pdb=" O VAL A 521 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N VAL A 523 " --> pdb=" O PHE A 395 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY A 397 " --> pdb=" O VAL A 523 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N PHE A 520 " --> pdb=" O LEU A 514 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER A 498 " --> pdb=" O GLU A 513 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 419 through 421 removed outlier: 6.956A pdb=" N ASP A 420 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N ASP A 435 " --> pdb=" O ASP A 420 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 473 through 480 removed outlier: 3.689A pdb=" N GLU A 476 " --> pdb=" O ARG A 453 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 87 through 89 removed outlier: 6.370A pdb=" N ILE D 4 " --> pdb=" O ILE D 145 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LEU D 147 " --> pdb=" O ILE D 4 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL D 6 " --> pdb=" O LEU D 147 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TYR D 3 " --> pdb=" O CYS D 176 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE D 178 " --> pdb=" O TYR D 3 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU D 5 " --> pdb=" O ILE D 178 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL D 180 " --> pdb=" O LEU D 5 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR D 7 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N LEU D 182 " --> pdb=" O THR D 7 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N LEU D 213 " --> pdb=" O PHE D 175 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN D 177 " --> pdb=" O LEU D 213 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL D 215 " --> pdb=" O ASN D 177 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N HIS D 179 " --> pdb=" O VAL D 215 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ARG D 217 " --> pdb=" O HIS D 179 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER D 181 " --> pdb=" O ARG D 217 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 59 through 60 Processing sheet with id=AA8, first strand: chain 'D' and resid 335 through 338 removed outlier: 6.668A pdb=" N ALA D 302 " --> pdb=" O LEU D 368 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE D 367 " --> pdb=" O LEU D 396 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N VAL D 398 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL D 369 " --> pdb=" O VAL D 398 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE D 395 " --> pdb=" O VAL D 521 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N VAL D 523 " --> pdb=" O PHE D 395 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY D 397 " --> pdb=" O VAL D 523 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N PHE D 520 " --> pdb=" O LEU D 514 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER D 498 " --> pdb=" O GLU D 513 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 419 through 421 removed outlier: 6.956A pdb=" N ASP D 420 " --> pdb=" O VAL D 433 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N ASP D 435 " --> pdb=" O ASP D 420 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 473 through 480 removed outlier: 3.690A pdb=" N GLU D 476 " --> pdb=" O ARG D 453 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 87 through 89 removed outlier: 6.370A pdb=" N ILE E 4 " --> pdb=" O ILE E 145 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU E 147 " --> pdb=" O ILE E 4 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL E 6 " --> pdb=" O LEU E 147 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TYR E 3 " --> pdb=" O CYS E 176 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE E 178 " --> pdb=" O TYR E 3 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU E 5 " --> pdb=" O ILE E 178 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL E 180 " --> pdb=" O LEU E 5 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N THR E 7 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 8.542A pdb=" N LEU E 182 " --> pdb=" O THR E 7 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N LEU E 213 " --> pdb=" O PHE E 175 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN E 177 " --> pdb=" O LEU E 213 " (cutoff:3.500A) removed outlier: 7.591A pdb=" N VAL E 215 " --> pdb=" O ASN E 177 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N HIS E 179 " --> pdb=" O VAL E 215 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ARG E 217 " --> pdb=" O HIS E 179 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER E 181 " --> pdb=" O ARG E 217 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 59 through 60 Processing sheet with id=AB4, first strand: chain 'E' and resid 335 through 338 removed outlier: 6.668A pdb=" N ALA E 302 " --> pdb=" O LEU E 368 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE E 367 " --> pdb=" O LEU E 396 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N VAL E 398 " --> pdb=" O ILE E 367 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL E 369 " --> pdb=" O VAL E 398 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE E 395 " --> pdb=" O VAL E 521 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N VAL E 523 " --> pdb=" O PHE E 395 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY E 397 " --> pdb=" O VAL E 523 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N PHE E 520 " --> pdb=" O LEU E 514 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N SER E 498 " --> pdb=" O GLU E 513 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 419 through 421 removed outlier: 6.956A pdb=" N ASP E 420 " --> pdb=" O VAL E 433 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N ASP E 435 " --> pdb=" O ASP E 420 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 473 through 480 removed outlier: 3.690A pdb=" N GLU E 476 " --> pdb=" O ARG E 453 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 87 through 89 removed outlier: 6.371A pdb=" N ILE F 4 " --> pdb=" O ILE F 145 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N LEU F 147 " --> pdb=" O ILE F 4 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N VAL F 6 " --> pdb=" O LEU F 147 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N TYR F 3 " --> pdb=" O CYS F 176 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N ILE F 178 " --> pdb=" O TYR F 3 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU F 5 " --> pdb=" O ILE F 178 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N VAL F 180 " --> pdb=" O LEU F 5 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR F 7 " --> pdb=" O VAL F 180 " (cutoff:3.500A) removed outlier: 8.541A pdb=" N LEU F 182 " --> pdb=" O THR F 7 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N LEU F 213 " --> pdb=" O PHE F 175 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N ASN F 177 " --> pdb=" O LEU F 213 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL F 215 " --> pdb=" O ASN F 177 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N HIS F 179 " --> pdb=" O VAL F 215 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N ARG F 217 " --> pdb=" O HIS F 179 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N SER F 181 " --> pdb=" O ARG F 217 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 59 through 60 Processing sheet with id=AB9, first strand: chain 'F' and resid 335 through 338 removed outlier: 6.668A pdb=" N ALA F 302 " --> pdb=" O LEU F 368 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE F 367 " --> pdb=" O LEU F 396 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N VAL F 398 " --> pdb=" O ILE F 367 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL F 369 " --> pdb=" O VAL F 398 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N PHE F 395 " --> pdb=" O VAL F 521 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N VAL F 523 " --> pdb=" O PHE F 395 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLY F 397 " --> pdb=" O VAL F 523 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N PHE F 520 " --> pdb=" O LEU F 514 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER F 498 " --> pdb=" O GLU F 513 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 419 through 421 removed outlier: 6.957A pdb=" N ASP F 420 " --> pdb=" O VAL F 433 " (cutoff:3.500A) removed outlier: 8.955A pdb=" N ASP F 435 " --> pdb=" O ASP F 420 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 473 through 480 removed outlier: 3.690A pdb=" N GLU F 476 " --> pdb=" O ARG F 453 " (cutoff:3.500A) 592 hydrogen bonds defined for protein. 