Starting phenix.real_space_refine on Thu Jan 23 22:47:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c4f_45184/01_2025/9c4f_45184.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c4f_45184/01_2025/9c4f_45184.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9c4f_45184/01_2025/9c4f_45184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c4f_45184/01_2025/9c4f_45184.map" model { file = "/net/cci-nas-00/data/ceres_data/9c4f_45184/01_2025/9c4f_45184.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c4f_45184/01_2025/9c4f_45184.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.005 sd= 0.050 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: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 13753 2.51 5 N 3649 2.21 5 O 4078 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 21560 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4021 Classifications: {'peptide': 517} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 472} Chain breaks: 4 Chain: "I" Number of atoms: 1455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1455 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Restraints were copied for chains: B, C, D, E Time building chain proxies: 12.31, per 1000 atoms: 0.57 Number of scatterers: 21560 At special positions: 0 Unit cell: (204.12, 174.96, 147.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 4078 8.00 N 3649 7.00 C 13753 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: 4.66 Conformation dependent library (CDL) restraints added in 2.9 seconds 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5032 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 72 sheets defined 13.8% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 94 through 99 removed outlier: 4.123A pdb=" N PHE A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 111 Processing helix chain 'A' and resid 196 through 199 removed outlier: 3.673A pdb=" N GLY A 199 " --> pdb=" O GLY A 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 196 through 199' Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 248 through 252 removed outlier: 3.798A pdb=" N MET A 252 " --> pdb=" O PHE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 524 through 528 removed outlier: 3.509A pdb=" N THR A 528 " --> pdb=" O PRO A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 536 Processing helix chain 'B' and resid 3 through 7 Processing helix chain 'B' and resid 94 through 99 removed outlier: 4.124A pdb=" N PHE B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 111 Processing helix chain 'B' and resid 196 through 199 removed outlier: 3.673A pdb=" N GLY B 199 " --> pdb=" O GLY B 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 196 through 199' Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 248 through 252 removed outlier: 3.797A pdb=" N MET B 252 " --> pdb=" O PHE B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 284 Processing helix chain 'B' and resid 377 through 382 Processing helix chain 'B' and resid 524 through 528 removed outlier: 3.508A pdb=" N THR B 528 " --> pdb=" O PRO B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 Processing helix chain 'E' and resid 3 through 7 Processing helix chain 'E' and resid 94 through 99 removed outlier: 4.123A pdb=" N PHE E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 111 Processing helix chain 'E' and resid 196 through 199 removed outlier: 3.672A pdb=" N GLY E 199 " --> pdb=" O GLY E 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 196 through 199' Processing helix chain 'E' and resid 213 through 217 Processing helix chain 'E' and resid 248 through 252 removed outlier: 3.798A pdb=" N MET E 252 " --> pdb=" O PHE E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 284 Processing helix chain 'E' and resid 377 through 382 Processing helix chain 'E' and resid 524 through 528 removed outlier: 3.509A pdb=" N THR E 528 " --> pdb=" O PRO E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 536 Processing helix chain 'C' and resid 3 through 7 Processing helix chain 'C' and resid 94 through 99 removed outlier: 4.124A pdb=" N PHE C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 111 Processing helix chain 'C' and resid 196 through 199 removed outlier: 3.673A pdb=" N GLY C 199 " --> pdb=" O GLY C 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 196 through 199' Processing helix chain 'C' and resid 213 through 217 Processing helix chain 'C' and resid 248 through 252 removed outlier: 3.797A pdb=" N MET C 252 " --> pdb=" O PHE C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 284 Processing helix chain 'C' and resid 377 through 382 Processing helix chain 'C' and resid 524 through 528 removed outlier: 3.509A pdb=" N THR C 528 " --> pdb=" O PRO C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 536 Processing helix chain 'D' and resid 3 through 7 Processing helix chain 'D' and resid 94 through 99 removed outlier: 4.123A pdb=" N PHE D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 111 Processing helix chain 'D' and resid 196 through 199 removed outlier: 3.673A pdb=" N GLY D 199 " --> pdb=" O GLY D 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 196 through 199' Processing helix chain 'D' and resid 213 through 217 Processing helix chain 'D' and resid 248 through 252 removed outlier: 3.798A pdb=" N MET D 252 " --> pdb=" O PHE D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 284 Processing helix chain 'D' and resid 377 through 382 Processing helix chain 'D' and resid 524 through 528 removed outlier: 3.509A pdb=" N THR D 528 " --> pdb=" O PRO D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 536 Processing helix chain 'I' and resid 282 through 286 removed outlier: 3.529A pdb=" N SER I 286 " --> pdb=" O GLY I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 303 Processing helix chain 'I' and resid 330 through 344 Processing helix chain 'I' and resid 351 through 365 Processing helix chain 'I' and resid 366 through 368 No H-bonds generated for 'chain 'I' and resid 366 through 368' Processing helix chain 'I' and resid 394 through 407 Processing helix chain 'I' and resid 422 through 432 Processing helix chain 'I' and resid 445 through 458 removed outlier: 3.559A pdb=" N GLU I 456 " --> pdb=" O ASP I 452 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL I 457 " --> pdb=" O PHE I 453 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 28 through 31 removed outlier: 6.444A pdb=" N TYR E 481 " --> pdb=" O VAL E 128 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL E 128 " --> pdb=" O TYR E 481 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL E 483 " --> pdb=" O ILE E 126 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE E 126 " --> pdb=" O VAL E 483 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LYS E 493 " --> pdb=" O PRO E 116 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY E 495 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE E 114 " --> pdb=" O GLY E 495 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 228 through 233 removed outlier: 8.837A pdb=" N SER A 10 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 9.200A pdb=" N VAL E 141 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLY A 12 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N ASP E 143 " --> pdb=" O GLY A 12 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 22 through 25 removed outlier: 5.995A pdb=" N ILE E 460 " --> pdb=" O PRO E 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 22 through 25 removed outlier: 5.995A pdb=" N ILE E 460 " --> pdb=" O PRO E 86 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N TYR E 83 " --> pdb=" O THR E 188 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR E 188 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N THR E 85 " --> pdb=" O TYR E 186 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N TYR E 186 " --> pdb=" O THR E 85 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N TRP E 87 " --> pdb=" O TYR E 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.444A pdb=" N TYR A 481 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL A 128 " --> pdb=" O TYR A 481 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL A 483 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE A 126 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LYS A 493 " --> pdb=" O PRO A 116 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY A 495 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE A 114 " --> pdb=" O GLY A 495 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 228 through 233 removed outlier: 7.440A pdb=" N VAL A 139 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY B 12 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 55 through 57 removed outlier: 7.252A pdb=" N TYR A 83 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR A 188 " --> pdb=" O TYR A 83 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N THR A 85 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N TYR A 186 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N TRP A 87 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 55 through 57 removed outlier: 5.995A pdb=" N ILE A 460 " --> pdb=" O PRO A 86 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 191 through 194 Processing sheet with id=AB1, first strand: chain 'A' and resid 244 through 245 removed outlier: 6.707A pdb=" N GLY A 244 " --> pdb=" O HIS A 552 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 262 through 266 removed outlier: 6.469A pdb=" N LYS A 272 " --> pdb=" O ASP A 265 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 289 through 290 removed outlier: 6.369A pdb=" N MET A 289 " --> pdb=" O VAL A 414 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 317 through 321 removed outlier: 6.595A pdb=" N THR A 324 " --> pdb=" O THR A 320 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 338 through 341 Processing sheet with id=AB6, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AB7, first strand: chain 'A' and resid 374 through 375 removed outlier: 6.497A pdb=" N PHE A 374 " --> pdb=" O LEU A 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB9, first strand: chain 'A' and resid 427 through 429 removed outlier: 6.049A pdb=" N SER A 428 " --> pdb=" O LEU A 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 477 through 478 removed outlier: 6.398A pdb=" N THR A 477 " --> pdb=" O THR C 11 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ALA C 13 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL B 139 " --> pdb=" O SER C 10 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY C 12 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 31 removed outlier: 6.443A pdb=" N TYR B 481 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL B 128 " --> pdb=" O TYR B 481 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B 483 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE B 126 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LYS B 493 " --> pdb=" O PRO B 116 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY B 495 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE B 114 " --> pdb=" O GLY B 495 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 55 through 57 removed outlier: 7.252A pdb=" N TYR B 83 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR B 188 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N THR B 85 " --> pdb=" O TYR B 186 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N TYR B 186 " --> pdb=" O THR B 85 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N TRP B 87 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 55 through 57 removed outlier: 5.995A pdb=" N ILE B 460 " --> pdb=" O PRO B 86 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 191 through 194 Processing sheet with id=AC6, first strand: chain 'B' and resid 244 through 245 removed outlier: 6.707A pdb=" N GLY B 244 " --> pdb=" O HIS B 552 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 262 through 266 removed outlier: 6.469A pdb=" N LYS B 272 " --> pdb=" O ASP B 265 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 289 through 290 removed outlier: 6.370A pdb=" N MET B 289 " --> pdb=" O VAL B 414 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 317 through 321 removed outlier: 6.595A pdb=" N THR B 324 " --> pdb=" O THR B 320 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 338 through 341 Processing sheet with id=AD2, first strand: chain 'B' and resid 356 through 357 Processing sheet with id=AD3, first strand: chain 'B' and resid 374 through 375 removed outlier: 6.497A pdb=" N PHE B 374 " --> pdb=" O LEU B 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD5, first strand: chain 'B' and resid 427 through 429 removed outlier: 6.050A pdb=" N SER B 428 " --> pdb=" O LEU B 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 477 through 478 removed outlier: 6.398A pdb=" N THR B 477 " --> pdb=" O THR D 11 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ALA D 13 " --> pdb=" O THR B 477 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL C 139 " --> pdb=" O SER D 10 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY D 12 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.444A pdb=" N TYR C 481 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL C 128 " --> pdb=" O TYR C 481 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL C 483 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE C 126 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LYS C 493 " --> pdb=" O PRO C 116 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLY C 495 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE C 114 " --> pdb=" O GLY C 495 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 477 through 478 removed outlier: 8.837A pdb=" N SER E 10 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 9.201A pdb=" N VAL D 141 " --> pdb=" O SER E 10 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLY E 12 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N ASP D 143 " --> pdb=" O GLY E 12 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 28 through 31 removed outlier: 6.443A pdb=" N TYR D 481 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL D 128 " --> pdb=" O TYR D 481 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL D 483 " --> pdb=" O ILE D 126 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE D 126 " --> pdb=" O VAL D 483 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LYS D 493 " --> pdb=" O PRO D 116 