1692 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: 2.83 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2964 1.30 - 1.43: 4519 1.43 - 1.55: 10545 1.55 - 1.68: 36 1.68 - 1.81: 140 Bond restraints: 18204 Sorted by residual: bond pdb=" CA TYR D 53 " pdb=" C TYR D 53 " ideal model delta sigma weight residual 1.524 1.433 0.091 1.27e-02 6.20e+03 5.16e+01 bond pdb=" CA TYR F 53 " pdb=" C TYR F 53 " ideal model delta sigma weight residual 1.524 1.433 0.091 1.27e-02 6.20e+03 5.15e+01 bond pdb=" CA TYR A 53 " pdb=" C TYR A 53 " ideal model delta sigma weight residual 1.524 1.433 0.091 1.27e-02 6.20e+03 5.15e+01 bond pdb=" CA TYR E 53 " pdb=" C TYR E 53 " ideal model delta sigma weight residual 1.524 1.433 0.090 1.27e-02 6.20e+03 5.07e+01 bond pdb=" CA ALA E 315 " pdb=" C ALA E 315 " ideal model delta sigma weight residual 1.523 1.434 0.089 1.30e-02 5.92e+03 4.71e+01 ... (remaining 18199 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.51: 24109 3.51 - 7.02: 482 7.02 - 10.53: 73 10.53 - 14.04: 8 14.04 - 17.56: 8 Bond angle restraints: 24680 Sorted by residual: angle pdb=" N SER A 51 " pdb=" CA SER A 51 " pdb=" C SER A 51 " ideal model delta sigma weight residual 109.64 92.08 17.56 1.56e+00 4.11e-01 1.27e+02 angle pdb=" N SER F 51 " pdb=" CA SER F 51 " pdb=" C SER F 51 " ideal model delta sigma weight residual 109.64 92.13 17.51 1.56e+00 4.11e-01 1.26e+02 angle pdb=" N SER D 51 " pdb=" CA SER D 51 " pdb=" C SER D 51 " ideal model delta sigma weight residual 109.64 92.13 17.51 1.56e+00 4.11e-01 1.26e+02 angle pdb=" N SER E 51 " pdb=" CA SER E 51 " pdb=" C SER E 51 " ideal model delta sigma weight residual 109.64 92.20 17.44 1.56e+00 4.11e-01 1.25e+02 angle pdb=" N GLU E 54 " pdb=" CA GLU E 54 " pdb=" C GLU E 54 " ideal model delta sigma weight residual 110.53 99.89 10.64 1.29e+00 6.01e-01 6.80e+01 ... (remaining 24675 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.94: 10801 33.94 - 67.87: 161 67.87 - 101.81: 16 101.81 - 135.74: 2 135.74 - 169.68: 4 Dihedral angle restraints: 10984 sinusoidal: 4580 harmonic: 6404 Sorted by residual: dihedral pdb=" CA ARG D 311 " pdb=" C ARG D 311 " pdb=" N ASP D 312 " pdb=" CA ASP D 312 " ideal model delta harmonic sigma weight residual -180.00 -118.06 -61.94 0 5.00e+00 4.00e-02 1.53e+02 dihedral pdb=" CA ARG E 311 " pdb=" C ARG E 311 " pdb=" N ASP E 312 " pdb=" CA ASP E 312 " ideal model delta harmonic sigma weight residual -180.00 -118.10 -61.90 0 5.00e+00 4.00e-02 1.53e+02 dihedral pdb=" CA ARG F 311 " pdb=" C ARG F 311 " pdb=" N ASP F 312 " pdb=" CA ASP F 312 " ideal model delta harmonic sigma weight residual -180.00 -118.11 -61.89 0 5.00e+00 4.00e-02 1.53e+02 ... (remaining 10981 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 2297 0.091 - 0.182: 395 0.182 - 0.273: 36 0.273 - 0.364: 8 0.364 - 0.455: 12 Chirality restraints: 2748 Sorted by residual: chirality pdb=" CB ILE F 214 " pdb=" CA ILE F 214 " pdb=" CG1 ILE F 214 " pdb=" CG2 ILE F 214 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" CB ILE A 214 " pdb=" CA ILE A 214 " pdb=" CG1 ILE A 214 " pdb=" CG2 ILE A 214 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.14e+00 chirality pdb=" CB ILE D 214 " pdb=" CA ILE D 214 " pdb=" CG1 ILE D 214 " pdb=" CG2 ILE D 214 " both_signs ideal model delta sigma weight residual False 2.64 2.19 0.45 2.00e-01 2.50e+01 5.14e+00 ... (remaining 2745 not shown) Planarity restraints: 3168 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 53 " -0.053 2.00e-02 2.50e+03 2.74e-02 1.50e+01 pdb=" CG TYR F 53 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR F 53 " 0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR F 53 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR F 53 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR F 53 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR F 53 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR F 53 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 53 " 0.053 2.00e-02 2.50e+03 2.74e-02 1.50e+01 pdb=" CG TYR E 53 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR E 53 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TYR E 53 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR E 53 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR E 53 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR E 53 " 0.006 2.00e-02 2.50e+03 pdb=" OH TYR E 53 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 53 " -0.053 2.00e-02 2.50e+03 2.73e-02 1.49e+01 pdb=" CG TYR A 53 " 0.044 2.00e-02 2.50e+03 pdb=" CD1 TYR A 53 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR A 53 " 0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 53 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 53 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR A 53 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR A 53 " -0.025 2.00e-02 2.50e+03 ... (remaining 3165 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.30: 18 2.30 - 2.95: 7998 2.95 - 3.60: 25595 3.60 - 4.25: 43234 4.25 - 4.90: 69646 Nonbonded interactions: 146491 Sorted by model distance: nonbonded pdb=" OE2 GLU A 155 " pdb=" O2' CTP A 602 " model vdw 1.655 3.040 nonbonded pdb=" OE2 GLU F 155 " pdb=" O2' CTP F 602 " model vdw 1.656 3.040 nonbonded pdb=" OE2 GLU E 155 " pdb=" O2' CTP E 602 " model vdw 1.656 3.040 nonbonded pdb=" OE2 GLU D 155 " pdb=" O2' CTP D 602 " model vdw 1.656 3.040 nonbonded pdb=" OD1 ASP A 153 " pdb=" NZ LYS D 195 " model vdw 1.872 3.120 ... (remaining 146486 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 'A' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.75 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 15.840 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 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 : 0.011 0.091 18204 Z= 0.571 Angle : 1.252 17.556 24680 Z= 0.695 Chirality : 0.075 0.455 2748 Planarity : 0.009 0.069 3168 Dihedral : 12.859 169.679 6872 Min Nonbonded Distance : 1.655 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.18 % Allowed : 8.60 % Favored : 91.22 % Rotamer: Outliers : 0.41 % Allowed : 5.98 % Favored : 93.61 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.57 % 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: -4.98 (0.14), residues: 2220 helix: -4.03 (0.10), residues: 812 sheet: -3.12 (0.28), residues: 316 loop : -2.68 (0.17), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 205 TYR 0.053 0.005 TYR A 53 PHE 0.032 0.004 PHE A 482 TRP 0.030 0.005 TRP D 124 HIS 0.012 0.002 HIS E 55 Details of bonding type rmsd covalent geometry : bond 0.01069 (18204) covalent geometry : angle 1.25195 (24680) hydrogen bonds : bond 0.31563 ( 592) hydrogen bonds : angle 10.45490 ( 1692) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 548 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 GLU cc_start: 0.7844 (tm-30) cc_final: 0.7518 (tm-30) REVERT: A 299 CYS cc_start: 0.7605 (m) cc_final: 0.7282 (m) REVERT: A 363 LYS cc_start: 0.8836 (tmmm) cc_final: 0.8495 (ttpt) REVERT: A 436 MET cc_start: 0.8353 (ttm) cc_final: 0.8152 (ttm) REVERT: D 57 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7504 (tm-30) REVERT: D 299 CYS cc_start: 0.7604 (m) cc_final: 0.7298 (m) REVERT: D 363 LYS cc_start: 0.8811 (tmmm) cc_final: 0.8468 (ttpt) REVERT: D 436 MET cc_start: 0.8360 (ttm) cc_final: 0.8130 (ttm) REVERT: E 157 MET cc_start: 0.7885 (mmt) cc_final: 0.7654 (mmt) REVERT: E 299 CYS cc_start: 0.7526 (m) cc_final: 0.7232 (m) REVERT: E 363 LYS cc_start: 0.8748 (tmmm) cc_final: 0.8433 (ttpt) REVERT: E 379 LEU cc_start: 0.8407 (tt) cc_final: 0.7912 (tt) REVERT: E 436 MET cc_start: 0.8290 (ttm) cc_final: 0.8073 (ttm) REVERT: F 157 MET cc_start: 0.7883 (mmt) cc_final: 0.7651 (mmt) REVERT: F 299 CYS cc_start: 0.7531 (m) cc_final: 0.7225 (m) REVERT: F 363 LYS cc_start: 0.8755 (tmmm) cc_final: 0.8433 (ttpt) REVERT: F 436 MET cc_start: 0.8345 (ttm) cc_final: 0.8123 (ttm) outliers start: 8 outliers final: 4 residues processed: 556 average time/residue: 0.1698 time to fit residues: 132.0917 Evaluate side-chains 281 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 277 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 GLU Chi-restraints excluded: chain D residue 322 GLU Chi-restraints excluded: chain E residue 322 GLU Chi-restraints excluded: chain F residue 322 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 5.9990 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 7.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 480 HIS A 495 ASN A 502 GLN ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 167 GLN D 412 ASN D 478 HIS D 495 ASN D 502 GLN ** D 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 167 GLN ** E 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 495 ASN E 502 GLN ** E 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 167 GLN F 412 ASN F 478 HIS F 495 ASN F 502 GLN ** F 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.127915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.107085 restraints weight = 31351.533| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 3.17 r_work: 0.3364 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.75 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3360 r_free = 0.3360 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3360 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 18204 Z= 0.209 Angle : 0.784 7.738 24680 Z= 0.398 Chirality : 0.051 0.200 2748 Planarity : 0.006 0.052 3168 Dihedral : 12.217 174.456 2516 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 3.71 % Allowed : 14.18 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -3.47 (0.16), residues: 2220 helix: -2.08 (0.15), residues: 836 sheet: -2.78 (0.23), residues: 408 loop : -2.11 (0.19), residues: 976 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 465 TYR 0.023 0.003 TYR F 307 PHE 0.021 0.002 PHE D 50 TRP 0.017 0.002 TRP A 285 HIS 0.004 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00483 (18204) covalent geometry : angle 0.78428 (24680) hydrogen bonds : bond 0.05306 ( 592) hydrogen bonds : angle 5.76634 ( 1692) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 345 time to evaluate : 0.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7565 (mt-10) REVERT: A 363 LYS cc_start: 0.8719 (tmmm) cc_final: 0.8459 (ttpt) REVERT: A 408 GLU cc_start: 0.8721 (tm-30) cc_final: 0.8284 (tm-30) REVERT: A 436 MET cc_start: 0.8592 (ttm) cc_final: 0.8363 (ttm) REVERT: A 438 GLU cc_start: 0.7552 (tp30) cc_final: 0.7294 (tp30) REVERT: D 75 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7571 (mt-10) REVERT: D 363 LYS cc_start: 0.8714 (tmmm) cc_final: 0.8463 (ttpt) REVERT: D 408 GLU cc_start: 0.8735 (tm-30) cc_final: 0.8293 (tm-30) REVERT: D 436 MET cc_start: 0.8616 (ttm) cc_final: 0.8244 (ttm) REVERT: D 438 GLU cc_start: 0.7793 (tp30) cc_final: 0.7546 (tp30) REVERT: E 75 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7569 (mt-10) REVERT: E 363 LYS cc_start: 0.8708 (tmmm) cc_final: 0.8454 (ttpt) REVERT: E 408 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8263 (tm-30) REVERT: E 436 MET cc_start: 0.8572 (ttm) cc_final: 0.8354 (ttm) REVERT: E 438 GLU cc_start: 0.7882 (tp30) cc_final: 0.7539 (mt-10) REVERT: E 508 ARG cc_start: 0.8144 (mtp85) cc_final: 0.7849 (mtm-85) REVERT: F 75 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7574 (mt-10) REVERT: F 363 LYS cc_start: 0.8704 (tmmm) cc_final: 0.8449 (ttpt) REVERT: F 408 GLU cc_start: 0.8720 (tm-30) cc_final: 0.8280 (tm-30) REVERT: F 436 MET cc_start: 0.8585 (ttm) cc_final: 0.8231 (ttm) REVERT: F 438 GLU cc_start: 0.7824 (tp30) cc_final: 0.7553 (tp30) outliers start: 72 outliers final: 34 residues processed: 399 average time/residue: 0.1395 time to fit residues: 82.5502 Evaluate side-chains 296 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 262 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 214 ILE Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 463 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 214 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 463 ILE Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 214 ILE Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 463 ILE Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 463 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 4 optimal weight: 0.6980 chunk 134 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 216 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 5.9990 chunk 218 optimal weight: 0.0010 chunk 56 optimal weight: 0.8980 chunk 10 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 165 optimal weight: 6.9990 overall best weight: 1.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 44 ASN ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 44 ASN ** D 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 44 ASN E 198 GLN E 478 HIS ** E 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 44 ASN F 198 GLN ** F 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 524 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.128087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.107331 restraints weight = 31748.016| |-----------------------------------------------------------------------------| r_work (start): 0.3445 rms_B_bonded: 3.21 r_work: 0.3326 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3377 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.82 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3377 r_free = 0.3377 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3377 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.3323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18204 Z= 0.155 Angle : 0.709 7.472 24680 Z= 0.351 Chirality : 0.049 0.223 2748 Planarity : 0.005 0.045 3168 Dihedral : 11.389 163.859 2504 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 3.56 % Allowed : 15.62 % Favored : 80.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -2.69 (0.17), residues: 2220 helix: -1.19 (0.17), residues: 860 sheet: -2.37 (0.25), residues: 348 loop : -2.00 (0.19), residues: 1012 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 465 TYR 0.020 0.002 TYR A 307 PHE 0.020 0.001 PHE D 50 TRP 0.014 0.002 TRP E 285 HIS 0.003 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00357 (18204) covalent geometry : angle 0.70898 (24680) hydrogen bonds : bond 0.03816 ( 592) hydrogen bonds : angle 5.11957 ( 1692) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 345 time to evaluate : 0.704 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 224 MET cc_start: 0.8446 (tpp) cc_final: 0.8235 (tpp) REVERT: A 363 LYS cc_start: 0.8544 (tmmm) cc_final: 0.8229 (ttpp) REVERT: A 408 GLU cc_start: 0.8830 (tm-30) cc_final: 0.8551 (tm-30) REVERT: A 436 MET cc_start: 0.8545 (ttm) cc_final: 0.8304 (ttm) REVERT: A 438 GLU cc_start: 0.7729 (tp30) cc_final: 0.7408 (tp30) REVERT: A 498 SER cc_start: 0.8334 (t) cc_final: 0.7989 (p) REVERT: A 510 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7999 (mm-30) REVERT: A 528 GLU cc_start: 0.8896 (mp0) cc_final: 0.8553 (mp0) REVERT: D 224 MET cc_start: 0.8440 (tpp) cc_final: 0.8229 (tpp) REVERT: D 363 LYS cc_start: 0.8564 (tmmm) cc_final: 0.8259 (ttpp) REVERT: D 436 MET cc_start: 0.8491 (ttm) cc_final: 0.8218 (ttm) REVERT: D 438 GLU cc_start: 0.7921 (tp30) cc_final: 0.7601 (tp30) REVERT: D 498 SER cc_start: 0.8332 (t) cc_final: 0.7988 (p) REVERT: D 510 GLU cc_start: 0.8308 (mm-30) cc_final: 0.8056 (mm-30) REVERT: D 528 GLU cc_start: 0.8878 (mp0) cc_final: 0.8539 (mp0) REVERT: E 224 MET cc_start: 0.8369 (tpp) cc_final: 0.8164 (tpp) REVERT: E 324 SER cc_start: 0.9140 (m) cc_final: 0.8929 (t) REVERT: E 363 LYS cc_start: 0.8556 (tmmm) cc_final: 0.8251 (ttpp) REVERT: E 408 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8675 (tm-30) REVERT: E 436 MET cc_start: 0.8445 (ttm) cc_final: 0.8226 (ttm) REVERT: E 438 GLU cc_start: 0.8077 (tp30) cc_final: 0.7797 (tp30) REVERT: E 498 SER cc_start: 0.8334 (t) cc_final: 0.7988 (p) REVERT: E 508 ARG cc_start: 0.8148 (mtp85) cc_final: 0.7893 (mtm-85) REVERT: E 510 GLU cc_start: 0.8302 (mm-30) cc_final: 0.8038 (mm-30) REVERT: E 528 GLU cc_start: 0.8874 (mp0) cc_final: 0.8535 (mp0) REVERT: F 224 MET cc_start: 0.8398 (tpp) cc_final: 0.8195 (tpp) REVERT: F 324 SER cc_start: 0.9174 (m) cc_final: 0.8970 (t) REVERT: F 363 LYS cc_start: 0.8553 (tmmm) cc_final: 0.8249 (ttpp) REVERT: F 408 GLU cc_start: 0.8894 (tm-30) cc_final: 0.8674 (tm-30) REVERT: F 436 MET cc_start: 0.8510 (ttm) cc_final: 0.8242 (ttm) REVERT: F 438 GLU cc_start: 0.7922 (tp30) cc_final: 0.7602 (tp30) REVERT: F 498 SER cc_start: 0.8336 (t) cc_final: 0.7989 (p) REVERT: F 510 GLU cc_start: 0.8312 (mm-30) cc_final: 0.8069 (mm-30) REVERT: F 528 GLU cc_start: 0.8873 (mp0) cc_final: 0.8523 (mp0) outliers start: 69 outliers final: 39 residues processed: 384 average time/residue: 0.1257 time to fit residues: 75.0562 Evaluate side-chains 300 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 261 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 THR Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 508 ARG Chi-restraints excluded: chain E residue 7 THR Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 508 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 0.8980 chunk 44 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 chunk 112 optimal weight: 7.9990 chunk 96 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 60 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 211 optimal weight: 0.0270 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 198 GLN ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 ASN D 198 GLN E 87 ASN ** E 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 87 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.130191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.109899 restraints weight = 31630.685| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.13 r_work: 0.3372 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3375 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3375 r_free = 0.3375 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3375 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8007 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18204 Z= 0.117 Angle : 0.645 6.632 24680 Z= 0.319 Chirality : 0.047 0.177 2748 Planarity : 0.005 0.043 3168 Dihedral : 10.631 146.685 2504 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 2.99 % Allowed : 17.78 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.96 (0.17), residues: 2220 helix: -0.33 (0.18), residues: 832 sheet: -2.15 (0.25), residues: 348 loop : -1.75 (0.19), residues: 1040 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 376 TYR 0.016 0.001 TYR D 307 PHE 0.020 0.001 PHE D 50 TRP 0.010 0.001 TRP F 285 HIS 0.003 0.001 HIS D 517 Details of bonding type rmsd covalent geometry : bond 0.00268 (18204) covalent geometry : angle 0.64538 (24680) hydrogen bonds : bond 0.03249 ( 592) hydrogen bonds : angle 4.77502 ( 1692) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 334 time to evaluate : 0.715 Fit side-chains REVERT: A 66 GLU cc_start: 0.8386 (mt-10) cc_final: 0.7993 (mt-10) REVERT: A 70 ASP cc_start: 0.8067 (m-30) cc_final: 0.7524 (t0) REVERT: A 161 GLU cc_start: 0.8328 (tp30) cc_final: 0.7942 (tm-30) REVERT: A 224 MET cc_start: 0.8364 (tpp) cc_final: 0.8088 (tpp) REVERT: A 363 LYS cc_start: 0.8528 (tmmm) cc_final: 0.8289 (ttmt) REVERT: A 436 MET cc_start: 0.8632 (ttm) cc_final: 0.8377 (ttm) REVERT: A 438 GLU cc_start: 0.7761 (tp30) cc_final: 0.7507 (tp30) REVERT: A 498 SER cc_start: 0.8403 (t) cc_final: 0.8038 (p) REVERT: D 70 ASP cc_start: 0.8037 (m-30) cc_final: 0.7510 (t0) REVERT: D 161 GLU cc_start: 0.8322 (tp30) cc_final: 0.7940 (tm-30) REVERT: D 224 MET cc_start: 0.8359 (tpp) cc_final: 0.8083 (tpp) REVERT: D 363 LYS cc_start: 0.8531 (tmmm) cc_final: 0.8298 (ttmt) REVERT: D 436 MET cc_start: 0.8503 (ttm) cc_final: 0.8210 (ttm) REVERT: D 438 GLU cc_start: 0.8027 (tp30) cc_final: 0.7805 (tp30) REVERT: D 498 SER cc_start: 0.8400 (t) cc_final: 0.8026 (p) REVERT: E 66 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7838 (mt-10) REVERT: E 70 ASP cc_start: 0.8103 (m-30) cc_final: 0.7602 (t0) REVERT: E 161 GLU cc_start: 0.8348 (tp30) cc_final: 0.7973 (tm-30) REVERT: E 224 MET cc_start: 0.8365 (tpp) cc_final: 0.8098 (tpp) REVERT: E 363 LYS cc_start: 0.8508 (tmmm) cc_final: 0.8282 (ttmt) REVERT: E 436 MET cc_start: 0.8453 (ttm) cc_final: 0.8230 (ttm) REVERT: E 438 GLU cc_start: 0.8085 (tp30) cc_final: 0.7798 (tp30) REVERT: E 498 SER cc_start: 0.8394 (t) cc_final: 0.8018 (p) REVERT: E 503 ASP cc_start: 0.7751 (p0) cc_final: 0.7447 (p0) REVERT: E 508 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7781 (mtm-85) REVERT: F 70 ASP cc_start: 0.8082 (m-30) cc_final: 0.7605 (t0) REVERT: F 161 GLU cc_start: 0.8329 (tp30) cc_final: 0.7958 (tm-30) REVERT: F 224 MET cc_start: 0.8425 (tpp) cc_final: 0.8147 (tpp) REVERT: F 363 LYS cc_start: 0.8511 (tmmm) cc_final: 0.8283 (ttmt) REVERT: F 436 MET cc_start: 0.8508 (ttm) cc_final: 0.8245 (ttm) REVERT: F 438 GLU cc_start: 0.8046 (tp30) cc_final: 0.7794 (tp30) REVERT: F 470 ASP cc_start: 0.7602 (t0) cc_final: 0.7395 (t0) REVERT: F 498 SER cc_start: 0.8396 (t) cc_final: 0.8020 (p) outliers start: 58 outliers final: 43 residues processed: 359 average time/residue: 0.1233 time to fit residues: 69.3106 Evaluate side-chains 300 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 256 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 313 CYS Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 503 ASP Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 313 CYS Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 508 ARG Chi-restraints excluded: chain E residue 551 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 313 CYS Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 503 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 175 optimal weight: 9.9990 chunk 68 optimal weight: 10.0000 chunk 59 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 122 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 115 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 93 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 57 optimal weight: 3.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 329 ASN ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 329 ASN ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 329 ASN ** E 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 329 ASN ** F 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.125351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.104889 restraints weight = 31926.020| |-----------------------------------------------------------------------------| r_work (start): 0.3462 rms_B_bonded: 3.11 r_work: 0.3354 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3352 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3352 r_free = 0.3352 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3352 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 18204 Z= 0.189 Angle : 0.703 9.935 24680 Z= 0.346 Chirality : 0.049 0.198 2748 Planarity : 0.005 0.046 3168 Dihedral : 10.337 143.556 2504 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 10.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 4.85 % Allowed : 18.56 % Favored : 76.