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY D 495 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE D 114 " --> pdb=" O GLY D 495 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 22 through 25 removed outlier: 5.995A pdb=" N ILE D 460 " --> pdb=" O PRO D 86 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 22 through 25 removed outlier: 5.995A pdb=" N ILE D 460 " --> pdb=" O PRO D 86 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N TYR D 83 " --> pdb=" O THR D 188 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N THR D 188 " --> pdb=" O TYR D 83 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N THR D 85 " --> pdb=" O TYR D 186 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N TYR D 186 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N TRP D 87 " --> pdb=" O TYR D 184 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 191 through 194 Processing sheet with id=AE4, first strand: chain 'E' and resid 244 through 245 removed outlier: 6.708A pdb=" N GLY E 244 " --> pdb=" O HIS E 552 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 262 through 266 removed outlier: 6.469A pdb=" N LYS E 272 " --> pdb=" O ASP E 265 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 289 through 290 removed outlier: 6.370A pdb=" N MET E 289 " --> pdb=" O VAL E 414 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'E' and resid 317 through 321 removed outlier: 6.595A pdb=" N THR E 324 " --> pdb=" O THR E 320 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 338 through 341 Processing sheet with id=AE9, first strand: chain 'E' and resid 356 through 357 Processing sheet with id=AF1, first strand: chain 'E' and resid 374 through 375 removed outlier: 6.497A pdb=" N PHE E 374 " --> pdb=" O LEU E 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'E' and resid 391 through 392 Processing sheet with id=AF3, first strand: chain 'E' and resid 427 through 429 removed outlier: 6.050A pdb=" N SER E 428 " --> pdb=" O LEU E 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 55 through 57 removed outlier: 7.253A pdb=" N TYR C 83 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR C 188 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N THR C 85 " --> pdb=" O TYR C 186 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N TYR C 186 " --> pdb=" O THR C 85 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N TRP C 87 " --> pdb=" O TYR C 184 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 55 through 57 removed outlier: 5.995A pdb=" N ILE C 460 " --> pdb=" O PRO C 86 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 191 through 194 Processing sheet with id=AF7, first strand: chain 'C' and resid 244 through 245 removed outlier: 6.707A pdb=" N GLY C 244 " --> pdb=" O HIS C 552 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'C' and resid 262 through 266 removed outlier: 6.469A pdb=" N LYS C 272 " --> pdb=" O ASP C 265 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 289 through 290 removed outlier: 6.370A pdb=" N MET C 289 " --> pdb=" O VAL C 414 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'C' and resid 317 through 321 removed outlier: 6.595A pdb=" N THR C 324 " --> pdb=" O THR C 320 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 338 through 341 Processing sheet with id=AG3, first strand: chain 'C' and resid 356 through 357 Processing sheet with id=AG4, first strand: chain 'C' and resid 374 through 375 removed outlier: 6.497A pdb=" N PHE C 374 " --> pdb=" O LEU C 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AG6, first strand: chain 'C' and resid 427 through 429 removed outlier: 6.049A pdb=" N SER C 428 " --> pdb=" O LEU C 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'D' and resid 191 through 194 Processing sheet with id=AG8, first strand: chain 'D' and resid 244 through 245 removed outlier: 6.708A pdb=" N GLY D 244 " --> pdb=" O HIS D 552 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'D' and resid 262 through 266 removed outlier: 6.469A pdb=" N LYS D 272 " --> pdb=" O ASP D 265 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 289 through 290 removed outlier: 6.370A pdb=" N MET D 289 " --> pdb=" O VAL D 414 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'D' and resid 317 through 321 removed outlier: 6.595A pdb=" N THR D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'D' and resid 338 through 341 Processing sheet with id=AH4, first strand: chain 'D' and resid 356 through 357 Processing sheet with id=AH5, first strand: chain 'D' and resid 374 through 375 removed outlier: 6.498A pdb=" N PHE D 374 " --> pdb=" O LEU D 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'D' and resid 391 through 392 Processing sheet with id=AH7, first strand: chain 'D' and resid 427 through 429 removed outlier: 6.049A pdb=" N SER D 428 " --> pdb=" O LEU D 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'I' and resid 319 through 321 Processing sheet with id=AH9, first strand: chain 'I' and resid 319 through 321 removed outlier: 6.025A pdb=" N LYS I 273 " --> pdb=" O GLN I 309 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ASN I 311 " --> pdb=" O LYS I 273 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL I 275 " --> pdb=" O ASN I 311 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE I 313 " --> pdb=" O VAL I 275 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE I 277 " --> pdb=" O ILE I 313 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N PHE I 315 " --> pdb=" O PHE I 277 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE I 279 " --> pdb=" O PHE I 315 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N SER I 378 " --> pdb=" O SER I 411 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N PHE I 413 " --> pdb=" O SER I 378 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE I 380 " --> pdb=" O PHE I 413 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LEU I 415 " --> pdb=" O ILE I 380 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU I 382 " --> pdb=" O LEU I 415 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N PHE I 417 " --> pdb=" O LEU I 382 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR I 384 " --> pdb=" O PHE I 417 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ARG I 438 " --> pdb=" O LEU I 412 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS I 414 " --> pdb=" O ARG I 438 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE I 440 " --> pdb=" O CYS I 414 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY I 416 " --> pdb=" O ILE I 440 " (cutoff:3.500A) 590 hydrogen bonds defined for protein. 1443 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: 8.13 Time building geometry restraints manager: 5.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5438 1.33 - 1.45: 4885 1.45 - 1.58: 11734 1.58 - 1.70: 0 1.70 - 1.82: 139 Bond restraints: 22196 Sorted by residual: bond pdb=" CD ARG I 403 " pdb=" NE ARG I 403 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.40e-02 5.10e+03 9.52e+00 bond pdb=" CD ARG I 307 " pdb=" NE ARG I 307 " ideal model delta sigma weight residual 1.458 1.501 -0.043 1.40e-02 5.10e+03 9.49e+00 bond pdb=" CE1 HIS I 441 " pdb=" NE2 HIS I 441 " ideal model delta sigma weight residual 1.321 1.351 -0.030 1.00e-02 1.00e+04 9.21e+00 bond pdb=" CD ARG I 338 " pdb=" NE ARG I 338 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.40e-02 5.10e+03 9.19e+00 bond pdb=" CD ARG I 294 " pdb=" NE ARG I 294 " ideal model delta sigma weight residual 1.458 1.500 -0.042 1.40e-02 5.10e+03 9.09e+00 ... (remaining 22191 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 29954 3.18 - 6.36: 291 6.36 - 9.55: 5 9.55 - 12.73: 1 12.73 - 15.91: 1 Bond angle restraints: 30252 Sorted by residual: angle pdb=" CA LEU I 372 " pdb=" C LEU I 372 " pdb=" N PRO I 373 " ideal model delta sigma weight residual 121.08 126.90 -5.82 1.08e+00 8.57e-01 2.90e+01 angle pdb=" C ARG I 323 " pdb=" N PRO I 324 " pdb=" CA PRO I 324 " ideal model delta sigma weight residual 119.84 126.57 -6.73 1.25e+00 6.40e-01 2.90e+01 angle pdb=" CA ASP I 420 " pdb=" CB ASP I 420 " pdb=" CG ASP I 420 " ideal model delta sigma weight residual 112.60 117.56 -4.96 1.00e+00 1.00e+00 2.46e+01 angle pdb=" N ALA I 342 " pdb=" CA ALA I 342 " pdb=" C ALA I 342 " ideal model delta sigma weight residual 111.36 116.51 -5.15 1.09e+00 8.42e-01 2.23e+01 angle pdb=" N PRO I 324 " pdb=" CA PRO I 324 " pdb=" C PRO I 324 " ideal model delta sigma weight residual 112.47 122.04 -9.57 2.06e+00 2.36e-01 2.16e+01 ... (remaining 30247 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 12283 17.77 - 35.54: 560 35.54 - 53.31: 133 53.31 - 71.08: 49 71.08 - 88.85: 22 Dihedral angle restraints: 13047 sinusoidal: 5139 harmonic: 7908 Sorted by residual: dihedral pdb=" CA ASP D 341 " pdb=" C ASP D 341 " pdb=" N THR D 342 " pdb=" CA THR D 342 " ideal model delta harmonic sigma weight residual -180.00 -151.96 -28.04 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA ASP C 341 " pdb=" C ASP C 341 " pdb=" N THR C 342 " pdb=" CA THR C 342 " ideal model delta harmonic sigma weight residual 180.00 -151.98 -28.02 0 5.00e+00 4.00e-02 3.14e+01 dihedral pdb=" CA ASP A 341 " pdb=" C ASP A 341 " pdb=" N THR A 342 " pdb=" CA THR A 342 " ideal model delta harmonic sigma weight residual 180.00 -152.00 -28.00 0 5.00e+00 4.00e-02 3.14e+01 ... (remaining 13044 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2646 0.061 - 0.122: 549 0.122 - 0.183: 48 0.183 - 0.245: 11 0.245 - 0.306: 4 Chirality restraints: 3258 Sorted by residual: chirality pdb=" CA ARG I 403 " pdb=" N ARG I 403 " pdb=" C ARG I 403 " pdb=" CB ARG I 403 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.34e+00 chirality pdb=" CA PRO I 324 " pdb=" N PRO I 324 " pdb=" C PRO I 324 " pdb=" CB PRO I 324 " both_signs ideal model delta sigma weight residual False 2.72 2.42 0.29 2.00e-01 2.50e+01 2.17e+00 chirality pdb=" CA ALA I 342 " pdb=" N ALA I 342 " pdb=" C ALA I 342 " pdb=" CB ALA I 342 " both_signs ideal model delta sigma weight residual False 2.48 2.21 0.27 2.00e-01 2.50e+01 1.84e+00 ... (remaining 3255 not shown) Planarity restraints: 3942 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP I 322 " 0.101 2.00e-02 2.50e+03 5.67e-02 8.04e+01 pdb=" CG TRP I 322 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TRP I 322 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TRP I 322 " -0.070 2.00e-02 2.50e+03 pdb=" NE1 TRP I 322 " -0.012 2.00e-02 2.50e+03 pdb=" CE2 TRP I 322 " -0.024 2.00e-02 2.50e+03 pdb=" CE3 TRP I 322 " -0.089 2.00e-02 2.50e+03 pdb=" CZ2 TRP I 322 " 0.022 2.00e-02 2.50e+03 pdb=" CZ3 TRP I 322 " 0.015 2.00e-02 2.50e+03 pdb=" CH2 TRP I 322 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE I 453 " 0.092 2.00e-02 2.50e+03 5.66e-02 5.61e+01 pdb=" CG PHE I 453 " -0.071 2.00e-02 2.50e+03 pdb=" CD1 PHE I 453 " -0.045 2.00e-02 2.50e+03 pdb=" CD2 PHE I 453 " -0.059 2.00e-02 2.50e+03 pdb=" CE1 PHE I 453 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 PHE I 453 " 0.020 2.00e-02 2.50e+03 pdb=" CZ PHE I 453 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 423 " -0.047 2.00e-02 2.50e+03 4.13e-02 3.42e+01 pdb=" CG TYR I 423 " -0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR I 423 " 0.019 2.00e-02 2.50e+03 pdb=" CD2 TYR I 423 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR I 423 " 0.040 2.00e-02 2.50e+03 pdb=" CE2 TYR I 423 " 0.046 2.00e-02 2.50e+03 pdb=" CZ TYR I 423 " 0.022 2.00e-02 2.50e+03 pdb=" OH TYR I 423 " -0.081 2.00e-02 2.50e+03 ... (remaining 3939 not shown) Histogram of nonbonded interaction distances: 1.66 - 2.31: 21 2.31 - 2.96: 10019 2.96 - 3.60: 31647 3.60 - 4.25: 54393 4.25 - 4.90: 86632 Nonbonded interactions: 182712 Sorted by model distance: nonbonded pdb=" OE1 GLU B 8 " pdb=" C GLY I 349 " model vdw 1.661 3.270 nonbonded pdb=" OE1 GLU A 27 " pdb=" O GLU E 215 " model vdw 1.784 3.040 nonbonded pdb=" O GLU B 215 " pdb=" OE1 GLU C 27 " model vdw 1.784 3.040 nonbonded pdb=" OE1 GLU E 27 " pdb=" O GLU D 215 " model vdw 1.785 3.040 nonbonded pdb=" O GLU C 215 " pdb=" OE1 GLU D 27 " model vdw 1.785 3.040 ... (remaining 182707 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.800 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 47.600 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 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 : 0.005 0.071 22196 Z= 0.356 Angle : 0.817 15.911 30252 Z= 0.494 Chirality : 0.050 0.306 3258 Planarity : 0.008 0.140 3942 Dihedral : 13.074 88.853 8015 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.53 % Favored : 97.39 % Rotamer: Outliers : 0.30 % Allowed : 0.55 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.14), residues: 2722 helix: -0.43 (0.39), residues: 175 sheet: 0.53 (0.19), residues: 676 loop : -0.79 (0.12), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.101 0.004 TRP I 322 HIS 0.010 0.002 HIS B 216 PHE 0.092 0.004 PHE I 453 TYR 0.081 0.005 TYR I 423 ARG 0.017 0.003 ARG C 502 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 727 time to evaluate : 2.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 SER cc_start: 0.7725 (m) cc_final: 0.7406 (m) REVERT: A 53 HIS cc_start: 0.7672 (p90) cc_final: 0.7126 (p-80) REVERT: A 215 GLU cc_start: 0.6949 (mp0) cc_final: 0.6167 (mp0) REVERT: A 229 THR cc_start: 0.8347 (m) cc_final: 0.8054 (p) REVERT: A 295 ASN cc_start: 0.7520 (t0) cc_final: 0.7274 (t0) REVERT: A 384 LEU cc_start: 0.8210 (mt) cc_final: 0.7885 (mt) REVERT: A 546 THR cc_start: 0.7973 (p) cc_final: 0.7745 (t) REVERT: B 32 SER cc_start: 0.8314 (p) cc_final: 0.8051 (t) REVERT: B 42 ARG cc_start: 0.8431 (mmt-90) cc_final: 0.8022 (mpt180) REVERT: B 53 HIS cc_start: 0.7484 (p90) cc_final: 0.7093 (p-80) REVERT: B 110 ASN cc_start: 0.7798 (m-40) cc_final: 0.7585 (m110) REVERT: B 156 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7303 (mt-10) REVERT: B 329 ARG cc_start: 0.8011 (mtt90) cc_final: 0.7712 (mtt180) REVERT: B 378 LYS cc_start: 0.7995 (pttm) cc_final: 0.7769 (ptmm) REVERT: B 498 LYS cc_start: 0.8453 (ttmt) cc_final: 0.8205 (mmmm) REVERT: B 523 TYR cc_start: 0.8737 (p90) cc_final: 0.8535 (p90) REVERT: B 524 ASP cc_start: 0.7858 (t0) cc_final: 0.7653 (t0) REVERT: E 24 MET cc_start: 0.7181 (mmm) cc_final: 0.6809 (mmm) REVERT: E 91 ASP cc_start: 0.6755 (t0) cc_final: 0.6474 (t0) REVERT: E 143 ASP cc_start: 0.6932 (m-30) cc_final: 0.6670 (m-30) REVERT: E 193 ASN cc_start: 0.7143 (t0) cc_final: 0.6851 (t0) REVERT: E 215 GLU cc_start: 0.7148 (mp0) cc_final: 0.6477 (mp0) REVERT: E 230 MET cc_start: 0.6878 (tmm) cc_final: 0.6651 (tmm) REVERT: E 295 ASN cc_start: 0.7735 (t0) cc_final: 0.7442 (t0) REVERT: E 432 ASN cc_start: 0.7931 (p0) cc_final: 0.7622 (p0) REVERT: E 510 TYR cc_start: 0.7879 (m-80) cc_final: 0.7494 (m-80) REVERT: C 154 ASP cc_start: 0.7179 (t0) cc_final: 0.6830 (t0) REVERT: C 180 PHE cc_start: 0.7615 (m-80) cc_final: 0.7205 (m-80) REVERT: C 287 ASN cc_start: 0.7086 (m-40) cc_final: 0.6818 (m110) REVERT: C 295 ASN cc_start: 0.7168 (t0) cc_final: 0.6877 (t0) REVERT: C 371 VAL cc_start: 0.9104 (t) cc_final: 0.8865 (p) REVERT: C 428 SER cc_start: 0.8087 (t) cc_final: 0.7882 (t) REVERT: D 24 MET cc_start: 0.7830 (mmm) cc_final: 0.7526 (mmm) REVERT: D 80 ILE cc_start: 0.8432 (pt) cc_final: 0.8216 (pt) REVERT: D 103 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6795 (mt-10) REVERT: D 130 ASP cc_start: 0.6638 (m-30) cc_final: 0.6408 (m-30) REVERT: D 154 ASP cc_start: 0.7304 (t0) cc_final: 0.6979 (t0) REVERT: D 168 ASP cc_start: 0.7308 (t0) cc_final: 0.7088 (t0) REVERT: D 287 ASN cc_start: 0.7228 (m-40) cc_final: 0.7022 (m110) REVERT: D 417 ARG cc_start: 0.7751 (mtm-85) cc_final: 0.7516 (mtm-85) outliers start: 7 outliers final: 5 residues processed: 731 average time/residue: 0.3980 time to fit residues: 432.2280 Evaluate side-chains 608 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 603 time to evaluate : 2.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain I residue 443 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 139 optimal weight: 0.0570 chunk 110 optimal weight: 0.9980 chunk 213 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 247 optimal weight: 3.9990 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN A 53 HIS A 155 HIS ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN A 335 GLN A 385 GLN A 451 GLN A 513 HIS ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 HIS B 195 GLN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN B 335 GLN B 380 GLN B 385 GLN B 425 GLN B 513 HIS B 534 HIS E 155 HIS E 216 HIS E 385 GLN C 5 ASN C 155 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 286 GLN C 335 GLN C 380 GLN ** C 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN D 5 ASN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D 380 GLN D 385 GLN ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 432 ASN I 274 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.111280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.092015 restraints weight = 35949.611| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.18 r_work: 0.2983 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 22196 Z= 0.266 Angle : 0.616 9.264 30252 Z= 0.319 Chirality : 0.044 0.286 3258 Planarity : 0.004 0.123 3942 Dihedral : 6.237 53.757 2977 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.10 % Favored : 98.86 % Rotamer: Outliers : 2.04 % Allowed : 7.56 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 2722 helix: 0.39 (0.38), residues: 183 sheet: 0.22 (0.19), residues: 668 loop : -0.28 (0.13), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 545 HIS 0.008 0.001 HIS D 53 PHE 0.020 0.002 PHE I 315 TYR 0.017 0.002 TYR D 159 ARG 0.006 0.001 ARG I 439 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 650 time to evaluate : 2.417 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 21 VAL cc_start: 0.8542 (t) cc_final: 0.8139 (m) REVERT: A 53 HIS cc_start: 0.8170 (p-80) cc_final: 0.7953 (p90) REVERT: A 109 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7615 (mt-10) REVERT: A 130 ASP cc_start: 0.7595 (m-30) cc_final: 0.7379 (m-30) REVERT: A 207 GLU cc_start: 0.6008 (tm-30) cc_final: 0.4106 (tm-30) REVERT: A 215 GLU cc_start: 0.8230 (mp0) cc_final: 0.7384 (mp0) REVERT: A 240 GLU cc_start: 0.8091 (tp30) cc_final: 0.7757 (tp30) REVERT: A 257 TYR cc_start: 0.8780 (m-80) cc_final: 0.8563 (m-80) REVERT: A 259 SER cc_start: 0.8892 (m) cc_final: 0.8470 (p) REVERT: A 295 ASN cc_start: 0.7949 (t0) cc_final: 0.7582 (t0) REVERT: A 384 LEU cc_start: 0.8838 (mt) cc_final: 0.8448 (mt) REVERT: A 434 ASP cc_start: 0.8273 (m-30) cc_final: 0.8019 (p0) REVERT: A 435 ASP cc_start: 0.6363 (p0) cc_final: 0.6129 (p0) REVERT: A 486 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8162 (ptm) REVERT: A 540 LYS cc_start: 0.8436 (mttt) cc_final: 0.8076 (mttm) REVERT: A 546 THR cc_start: 0.8550 (p) cc_final: 0.8146 (t) REVERT: B 2 THR cc_start: 0.8256 (p) cc_final: 0.8047 (m) REVERT: B 24 MET cc_start: 0.8344 (mmm) cc_final: 0.7908 (tpp) REVERT: B 53 HIS cc_start: 0.7882 (p90) cc_final: 0.7586 (p90) REVERT: B 55 LYS cc_start: 0.8715 (mttt) cc_final: 0.8483 (mttt) REVERT: B 110 ASN cc_start: 0.8458 (m-40) cc_final: 0.8167 (m110) REVERT: B 130 ASP cc_start: 0.7959 (m-30) cc_final: 0.7672 (m-30) REVERT: B 134 LYS cc_start: 0.8654 (tttt) cc_final: 0.8315 (ttpp) REVERT: B 154 ASP cc_start: 0.7599 (t0) cc_final: 0.7292 (t0) REVERT: B 156 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7917 (mt-10) REVERT: B 215 GLU cc_start: 0.8123 (mp0) cc_final: 0.7820 (mp0) REVERT: B 230 MET cc_start: 0.8215 (tmm) cc_final: 0.7811 (tmm) REVERT: B 295 ASN cc_start: 0.7920 (t0) cc_final: 0.7643 (t0) REVERT: B 296 SER cc_start: 0.8770 (t) cc_final: 0.8562 (m) REVERT: B 374 PHE cc_start: 0.8596 (m-80) cc_final: 0.8355 (m-80) REVERT: B 378 LYS cc_start: 0.8117 (pttm) cc_final: 0.7901 (pttm) REVERT: B 498 LYS cc_start: 0.8754 (ttmt) cc_final: 0.8539 (ttmm) REVERT: B 523 TYR cc_start: 0.8910 (p90) cc_final: 0.8257 (p90) REVERT: B 524 ASP cc_start: 0.8628 (t0) cc_final: 0.8235 (t0) REVERT: B 543 GLU cc_start: 0.8156 (mt-10) cc_final: 0.7917 (tt0) REVERT: E 53 HIS cc_start: 0.7364 (p90) cc_final: 0.7118 (p90) REVERT: E 57 PHE cc_start: 0.7851 (t80) cc_final: 0.7567 (t80) REVERT: E 91 ASP cc_start: 0.7645 (t0) cc_final: 0.7427 (t0) REVERT: E 129 LYS cc_start: 0.8222 (mttp) cc_final: 0.8003 (mttp) REVERT: E 130 ASP cc_start: 0.7768 (m-30) cc_final: 0.7490 (m-30) REVERT: E 134 LYS cc_start: 0.8008 (tttt) cc_final: 0.7790 (ttpp) REVERT: E 154 ASP cc_start: 0.8408 (t0) cc_final: 0.8156 (t0) REVERT: E 191 ASP cc_start: 0.7993 (m-30) cc_final: 0.7786 (m-30) REVERT: E 193 ASN cc_start: 0.8094 (t0) cc_final: 0.7474 (t0) REVERT: E 202 LYS cc_start: 0.8780 (mttt) cc_final: 0.8548 (mttt) REVERT: E 215 GLU cc_start: 0.8269 (mp0) cc_final: 0.7345 (mp0) REVERT: E 289 MET cc_start: 0.8359 (mmm) cc_final: 0.8118 (mmm) REVERT: E 295 ASN cc_start: 0.8426 (t0) cc_final: 0.7713 (t0) REVERT: E 379 GLU cc_start: 0.7904 (mm-30) cc_final: 0.7613 (mm-30) REVERT: E 382 LYS cc_start: 0.8353 (mtmt) cc_final: 0.8001 (mtmt) REVERT: E 410 MET cc_start: 0.8545 (mtm) cc_final: 0.8313 (mtm) REVERT: E 432 ASN cc_start: 0.8297 (p0) cc_final: 0.7965 (p0) REVERT: E 510 TYR cc_start: 0.8321 (m-80) cc_final: 0.7598 (m-80) REVERT: C 103 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7333 (mt-10) REVERT: C 143 ASP cc_start: 0.7445 (m-30) cc_final: 0.7135 (m-30) REVERT: C 180 PHE cc_start: 0.8557 (m-80) cc_final: 0.8005 (m-80) REVERT: C 191 ASP cc_start: 0.7807 (m-30) cc_final: 0.7563 (m-30) REVERT: C 193 ASN cc_start: 0.7720 (t0) cc_final: 0.7435 (t0) REVERT: C 194 THR cc_start: 0.8063 (m) cc_final: 0.7811 (m) REVERT: C 200 ASP cc_start: 0.6864 (m-30) cc_final: 0.6493 (m-30) REVERT: C 295 ASN cc_start: 0.7911 (t0) cc_final: 0.7596 (t0) REVERT: C 371 VAL cc_start: 0.8972 (t) cc_final: 0.8643 (p) REVERT: C 423 GLU cc_start: 0.8272 (mt-10) cc_final: 0.8033 (mt-10) REVERT: C 440 GLN cc_start: 0.8356 (mp10) cc_final: 0.7768 (mp10) REVERT: C 521 VAL cc_start: 0.8652 (t) cc_final: 0.8288 (p) REVERT: C 546 THR cc_start: 0.8381 (p) cc_final: 0.8176 (p) REVERT: D 21 VAL cc_start: 0.8757 (t) cc_final: 0.8421 (m) REVERT: D 24 MET cc_start: 0.8503 (mmm) cc_final: 0.7788 (mmm) REVERT: D 58 SER cc_start: 0.8369 (t) cc_final: 0.7674 (p) REVERT: D 130 ASP cc_start: 0.7760 (m-30) cc_final: 0.7470 (m-30) REVERT: D 154 ASP cc_start: 0.8058 (t0) cc_final: 0.7494 (t70) REVERT: D 168 ASP cc_start: 0.7934 (t0) cc_final: 0.7651 (t0) REVERT: D 203 LYS cc_start: 0.8584 (ttmm) cc_final: 0.8321 (ttmm) REVERT: D 215 GLU cc_start: 0.8379 (mp0) cc_final: 0.7485 (mp0) REVERT: D 242 LEU cc_start: 0.8552 (mt) cc_final: 0.8267 (mp) REVERT: D 289 MET cc_start: 0.8688 (mmm) cc_final: 0.8364 (mmt) REVERT: D 341 ASP cc_start: 0.8109 (OUTLIER) cc_final: 0.7783 (m-30) REVERT: D 382 LYS cc_start: 0.8557 (mtmt) cc_final: 0.8291 (mtmt) REVERT: D 389 MET cc_start: 0.8676 (mmm) cc_final: 0.8416 (mmm) REVERT: D 435 ASP cc_start: 0.7887 (t0) cc_final: 0.7122 (p0) REVERT: D 461 LEU cc_start: 0.8587 (tp) cc_final: 0.8370 (tp) REVERT: I 271 MET cc_start: 0.5595 (pmm) cc_final: 0.5094 (pmm) REVERT: I 358 MET cc_start: 0.7071 (mmp) cc_final: 0.6682 (mmp) outliers start: 48 outliers final: 29 residues processed: 669 average time/residue: 0.3708 time to fit residues: 369.0754 Evaluate side-chains 639 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 608 time to evaluate : 2.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 274 ARG Chi-restraints excluded: chain E residue 459 LYS Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain I residue 278 VAL Chi-restraints excluded: chain I residue 443 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 84 optimal weight: 7.9990 chunk 211 optimal weight: 5.9990 chunk 186 optimal weight: 6.9990 chunk 96 optimal weight: 4.9990 chunk 51 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 162 optimal weight: 0.8980 chunk 238 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 233 optimal weight: 8.9990 chunk 28 optimal weight: 5.9990 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 ASN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN B 356 GLN ** B 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN C 43 GLN C 155 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 287 ASN C 356 GLN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 GLN C 425 GLN D 43 GLN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS D 323 ASN D 380 GLN ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 432 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.106795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.088125 restraints weight = 36049.521| |-----------------------------------------------------------------------------| r_work (start): 0.3020 rms_B_bonded: 2.13 r_work: 0.2912 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.3362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.120 22196 Z= 0.703 Angle : 0.717 8.488 30252 Z= 0.372 Chirality : 0.051 0.277 3258 Planarity : 0.006 0.121 3942 Dihedral : 6.302 55.685 2975 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.76 % Favored : 98.20 % Rotamer: Outliers : 3.06 % Allowed : 9.85 % Favored : 87.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.50 (0.15), residues: 2722 helix: 0.10 (0.37), residues: 183 sheet: 0.08 (0.19), residues: 633 loop : -0.51 (0.13), residues: 1906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 25 HIS 0.012 0.002 HIS B 106 PHE 0.032 0.003 PHE B 219 TYR 0.023 0.003 TYR C 422 ARG 0.009 0.001 ARG E 373 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 757 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 685 time to evaluate : 2.478 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 21 VAL cc_start: 0.8587 (t) cc_final: 0.8180 (m) REVERT: A 22 LYS cc_start: 0.8251 (mttt) cc_final: 0.7897 (mttt) REVERT: A 24 MET cc_start: 0.8418 (mmm) cc_final: 0.7908 (mmm) REVERT: A 76 THR cc_start: 0.8748 (p) cc_final: 0.8528 (p) REVERT: A 124 SER cc_start: 0.8618 (m) cc_final: 0.8273 (p) REVERT: A 197 ILE cc_start: 0.8609 (OUTLIER) cc_final: 0.8365 (mt) REVERT: A 204 LEU cc_start: 0.8382 (OUTLIER) cc_final: 0.8083 (mp) REVERT: A 207 GLU cc_start: 0.6947 (tm-30) cc_final: 0.4320 (tt0) REVERT: A 240 GLU cc_start: 0.8230 (tp30) cc_final: 0.7959 (tp30) REVERT: A 295 ASN cc_start: 0.8014 (t0) cc_final: 0.7706 (t0) REVERT: A 341 ASP cc_start: 0.8298 (OUTLIER) cc_final: 0.8083 (m-30) REVERT: A 405 ILE cc_start: 0.8872 (mp) cc_final: 0.8611 (mm) REVERT: A 486 MET cc_start: 0.8509 (OUTLIER) cc_final: 0.8283 (ptm) REVERT: A 507 PRO cc_start: 0.8841 (Cg_exo) cc_final: 0.8570 (Cg_endo) REVERT: A 540 LYS cc_start: 0.8603 (mttt) cc_final: 0.8266 (mttm) REVERT: A 546 THR cc_start: 0.8647 (p) cc_final: 0.8218 (t) REVERT: A 548 LYS cc_start: 0.8812 (mttm) cc_final: 0.8593 (mttp) REVERT: B 24 MET cc_start: 0.8226 (mmm) cc_final: 0.8026 (mmm) REVERT: B 51 GLU cc_start: 0.7422 (tt0) cc_final: 0.6782 (tt0) REVERT: B 53 HIS cc_start: 0.7806 (p90) cc_final: 0.7321 (p90) REVERT: B 55 LYS cc_start: 0.8705 (mttt) cc_final: 0.8484 (mttt) REVERT: B 110 ASN cc_start: 0.8326 (m-40) cc_final: 0.8036 (m110) REVERT: B 130 ASP cc_start: 0.8017 (m-30) cc_final: 0.7620 (m-30) REVERT: B 134 LYS cc_start: 0.8832 (tttt) cc_final: 0.8394 (ttpp) REVERT: B 154 ASP cc_start: 0.7605 (t0) cc_final: 0.7189 (t0) REVERT: B 215 GLU cc_start: 0.8114 (mp0) cc_final: 0.7833 (mp0) REVERT: B 230 MET cc_start: 0.8019 (OUTLIER) cc_final: 0.7713 (tmm) REVERT: B 294 VAL cc_start: 0.8648 (t) cc_final: 0.8389 (p) REVERT: B 296 SER cc_start: 0.8806 (t) cc_final: 0.8322 (p) REVERT: B 349 ILE cc_start: 0.8977 (tp) cc_final: 0.8755 (tt) REVERT: B 376 ASN cc_start: 0.8279 (t0) cc_final: 0.8000 (t0) REVERT: B 377 GLU cc_start: 0.7258 (mm-30) cc_final: 0.6968 (mm-30) REVERT: B 378 LYS cc_start: 0.8455 (pttm) cc_final: 0.8170 (pttm) REVERT: B 523 TYR cc_start: 0.8953 (p90) cc_final: 0.8742 (p90) REVERT: B 524 ASP cc_start: 0.8685 (t0) cc_final: 0.8203 (t0) REVERT: B 526 THR cc_start: 0.8717 (p) cc_final: 0.8498 (t) REVERT: B 543 GLU cc_start: 0.8079 (mt-10) cc_final: 0.7763 (tt0) REVERT: B 546 THR cc_start: 0.8368 (OUTLIER) cc_final: 0.8025 (t) REVERT: E 81 MET cc_start: 0.8712 (tmm) cc_final: 0.8275 (ttp) REVERT: E 125 GLU cc_start: 0.8548 (mm-30) cc_final: 0.8324 (mm-30) REVERT: E 129 LYS cc_start: 0.8295 (mttp) cc_final: 0.8015 (mtpp) REVERT: E 130 ASP cc_start: 0.7743 (m-30) cc_final: 0.7464 (m-30) REVERT: E 133 ASP cc_start: 0.8063 (m-30) cc_final: 0.7827 (m-30) REVERT: E 134 LYS cc_start: 0.8061 (tttt) cc_final: 0.7709 (ttpp) REVERT: E 191 ASP cc_start: 0.7932 (m-30) cc_final: 0.7647 (m-30) REVERT: E 193 ASN cc_start: 0.8275 (t0) cc_final: 0.7845 (t0) REVERT: E 207 GLU cc_start: 0.8003 (mt-10) cc_final: 0.7634 (tm-30) REVERT: E 215 GLU cc_start: 0.8299 (mp0) cc_final: 0.7232 (mp0) REVERT: E 294 VAL cc_start: 0.8776 (t) cc_final: 0.8377 (p) REVERT: E 295 ASN cc_start: 0.8447 (t0) cc_final: 0.7658 (t0) REVERT: E 379 GLU cc_start: 