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.98 (0.17), residues: 2220 helix: -0.33 (0.18), residues: 876 sheet: -2.05 (0.26), residues: 340 loop : -1.87 (0.19), residues: 1004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG F 479 TYR 0.015 0.002 TYR F 307 PHE 0.025 0.002 PHE A 50 TRP 0.011 0.002 TRP D 285 HIS 0.003 0.001 HIS E 96 Details of bonding type rmsd covalent geometry : bond 0.00449 (18204) covalent geometry : angle 0.70317 (24680) hydrogen bonds : bond 0.03369 ( 592) hydrogen bonds : angle 4.82020 ( 1692) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 271 time to evaluate : 0.648 Fit side-chains REVERT: A 70 ASP cc_start: 0.8059 (m-30) cc_final: 0.7558 (t0) REVERT: A 161 GLU cc_start: 0.8331 (tp30) cc_final: 0.7923 (tm-30) REVERT: A 224 MET cc_start: 0.8461 (tpp) cc_final: 0.8181 (tpp) REVERT: A 363 LYS cc_start: 0.8526 (tmmm) cc_final: 0.8296 (ttmt) REVERT: A 438 GLU cc_start: 0.8019 (tp30) cc_final: 0.7788 (tp30) REVERT: A 498 SER cc_start: 0.8438 (t) cc_final: 0.8062 (p) REVERT: A 510 GLU cc_start: 0.8158 (mm-30) cc_final: 0.7689 (mm-30) REVERT: D 70 ASP cc_start: 0.8023 (m-30) cc_final: 0.7546 (t0) REVERT: D 161 GLU cc_start: 0.8340 (tp30) cc_final: 0.7937 (tm-30) REVERT: D 224 MET cc_start: 0.8443 (tpp) cc_final: 0.8173 (tpp) REVERT: D 363 LYS cc_start: 0.8525 (tmmm) cc_final: 0.8297 (ttmt) REVERT: D 436 MET cc_start: 0.8490 (ttm) cc_final: 0.8197 (ttm) REVERT: D 438 GLU cc_start: 0.8187 (tp30) cc_final: 0.7922 (tp30) REVERT: D 481 ARG cc_start: 0.7683 (mtp180) cc_final: 0.7380 (ttp-170) REVERT: D 498 SER cc_start: 0.8437 (t) cc_final: 0.8061 (p) REVERT: D 510 GLU cc_start: 0.8255 (mm-30) cc_final: 0.7733 (mm-30) REVERT: E 70 ASP cc_start: 0.8085 (m-30) cc_final: 0.7596 (t0) REVERT: E 161 GLU cc_start: 0.8374 (tp30) cc_final: 0.7977 (tm-30) REVERT: E 224 MET cc_start: 0.8474 (tpp) cc_final: 0.8205 (tpp) REVERT: E 363 LYS cc_start: 0.8481 (tmmm) cc_final: 0.8251 (ttmt) REVERT: E 438 GLU cc_start: 0.8166 (tp30) cc_final: 0.7910 (tp30) REVERT: E 498 SER cc_start: 0.8451 (t) cc_final: 0.8069 (p) REVERT: E 503 ASP cc_start: 0.8053 (p0) cc_final: 0.7291 (p0) REVERT: E 508 ARG cc_start: 0.8266 (OUTLIER) cc_final: 0.7878 (ptp90) REVERT: E 510 GLU cc_start: 0.8238 (mm-30) cc_final: 0.8018 (mm-30) REVERT: F 70 ASP cc_start: 0.8089 (m-30) cc_final: 0.7596 (t0) REVERT: F 161 GLU cc_start: 0.8354 (tp30) cc_final: 0.7965 (tm-30) REVERT: F 224 MET cc_start: 0.8476 (tpp) cc_final: 0.8207 (tpp) REVERT: F 363 LYS cc_start: 0.8539 (tmmm) cc_final: 0.8313 (ttmt) REVERT: F 436 MET cc_start: 0.8516 (ttm) cc_final: 0.8221 (ttm) REVERT: F 438 GLU cc_start: 0.8180 (tp30) cc_final: 0.7910 (tp30) REVERT: F 498 SER cc_start: 0.8455 (t) cc_final: 0.8073 (p) REVERT: F 510 GLU cc_start: 0.8277 (mm-30) cc_final: 0.7747 (mm-30) outliers start: 94 outliers final: 68 residues processed: 331 average time/residue: 0.1235 time to fit residues: 62.9757 Evaluate side-chains 320 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 251 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 78 LEU Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 313 CYS Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 417 LYS Chi-restraints excluded: chain D residue 424 PHE Chi-restraints excluded: chain D residue 551 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 313 CYS Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain E residue 417 LYS Chi-restraints excluded: chain E residue 489 ILE Chi-restraints excluded: chain E residue 508 ARG Chi-restraints excluded: chain E residue 551 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 313 CYS Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 417 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 146 optimal weight: 2.9990 chunk 145 optimal weight: 8.9990 chunk 51 optimal weight: 0.4980 chunk 49 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 126 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 197 optimal weight: 7.9990 chunk 207 optimal weight: 9.9990 chunk 17 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 480 HIS ** 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 = 0.3771 r_free = 0.3771 target = 0.126845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.106566 restraints weight = 31554.504| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 3.08 r_work: 0.3383 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3383 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3381 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3381 r_free = 0.3381 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3381 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 18204 Z= 0.145 Angle : 0.667 11.967 24680 Z= 0.324 Chirality : 0.047 0.207 2748 Planarity : 0.005 0.045 3168 Dihedral : 9.769 132.379 2504 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.54 % Favored : 94.46 % Rotamer: Outliers : 4.59 % Allowed : 18.61 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.50 (0.18), residues: 2220 helix: 0.14 (0.18), residues: 852 sheet: -1.94 (0.27), residues: 340 loop : -1.58 (0.19), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 454 TYR 0.015 0.002 TYR F 307 PHE 0.022 0.001 PHE D 50 TRP 0.011 0.001 TRP F 124 HIS 0.003 0.001 HIS E 96 Details of bonding type rmsd covalent geometry : bond 0.00342 (18204) covalent geometry : angle 0.66651 (24680) hydrogen bonds : bond 0.03092 ( 592) hydrogen bonds : angle 4.63942 ( 1692) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 291 time to evaluate : 0.682 Fit side-chains REVERT: A 70 ASP cc_start: 0.8135 (m-30) cc_final: 0.7569 (t0) REVERT: A 161 GLU cc_start: 0.8347 (tp30) cc_final: 0.7931 (tm-30) REVERT: A 224 MET cc_start: 0.8435 (tpp) cc_final: 0.8175 (tpp) REVERT: A 256 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8671 (tt) REVERT: A 363 LYS cc_start: 0.8516 (tmmm) cc_final: 0.8291 (ttmt) REVERT: A 436 MET cc_start: 0.8437 (ttm) cc_final: 0.8030 (ttm) REVERT: A 470 ASP cc_start: 0.7653 (t0) cc_final: 0.7414 (t0) REVERT: A 498 SER cc_start: 0.8332 (t) cc_final: 0.7947 (p) REVERT: A 510 GLU cc_start: 0.8252 (mm-30) cc_final: 0.7787 (mm-30) REVERT: D 70 ASP cc_start: 0.8146 (m-30) cc_final: 0.7580 (t0) REVERT: D 161 GLU cc_start: 0.8333 (tp30) cc_final: 0.7910 (tm-30) REVERT: D 224 MET cc_start: 0.8437 (tpp) cc_final: 0.8176 (tpp) REVERT: D 256 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8675 (tt) REVERT: D 363 LYS cc_start: 0.8519 (tmmm) cc_final: 0.8294 (ttmt) REVERT: D 436 MET cc_start: 0.8480 (ttm) cc_final: 0.8087 (ttm) REVERT: D 438 GLU cc_start: 0.8136 (tp30) cc_final: 0.7791 (tp30) REVERT: D 481 ARG cc_start: 0.7757 (mtp180) cc_final: 0.7195 (ttp-170) REVERT: D 498 SER cc_start: 0.8325 (t) cc_final: 0.7943 (p) REVERT: D 510 GLU cc_start: 0.8299 (mm-30) cc_final: 0.7822 (mm-30) REVERT: E 70 ASP cc_start: 0.8190 (m-30) cc_final: 0.7628 (t0) REVERT: E 161 GLU cc_start: 0.8347 (tp30) cc_final: 0.7916 (tm-30) REVERT: E 224 MET cc_start: 0.8458 (tpp) cc_final: 0.8197 (tpp) REVERT: E 256 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8644 (tt) REVERT: E 363 LYS cc_start: 0.8492 (tmmm) cc_final: 0.8263 (ttmt) REVERT: E 498 SER cc_start: 0.8312 (t) cc_final: 0.7932 (p) REVERT: E 503 ASP cc_start: 0.8004 (p0) cc_final: 0.7795 (p0) REVERT: E 508 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7873 (mtm-85) REVERT: E 510 GLU cc_start: 0.8287 (mm-30) cc_final: 0.8077 (mm-30) REVERT: F 70 ASP cc_start: 0.8164 (m-30) cc_final: 0.7615 (t0) REVERT: F 161 GLU cc_start: 0.8335 (tp30) cc_final: 0.7913 (tm-30) REVERT: F 224 MET cc_start: 0.8469 (tpp) cc_final: 0.8203 (tpp) REVERT: F 256 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8652 (tt) REVERT: F 363 LYS cc_start: 0.8517 (tmmm) cc_final: 0.8290 (ttmt) REVERT: F 436 MET cc_start: 0.8515 (ttm) cc_final: 0.8121 (ttm) REVERT: F 438 GLU cc_start: 0.8124 (tp30) cc_final: 0.7781 (tp30) REVERT: F 481 ARG cc_start: 0.7891 (mtp180) cc_final: 0.7351 (ttp-170) REVERT: F 498 SER cc_start: 0.8329 (t) cc_final: 0.7941 (p) REVERT: F 510 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7841 (mm-30) outliers start: 89 outliers final: 75 residues processed: 339 average time/residue: 0.1275 time to fit residues: 67.4417 Evaluate side-chains 347 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 267 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 246 ASP Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 313 CYS Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 503 ASP Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 246 ASP Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 313 CYS Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 508 ARG Chi-restraints excluded: chain E residue 551 LEU Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 313 CYS Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 503 ASP Chi-restraints excluded: chain F residue 555 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 147 optimal weight: 10.0000 chunk 211 optimal weight: 4.9990 chunk 200 optimal weight: 10.0000 chunk 0 optimal weight: 7.9990 chunk 166 optimal weight: 0.9980 chunk 219 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 157 optimal weight: 4.9990 chunk 145 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 146 optimal weight: 0.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 412 ASN ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.125986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.105551 restraints weight = 31914.527| |-----------------------------------------------------------------------------| r_work (start): 0.3470 rms_B_bonded: 3.12 r_work: 0.3363 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3362 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.85 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 18204 Z= 0.162 Angle : 0.679 12.266 24680 Z= 0.331 Chirality : 0.048 0.222 2748 Planarity : 0.005 0.045 3168 Dihedral : 9.451 128.953 2504 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 4.79 % Allowed : 18.04 % Favored : 77.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.40 (0.18), residues: 2220 helix: 0.23 (0.19), residues: 852 sheet: -1.86 (0.27), residues: 340 loop : -1.55 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 479 TYR 0.014 0.002 TYR F 307 PHE 0.022 0.001 PHE D 50 TRP 0.013 0.002 TRP F 124 HIS 0.003 0.001 HIS F 96 Details of bonding type rmsd covalent geometry : bond 0.00385 (18204) covalent geometry : angle 0.67868 (24680) hydrogen bonds : bond 0.03083 ( 592) hydrogen bonds : angle 4.59961 ( 1692) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 265 time to evaluate : 0.705 Fit side-chains REVERT: A 70 ASP cc_start: 0.8173 (m-30) cc_final: 0.7596 (t0) REVERT: A 224 MET cc_start: 0.8435 (tpp) cc_final: 0.8179 (tpp) REVERT: A 256 LEU cc_start: 0.8958 (OUTLIER) cc_final: 0.8707 (tt) REVERT: A 363 LYS cc_start: 0.8468 (tmmm) cc_final: 0.8262 (ttmt) REVERT: A 436 MET cc_start: 0.8378 (ttm) cc_final: 0.7941 (ttm) REVERT: A 470 ASP cc_start: 0.7668 (t0) cc_final: 0.7429 (t0) REVERT: A 498 SER cc_start: 0.8336 (t) cc_final: 0.7959 (p) REVERT: A 510 GLU cc_start: 0.8246 (mm-30) cc_final: 0.7721 (mm-30) REVERT: D 70 ASP cc_start: 0.8176 (m-30) cc_final: 0.7586 (t0) REVERT: D 224 MET cc_start: 0.8406 (tpp) cc_final: 0.8158 (tpp) REVERT: D 256 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8705 (tt) REVERT: D 363 LYS cc_start: 0.8501 (tmmm) cc_final: 0.8267 (ttmt) REVERT: D 436 MET cc_start: 0.8434 (ttm) cc_final: 0.7920 (ttm) REVERT: D 498 SER cc_start: 0.8343 (t) cc_final: 0.7967 (p) REVERT: D 510 GLU cc_start: 0.8258 (mm-30) cc_final: 0.7744 (mm-30) REVERT: E 70 ASP cc_start: 0.8162 (m-30) cc_final: 0.7631 (t0) REVERT: E 224 MET cc_start: 0.8458 (tpp) cc_final: 0.8208 (tpp) REVERT: E 256 LEU cc_start: 0.8930 (OUTLIER) cc_final: 0.8707 (tt) REVERT: E 363 LYS cc_start: 0.8487 (tmmm) cc_final: 0.8286 (ttmt) REVERT: E 470 ASP cc_start: 0.7694 (t0) cc_final: 0.7468 (t0) REVERT: E 498 SER cc_start: 0.8399 (t) cc_final: 0.8019 (p) REVERT: E 503 ASP cc_start: 0.8065 (p0) cc_final: 0.7861 (p0) REVERT: E 508 ARG cc_start: 0.8334 (OUTLIER) cc_final: 0.7962 (mtm-85) REVERT: F 70 ASP cc_start: 0.8143 (m-30) cc_final: 0.7584 (t0) REVERT: F 157 MET cc_start: 0.8249 (mmt) cc_final: 0.7855 (mmt) REVERT: F 224 MET cc_start: 0.8416 (tpp) cc_final: 0.8175 (tpp) REVERT: F 256 LEU cc_start: 0.8940 (OUTLIER) cc_final: 0.8715 (tt) REVERT: F 363 LYS cc_start: 0.8469 (tmmm) cc_final: 0.8265 (ttmt) REVERT: F 436 MET cc_start: 0.8462 (ttm) cc_final: 0.7840 (ttm) REVERT: F 438 GLU cc_start: 0.8059 (tp30) cc_final: 0.7824 (tp30) REVERT: F 470 ASP cc_start: 0.7712 (t0) cc_final: 0.7497 (t0) REVERT: F 498 SER cc_start: 0.8338 (t) cc_final: 0.7956 (p) REVERT: F 510 GLU cc_start: 0.8283 (mm-30) cc_final: 0.7762 (mm-30) outliers start: 93 outliers final: 83 residues processed: 320 average time/residue: 0.1288 time to fit residues: 63.9130 Evaluate side-chains 335 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 247 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 386 SER Chi-restraints excluded: chain A residue 417 LYS Chi-restraints excluded: chain A residue 424 PHE Chi-restraints excluded: chain A residue 489 ILE Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 78 LEU Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 119 ASP Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 313 CYS Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 386 SER Chi-restraints excluded: chain D residue 417 LYS Chi-restraints excluded: chain D residue 424 PHE Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain D residue 503 ASP Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 78 LEU Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 119 ASP Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 313 CYS Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain E residue 424 PHE Chi-restraints excluded: chain E residue 508 ARG Chi-restraints excluded: chain E residue 551 LEU Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 78 LEU Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 119 ASP Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 256 LEU Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 313 CYS Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 424 PHE Chi-restraints excluded: chain F residue 503 ASP Chi-restraints excluded: chain F residue 555 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 166 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 164 optimal weight: 1.9990 chunk 168 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 176 optimal weight: 0.7980 chunk 186 optimal weight: 1.9990 chunk 160 optimal weight: 9.9990 chunk 77 optimal weight: 0.0670 chunk 117 optimal weight: 0.9980 chunk 197 optimal weight: 0.9980 overall best weight: 0.7720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 412 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.129177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.108824 restraints weight = 31496.256| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 3.12 r_work: 0.3411 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3419 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.84 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3419 r_free = 0.3419 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3419 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8034 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18204 Z= 0.117 Angle : 0.648 10.780 24680 Z= 0.313 Chirality : 0.046 0.181 2748 Planarity : 0.005 0.045 3168 Dihedral : 8.631 108.222 2504 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 10.