0.7836 (mm-30) cc_final: 0.7595 (mm-30) REVERT: E 382 LYS cc_start: 0.8598 (mtmt) cc_final: 0.8344 (mtmm) REVERT: E 410 MET cc_start: 0.8567 (mtm) cc_final: 0.8339 (mtm) REVERT: E 423 GLU cc_start: 0.8239 (mt-10) cc_final: 0.8013 (mt-10) REVERT: E 438 LYS cc_start: 0.8715 (mttm) cc_final: 0.6529 (pptt) REVERT: E 490 MET cc_start: 0.8449 (tpp) cc_final: 0.8215 (ttm) REVERT: E 524 ASP cc_start: 0.8324 (t0) cc_final: 0.7937 (t0) REVERT: E 540 LYS cc_start: 0.8782 (OUTLIER) cc_final: 0.8534 (mtpt) REVERT: E 543 GLU cc_start: 0.8165 (tt0) cc_final: 0.7926 (tt0) REVERT: E 554 LEU cc_start: 0.7318 (OUTLIER) cc_final: 0.7019 (mp) REVERT: C 51 GLU cc_start: 0.8123 (tt0) cc_final: 0.7776 (tt0) REVERT: C 103 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7000 (mt-10) REVERT: C 154 ASP cc_start: 0.8047 (t0) cc_final: 0.7536 (t0) REVERT: C 158 LYS cc_start: 0.6030 (tptp) cc_final: 0.5519 (tttp) REVERT: C 191 ASP cc_start: 0.7836 (m-30) cc_final: 0.7579 (m-30) REVERT: C 192 VAL cc_start: 0.8744 (t) cc_final: 0.8503 (p) REVERT: C 193 ASN cc_start: 0.7845 (t0) cc_final: 0.7572 (t0) REVERT: C 204 LEU cc_start: 0.8355 (mt) cc_final: 0.8119 (mm) REVERT: C 230 MET cc_start: 0.8328 (tmm) cc_final: 0.8093 (tmm) REVERT: C 272 LYS cc_start: 0.7993 (mmtt) cc_final: 0.7587 (tptp) REVERT: C 274 ARG cc_start: 0.8131 (tmm-80) cc_final: 0.7754 (tmm-80) REVERT: C 294 VAL cc_start: 0.8608 (t) cc_final: 0.8319 (p) REVERT: C 295 ASN cc_start: 0.8200 (t0) cc_final: 0.7804 (t0) REVERT: C 296 SER cc_start: 0.8937 (t) cc_final: 0.8554 (p) REVERT: C 329 ARG cc_start: 0.8040 (mtt90) cc_final: 0.7798 (mtt-85) REVERT: C 371 VAL cc_start: 0.9018 (t) cc_final: 0.8683 (p) REVERT: C 471 LYS cc_start: 0.8377 (mmtt) cc_final: 0.7860 (mmtt) REVERT: C 521 VAL cc_start: 0.8650 (t) cc_final: 0.8344 (p) REVERT: C 524 ASP cc_start: 0.8152 (t0) cc_final: 0.7848 (t0) REVERT: C 534 HIS cc_start: 0.7997 (m-70) cc_final: 0.7722 (m-70) REVERT: C 542 GLU cc_start: 0.8138 (pt0) cc_final: 0.7895 (pt0) REVERT: C 546 THR cc_start: 0.8429 (p) cc_final: 0.7921 (m) REVERT: D 21 VAL cc_start: 0.8732 (t) cc_final: 0.8428 (m) REVERT: D 24 MET cc_start: 0.8477 (mmm) cc_final: 0.7745 (mmm) REVERT: D 49 ASP cc_start: 0.8492 (t0) cc_final: 0.8187 (t0) REVERT: D 51 GLU cc_start: 0.7656 (tt0) cc_final: 0.7350 (tt0) REVERT: D 58 SER cc_start: 0.8368 (t) cc_final: 0.7821 (p) REVERT: D 103 GLU cc_start: 0.8049 (mt-10) cc_final: 0.7789 (mt-10) REVERT: D 135 THR cc_start: 0.8661 (m) cc_final: 0.8397 (t) REVERT: D 151 MET cc_start: 0.8500 (ttp) cc_final: 0.8215 (ttp) REVERT: D 168 ASP cc_start: 0.8145 (t0) cc_final: 0.7837 (t0) REVERT: D 192 VAL cc_start: 0.8942 (t) cc_final: 0.8727 (p) REVERT: D 203 LYS cc_start: 0.8612 (ttmm) cc_final: 0.8327 (ttmm) REVERT: D 207 GLU cc_start: 0.6054 (tm-30) cc_final: 0.5192 (tm-30) REVERT: D 215 GLU cc_start: 0.8375 (mp0) cc_final: 0.7510 (mp0) REVERT: D 289 MET cc_start: 0.8779 (mmm) cc_final: 0.8414 (mmp) REVERT: D 341 ASP cc_start: 0.8059 (OUTLIER) cc_final: 0.7700 (m-30) REVERT: D 346 VAL cc_start: 0.8817 (t) cc_final: 0.8507 (p) REVERT: D 382 LYS cc_start: 0.8755 (mtmt) cc_final: 0.8409 (mtpt) REVERT: D 417 ARG cc_start: 0.8340 (ttm110) cc_final: 0.7845 (mtm110) REVERT: D 435 ASP cc_start: 0.8073 (t0) cc_final: 0.7587 (p0) REVERT: D 461 LEU cc_start: 0.8708 (tp) cc_final: 0.8501 (tt) REVERT: D 490 MET cc_start: 0.8491 (OUTLIER) cc_final: 0.8253 (ttt) REVERT: D 524 ASP cc_start: 0.8170 (t0) cc_final: 0.7709 (t0) REVERT: I 271 MET cc_start: 0.5538 (pmm) cc_final: 0.5150 (pmm) REVERT: I 358 MET cc_start: 0.7454 (mmp) cc_final: 0.6966 (mmp) REVERT: I 399 GLN cc_start: 0.7967 (mt0) cc_final: 0.7767 (mt0) outliers start: 72 outliers final: 44 residues processed: 706 average time/residue: 0.3596 time to fit residues: 379.6688 Evaluate side-chains 712 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 658 time to evaluate : 2.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 341 ASP Chi-restraints excluded: chain A residue 344 LYS Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 23 SER Chi-restraints excluded: chain B residue 77 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 274 ARG Chi-restraints excluded: chain E residue 344 LYS Chi-restraints excluded: chain E residue 459 LYS Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 486 MET Chi-restraints excluded: chain E residue 540 LYS Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 139 VAL Chi-restraints excluded: chain D residue 142 THR Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 490 MET Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain I residue 443 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 76 optimal weight: 0.0980 chunk 28 optimal weight: 0.7980 chunk 131 optimal weight: 2.9990 chunk 195 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 141 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 205 optimal weight: 3.9990 chunk 4 optimal weight: 0.6980 chunk 194 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 HIS ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 GLN ** B 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 43 GLN C 43 GLN C 106 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 ASN C 380 GLN C 533 HIS D 43 GLN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 GLN ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 432 ASN D 463 GLN D 552 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.113452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.095411 restraints weight = 35194.485| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.05 r_work: 0.2980 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3503 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 22196 Z= 0.188 Angle : 0.549 8.618 30252 Z= 0.282 Chirality : 0.041 0.276 3258 Planarity : 0.005 0.118 3942 Dihedral : 5.326 57.331 2971 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.54 % Favored : 98.42 % Rotamer: Outliers : 2.00 % Allowed : 12.31 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.15), residues: 2722 helix: 0.53 (0.39), residues: 183 sheet: -0.10 (0.19), residues: 673 loop : -0.25 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 545 HIS 0.005 0.001 HIS D 53 PHE 0.024 0.002 PHE B 374 TYR 0.017 0.001 TYR D 523 ARG 0.006 0.000 ARG C 417 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 730 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 683 time to evaluate : 2.331 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 24 MET cc_start: 0.8282 (mmm) cc_final: 0.7831 (mmm) REVERT: A 76 THR cc_start: 0.8781 (p) cc_final: 0.8566 (p) REVERT: A 124 SER cc_start: 0.8606 (m) cc_final: 0.8304 (p) REVERT: A 134 LYS cc_start: 0.8840 (ttpp) cc_final: 0.8575 (ttpp) REVERT: A 207 GLU cc_start: 0.6614 (tm-30) cc_final: 0.4254 (tt0) REVERT: A 240 GLU cc_start: 0.8159 (tp30) cc_final: 0.7839 (tp30) REVERT: A 295 ASN cc_start: 0.7965 (t0) cc_final: 0.7595 (t0) REVERT: A 405 ILE cc_start: 0.8798 (mp) cc_final: 0.8569 (mm) REVERT: A 486 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8290 (ptm) REVERT: A 507 PRO cc_start: 0.8887 (Cg_exo) cc_final: 0.8617 (Cg_endo) REVERT: A 540 LYS cc_start: 0.8569 (mttt) cc_final: 0.8149 (mttm) REVERT: A 546 THR cc_start: 0.8626 (p) cc_final: 0.8237 (t) REVERT: B 42 ARG cc_start: 0.8526 (mmt-90) cc_final: 0.8189 (mpt180) REVERT: B 51 GLU cc_start: 0.7384 (tt0) cc_final: 0.6790 (tt0) REVERT: B 53 HIS cc_start: 0.7833 (p90) cc_final: 0.7339 (p90) REVERT: B 110 ASN cc_start: 0.8325 (m-40) cc_final: 0.7964 (m110) REVERT: B 130 ASP cc_start: 0.7971 (m-30) cc_final: 0.7606 (m-30) REVERT: B 134 LYS cc_start: 0.8648 (tttt) cc_final: 0.8193 (ttpp) REVERT: B 154 ASP cc_start: 0.7649 (t0) cc_final: 0.7306 (t0) REVERT: B 156 GLU cc_start: 0.8275 (mt-10) cc_final: 0.8057 (mt-10) REVERT: B 157 TYR cc_start: 0.8318 (m-80) cc_final: 0.7649 (m-80) REVERT: B 215 GLU cc_start: 0.8070 (mp0) cc_final: 0.7678 (mp0) REVERT: B 230 MET cc_start: 0.8135 (tmm) cc_final: 0.7736 (tmm) REVERT: B 294 VAL cc_start: 0.8585 (t) cc_final: 0.8365 (p) REVERT: B 296 SER cc_start: 0.8724 (t) cc_final: 0.8170 (p) REVERT: B 325 ARG cc_start: 0.8422 (mtp180) cc_final: 0.8216 (mtm180) REVERT: B 329 ARG cc_start: 0.8526 (mtt90) cc_final: 0.8002 (mtt-85) REVERT: B 376 ASN cc_start: 0.8212 (t0) cc_final: 0.7931 (t0) REVERT: B 523 TYR cc_start: 0.8866 (p90) cc_final: 0.8445 (p90) REVERT: B 524 ASP cc_start: 0.8631 (t0) cc_final: 0.8285 (t0) REVERT: B 526 THR cc_start: 0.8700 (p) cc_final: 0.8497 (t) REVERT: B 532 GLN cc_start: 0.8212 (mm110) cc_final: 0.7747 (mm-40) REVERT: B 543 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7640 (tt0) REVERT: B 546 THR cc_start: 0.8294 (p) cc_final: 0.8000 (t) REVERT: B 554 LEU cc_start: 0.7258 (OUTLIER) cc_final: 0.7012 (mp) REVERT: E 19 ASN cc_start: 0.8575 (t0) cc_final: 0.8266 (t0) REVERT: E 81 MET cc_start: 0.8611 (tmm) cc_final: 0.8207 (ttp) REVERT: E 120 THR cc_start: 0.8445 (m) cc_final: 0.8161 (t) REVERT: E 129 LYS cc_start: 0.8273 (mttp) cc_final: 0.7946 (mttp) REVERT: E 130 ASP cc_start: 0.7804 (m-30) cc_final: 0.7500 (m-30) REVERT: E 134 LYS cc_start: 0.7883 (tttt) cc_final: 0.7611 (ttpp) REVERT: E 191 ASP cc_start: 0.7870 (m-30) cc_final: 0.7595 (m-30) REVERT: E 193 ASN cc_start: 0.8198 (t0) cc_final: 0.7685 (t0) REVERT: E 207 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7358 (tm-30) REVERT: E 215 GLU cc_start: 0.8214 (mp0) cc_final: 0.7288 (mp0) REVERT: E 294 VAL cc_start: 0.8732 (t) cc_final: 0.8365 (p) REVERT: E 295 ASN cc_start: 0.8371 (t0) cc_final: 0.7599 (t0) REVERT: E 347 THR cc_start: 0.8497 (m) cc_final: 0.8208 (p) REVERT: E 379 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7394 (mm-30) REVERT: E 382 LYS cc_start: 0.8556 (mtmt) cc_final: 0.8039 (mtmt) REVERT: E 389 MET cc_start: 0.8533 (tpp) cc_final: 0.8144 (tpt) REVERT: E 410 MET cc_start: 0.8524 (mtm) cc_final: 0.8282 (mtp) REVERT: E 423 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7905 (mt-10) REVERT: E 427 TRP cc_start: 0.8650 (p90) cc_final: 0.8348 (p90) REVERT: E 524 ASP cc_start: 0.8260 (t0) cc_final: 0.7829 (t0) REVERT: E 540 LYS cc_start: 0.8649 (OUTLIER) cc_final: 0.8391 (mtpt) REVERT: E 543 GLU cc_start: 0.7945 (tt0) cc_final: 0.7687 (tt0) REVERT: C 158 LYS cc_start: 0.5954 (tptp) cc_final: 0.5300 (tttp) REVERT: C 191 ASP cc_start: 0.7793 (m-30) cc_final: 0.7570 (m-30) REVERT: C 192 VAL cc_start: 0.8742 (t) cc_final: 0.8463 (p) REVERT: C 193 ASN cc_start: 0.7795 (t0) cc_final: 0.7469 (t0) REVERT: C 215 GLU cc_start: 0.8198 (mp0) cc_final: 0.7898 (mp0) REVERT: C 272 LYS cc_start: 0.7976 (mmtt) cc_final: 0.7532 (tptt) REVERT: C 274 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7728 (tmm-80) REVERT: C 294 VAL cc_start: 0.8607 (t) cc_final: 0.8339 (p) REVERT: C 295 ASN cc_start: 0.8013 (t0) cc_final: 0.7708 (t0) REVERT: C 329 ARG cc_start: 0.7971 (mtt90) cc_final: 0.7515 (mtt-85) REVERT: C 371 VAL cc_start: 0.8926 (t) cc_final: 0.8600 (p) REVERT: C 374 PHE cc_start: 0.8625 (m-80) cc_final: 0.8267 (m-80) REVERT: C 471 LYS cc_start: 0.8323 (mmtt) cc_final: 0.7835 (mmtt) REVERT: C 521 VAL cc_start: 0.8647 (t) cc_final: 0.8350 (p) REVERT: C 524 ASP cc_start: 0.8201 (t0) cc_final: 0.7753 (t0) REVERT: C 534 HIS cc_start: 0.7914 (m-70) cc_final: 0.7626 (m-70) REVERT: C 543 GLU cc_start: 0.7940 (mt-10) cc_final: 0.7687 (tt0) REVERT: C 546 THR cc_start: 0.8472 (p) cc_final: 0.8074 (m) REVERT: D 21 VAL cc_start: 0.8713 (t) cc_final: 0.8379 (m) REVERT: D 24 MET cc_start: 0.8397 (mmm) cc_final: 0.7727 (mmm) REVERT: D 49 ASP cc_start: 0.8506 (t0) cc_final: 0.8181 (t0) REVERT: D 51 GLU cc_start: 0.7747 (tt0) cc_final: 0.7435 (tt0) REVERT: D 55 LYS cc_start: 0.8798 (mttp) cc_final: 0.8442 (mttp) REVERT: D 58 SER cc_start: 0.8355 (t) cc_final: 0.7861 (p) REVERT: D 103 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7711 (mt-10) REVERT: D 134 LYS cc_start: 0.8890 (ttpp) cc_final: 0.8341 (ttpp) REVERT: D 135 THR cc_start: 0.8618 (m) cc_final: 0.8372 (t) REVERT: D 151 MET cc_start: 0.8474 (ttp) cc_final: 0.8146 (ttp) REVERT: D 168 ASP cc_start: 0.8028 (t0) cc_final: 0.7783 (t0) REVERT: D 192 VAL cc_start: 0.8903 (t) cc_final: 0.8654 (p) REVERT: D 203 LYS cc_start: 0.8598 (ttmm) cc_final: 0.8323 (ttmm) REVERT: D 207 GLU cc_start: 0.5932 (tm-30) cc_final: 0.4465 (tm-30) REVERT: D 215 GLU cc_start: 0.8334 (mp0) cc_final: 0.7529 (mp0) REVERT: D 341 ASP cc_start: 0.8035 (OUTLIER) cc_final: 0.7726 (m-30) REVERT: D 346 VAL cc_start: 0.8717 (t) cc_final: 0.8416 (p) REVERT: D 382 LYS cc_start: 0.8732 (mtmt) cc_final: 0.8356 (mtmt) REVERT: D 417 ARG cc_start: 0.8305 (ttm110) cc_final: 0.7879 (mtm110) REVERT: D 435 ASP cc_start: 0.8032 (t0) cc_final: 0.7530 (p0) REVERT: D 490 MET cc_start: 0.8433 (OUTLIER) cc_final: 0.8201 (ttt) REVERT: I 271 MET cc_start: 0.5275 (pmm) cc_final: 0.4871 (pmm) REVERT: I 338 ARG cc_start: 0.7421 (ttp80) cc_final: 0.7194 (ttp80) REVERT: I 357 LEU cc_start: 0.8382 (mt) cc_final: 0.8095 (mt) REVERT: I 358 MET cc_start: 0.7523 (mmp) cc_final: 0.7013 (mmp) outliers start: 47 outliers final: 29 residues processed: 695 average time/residue: 0.3974 time to fit residues: 413.4579 Evaluate side-chains 691 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 656 time to evaluate : 2.