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 3.71 % Allowed : 19.64 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.25 (0.18), residues: 2220 helix: 0.40 (0.19), residues: 852 sheet: -1.77 (0.27), residues: 340 loop : -1.51 (0.20), residues: 1028 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 508 TYR 0.016 0.001 TYR E 265 PHE 0.021 0.001 PHE F 482 TRP 0.006 0.001 TRP A 285 HIS 0.002 0.001 HIS E 517 Details of bonding type rmsd covalent geometry : bond 0.00267 (18204) covalent geometry : angle 0.64767 (24680) hydrogen bonds : bond 0.02811 ( 592) hydrogen bonds : angle 4.47338 ( 1692) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 298 time to evaluate : 0.540 Fit side-chains REVERT: A 70 ASP cc_start: 0.8181 (m-30) cc_final: 0.7657 (t0) REVERT: A 126 MET cc_start: 0.8595 (tpp) cc_final: 0.8374 (mmt) REVERT: A 224 MET cc_start: 0.8365 (tpp) cc_final: 0.8106 (tpp) REVERT: A 256 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8672 (tt) REVERT: A 402 MET cc_start: 0.8256 (ttm) cc_final: 0.7900 (ttm) REVERT: A 436 MET cc_start: 0.8427 (ttm) cc_final: 0.8001 (ttm) REVERT: A 438 GLU cc_start: 0.7866 (tp30) cc_final: 0.7649 (tp30) REVERT: A 461 ASN cc_start: 0.7767 (p0) cc_final: 0.7375 (m110) REVERT: A 470 ASP cc_start: 0.7635 (t0) cc_final: 0.7388 (t0) REVERT: A 498 SER cc_start: 0.8291 (t) cc_final: 0.7922 (p) REVERT: A 510 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7617 (mm-30) REVERT: D 70 ASP cc_start: 0.8176 (m-30) cc_final: 0.7629 (t0) REVERT: D 126 MET cc_start: 0.8588 (tpp) cc_final: 0.8367 (mmt) REVERT: D 224 MET cc_start: 0.8341 (tpp) cc_final: 0.8089 (tpp) REVERT: D 256 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8666 (tt) REVERT: D 363 LYS cc_start: 0.8464 (tmmm) cc_final: 0.8243 (ttmt) REVERT: D 436 MET cc_start: 0.8446 (ttm) cc_final: 0.7998 (ttm) REVERT: D 470 ASP cc_start: 0.7659 (t0) cc_final: 0.7419 (t0) REVERT: D 498 SER cc_start: 0.8207 (t) cc_final: 0.7857 (p) REVERT: D 510 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7713 (mm-30) REVERT: E 70 ASP cc_start: 0.8175 (m-30) cc_final: 0.7636 (t0) REVERT: E 126 MET cc_start: 0.8634 (tpp) cc_final: 0.8416 (mmt) REVERT: E 224 MET cc_start: 0.8377 (tpp) cc_final: 0.8121 (tpp) REVERT: E 260 GLN cc_start: 0.8560 (mm-40) cc_final: 0.8158 (mt0) REVERT: E 402 MET cc_start: 0.8188 (ttm) cc_final: 0.7729 (ttm) REVERT: E 461 ASN cc_start: 0.7733 (p0) cc_final: 0.7322 (m110) REVERT: E 470 ASP cc_start: 0.7637 (t0) cc_final: 0.7394 (t0) REVERT: E 498 SER cc_start: 0.8293 (t) cc_final: 0.7937 (p) REVERT: E 503 ASP cc_start: 0.7799 (p0) cc_final: 0.7550 (p0) REVERT: E 508 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7916 (mtm-85) REVERT: F 70 ASP cc_start: 0.8128 (m-30) cc_final: 0.7615 (t0) REVERT: F 126 MET cc_start: 0.8627 (tpp) cc_final: 0.8406 (mmt) REVERT: F 224 MET cc_start: 0.8345 (tpp) cc_final: 0.8099 (tpp) REVERT: F 260 GLN cc_start: 0.8554 (mm-40) cc_final: 0.8149 (mt0) REVERT: F 363 LYS cc_start: 0.8441 (tmmm) cc_final: 0.8239 (ttmt) REVERT: F 436 MET cc_start: 0.8438 (ttm) cc_final: 0.7967 (ttm) REVERT: F 470 ASP cc_start: 0.7666 (t0) cc_final: 0.7416 (t0) REVERT: F 498 SER cc_start: 0.8269 (t) cc_final: 0.7899 (p) REVERT: F 510 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7731 (mm-30) outliers start: 72 outliers final: 64 residues processed: 344 average time/residue: 0.1195 time to fit residues: 65.1196 Evaluate side-chains 340 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 273 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 288 MET Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 342 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 503 ASP Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 313 CYS Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 342 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 503 ASP Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 45 ILE Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 151 ILE Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 313 CYS Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 386 SER Chi-restraints excluded: chain E residue 508 ARG Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain F residue 45 ILE Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 151 ILE Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 313 CYS Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 342 LEU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 386 SER Chi-restraints excluded: chain F residue 503 ASP Chi-restraints excluded: chain F residue 555 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 67 optimal weight: 0.0020 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 chunk 115 optimal weight: 0.0770 chunk 53 optimal weight: 0.9980 chunk 144 optimal weight: 0.0970 chunk 196 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 75 optimal weight: 0.0000 chunk 78 optimal weight: 0.3980 overall best weight: 0.1148 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 480 HIS ** 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 = 0.3848 r_free = 0.3848 target = 0.134424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.113483 restraints weight = 31939.536| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 3.25 r_work: 0.3488 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3485 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.86 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3485 r_free = 0.3485 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3485 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.4860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 18204 Z= 0.108 Angle : 0.654 14.646 24680 Z= 0.310 Chirality : 0.045 0.154 2748 Planarity : 0.005 0.045 3168 Dihedral : 7.665 75.009 2504 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 2.84 % Allowed : 21.39 % Favored : 75.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.01 (0.18), residues: 2220 helix: 0.64 (0.19), residues: 844 sheet: -1.56 (0.28), residues: 340 loop : -1.44 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 376 TYR 0.015 0.001 TYR E 307 PHE 0.015 0.001 PHE A 50 TRP 0.005 0.001 TRP A 285 HIS 0.003 0.001 HIS A 517 Details of bonding type rmsd covalent geometry : bond 0.00239 (18204) covalent geometry : angle 0.65388 (24680) hydrogen bonds : bond 0.02666 ( 592) hydrogen bonds : angle 4.38456 ( 1692) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 310 time to evaluate : 0.701 Fit side-chains REVERT: A 70 ASP cc_start: 0.8207 (m-30) cc_final: 0.7697 (t0) REVERT: A 260 GLN cc_start: 0.8627 (mm-40) cc_final: 0.8358 (mt0) REVERT: A 344 LYS cc_start: 0.7810 (mmtt) cc_final: 0.7578 (mmtp) REVERT: A 368 LEU cc_start: 0.8944 (tp) cc_final: 0.8731 (tt) REVERT: A 402 MET cc_start: 0.8180 (ttm) cc_final: 0.7845 (ttm) REVERT: A 436 MET cc_start: 0.8245 (ttm) cc_final: 0.7831 (ttm) REVERT: A 438 GLU cc_start: 0.7695 (tp30) cc_final: 0.7463 (tp30) REVERT: A 461 ASN cc_start: 0.7673 (p0) cc_final: 0.7309 (m110) REVERT: A 470 ASP cc_start: 0.7646 (t0) cc_final: 0.7378 (t0) REVERT: A 498 SER cc_start: 0.8002 (t) cc_final: 0.7664 (p) REVERT: A 510 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7534 (mm-30) REVERT: D 70 ASP cc_start: 0.8203 (m-30) cc_final: 0.7684 (t0) REVERT: D 260 GLN cc_start: 0.8630 (mm-40) cc_final: 0.8362 (mt0) REVERT: D 368 LEU cc_start: 0.8949 (tp) cc_final: 0.8712 (tt) REVERT: D 436 MET cc_start: 0.8542 (ttm) cc_final: 0.8122 (ttm) REVERT: D 438 GLU cc_start: 0.8123 (tp30) cc_final: 0.7636 (tp30) REVERT: D 470 ASP cc_start: 0.7663 (t0) cc_final: 0.7414 (t0) REVERT: D 498 SER cc_start: 0.8010 (t) cc_final: 0.7674 (p) REVERT: D 510 GLU cc_start: 0.7956 (mm-30) cc_final: 0.7714 (mm-30) REVERT: E 70 ASP cc_start: 0.8157 (m-30) cc_final: 0.7664 (t0) REVERT: E 260 GLN cc_start: 0.8606 (mm-40) cc_final: 0.8318 (mt0) REVERT: E 436 MET cc_start: 0.8418 (ttm) cc_final: 0.8217 (ttm) REVERT: E 461 ASN cc_start: 0.7639 (p0) cc_final: 0.7272 (m110) REVERT: E 470 ASP cc_start: 0.7636 (t0) cc_final: 0.7377 (t0) REVERT: E 498 SER cc_start: 0.7974 (t) cc_final: 0.7591 (p) REVERT: E 503 ASP cc_start: 0.7664 (p0) cc_final: 0.7414 (p0) REVERT: E 507 ASP cc_start: 0.7798 (m-30) cc_final: 0.7589 (m-30) REVERT: F 70 ASP cc_start: 0.8131 (m-30) cc_final: 0.7650 (t0) REVERT: F 224 MET cc_start: 0.8297 (tpp) cc_final: 0.8095 (tpp) REVERT: F 260 GLN cc_start: 0.8614 (mm-40) cc_final: 0.8307 (mt0) REVERT: F 436 MET cc_start: 0.8565 (ttm) cc_final: 0.8151 (ttm) REVERT: F 438 GLU cc_start: 0.8046 (tp30) cc_final: 0.7593 (tp30) REVERT: F 470 ASP cc_start: 0.7659 (t0) cc_final: 0.7405 (t0) REVERT: F 498 SER cc_start: 0.7994 (t) cc_final: 0.7679 (p) REVERT: F 510 GLU cc_start: 0.8003 (mm-30) cc_final: 0.7752 (mm-30) outliers start: 55 outliers final: 49 residues processed: 341 average time/residue: 0.1195 time to fit residues: 64.4720 Evaluate side-chains 318 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 269 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 313 CYS Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 313 CYS Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 246 ASP Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 313 CYS Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 555 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 202 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 194 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 198 GLN E 480 HIS F 198 GLN ** F 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.130819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.110495 restraints weight = 31674.438| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 3.13 r_work: 0.3444 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3440 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.87 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3440 r_free = 0.3440 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3440 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8013 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18204 Z= 0.125 Angle : 0.674 13.622 24680 Z= 0.321 Chirality : 0.046 0.150 2748 Planarity : 0.005 0.044 3168 Dihedral : 7.453 72.973 2504 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 10.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 2.78 % Allowed : 21.34 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.90 (0.18), residues: 2220 helix: 0.69 (0.19), residues: 844 sheet: -1.46 (0.28), residues: 340 loop : -1.35 (0.20), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 479 TYR 0.014 0.001 TYR F 307 PHE 0.033 0.001 PHE A 50 TRP 0.009 0.001 TRP A 124 HIS 0.002 0.001 HIS F 526 Details of bonding type rmsd covalent geometry : bond 0.00293 (18204) covalent geometry : angle 0.67414 (24680) hydrogen bonds : bond 0.02702 ( 592) hydrogen bonds : angle 4.35121 ( 1692) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 282 time to evaluate : 0.721 Fit side-chains REVERT: A 57 GLU cc_start: 0.7222 (tt0) cc_final: 0.6980 (tt0) REVERT: A 70 ASP cc_start: 0.8222 (m-30) cc_final: 0.7675 (t0) REVERT: A 402 MET cc_start: 0.8248 (ttm) cc_final: 0.7917 (ttm) REVERT: A 436 MET cc_start: 0.8226 (ttm) cc_final: 0.7772 (ttm) REVERT: A 461 ASN cc_start: 0.7709 (p0) cc_final: 0.7329 (m110) REVERT: A 498 SER cc_start: 0.7994 (t) cc_final: 0.7652 (p) REVERT: A 510 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7617 (mm-30) REVERT: D 70 ASP cc_start: 0.8235 (m-30) cc_final: 0.7660 (t0) REVERT: D 344 LYS cc_start: 0.7740 (mmtt) cc_final: 0.7524 (mmtp) REVERT: D 436 MET cc_start: 0.8432 (ttm) cc_final: 0.8085 (ttm) REVERT: D 438 GLU cc_start: 0.8053 (tp30) cc_final: 0.7818 (tp30) REVERT: D 498 SER cc_start: 0.8208 (t) cc_final: 0.7863 (p) REVERT: D 510 GLU cc_start: 0.8047 (mm-30) cc_final: 0.7761 (mm-30) REVERT: E 70 ASP cc_start: 0.8145 (m-30) cc_final: 0.7617 (t0) REVERT: E 408 GLU cc_start: 0.8458 (tm-30) cc_final: 0.8213 (tm-30) REVERT: E 461 ASN cc_start: 0.7681 (p0) cc_final: 0.7281 (m110) REVERT: E 470 ASP cc_start: 0.7649 (t0) cc_final: 0.7392 (t0) REVERT: E 498 SER cc_start: 0.7985 (t) cc_final: 0.7611 (p) REVERT: E 503 ASP cc_start: 0.7672 (p0) cc_final: 0.7456 (p0) REVERT: F 70 ASP cc_start: 0.8141 (m-30) cc_final: 0.7617 (t0) REVERT: F 224 MET cc_start: 0.8320 (tpp) cc_final: 0.8102 (tpp) REVERT: F 240 GLN cc_start: 0.8069 (mp10) cc_final: 0.7831 (mp10) REVERT: F 408 GLU cc_start: 0.8412 (tm-30) cc_final: 0.8180 (tm-30) REVERT: F 436 MET cc_start: 0.8535 (ttm) cc_final: 0.8063 (ttm) REVERT: F 438 GLU cc_start: 0.8046 (tp30) cc_final: 0.7829 (tp30) REVERT: F 498 SER cc_start: 0.8022 (t) cc_final: 0.7672 (p) REVERT: F 510 GLU cc_start: 0.8007 (mm-30) cc_final: 0.7789 (mm-30) outliers start: 54 outliers final: 51 residues processed: 314 average time/residue: 0.1171 time to fit residues: 58.7390 Evaluate side-chains 307 residues out of total 1940 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 256 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 SER Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 231 SER Chi-restraints excluded: chain A residue 272 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 313 CYS Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 555 LEU Chi-restraints excluded: chain D residue 51 SER Chi-restraints excluded: chain D residue 58 VAL Chi-restraints excluded: chain D residue 68 ASP Chi-restraints excluded: chain D residue 101 GLU Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 231 SER Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 281 LEU Chi-restraints excluded: chain D residue 288 MET Chi-restraints excluded: chain D residue 313 CYS Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 352 VAL Chi-restraints excluded: chain D residue 555 LEU Chi-restraints excluded: chain E residue 51 SER Chi-restraints excluded: chain E residue 58 VAL Chi-restraints excluded: chain E residue 68 ASP Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 272 LEU Chi-restraints excluded: chain E residue 281 LEU Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 313 CYS Chi-restraints excluded: chain E residue 332 LEU Chi-restraints excluded: chain E residue 352 VAL Chi-restraints excluded: chain E residue 555 LEU Chi-restraints excluded: chain F residue 51 SER Chi-restraints excluded: chain F residue 58 VAL Chi-restraints excluded: chain F residue 68 ASP Chi-restraints excluded: chain F residue 101 GLU Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 231 SER Chi-restraints excluded: chain F residue 272 LEU Chi-restraints excluded: chain F residue 281 LEU Chi-restraints excluded: chain F residue 288 MET Chi-restraints excluded: chain F residue 313 CYS Chi-restraints excluded: chain F residue 332 LEU Chi-restraints excluded: chain F residue 352 VAL Chi-restraints excluded: chain F residue 555 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 109 optimal weight: 4.9990 chunk 80 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 45 optimal weight: 8.9990 chunk 117 optimal weight: 0.8980 chunk 149 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 129 optimal weight: 1.9990 chunk 158 optimal weight: 0.0020 overall best weight: 1.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 478 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 192 GLN F 192 GLN ** F 480 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.127305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.106747 restraints weight = 31705.906| |-----------------------------------------------------------------------------| r_work (start): 0.3507 rms_B_bonded: 3.19 r_work: 0.3393 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3393 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3393 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.90 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3393 r_free = 0.3393 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.92 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3393 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18204 Z= 0.142 Angle : 0.694 13.463 24680 Z= 0.331 Chirality : 0.047 0.167 2748 Planarity : 0.005 0.044 3168 Dihedral : 7.426 72.502 2504 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.84 % Allowed : 21.55 % Favored : 75.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.04 (0.18), residues: 2220 helix: 0.52 (0.18), residues: 892 sheet: -1.37 (0.29), residues: 340 loop : -1.54 (0.20), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 479 TYR 0.029 0.002 TYR F 265 PHE 0.031 0.001 PHE E 50 TRP 0.009 0.001 TRP E 124 HIS 0.003 0.001 HIS D 96 Details of bonding type rmsd covalent geometry : bond 0.00334 (18204) covalent geometry : angle 0.69368 (24680) hydrogen bonds : bond 0.02842 ( 592) hydrogen bonds : angle 4.39426 ( 1692) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3536.30 seconds wall clock time: 61 minutes 44.64 seconds (3704.64 seconds total)