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 274 ARG Chi-restraints excluded: chain E residue 344 LYS Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 540 LYS Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 274 ARG Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 490 MET Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain I residue 443 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 6.9990 chunk 126 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 chunk 195 optimal weight: 0.8980 chunk 177 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 161 optimal weight: 3.9990 chunk 83 optimal weight: 3.9990 chunk 260 optimal weight: 9.9990 chunk 122 optimal weight: 1.9990 chunk 252 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 ASN C 356 GLN C 451 GLN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS D 284 GLN ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 513 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3381 r_free = 0.3381 target = 0.111416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.093566 restraints weight = 34951.518| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 2.00 r_work: 0.2950 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 22196 Z= 0.443 Angle : 0.608 9.346 30252 Z= 0.311 Chirality : 0.044 0.276 3258 Planarity : 0.005 0.116 3942 Dihedral : 5.363 57.480 2969 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.02 % Favored : 97.94 % Rotamer: Outliers : 3.06 % Allowed : 12.91 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.15), residues: 2722 helix: 0.36 (0.38), residues: 183 sheet: -0.02 (0.19), residues: 638 loop : -0.42 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 415 HIS 0.007 0.001 HIS B 536 PHE 0.022 0.002 PHE B 219 TYR 0.020 0.002 TYR D 523 ARG 0.006 0.001 ARG D 88 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 662 time to evaluate : 2.536 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8250 (mttt) cc_final: 0.7863 (mttt) REVERT: A 24 MET cc_start: 0.8364 (mmm) cc_final: 0.7915 (mmm) REVERT: A 42 ARG cc_start: 0.8557 (mmt-90) cc_final: 0.8303 (mmt-90) REVERT: A 124 SER cc_start: 0.8567 (m) cc_final: 0.8199 (p) REVERT: A 134 LYS cc_start: 0.8784 (ttpp) cc_final: 0.8286 (ttpp) REVERT: A 207 GLU cc_start: 0.6865 (tm-30) cc_final: 0.4276 (tt0) REVERT: A 240 GLU cc_start: 0.8234 (tp30) cc_final: 0.7883 (tp30) REVERT: A 295 ASN cc_start: 0.8002 (t0) cc_final: 0.7656 (t0) REVERT: A 405 ILE cc_start: 0.8821 (mp) cc_final: 0.8618 (mm) REVERT: A 434 ASP cc_start: 0.8113 (m-30) cc_final: 0.7759 (p0) REVERT: A 486 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8228 (ptm) REVERT: A 507 PRO cc_start: 0.8894 (Cg_exo) cc_final: 0.8625 (Cg_endo) REVERT: A 540 LYS cc_start: 0.8589 (mttt) cc_final: 0.8177 (mttt) REVERT: A 546 THR cc_start: 0.8660 (p) cc_final: 0.8288 (t) REVERT: B 51 GLU cc_start: 0.7407 (tt0) cc_final: 0.6812 (tt0) REVERT: B 53 HIS cc_start: 0.7813 (p90) cc_final: 0.7346 (p90) REVERT: B 110 ASN cc_start: 0.8315 (m-40) cc_final: 0.7991 (m110) REVERT: B 130 ASP cc_start: 0.7954 (m-30) cc_final: 0.7571 (m-30) REVERT: B 134 LYS cc_start: 0.8687 (tttt) cc_final: 0.8221 (ttpp) REVERT: B 154 ASP cc_start: 0.7613 (t0) cc_final: 0.7221 (t0) REVERT: B 156 GLU cc_start: 0.8272 (mt-10) cc_final: 0.8041 (mt-10) REVERT: B 157 TYR cc_start: 0.8313 (m-80) cc_final: 0.7651 (m-80) REVERT: B 215 GLU cc_start: 0.8078 (mp0) cc_final: 0.7720 (mp0) REVERT: B 230 MET cc_start: 0.8101 (OUTLIER) cc_final: 0.7700 (tmm) REVERT: B 294 VAL cc_start: 0.8636 (t) cc_final: 0.8418 (p) REVERT: B 296 SER cc_start: 0.8717 (t) cc_final: 0.8186 (p) REVERT: B 376 ASN cc_start: 0.8224 (t0) cc_final: 0.7905 (t0) REVERT: B 389 MET cc_start: 0.8555 (tpp) cc_final: 0.8029 (tpt) REVERT: B 417 ARG cc_start: 0.8349 (mtm-85) cc_final: 0.8129 (mtm-85) REVERT: B 524 ASP cc_start: 0.8617 (t0) cc_final: 0.8110 (t0) REVERT: B 532 GLN cc_start: 0.8184 (mm110) cc_final: 0.7733 (mm-40) REVERT: B 543 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7639 (tt0) REVERT: B 546 THR cc_start: 0.8385 (p) cc_final: 0.8055 (t) REVERT: B 554 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.7019 (mp) REVERT: E 55 LYS cc_start: 0.8618 (mtmt) cc_final: 0.8233 (mtmm) REVERT: E 81 MET cc_start: 0.8662 (tmm) cc_final: 0.8246 (ttp) REVERT: E 120 THR cc_start: 0.8344 (m) cc_final: 0.8068 (t) REVERT: E 129 LYS cc_start: 0.8309 (mttp) cc_final: 0.7969 (mtpp) REVERT: E 130 ASP cc_start: 0.7782 (m-30) cc_final: 0.7499 (m-30) REVERT: E 133 ASP cc_start: 0.7969 (m-30) cc_final: 0.7477 (m-30) REVERT: E 134 LYS cc_start: 0.7905 (tttt) cc_final: 0.7568 (ttpp) REVERT: E 191 ASP cc_start: 0.7898 (m-30) cc_final: 0.7599 (m-30) REVERT: E 193 ASN cc_start: 0.8257 (t0) cc_final: 0.7857 (t0) REVERT: E 207 GLU cc_start: 0.8000 (mt-10) cc_final: 0.7639 (tm-30) REVERT: E 215 GLU cc_start: 0.8236 (mp0) cc_final: 0.7285 (mp0) REVERT: E 294 VAL cc_start: 0.8727 (t) cc_final: 0.8354 (p) REVERT: E 295 ASN cc_start: 0.8433 (t0) cc_final: 0.7656 (t0) REVERT: E 347 THR cc_start: 0.8530 (m) cc_final: 0.8272 (p) REVERT: E 379 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7440 (mm-30) REVERT: E 382 LYS cc_start: 0.8608 (mtmt) cc_final: 0.8305 (mtmm) REVERT: E 389 MET cc_start: 0.8566 (tpp) cc_final: 0.8168 (tpt) REVERT: E 410 MET cc_start: 0.8572 (mtm) cc_final: 0.8336 (mtp) REVERT: E 423 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7868 (mt-10) REVERT: E 524 ASP cc_start: 0.8372 (t0) cc_final: 0.7934 (t0) REVERT: E 540 LYS cc_start: 0.8700 (OUTLIER) cc_final: 0.8457 (mtpt) REVERT: E 543 GLU cc_start: 0.7963 (tt0) cc_final: 0.7691 (tt0) REVERT: E 548 LYS cc_start: 0.8884 (mttp) cc_final: 0.8611 (mttp) REVERT: E 554 LEU cc_start: 0.7158 (OUTLIER) cc_final: 0.6889 (mp) REVERT: C 21 VAL cc_start: 0.8650 (t) cc_final: 0.8335 (m) REVERT: C 51 GLU cc_start: 0.8032 (tt0) cc_final: 0.7739 (tt0) REVERT: C 143 ASP cc_start: 0.7373 (m-30) cc_final: 0.6959 (m-30) REVERT: C 151 MET cc_start: 0.8580 (OUTLIER) cc_final: 0.8164 (ttp) REVERT: C 154 ASP cc_start: 0.8009 (t0) cc_final: 0.7533 (t0) REVERT: C 158 LYS cc_start: 0.6029 (tptp) cc_final: 0.5425 (tttp) REVERT: C 191 ASP cc_start: 0.7810 (m-30) cc_final: 0.7570 (m-30) REVERT: C 192 VAL cc_start: 0.8728 (t) cc_final: 0.8462 (p) REVERT: C 193 ASN cc_start: 0.7802 (t0) cc_final: 0.7478 (t0) REVERT: C 204 LEU cc_start: 0.8283 (mt) cc_final: 0.8043 (mm) REVERT: C 207 GLU cc_start: 0.6011 (tm-30) cc_final: 0.4459 (tm-30) REVERT: C 215 GLU cc_start: 0.8250 (mp0) cc_final: 0.7914 (mp0) REVERT: C 230 MET cc_start: 0.8274 (tmm) cc_final: 0.8069 (tmm) REVERT: C 272 LYS cc_start: 0.7873 (mmtt) cc_final: 0.7398 (tptt) REVERT: C 274 ARG cc_start: 0.8117 (tmm-80) cc_final: 0.7692 (tmm-80) REVERT: C 294 VAL cc_start: 0.8671 (t) cc_final: 0.8365 (p) REVERT: C 295 ASN cc_start: 0.8246 (t0) cc_final: 0.7869 (t0) REVERT: C 329 ARG cc_start: 0.8178 (mtt90) cc_final: 0.7712 (mtt-85) REVERT: C 371 VAL cc_start: 0.8950 (t) cc_final: 0.8632 (p) REVERT: C 374 PHE cc_start: 0.8627 (m-80) cc_final: 0.8290 (m-80) REVERT: C 435 ASP cc_start: 0.5689 (OUTLIER) cc_final: 0.5121 (t70) REVERT: C 471 LYS cc_start: 0.8389 (mmtt) cc_final: 0.7908 (mmtt) REVERT: C 521 VAL cc_start: 0.8614 (t) cc_final: 0.8335 (p) REVERT: C 524 ASP cc_start: 0.8181 (t0) cc_final: 0.7728 (t0) REVERT: C 534 HIS cc_start: 0.7977 (m-70) cc_final: 0.7667 (m-70) REVERT: C 543 GLU cc_start: 0.7930 (mt-10) cc_final: 0.7643 (tt0) REVERT: C 546 THR cc_start: 0.8436 (p) cc_final: 0.8082 (m) REVERT: D 21 VAL cc_start: 0.8742 (t) cc_final: 0.8430 (m) REVERT: D 24 MET cc_start: 0.8476 (mmm) cc_final: 0.7815 (mmm) REVERT: D 49 ASP cc_start: 0.8467 (t0) cc_final: 0.8163 (t0) REVERT: D 51 GLU cc_start: 0.7691 (tt0) cc_final: 0.7342 (tt0) REVERT: D 55 LYS cc_start: 0.8791 (mttp) cc_final: 0.8443 (mttp) REVERT: D 58 SER cc_start: 0.8298 (t) cc_final: 0.7825 (p) REVERT: D 103 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7742 (mt-10) REVERT: D 135 THR cc_start: 0.8578 (m) cc_final: 0.8362 (t) REVERT: D 151 MET cc_start: 0.8455 (ttp) cc_final: 0.8177 (ttp) REVERT: D 168 ASP cc_start: 0.8051 (t0) cc_final: 0.7794 (t0) REVERT: D 192 VAL cc_start: 0.8888 (t) cc_final: 0.8650 (p) REVERT: D 201 SER cc_start: 0.8281 (OUTLIER) cc_final: 0.7984 (m) REVERT: D 203 LYS cc_start: 0.8527 (ttmm) cc_final: 0.8297 (ttmm) REVERT: D 207 GLU cc_start: 0.5609 (tm-30) cc_final: 0.4141 (tm-30) REVERT: D 215 GLU cc_start: 0.8368 (mp0) cc_final: 0.7529 (mp0) REVERT: D 341 ASP cc_start: 0.8034 (OUTLIER) cc_final: 0.7713 (m-30) REVERT: D 346 VAL cc_start: 0.8776 (t) cc_final: 0.8494 (p) REVERT: D 382 LYS cc_start: 0.8750 (mtmt) cc_final: 0.8408 (mtmt) REVERT: D 435 ASP cc_start: 0.8012 (t0) cc_final: 0.7503 (p0) REVERT: D 490 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8272 (ttt) REVERT: I 271 MET cc_start: 0.5317 (pmm) cc_final: 0.4895 (pmm) REVERT: I 358 MET cc_start: 0.7569 (mmp) cc_final: 0.7170 (mmp) REVERT: I 383 LEU cc_start: 0.6626 (OUTLIER) cc_final: 0.6412 (tp) outliers start: 72 outliers final: 50 residues processed: 685 average time/residue: 0.3810 time to fit residues: 387.3282 Evaluate side-chains 715 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 654 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 488 VAL Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 132 THR Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 231 SER Chi-restraints excluded: chain E residue 274 ARG Chi-restraints excluded: chain E residue 344 LYS Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 540 LYS Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 435 ASP Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 201 SER Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 490 MET Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain I residue 383 LEU Chi-restraints excluded: chain I residue 443 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 26 optimal weight: 0.0170 chunk 94 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 227 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 239 optimal weight: 1.9990 chunk 257 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 174 optimal weight: 4.9990 chunk 95 optimal weight: 0.9980 overall best weight: 1.2022 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 532 GLN C 43 GLN ** C 155 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 ASN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 GLN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 380 GLN ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 367 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.112738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.094911 restraints weight = 35005.979| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.03 r_work: 0.2972 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 22196 Z= 0.246 Angle : 0.549 8.561 30252 Z= 0.281 Chirality : 0.041 0.270 3258 Planarity : 0.005 0.114 3942 Dihedral : 5.066 57.753 2969 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.65 % Favored : 98.31 % Rotamer: Outliers : 3.10 % Allowed : 13.04 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 2722 helix: 0.47 (0.39), residues: 183 sheet: -0.05 (0.19), residues: 638 loop : -0.38 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP E 415 HIS 0.007 0.001 HIS C 155 PHE 0.017 0.002 PHE D 492 TYR 0.016 0.001 TYR D 523 ARG 0.004 0.000 ARG D 88 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 739 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 666 time to evaluate : 2.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8205 (mttt) cc_final: 0.7819 (mttt) REVERT: A 24 MET cc_start: 0.8353 (mmm) cc_final: 0.7904 (mmm) REVERT: A 42 ARG cc_start: 0.8556 (mmt-90) cc_final: 0.8290 (mmt-90) REVERT: A 55 LYS cc_start: 0.8352 (mtpp) cc_final: 0.8113 (mtpp) REVERT: A 124 SER cc_start: 0.8598 (m) cc_final: 0.8238 (p) REVERT: A 134 LYS cc_start: 0.8787 (ttpp) cc_final: 0.8258 (ttpp) REVERT: A 197 ILE cc_start: 0.8555 (OUTLIER) cc_final: 0.8314 (mt) REVERT: A 207 GLU cc_start: 0.6775 (tm-30) cc_final: 0.4536 (tt0) REVERT: A 240 GLU cc_start: 0.8200 (tp30) cc_final: 0.7869 (tp30) REVERT: A 295 ASN cc_start: 0.7983 (t0) cc_final: 0.7428 (t0) REVERT: A 296 SER cc_start: 0.8604 (t) cc_final: 0.8081 (p) REVERT: A 389 MET cc_start: 0.8487 (tpp) cc_final: 0.8160 (ttm) REVERT: A 405 ILE cc_start: 0.8838 (mp) cc_final: 0.8598 (mm) REVERT: A 434 ASP cc_start: 0.8099 (m-30) cc_final: 0.7687 (p0) REVERT: A 486 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8197 (ptm) REVERT: A 540 LYS cc_start: 0.8584 (mttt) cc_final: 0.8138 (mttt) REVERT: A 546 THR cc_start: 0.8661 (p) cc_final: 0.8276 (t) REVERT: B 8 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7447 (mt-10) REVERT: B 24 MET cc_start: 0.8177 (mmm) cc_final: 0.7893 (tpp) REVERT: B 42 ARG cc_start: 0.8590 (mmt-90) cc_final: 0.8279 (mpt180) REVERT: B 51 GLU cc_start: 0.7431 (tt0) cc_final: 0.6825 (tt0) REVERT: B 53 HIS cc_start: 0.7812 (p90) cc_final: 0.7292 (p90) REVERT: B 110 ASN cc_start: 0.8270 (m-40) cc_final: 0.7940 (m110) REVERT: B 130 ASP cc_start: 0.7943 (m-30) cc_final: 0.7556 (m-30) REVERT: B 134 LYS cc_start: 0.8655 (tttt) cc_final: 0.8211 (ttpp) REVERT: B 154 ASP cc_start: 0.7637 (t0) cc_final: 0.7244 (t0) REVERT: B 156 GLU cc_start: 0.8273 (mt-10) cc_final: 0.8069 (mt-10) REVERT: B 215 GLU cc_start: 0.8057 (mp0) cc_final: 0.7675 (mp0) REVERT: B 230 MET cc_start: 0.8087 (OUTLIER) cc_final: 0.7682 (tmm) REVERT: B 294 VAL cc_start: 0.8604 (t) cc_final: 0.8383 (p) REVERT: B 296 SER cc_start: 0.8703 (t) cc_final: 0.8151 (p) REVERT: B 329 ARG cc_start: 0.8561 (mtt90) cc_final: 0.8066 (mtt-85) REVERT: B 376 ASN cc_start: 0.8187 (t0) cc_final: 0.7856 (t0) REVERT: B 377 GLU cc_start: 0.7231 (mm-30) cc_final: 0.6788 (mm-30) REVERT: B 389 MET cc_start: 0.8511 (tpp) cc_final: 0.7993 (tpt) REVERT: B 435 ASP cc_start: 0.8435 (t0) cc_final: 0.7587 (p0) REVERT: B 470 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8039 (pt) REVERT: B 524 ASP cc_start: 0.8633 (t0) cc_final: 0.8123 (t0) REVERT: B 532 GLN cc_start: 0.8166 (mm-40) cc_final: 0.7842 (mm-40) REVERT: B 543 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7582 (tt0) REVERT: B 546 THR cc_start: 0.8364 (p) cc_final: 0.8040 (t) REVERT: B 554 LEU cc_start: 0.7274 (OUTLIER) cc_final: 0.7022 (mp) REVERT: E 19 ASN cc_start: 0.8684 (t0) cc_final: 0.8411 (t0) REVERT: E 81 MET cc_start: 0.8659 (tmm) cc_final: 0.8270 (ttp) REVERT: E 117 ASP cc_start: 0.7896 (t0) cc_final: 0.7644 (t0) REVERT: E 120 THR cc_start: 0.8402 (m) cc_final: 0.8101 (t) REVERT: E 129 LYS cc_start: 0.8341 (mttp) cc_final: 0.7954 (mtpp) REVERT: E 130 ASP cc_start: 0.7755 (m-30) cc_final: 0.7505 (m-30) REVERT: E 133 ASP cc_start: 0.7966 (m-30) cc_final: 0.7403 (m-30) REVERT: E 134 LYS cc_start: 0.7843 (tttt) cc_final: 0.7518 (ttpp) REVERT: E 148 ARG cc_start: 0.8507 (mmt-90) cc_final: 0.8302 (mmt-90) REVERT: E 191 ASP cc_start: 0.7918 (m-30) cc_final: 0.7619 (m-30) REVERT: E 193 ASN cc_start: 0.8235 (t0) cc_final: 0.7830 (t0) REVERT: E 207 GLU cc_start: 0.7863 (mt-10) cc_final: 0.7580 (tm-30) REVERT: E 215 GLU cc_start: 0.8200 (mp0) cc_final: 0.7326 (mp0) REVERT: E 217 SER cc_start: 0.8773 (OUTLIER) cc_final: 0.8561 (p) REVERT: E 294 VAL cc_start: 0.8713 (t) cc_final: 0.8362 (p) REVERT: E 347 THR cc_start: 0.8503 (m) cc_final: 0.8238 (p) REVERT: E 379 GLU cc_start: 0.7664 (mm-30) cc_final: 0.7444 (mm-30) REVERT: E 382 LYS cc_start: 0.8647 (mtmt) cc_final: 0.8342 (mtmm) REVERT: E 389 MET cc_start: 0.8534 (tpp) cc_final: 0.8177 (tpt) REVERT: E 423 GLU cc_start: 0.8144 (mt-10) cc_final: 0.7843 (mt-10) REVERT: E 427 TRP cc_start: 0.8648 (p90) cc_final: 0.8362 (p90) REVERT: E 490 MET cc_start: 0.8551 (ttm) cc_final: 0.8181 (ttm) REVERT: E 524 ASP cc_start: 0.8397 (t0) cc_final: 0.8046 (t0) REVERT: E 540 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8373 (mtpt) REVERT: E 543 GLU cc_start: 0.7896 (tt0) cc_final: 0.7597 (tt0) REVERT: E 554 LEU cc_start: 0.7083 (OUTLIER) cc_final: 0.6880 (mp) REVERT: C 21 VAL cc_start: 0.8641 (t) cc_final: 0.8355 (m) REVERT: C 51 GLU cc_start: 0.8018 (tt0) cc_final: 0.7690 (tt0) REVERT: C 103 GLU cc_start: 0.7808 (mt-10) cc_final: 0.7559 (mt-10) REVERT: C 151 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8283 (ttp) REVERT: C 154 ASP cc_start: 0.7981 (t0) cc_final: 0.7492 (t0) REVERT: C 158 LYS cc_start: 0.5740 (tptp) cc_final: 0.5069 (tttp) REVERT: C 191 ASP cc_start: 0.7862 (m-30) cc_final: 0.7613 (m-30) REVERT: C 192 VAL cc_start: 0.8736 (t) cc_final: 0.8453 (p) REVERT: C 193 ASN cc_start: 0.7798 (t0) cc_final: 0.7475 (t0) REVERT: C 204 LEU cc_start: 0.8224 (mt) cc_final: 0.7996 (mm) REVERT: C 215 GLU cc_start: 0.8228 (mp0) cc_final: 0.7258 (mp0) REVERT: C 274 ARG cc_start: 0.8141 (OUTLIER) cc_final: 0.7680 (tmm-80) REVERT: C 294 VAL cc_start: 0.8639 (t) cc_final: 0.8332 (p) REVERT: C 295 ASN cc_start: 0.8213 (t0) cc_final: 0.7828 (t0) REVERT: C 329 ARG cc_start: 0.8101 (mtt90) cc_final: 0.7626 (mtt-85) REVERT: C 371 VAL cc_start: 0.8913 (t) cc_final: 0.8597 (p) REVERT: C 374 PHE cc_start: 0.8627 (m-80) cc_final: 0.8403 (m-80) REVERT: C 435 ASP cc_start: 0.5572 (OUTLIER) cc_final: 0.5078 (t70) REVERT: C 471 LYS cc_start: 0.8412 (mmtt) cc_final: 0.7907 (mmtt) REVERT: C 521 VAL cc_start: 0.8590 (t) cc_final: 0.8325 (p) REVERT: C 524 ASP cc_start: 0.8188 (t0) cc_final: 0.7712 (t0) REVERT: C 534 HIS cc_start: 0.7938 (m-70) cc_final: 0.7635 (m-70) REVERT: C 543 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7646 (tt0) REVERT: C 546 THR cc_start: 0.8452 (p) cc_final: 0.8124 (m) REVERT: D 21 VAL cc_start: 0.8765 (t) cc_final: 0.8466 (m) REVERT: D 24 MET cc_start: 0.8390 (mmm) cc_final: 0.7834 (mmm) REVERT: D 49 ASP cc_start: 0.8479 (t0) cc_final: 0.8167 (t0) REVERT: D 51 GLU cc_start: 0.7760 (tt0) cc_final: 0.7420 (tt0) REVERT: D 55 LYS cc_start: 0.8793 (mttp) cc_final: 0.8440 (mttp) REVERT: D 58 SER cc_start: 0.8336 (t) cc_final: 0.8107 (p) REVERT: D 103 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7667 (mt-10) REVERT: D 151 MET cc_start: 0.8437 (ttp) cc_final: 0.8155 (ttp) REVERT: D 168 ASP cc_start: 0.8050 (t0) cc_final: 0.7793 (t0) REVERT: D 192 VAL cc_start: 0.8863 (t) cc_final: 0.8636 (p) REVERT: D 201 SER cc_start: 0.8264 (p) cc_final: 0.7954 (m) REVERT: D 203 LYS cc_start: 0.8488 (ttmm) cc_final: 0.8262 (ttmm) REVERT: D 207 GLU cc_start: 0.5734 (tm-30) cc_final: 0.4319 (tm-30) REVERT: D 215 GLU cc_start: 0.8314 (mp0) cc_final: 0.7503 (mp0) REVERT: D 266 THR cc_start: 0.7670 (t) cc_final: 0.7222 (p) REVERT: D 341 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7742 (m-30) REVERT: D 346 VAL cc_start: 0.8806 (t) cc_final: 0.8530 (p) REVERT: D 382 LYS cc_start: 0.8736 (mtmt) cc_final: 0.8451 (mtmt) REVERT: D 435 ASP cc_start: 0.8066 (t0) cc_final: 0.7541 (p0) REVERT: D 490 MET cc_start: 0.8470 (OUTLIER) cc_final: 0.8231 (ttt) REVERT: I 271 MET cc_start: 0.5170 (pmm) cc_final: 0.4738 (pmm) REVERT: I 358 MET cc_start: 0.7541 (mmp) cc_final: 0.7148 (mmp) outliers start: 73 outliers final: 48 residues processed: 685 average time/residue: 0.3812 time to fit residues: 386.2441 Evaluate side-chains 718 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 655 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 410 MET Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 274 ARG Chi-restraints excluded: chain E residue 344 LYS Chi-restraints excluded: chain E residue 406 GLU Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 540 LYS Chi-restraints excluded: chain E residue 554 LEU Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 75 CYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 274 ARG Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 435 ASP Chi-restraints excluded: chain C residue 543 GLU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 490 MET Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain I residue 443 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 163 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 132 optimal weight: 0.8980 chunk 198 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 264 optimal weight: 20.0000 chunk 162 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 153 optimal weight: 0.0670 chunk 41 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 overall best weight: 0.9522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 GLN C 513 HIS ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 421 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 = 0.3361 r_free = 0.3361 target = 0.110133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.091539 restraints weight = 35703.961| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.15 r_work: 0.2964 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 22196 Z= 0.213 Angle : 0.535 8.233 30252 Z= 0.272 Chirality : 0.041 0.266 3258 Planarity : 0.005 0.112 3942 Dihedral : 4.874 57.393 2969 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.91 % Favored : 98.05 % Rotamer: Outliers : 2.89 % Allowed : 13.97 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 2722 helix: 0.66 (0.40), residues: 183 sheet: -0.02 (0.19), residues: 638 loop : -0.35 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 415 HIS 0.004 0.001 HIS D 53 PHE 0.019 0.001 PHE E 57 TYR 0.014 0.001 TYR A 523 ARG 0.004 0.000 ARG D 88 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 747 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 679 time to evaluate : 2.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8215 (mttt) cc_final: 0.7834 (mttt) REVERT: A 24 MET cc_start: 0.8337 (mmm) cc_final: 0.7893 (mmm) REVERT: A 42 ARG cc_start: 0.8548 (mmt-90) cc_final: 0.8283 (mmt-90) REVERT: A 55 LYS cc_start: 0.8331 (mtpp) cc_final: 0.8109 (mtpp) REVERT: A 124 SER cc_start: 0.8602 (m) cc_final: 0.8282 (p) REVERT: A 134 LYS cc_start: 0.8750 (ttpp) cc_final: 0.8252 (ttpp) REVERT: A 152 LEU cc_start: 0.8723 (tp) cc_final: 0.8437 (tp) REVERT: A 197 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8234 (mt) REVERT: A 207 GLU cc_start: 0.6827 (tm-30) cc_final: 0.4365 (tt0) REVERT: A 240 GLU cc_start: 0.8245 (tp30) cc_final: 0.7923 (tp30) REVERT: A 251 GLU cc_start: 0.6129 (tm-30) cc_final: 0.5876 (tm-30) REVERT: A 295 ASN cc_start: 0.8007 (t0) cc_final: 0.7658 (t0) REVERT: A 405 ILE cc_start: 0.8861 (mp) cc_final: 0.8631 (mm) REVERT: A 434 ASP cc_start: 0.8137 (m-30) cc_final: 0.7677 (p0) REVERT: A 486 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8254 (ptm) REVERT: A 540 LYS cc_start: 0.8565 (mttt) cc_final: 0.8123 (mttt) REVERT: A 546 THR cc_start: 0.8623 (p) cc_final: 0.8278 (t) REVERT: B 8 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7411 (mt-10) REVERT: B 42 ARG cc_start: 0.8576 (mmt-90) cc_final: 0.8272 (mpt180) REVERT: B 51 GLU cc_start: 0.7457 (tt0) cc_final: 0.6844 (tt0) REVERT: B 53 HIS cc_start: 0.7810 (p90) cc_final: 0.7314 (p90) REVERT: B 110 ASN cc_start: 0.8246 (m-40) cc_final: 0.7893 (m110) REVERT: B 130 ASP cc_start: 0.8016 (m-30) cc_final: 0.7643 (m-30) REVERT: B 134 LYS cc_start: 0.8592 (tttt) cc_final: 0.8163 (ttpp) REVERT: B 154 ASP cc_start: 0.7667 (t0) cc_final: 0.7324 (t0) REVERT: B 215 GLU cc_start: 0.8066 (mp0) cc_final: 0.7660 (mp0) REVERT: B 230 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7764 (tmm) REVERT: B 294 VAL cc_start: 0.8596 (t) cc_final: 0.8374 (p) REVERT: B 296 SER cc_start: 0.8727 (t) cc_final: 0.8152 (p) REVERT: B 329 ARG cc_start: 0.8565 (mtt90) cc_final: 0.8063 (mtt-85) REVERT: B 349 ILE cc_start: 0.8794 (tp) cc_final: 0.8175 (tt) REVERT: B 376 ASN cc_start: 0.8191 (t0) cc_final: 0.7816 (t0) REVERT: B 377 GLU cc_start: 0.7246 (mm-30) cc_final: 0.6798 (mm-30) REVERT: B 389 MET cc_start: 0.8493 (tpp) cc_final: 0.7993 (tpt) REVERT: B 435 ASP cc_start: 0.8462 (t0) cc_final: 0.7573 (p0) REVERT: B 470 ILE cc_start: 0.8058 (OUTLIER) cc_final: 0.7857 (pt) REVERT: B 522 LEU cc_start: 0.8682 (tp) cc_final: 0.8469 (tp) REVERT: B 524 ASP cc_start: 0.8639 (t0) cc_final: 0.8124 (t0) REVERT: B 532 GLN cc_start: 0.8120 (mm-40) cc_final: 0.7682 (mm-40) REVERT: B 543 GLU cc_start: 0.7892 (OUTLIER) cc_final: 0.7587 (tt0) REVERT: B 546 THR cc_start: 0.8374 (p) cc_final: 0.8063 (t) REVERT: B 554 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.7054 (mp) REVERT: E 10 SER cc_start: 0.8420 (m) cc_final: 0.7899 (p) REVERT: E 19 ASN cc_start: 0.8699 (t0) cc_final: 0.8407 (t0) REVERT: E 81 MET cc_start: 0.8662 (tmm) cc_final: 0.8307 (ttp) REVERT: E 117 ASP cc_start: 0.7849 (t0) cc_final: 0.7588 (t0) REVERT: E 120 THR cc_start: 0.8346 (m) cc_final: 0.8030 (t) REVERT: E 129 LYS cc_start: 0.8380 (mttp) cc_final: 0.7988 (mtpp) REVERT: E 130 ASP cc_start: 0.7852 (m-30) cc_final: 0.7572 (m-30) REVERT: E 133 ASP cc_start: 0.7979 (m-30) cc_final: 0.7479 (m-30) REVERT: E 134 LYS cc_start: 0.7802 (tttt) cc_final: 0.7457 (ttpp) REVERT: E 191 ASP cc_start: 0.7942 (m-30) cc_final: 0.7635 (m-30) REVERT: E 193 ASN cc_start: 0.8243 (t0) cc_final: 0.7840 (t0) REVERT: E 207 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7522 (tm-30) REVERT: E 215 GLU cc_start: 0.8224 (mp0) cc_final: 0.7347 (mp0) REVERT: E 217 SER cc_start: 0.8741 (OUTLIER) cc_final: 0.8512 (p) REVERT: E 294 VAL cc_start: 0.8696 (t) cc_final: 0.8336 (p) REVERT: E 347 THR cc_start: 0.8506 (m) cc_final: 0.8228 (p) REVERT: E 379 GLU cc_start: 0.7589 (mm-30) cc_final: 0.7351 (mm-30) REVERT: E 382 LYS cc_start: 0.8671 (mtmt) cc_final: 0.8338 (mtmm) REVERT: E 389 MET cc_start: 0.8556 (tpp) cc_final: 0.8174 (tpt) REVERT: E 423 GLU cc_start: 0.8158 (mt-10) cc_final: 0.7892 (mt-10) REVERT: E 427 TRP cc_start: 0.8656 (p90) cc_final: 0.8370 (p90) REVERT: E 490 MET cc_start: 0.8589 (ttm) cc_final: 0.8241 (ttm) REVERT: E 524 ASP cc_start: 0.8453 (t0) cc_final: 0.8133 (t0) REVERT: E 540 LYS cc_start: 0.8596 (OUTLIER) cc_final: 0.8332 (mtpt) REVERT: E 543 GLU cc_start: 0.7871 (tt0) cc_final: 0.7575 (tt0) REVERT: C 5 ASN cc_start: 0.8051 (m-40) cc_final: 0.7666 (m-40) REVERT: C 21 VAL cc_start: 0.8575 (t) cc_final: 0.8291 (m) REVERT: C 103 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7553 (mt-10) REVERT: C 151 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8324 (ttp) REVERT: C 154 ASP cc_start: 0.8018 (t0) cc_final: 0.7519 (t0) REVERT: C 158 LYS cc_start: 0.5738 (tptp) cc_final: 0.5051 (tttp) REVERT: C 191 ASP cc_start: 0.7905 (m-30) cc_final: 0.7642 (m-30) REVERT: C 192 VAL cc_start: 0.8761 (t) cc_final: 0.8466 (p) REVERT: C 193 ASN cc_start: 0.7795 (t0) cc_final: 0.7475 (t0) REVERT: C 204 LEU cc_start: 0.8196 (mt) cc_final: 0.7962 (mm) REVERT: C 215 GLU cc_start: 0.8246 (mp0) cc_final: 0.7287 (mp0) REVERT: C 231 SER cc_start: 0.8659 (t) cc_final: 0.8265 (p) REVERT: C 274 ARG cc_start: 0.8104 (OUTLIER) cc_final: 0.7637 (tmm-80) REVERT: C 294 VAL cc_start: 0.8639 (t) cc_final: 0.8315 (p) REVERT: C 295 ASN cc_start: 0.8071 (t0) cc_final: 0.7731 (t0) REVERT: C 329 ARG cc_start: 0.8187 (mtt90) cc_final: 0.7956 (mtt-85) REVERT: C 371 VAL cc_start: 0.8879 (t) cc_final: 0.8539 (p) REVERT: C 435 ASP cc_start: 0.5517 (OUTLIER) cc_final: 0.5002 (t70) REVERT: C 471 LYS cc_start: 0.8445 (mmtt) cc_final: 0.7911 (mmtt) REVERT: C 521 VAL cc_start: 0.8576 (t) cc_final: 0.8304 (p) REVERT: C 524 ASP cc_start: 0.8271 (t0) cc_final: 0.7838 (t0) REVERT: C 534 HIS cc_start: 0.7975 (m-70) cc_final: 0.7666 (m-70) REVERT: C 543 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7633 (tt0) REVERT: C 546 THR cc_start: 0.8444 (p) cc_final: 0.8142 (m) REVERT: D 21 VAL cc_start: 0.8752 (t) cc_final: 0.8447 (m) REVERT: D 49 ASP cc_start: 0.8504 (t0) cc_final: 0.8183 (t0) REVERT: D 51 GLU cc_start: 0.7665 (tt0) cc_final: 0.7341 (tt0) REVERT: D 55 LYS cc_start: 0.8784 (mttp) cc_final: 0.8429 (mttp) REVERT: D 58 SER cc_start: 0.8362 (t) cc_final: 0.8126 (p) REVERT: D 103 GLU cc_start: 0.7954 (mt-10) cc_final: 0.7679 (mt-10) REVERT: D 151 MET cc_start: 0.8415 (ttp) cc_final: 0.8130 (ttp) REVERT: D 168 ASP cc_start: 0.8070 (t0) cc_final: 0.7816 (t0) REVERT: D 192 VAL cc_start: 0.8856 (t) cc_final: 0.8626 (p) REVERT: D 201 SER cc_start: 0.8224 (p) cc_final: 0.7949 (m) REVERT: D 203 LYS cc_start: 0.8448 (ttmm) cc_final: 0.8210 (ttmm) REVERT: D 215 GLU cc_start: 0.8334 (mp0) cc_final: 0.7507 (mp0) REVERT: D 242 LEU cc_start: 0.8555 (mt) cc_final: 0.8268 (mp) REVERT: D 266 THR cc_start: 0.7613 (t) cc_final: 0.7258 (p) REVERT: D 341 ASP cc_start: 0.8036 (t0) cc_final: 0.7787 (m-30) REVERT: D 346 VAL cc_start: 0.8798 (t) cc_final: 0.8530 (p) REVERT: D 382 LYS cc_start: 0.8746 (mtmt) cc_final: 0.8458 (mtmt) REVERT: D 389 MET cc_start: 0.8561 (mmm) cc_final: 0.8160 (tpt) REVERT: D 435 ASP cc_start: 0.8086 (t0) cc_final: 0.7528 (p0) REVERT: D 490 MET cc_start: 0.8467 (OUTLIER) cc_final: 0.8229 (ttt) REVERT: D 521 VAL cc_start: 0.8541 (t) cc_final: 0.8227 (p) REVERT: I 271 MET cc_start: 0.4715 (pmm) cc_final: 0.4248 (pmm) REVERT: I 358 MET cc_start: 0.7598 (mmp) cc_final: 0.7192 (mmp) outliers start: 68 outliers final: 48 residues processed: 698 average time/residue: 0.3836 time to fit residues: 397.1062 Evaluate side-chains 718 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 657 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 548 LYS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 217 SER Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 274 ARG Chi-restraints excluded: chain E residue 406 GLU Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 540 LYS Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 75 CYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 151 MET Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 274 ARG Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 435 ASP Chi-restraints excluded: chain C residue 543 GLU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 490 MET Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain I residue 383 LEU Chi-restraints excluded: chain I residue 399 GLN Chi-restraints excluded: chain I residue 443 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 71 optimal weight: 3.9990 chunk 46 optimal weight: 0.0050 chunk 212 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 198 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 144 optimal weight: 3.9990 chunk 200 optimal weight: 8.9990 chunk 129 optimal weight: 4.9990 chunk 230 optimal weight: 1.9990 chunk 175 optimal weight: 2.9990 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 5 ASN E 53 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 GLN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS ** D 421 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 = 0.3397 r_free = 0.3397 target = 0.112538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.094403 restraints weight = 34995.941| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.05 r_work: 0.2966 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2828 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.4024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 22196 Z= 0.317 Angle : 0.563 8.504 30252 Z= 0.286 Chirality : 0.042 0.258 3258 Planarity : 0.005 0.109 3942 Dihedral : 4.952 57.059 2969 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.02 % Favored : 97.94 % Rotamer: Outliers : 2.93 % Allowed : 14.01 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.15), residues: 2722 helix: -0.04 (0.36), residues: 213 sheet: -0.04 (0.19), residues: 638 loop : -0.40 (0.13), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 415 HIS 0.004 0.001 HIS D 53 PHE 0.021 0.002 PHE C 374 TYR 0.015 0.001 TYR A 523 ARG 0.008 0.001 ARG C 417 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 660 time to evaluate : 2.426 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8268 (mttt) cc_final: 0.7856 (mttt) REVERT: A 24 MET cc_start: 0.8360 (mmm) cc_final: 0.7931 (mmm) REVERT: A 55 LYS cc_start: 0.8315 (mtpp) cc_final: 0.8071 (mtpp) REVERT: A 124 SER cc_start: 0.8624 (m) cc_final: 0.8292 (p) REVERT: A 134 LYS cc_start: 0.8796 (ttpp) cc_final: 0.8304 (ttpp) REVERT: A 151 MET cc_start: 0.8489 (ttp) cc_final: 0.8281 (ttp) REVERT: A 152 LEU cc_start: 0.8724 (tp) cc_final: 0.8393 (tp) REVERT: A 197 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8280 (mt) REVERT: A 207 GLU cc_start: 0.6826 (tm-30) cc_final: 0.4525 (tt0) REVERT: A 240 GLU cc_start: 0.8258 (tp30) cc_final: 0.7932 (tp30) REVERT: A 251 GLU cc_start: 0.6144 (tm-30) cc_final: 0.5887 (tm-30) REVERT: A 295 ASN cc_start: 0.8044 (t0) cc_final: 0.7672 (t0) REVERT: A 388 ASN cc_start: 0.8645 (m-40) cc_final: 0.8269 (m110) REVERT: A 389 MET cc_start: 0.8530 (tpp) cc_final: 0.8293 (ttm) REVERT: A 405 ILE cc_start: 0.8897 (mp) cc_final: 0.8651 (mm) REVERT: A 486 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8236 (ptm) REVERT: A 540 LYS cc_start: 0.8560 (mttt) cc_final: 0.8126 (mttt) REVERT: A 546 THR cc_start: 0.8616 (p) cc_final: 0.8280 (t) REVERT: B 8 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7420 (mt-10) REVERT: B 42 ARG cc_start: 0.8567 (mmt-90) cc_final: 0.8280 (mpt180) REVERT: B 51 GLU cc_start: 0.7455 (tt0) cc_final: 0.6839 (tt0) REVERT: B 53 HIS cc_start: 0.7846 (p90) cc_final: 0.7333 (p90) REVERT: B 110 ASN cc_start: 0.8258 (m-40) cc_final: 0.7929 (m110) REVERT: B 130 ASP cc_start: 0.7962 (m-30) cc_final: 0.7609 (m-30) REVERT: B 134 LYS cc_start: 0.8648 (tttt) cc_final: 0.8214 (ttpp) REVERT: B 154 ASP cc_start: 0.7603 (t0) cc_final: 0.7205 (t0) REVERT: B 215 GLU cc_start: 0.8068 (mp0) cc_final: 0.7662 (mp0) REVERT: B 230 MET cc_start: 0.8151 (OUTLIER) cc_final: 0.7733 (tmm) REVERT: B 294 VAL cc_start: 0.8614 (t) cc_final: 0.8394 (p) REVERT: B 296 SER cc_start: 0.8717 (t) cc_final: 0.8159 (p) REVERT: B 329 ARG cc_start: 0.8648 (mtt90) cc_final: 0.8206 (mtt-85) REVERT: B 349 ILE cc_start: 0.8854 (tp) cc_final: 0.8315 (tt) REVERT: B 376 ASN cc_start: 0.8199 (t0) cc_final: 0.7752 (t0) REVERT: B 389 MET cc_start: 0.8526 (tpp) cc_final: 0.8064 (tpt) REVERT: B 435 ASP cc_start: 0.8444 (t0) cc_final: 0.7562 (p0) REVERT: B 470 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.8086 (pt) REVERT: B 510 TYR cc_start: 0.8583 (m-10) cc_final: 0.8289 (m-10) REVERT: B 524 ASP cc_start: 0.8611 (t0) cc_final: 0.8186 (t0) REVERT: B 532 GLN cc_start: 0.8186 (mm-40) cc_final: 0.7816 (mm-40) REVERT: B 539 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.8065 (tt0) REVERT: B 543 GLU cc_start: 0.7863 (OUTLIER) cc_final: 0.7566 (tt0) REVERT: B 546 THR cc_start: 0.8433 (p) cc_final: 0.8129 (t) REVERT: B 554 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.7036 (mp) REVERT: E 19 ASN cc_start: 0.8685 (t0) cc_final: 0.8435 (t0) REVERT: E 81 MET cc_start: 0.8641 (tmm) cc_final: 0.8285 (ttp) REVERT: E 117 ASP cc_start: 0.7833 (t0) cc_final: 0.7554 (t0) REVERT: E 120 THR cc_start: 0.8387 (m) cc_final: 0.8083 (t) REVERT: E 129 LYS cc_start: 0.8421 (mttp) cc_final: 0.8109 (mtpp) REVERT: E 130 ASP cc_start: 0.7831 (m-30) cc_final: 0.7570 (m-30) REVERT: E 133 ASP cc_start: 0.7952 (m-30) cc_final: 0.7467 (m-30) REVERT: E 134 LYS cc_start: 0.7824 (tttt) cc_final: 0.7493 (ttpp) REVERT: E 191 ASP cc_start: 0.7909 (m-30) cc_final: 0.7600 (m-30) REVERT: E 193 ASN cc_start: 0.8251 (t0) cc_final: 0.7870 (t0) REVERT: E 207 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7631 (tm-30) REVERT: E 215 GLU cc_start: 0.8223 (mp0) cc_final: 0.7356 (mp0) REVERT: E 294 VAL cc_start: 0.8705 (t) cc_final: 0.8348 (p) REVERT: E 347 THR cc_start: 0.8520 (m) cc_final: 0.8268 (p) REVERT: E 379 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7476 (mm-30) REVERT: E 382 LYS cc_start: 0.8688 (mtmt) cc_final: 0.8341 (mtmt) REVERT: E 389 MET cc_start: 0.8530 (tpp) cc_final: 0.8164 (tpt) REVERT: E 423 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7887 (mt-10) REVERT: E 427 TRP cc_start: 0.8660 (p90) cc_final: 0.8386 (p90) REVERT: E 459 LYS cc_start: 0.8583 (ttpt) cc_final: 0.8354 (tttt) REVERT: E 490 MET cc_start: 0.8582 (ttm) cc_final: 0.8260 (ttm) REVERT: E 524 ASP cc_start: 0.8495 (t0) cc_final: 0.8193 (t0) REVERT: E 540 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8350 (mtpt) REVERT: E 543 GLU cc_start: 0.7878 (tt0) cc_final: 0.7585 (tt0) REVERT: E 548 LYS cc_start: 0.8894 (mmtp) cc_final: 0.8579 (mmtm) REVERT: C 5 ASN cc_start: 0.8091 (m-40) cc_final: 0.7799 (m-40) REVERT: C 21 VAL cc_start: 0.8584 (t) cc_final: 0.8321 (m) REVERT: C 103 GLU cc_start: 0.7842 (mt-10) cc_final: 0.7542 (mt-10) REVERT: C 154 ASP cc_start: 0.7985 (t0) cc_final: 0.7504 (t0) REVERT: C 158 LYS cc_start: 0.5898 (tptp) cc_final: 0.5272 (tttp) REVERT: C 191 ASP cc_start: 0.7857 (m-30) cc_final: 0.7593 (m-30) REVERT: C 192 VAL cc_start: 0.8728 (t) cc_final: 0.8459 (p) REVERT: C 193 ASN cc_start: 0.7807 (t0) cc_final: 0.7495 (t0) REVERT: C 204 LEU cc_start: 0.8239 (mt) cc_final: 0.7997 (mm) REVERT: C 215 GLU cc_start: 0.8264 (mp0) cc_final: 0.7918 (mp0) REVERT: C 231 SER cc_start: 0.8571 (t) cc_final: 0.8146 (p) REVERT: C 274 ARG cc_start: 0.8128 (tmm-80) cc_final: 0.7663 (tmm-80) REVERT: C 294 VAL cc_start: 0.8646 (t) cc_final: 0.8340 (p) REVERT: C 295 ASN cc_start: 0.8220 (t0) cc_final: 0.7836 (t0) REVERT: C 329 ARG cc_start: 0.8153 (mtt90) cc_final: 0.7948 (mtt-85) REVERT: C 371 VAL cc_start: 0.8881 (t) cc_final: 0.8566 (p) REVERT: C 435 ASP cc_start: 0.5550 (OUTLIER) cc_final: 0.5041 (t70) REVERT: C 471 LYS cc_start: 0.8527 (mmtt) cc_final: 0.8013 (mmtt) REVERT: C 521 VAL cc_start: 0.8582 (t) cc_final: 0.8317 (p) REVERT: C 524 ASP cc_start: 0.8232 (t0) cc_final: 0.7723 (t0) REVERT: C 534 HIS cc_start: 0.7928 (m-70) cc_final: 0.7648 (m-70) REVERT: C 543 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7610 (tt0) REVERT: C 546 THR cc_start: 0.8419 (p) cc_final: 0.8131 (m) REVERT: D 21 VAL cc_start: 0.8734 (t) cc_final: 0.8415 (m) REVERT: D 22 LYS cc_start: 0.8204 (mttm) cc_final: 0.7994 (mttm) REVERT: D 49 ASP cc_start: 0.8472 (t0) cc_final: 0.8167 (t0) REVERT: D 51 GLU cc_start: 0.7652 (tt0) cc_final: 0.7325 (tt0) REVERT: D 55 LYS cc_start: 0.8794 (mttp) cc_final: 0.8446 (mttp) REVERT: D 58 SER cc_start: 0.8347 (t) cc_final: 0.8116 (p) REVERT: D 103 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7663 (mt-10) REVERT: D 151 MET cc_start: 0.8395 (ttp) cc_final: 0.8125 (ttp) REVERT: D 168 ASP cc_start: 0.8075 (t0) cc_final: 0.7811 (t0) REVERT: D 192 VAL cc_start: 0.8855 (t) cc_final: 0.8633 (p) REVERT: D 201 SER cc_start: 0.8269 (p) cc_final: 0.7985 (m) REVERT: D 203 LYS cc_start: 0.8481 (ttmm) cc_final: 0.8253 (ttmm) REVERT: D 215 GLU cc_start: 0.8349 (mp0) cc_final: 0.7518 (mp0) REVERT: D 242 LEU cc_start: 0.8576 (mt) cc_final: 0.8275 (mp) REVERT: D 341 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7773 (m-30) REVERT: D 346 VAL cc_start: 0.8830 (t) cc_final: 0.8561 (p) REVERT: D 382 LYS cc_start: 0.8756 (mtmt) cc_final: 0.8413 (mtmt) REVERT: D 389 MET cc_start: 0.8546 (mmm) cc_final: 0.8170 (tpt) REVERT: D 435 ASP cc_start: 0.8050 (t0) cc_final: 0.7509 (p0) REVERT: D 490 MET cc_start: 0.8478 (OUTLIER) cc_final: 0.8243 (ttt) REVERT: D 521 VAL cc_start: 0.8560 (t) cc_final: 0.8263 (p) REVERT: I 271 MET cc_start: 0.4413 (pmm) cc_final: 0.3973 (pmm) REVERT: I 338 ARG cc_start: 0.7229 (ttp80) cc_final: 0.6905 (ttp80) REVERT: I 358 MET cc_start: 0.7665 (mmp) cc_final: 0.7232 (mmp) outliers start: 69 outliers final: 52 residues processed: 680 average time/residue: 0.3756 time to fit residues: 379.7375 Evaluate side-chains 711 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 647 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 548 LYS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 470 ILE Chi-restraints excluded: chain B residue 539 GLU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 274 ARG Chi-restraints excluded: chain E residue 344 LYS Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 540 LYS Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 75 CYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 378 LYS Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 435 ASP Chi-restraints excluded: chain C residue 543 GLU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 490 MET Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain I residue 383 LEU Chi-restraints excluded: chain I residue 399 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 198 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 181 optimal weight: 2.9990 chunk 76 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 204 optimal weight: 7.9990 chunk 69 optimal weight: 0.0270 chunk 186 optimal weight: 7.9990 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 195 GLN ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 449 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.110430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.091980 restraints weight = 35889.552| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.17 r_work: 0.2982 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 22196 Z= 0.190 Angle : 0.536 9.640 30252 Z= 0.270 Chirality : 0.041 0.258 3258 Planarity : 0.005 0.106 3942 Dihedral : 4.620 21.238 2967 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.65 % Favored : 98.31 % Rotamer: Outliers : 2.34 % Allowed : 15.16 % Favored : 82.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.15), residues: 2722 helix: -0.14 (0.36), residues: 218 sheet: 0.00 (0.19), residues: 638 loop : -0.32 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 415 HIS 0.005 0.001 HIS C 53 PHE 0.019 0.001 PHE C 374 TYR 0.014 0.001 TYR A 523 ARG 0.007 0.000 ARG C 417 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 722 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 667 time to evaluate : 2.562 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 21 VAL cc_start: 0.8562 (t) cc_final: 0.8129 (m) REVERT: A 22 LYS cc_start: 0.8234 (mttt) cc_final: 0.7849 (mttt) REVERT: A 24 MET cc_start: 0.8334 (mmm) cc_final: 0.7887 (mmm) REVERT: A 55 LYS cc_start: 0.8347 (mtpp) cc_final: 0.8113 (mtpp) REVERT: A 58 SER cc_start: 0.8460 (t) cc_final: 0.7941 (p) REVERT: A 124 SER cc_start: 0.8624 (m) cc_final: 0.8301 (p) REVERT: A 134 LYS cc_start: 0.8744 (ttpp) cc_final: 0.8454 (ttpp) REVERT: A 152 LEU cc_start: 0.8728 (tp) cc_final: 0.8420 (tp) REVERT: A 197 ILE cc_start: 0.8543 (OUTLIER) cc_final: 0.8230 (mt) REVERT: A 207 GLU cc_start: 0.6696 (tm-30) cc_final: 0.4391 (tt0) REVERT: A 240 GLU cc_start: 0.8311 (tp30) cc_final: 0.7992 (tp30) REVERT: A 251 GLU cc_start: 0.6134 (tm-30) cc_final: 0.5863 (tm-30) REVERT: A 295 ASN cc_start: 0.8012 (t0) cc_final: 0.7437 (t0) REVERT: A 382 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7782 (ptpt) REVERT: A 389 MET cc_start: 0.8456 (tpp) cc_final: 0.8246 (ttm) REVERT: A 405 ILE cc_start: 0.8865 (mp) cc_final: 0.8616 (mm) REVERT: A 486 MET cc_start: 0.8498 (OUTLIER) cc_final: 0.8260 (ptm) REVERT: A 540 LYS cc_start: 0.8522 (mttt) cc_final: 0.8122 (mttt) REVERT: A 546 THR cc_start: 0.8579 (p) cc_final: 0.8252 (t) REVERT: B 8 GLU cc_start: 0.7908 (mt-10) cc_final: 0.7364 (mt-10) REVERT: B 34 ASN cc_start: 0.7766 (m-40) cc_final: 0.7561 (m-40) REVERT: B 42 ARG cc_start: 0.8570 (mmt-90) cc_final: 0.8275 (mpt180) REVERT: B 51 GLU cc_start: 0.7527 (tt0) cc_final: 0.6936 (tt0) REVERT: B 53 HIS cc_start: 0.7896 (p90) cc_final: 0.7446 (p90) REVERT: B 110 ASN cc_start: 0.8245 (m-40) cc_final: 0.7861 (m110) REVERT: B 120 THR cc_start: 0.8387 (m) cc_final: 0.8184 (t) REVERT: B 130 ASP cc_start: 0.7997 (m-30) cc_final: 0.7620 (m-30) REVERT: B 134 LYS cc_start: 0.8563 (tttt) cc_final: 0.8204 (ttpp) REVERT: B 154 ASP cc_start: 0.7653 (t0) cc_final: 0.7171 (t0) REVERT: B 215 GLU cc_start: 0.8133 (mp0) cc_final: 0.7732 (mp0) REVERT: B 230 MET cc_start: 0.8190 (OUTLIER) cc_final: 0.7745 (tmm) REVERT: B 273 PHE cc_start: 0.7940 (m-80) cc_final: 0.7678 (m-80) REVERT: B 294 VAL cc_start: 0.8599 (t) cc_final: 0.8383 (p) REVERT: B 296 SER cc_start: 0.8735 (t) cc_final: 0.8161 (p) REVERT: B 329 ARG cc_start: 0.8637 (mtt90) cc_final: 0.8165 (mtt-85) REVERT: B 349 ILE cc_start: 0.8774 (tp) cc_final: 0.8159 (tt) REVERT: B 376 ASN cc_start: 0.8147 (t0) cc_final: 0.7742 (t0) REVERT: B 389 MET cc_start: 0.8475 (tpp) cc_final: 0.7989 (tpt) REVERT: B 435 ASP cc_start: 0.8464 (t0) cc_final: 0.7562 (p0) REVERT: B 510 TYR cc_start: 0.8603 (m-10) cc_final: 0.8319 (m-10) REVERT: B 524 ASP cc_start: 0.8596 (t0) cc_final: 0.8151 (t0) REVERT: B 532 GLN cc_start: 0.8115 (mm-40) cc_final: 0.7762 (mm-40) REVERT: B 539 GLU cc_start: 0.8301 (tt0) cc_final: 0.8045 (tt0) REVERT: B 543 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7609 (tt0) REVERT: B 546 THR cc_start: 0.8432 (p) cc_final: 0.8132 (t) REVERT: B 554 LEU cc_start: 0.7247 (OUTLIER) cc_final: 0.7041 (mp) REVERT: E 19 ASN cc_start: 0.8692 (t0) cc_final: 0.8392 (t0) REVERT: E 81 MET cc_start: 0.8653 (tmm) cc_final: 0.8315 (ttp) REVERT: E 120 THR cc_start: 0.8309 (m) cc_final: 0.8037 (t) REVERT: E 129 LYS cc_start: 0.8375 (mttp) cc_final: 0.8073 (mtpp) REVERT: E 130 ASP cc_start: 0.7837 (m-30) cc_final: 0.7589 (m-30) REVERT: E 134 LYS cc_start: 0.7795 (tttt) cc_final: 0.7465 (ttpp) REVERT: E 148 ARG cc_start: 0.8660 (mmt-90) cc_final: 0.8435 (mmt-90) REVERT: E 191 ASP cc_start: 0.7941 (m-30) cc_final: 0.7631 (m-30) REVERT: E 193 ASN cc_start: 0.8236 (t0) cc_final: 0.7850 (t0) REVERT: E 207 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7621 (tm-30) REVERT: E 215 GLU cc_start: 0.8216 (mp0) cc_final: 0.7377 (mp0) REVERT: E 294 VAL cc_start: 0.8685 (t) cc_final: 0.8335 (p) REVERT: E 379 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7506 (mm-30) REVERT: E 389 MET cc_start: 0.8534 (tpp) cc_final: 0.8156 (tpt) REVERT: E 423 GLU cc_start: 0.8161 (mt-10) cc_final: 0.7929 (mt-10) REVERT: E 427 TRP cc_start: 0.8703 (p90) cc_final: 0.8427 (p90) REVERT: E 459 LYS cc_start: 0.8579 (ttpt) cc_final: 0.8324 (tttt) REVERT: E 490 MET cc_start: 0.8585 (ttm) cc_final: 0.8279 (ttm) REVERT: E 524 ASP cc_start: 0.8488 (t0) cc_final: 0.8186 (t0) REVERT: E 540 LYS cc_start: 0.8635 (OUTLIER) cc_final: 0.8342 (mtpt) REVERT: E 543 GLU cc_start: 0.7798 (tt0) cc_final: 0.7525 (tt0) REVERT: E 548 LYS cc_start: 0.8886 (mmtp) cc_final: 0.8566 (mmtm) REVERT: C 103 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7604 (mt-10) REVERT: C 154 ASP cc_start: 0.8003 (t0) cc_final: 0.7505 (t0) REVERT: C 158 LYS cc_start: 0.5869 (tptp) cc_final: 0.5187 (tttp) REVERT: C 191 ASP cc_start: 0.7908 (m-30) cc_final: 0.7625 (m-30) REVERT: C 192 VAL cc_start: 0.8739 (t) cc_final: 0.8461 (p) REVERT: C 193 ASN cc_start: 0.7806 (t0) cc_final: 0.7502 (t0) REVERT: C 204 LEU cc_start: 0.8190 (mt) cc_final: 0.7946 (mm) REVERT: C 215 GLU cc_start: 0.8248 (mp0) cc_final: 0.7287 (mp0) REVERT: C 229 THR cc_start: 0.8669 (m) cc_final: 0.8386 (p) REVERT: C 231 SER cc_start: 0.8540 (t) cc_final: 0.8063 (p) REVERT: C 294 VAL cc_start: 0.8644 (t) cc_final: 0.8331 (p) REVERT: C 295 ASN cc_start: 0.8072 (t0) cc_final: 0.7725 (t0) REVERT: C 329 ARG cc_start: 0.8168 (mtt90) cc_final: 0.7945 (mtt-85) REVERT: C 371 VAL cc_start: 0.8828 (t) cc_final: 0.8498 (p) REVERT: C 435 ASP cc_start: 0.5503 (OUTLIER) cc_final: 0.5015 (t70) REVERT: C 471 LYS cc_start: 0.8536 (mmtt) cc_final: 0.7999 (mmtt) REVERT: C 521 VAL cc_start: 0.8570 (t) cc_final: 0.8305 (p) REVERT: C 524 ASP cc_start: 0.8270 (t0) cc_final: 0.7800 (t0) REVERT: C 534 HIS cc_start: 0.7979 (m-70) cc_final: 0.7669 (m-70) REVERT: C 543 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7682 (tt0) REVERT: C 546 THR cc_start: 0.8416 (p) cc_final: 0.8145 (m) REVERT: D 21 VAL cc_start: 0.8741 (t) cc_final: 0.8432 (m) REVERT: D 22 LYS cc_start: 0.8140 (mttm) cc_final: 0.7913 (mttm) REVERT: D 49 ASP cc_start: 0.8502 (t0) cc_final: 0.8186 (t0) REVERT: D 51 GLU cc_start: 0.7659 (tt0) cc_final: 0.7370 (tt0) REVERT: D 55 LYS cc_start: 0.8792 (mttp) cc_final: 0.8440 (mttp) REVERT: D 58 SER cc_start: 0.8351 (t) cc_final: 0.8134 (p) REVERT: D 103 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7656 (mt-10) REVERT: D 134 LYS cc_start: 0.8879 (ttpp) cc_final: 0.8387 (ttpp) REVERT: D 151 MET cc_start: 0.8403 (ttp) cc_final: 0.8145 (ttp) REVERT: D 168 ASP cc_start: 0.8040 (t0) cc_final: 0.7794 (t0) REVERT: D 192 VAL cc_start: 0.8817 (t) cc_final: 0.8591 (p) REVERT: D 201 SER cc_start: 0.8263 (p) cc_final: 0.7979 (m) REVERT: D 203 LYS cc_start: 0.8465 (ttmm) cc_final: 0.8217 (ttmm) REVERT: D 215 GLU cc_start: 0.8307 (mp0) cc_final: 0.7511 (mp0) REVERT: D 242 LEU cc_start: 0.8558 (mt) cc_final: 0.8258 (mp) REVERT: D 266 THR cc_start: 0.7564 (t) cc_final: 0.7241 (p) REVERT: D 341 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7831 (m-30) REVERT: D 346 VAL cc_start: 0.8791 (t) cc_final: 0.8534 (p) REVERT: D 382 LYS cc_start: 0.8740 (mtmt) cc_final: 0.8469 (mtmt) REVERT: D 389 MET cc_start: 0.8546 (mmm) cc_final: 0.8216 (tpt) REVERT: D 435 ASP cc_start: 0.8090 (t0) cc_final: 0.7535 (p0) REVERT: D 447 TRP cc_start: 0.8812 (m-90) cc_final: 0.8321 (m-90) REVERT: D 463 GLN cc_start: 0.8983 (mm-40) cc_final: 0.8779 (mm-40) REVERT: D 490 MET cc_start: 0.8461 (OUTLIER) cc_final: 0.8227 (ttt) REVERT: D 521 VAL cc_start: 0.8567 (t) cc_final: 0.8269 (p) REVERT: I 271 MET cc_start: 0.4313 (pmm) cc_final: 0.3847 (pmm) REVERT: I 338 ARG cc_start: 0.7227 (ttp80) cc_final: 0.6883 (ttp80) REVERT: I 358 MET cc_start: 0.7735 (mmp) cc_final: 0.7316 (mmp) outliers start: 55 outliers final: 38 residues processed: 683 average time/residue: 0.3781 time to fit residues: 382.3204 Evaluate side-chains 705 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 656 time to evaluate : 2.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 549 SER Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 274 ARG Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 540 LYS Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 208 GLU Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 435 ASP Chi-restraints excluded: chain C residue 543 GLU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 490 MET Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain I residue 383 LEU Chi-restraints excluded: chain I residue 399 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 242 optimal weight: 5.9990 chunk 83 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 chunk 218 optimal weight: 0.0370 chunk 214 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 82 optimal weight: 0.0770 chunk 80 optimal weight: 0.1980 chunk 230 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 ASN ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 HIS E 517 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 GLN ** D 421 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 = 0.3437 r_free = 0.3437 target = 0.115238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.097737 restraints weight = 35146.472| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.03 r_work: 0.3003 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.069 22196 Z= 0.159 Angle : 0.539 9.525 30252 Z= 0.269 Chirality : 0.040 0.253 3258 Planarity : 0.005 0.103 3942 Dihedral : 4.493 23.582 2967 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.84 % Favored : 98.13 % Rotamer: Outliers : 2.21 % Allowed : 15.54 % Favored : 82.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.15), residues: 2722 helix: -0.05 (0.36), residues: 218 sheet: 0.00 (0.20), residues: 613 loop : -0.25 (0.13), residues: 1891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 87 HIS 0.004 0.001 HIS C 53 PHE 0.019 0.001 PHE C 374 TYR 0.023 0.001 TYR C 250 ARG 0.007 0.000 ARG C 417 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 680 time to evaluate : 2.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 LYS cc_start: 0.8171 (mttt) cc_final: 0.7777 (mttt) REVERT: A 24 MET cc_start: 0.8252 (mmm) cc_final: 0.7837 (mmm) REVERT: A 42 ARG cc_start: 0.8546 (mmt-90) cc_final: 0.8205 (mmt-90) REVERT: A 55 LYS cc_start: 0.8312 (mtpp) cc_final: 0.8095 (mtpp) REVERT: A 58 SER cc_start: 0.8448 (t) cc_final: 0.7941 (p) REVERT: A 124 SER cc_start: 0.8568 (m) cc_final: 0.8243 (p) REVERT: A 130 ASP cc_start: 0.7585 (m-30) cc_final: 0.7383 (m-30) REVERT: A 134 LYS cc_start: 0.8757 (ttpp) cc_final: 0.8459 (ttpp) REVERT: A 152 LEU cc_start: 0.8666 (tp) cc_final: 0.8389 (tp) REVERT: A 197 ILE cc_start: 0.8454 (OUTLIER) cc_final: 0.8137 (mt) REVERT: A 207 GLU cc_start: 0.6677 (tm-30) cc_final: 0.4390 (tt0) REVERT: A 240 GLU cc_start: 0.8271 (tp30) cc_final: 0.7941 (tp30) REVERT: A 251 GLU cc_start: 0.6086 (tm-30) cc_final: 0.5841 (tm-30) REVERT: A 295 ASN cc_start: 0.7994 (t0) cc_final: 0.7415 (t0) REVERT: A 325 ARG cc_start: 0.8418 (mtm180) cc_final: 0.5661 (mtt180) REVERT: A 382 LYS cc_start: 0.8219 (OUTLIER) cc_final: 0.7842 (ptpt) REVERT: A 486 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8262 (ptm) REVERT: A 540 LYS cc_start: 0.8452 (mttt) cc_final: 0.8057 (mttt) REVERT: A 546 THR cc_start: 0.8517 (p) cc_final: 0.8147 (t) REVERT: B 8 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7361 (mt-10) REVERT: B 34 ASN cc_start: 0.7677 (m-40) cc_final: 0.7468 (m-40) REVERT: B 42 ARG cc_start: 0.8545 (mmt-90) cc_final: 0.8249 (mpt180) REVERT: B 51 GLU cc_start: 0.7439 (tt0) cc_final: 0.6869 (tt0) REVERT: B 53 HIS cc_start: 0.7881 (p90) cc_final: 0.7432 (p90) REVERT: B 110 ASN cc_start: 0.8159 (m-40) cc_final: 0.7735 (m110) REVERT: B 130 ASP cc_start: 0.7978 (m-30) cc_final: 0.7630 (m-30) REVERT: B 134 LYS cc_start: 0.8500 (tttt) cc_final: 0.8268 (ttpp) REVERT: B 154 ASP cc_start: 0.7619 (t0) cc_final: 0.7137 (t0) REVERT: B 215 GLU cc_start: 0.8083 (mp0) cc_final: 0.7651 (mp0) REVERT: B 220 GLN cc_start: 0.8112 (mt0) cc_final: 0.7837 (mt0) REVERT: B 230 MET cc_start: 0.8200 (OUTLIER) cc_final: 0.7760 (tmm) REVERT: B 231 SER cc_start: 0.8403 (t) cc_final: 0.8026 (m) REVERT: B 243 GLU cc_start: 0.6939 (mt-10) cc_final: 0.6613 (mt-10) REVERT: B 273 PHE cc_start: 0.7815 (m-80) cc_final: 0.7553 (m-80) REVERT: B 296 SER cc_start: 0.8691 (t) cc_final: 0.8125 (p) REVERT: B 329 ARG cc_start: 0.8626 (mtt90) cc_final: 0.8151 (mtt-85) REVERT: B 349 ILE cc_start: 0.8717 (tp) cc_final: 0.8094 (tt) REVERT: B 376 ASN cc_start: 0.8137 (t0) cc_final: 0.7717 (t0) REVERT: B 389 MET cc_start: 0.8401 (tpp) cc_final: 0.7926 (tpt) REVERT: B 435 ASP cc_start: 0.8413 (t0) cc_final: 0.7521 (p0) REVERT: B 510 TYR cc_start: 0.8563 (m-10) cc_final: 0.8230 (m-10) REVERT: B 513 HIS cc_start: 0.8313 (p-80) cc_final: 0.8082 (p-80) REVERT: B 524 ASP cc_start: 0.8556 (t0) cc_final: 0.8107 (t0) REVERT: B 532 GLN cc_start: 0.8131 (mm-40) cc_final: 0.7782 (mm-40) REVERT: B 535 ARG cc_start: 0.7794 (mtt180) cc_final: 0.7481 (mtt180) REVERT: B 539 GLU cc_start: 0.8135 (tt0) cc_final: 0.7922 (tt0) REVERT: B 543 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7511 (tt0) REVERT: B 546 THR cc_start: 0.8395 (p) cc_final: 0.8101 (t) REVERT: E 19 ASN cc_start: 0.8689 (t0) cc_final: 0.8395 (t0) REVERT: E 55 LYS cc_start: 0.8470 (mtmt) cc_final: 0.8067 (mtmt) REVERT: E 81 MET cc_start: 0.8627 (tmm) cc_final: 0.8313 (ttp) REVERT: E 120 THR cc_start: 0.8266 (m) cc_final: 0.7994 (t) REVERT: E 129 LYS cc_start: 0.8359 (mttp) cc_final: 0.8090 (mtpp) REVERT: E 134 LYS cc_start: 0.7741 (tttt) cc_final: 0.7413 (ttpp) REVERT: E 148 ARG cc_start: 0.8586 (mmt-90) cc_final: 0.8374 (mpt180) REVERT: E 191 ASP cc_start: 0.7903 (m-30) cc_final: 0.7658 (m-30) REVERT: E 193 ASN cc_start: 0.8176 (t0) cc_final: 0.7698 (t0) REVERT: E 207 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7508 (tm-30) REVERT: E 215 GLU cc_start: 0.8166 (mp0) cc_final: 0.7353 (mp0) REVERT: E 294 VAL cc_start: 0.8659 (t) cc_final: 0.8290 (p) REVERT: E 295 ASN cc_start: 0.8400 (t0) cc_final: 0.7614 (t0) REVERT: E 423 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7856 (mt-10) REVERT: E 427 TRP cc_start: 0.8668 (p90) cc_final: 0.8397 (p90) REVERT: E 459 LYS cc_start: 0.8620 (ttpt) cc_final: 0.8369 (tttt) REVERT: E 490 MET cc_start: 0.8543 (ttm) cc_final: 0.8241 (ttm) REVERT: E 524 ASP cc_start: 0.8450 (t0) cc_final: 0.8162 (t0) REVERT: E 540 LYS cc_start: 0.8554 (OUTLIER) cc_final: 0.8219 (mtpt) REVERT: E 543 GLU cc_start: 0.7770 (tt0) cc_final: 0.7511 (tt0) REVERT: C 21 VAL cc_start: 0.8576 (t) cc_final: 0.8286 (m) REVERT: C 103 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7571 (mt-10) REVERT: C 154 ASP cc_start: 0.7950 (t0) cc_final: 0.7350 (t0) REVERT: C 158 LYS cc_start: 0.5656 (tptp) cc_final: 0.4984 (tttp) REVERT: C 191 ASP cc_start: 0.7879 (m-30) cc_final: 0.7591 (m-30) REVERT: C 192 VAL cc_start: 0.8729 (t) cc_final: 0.8445 (p) REVERT: C 193 ASN cc_start: 0.7787 (t0) cc_final: 0.7475 (t0) REVERT: C 204 LEU cc_start: 0.8125 (mt) cc_final: 0.7890 (mm) REVERT: C 215 GLU cc_start: 0.8221 (mp0) cc_final: 0.7303 (mp0) REVERT: C 230 MET cc_start: 0.7957 (ppp) cc_final: 0.7647 (ppp) REVERT: C 231 SER cc_start: 0.8345 (t) cc_final: 0.8062 (m) REVERT: C 251 GLU cc_start: 0.8058 (mt-10) cc_final: 0.6988 (tm-30) REVERT: C 266 THR cc_start: 0.7859 (m) cc_final: 0.7509 (p) REVERT: C 294 VAL cc_start: 0.8627 (t) cc_final: 0.8309 (p) REVERT: C 295 ASN cc_start: 0.8050 (t0) cc_final: 0.7702 (t0) REVERT: C 329 ARG cc_start: 0.8102 (mtt90) cc_final: 0.7883 (mtt-85) REVERT: C 371 VAL cc_start: 0.8789 (t) cc_final: 0.8467 (p) REVERT: C 435 ASP cc_start: 0.5409 (OUTLIER) cc_final: 0.4936 (t70) REVERT: C 440 GLN cc_start: 0.8326 (mp10) cc_final: 0.7833 (mt0) REVERT: C 471 LYS cc_start: 0.8470 (mmtt) cc_final: 0.7946 (mmtt) REVERT: C 521 VAL cc_start: 0.8536 (t) cc_final: 0.8269 (p) REVERT: C 524 ASP cc_start: 0.8223 (t0) cc_final: 0.7756 (t0) REVERT: C 534 HIS cc_start: 0.7925 (m-70) cc_final: 0.7622 (m-70) REVERT: C 543 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7640 (tt0) REVERT: C 546 THR cc_start: 0.8363 (p) cc_final: 0.8085 (m) REVERT: D 21 VAL cc_start: 0.8753 (t) cc_final: 0.8455 (m) REVERT: D 49 ASP cc_start: 0.8477 (t0) cc_final: 0.8182 (t0) REVERT: D 51 GLU cc_start: 0.7619 (tt0) cc_final: 0.7348 (tt0) REVERT: D 55 LYS cc_start: 0.8734 (mttp) cc_final: 0.8357 (mttp) REVERT: D 58 SER cc_start: 0.8334 (t) cc_final: 0.8125 (p) REVERT: D 103 GLU cc_start: 0.7884 (mt-10) cc_final: 0.7605 (mt-10) REVERT: D 134 LYS cc_start: 0.8825 (ttpp) cc_final: 0.8329 (tttp) REVERT: D 151 MET cc_start: 0.8375 (ttp) cc_final: 0.8128 (ttp) REVERT: D 168 ASP cc_start: 0.7964 (t0) cc_final: 0.7724 (t0) REVERT: D 192 VAL cc_start: 0.8790 (t) cc_final: 0.8540 (p) REVERT: D 201 SER cc_start: 0.8194 (p) cc_final: 0.7945 (m) REVERT: D 203 LYS cc_start: 0.8495 (ttmm) cc_final: 0.8250 (ttmm) REVERT: D 215 GLU cc_start: 0.8271 (mp0) cc_final: 0.7462 (mp0) REVERT: D 242 LEU cc_start: 0.8529 (mt) cc_final: 0.8245 (mp) REVERT: D 266 THR cc_start: 0.7554 (t) cc_final: 0.7266 (p) REVERT: D 341 ASP cc_start: 0.8017 (OUTLIER) cc_final: 0.7803 (m-30) REVERT: D 346 VAL cc_start: 0.8796 (t) cc_final: 0.8546 (p) REVERT: D 382 LYS cc_start: 0.8729 (mtmt) cc_final: 0.8338 (mtmt) REVERT: D 389 MET cc_start: 0.8468 (mmm) cc_final: 0.8111 (tpt) REVERT: D 435 ASP cc_start: 0.8031 (t0) cc_final: 0.7514 (p0) REVERT: D 447 TRP cc_start: 0.8767 (m-90) cc_final: 0.8330 (m-90) REVERT: D 490 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8185 (ttt) REVERT: D 493 LYS cc_start: 0.8432 (mtmt) cc_final: 0.8168 (mtmt) REVERT: D 521 VAL cc_start: 0.8482 (t) cc_final: 0.8213 (p) REVERT: I 271 MET cc_start: 0.4301 (pmm) cc_final: 0.3805 (pmm) REVERT: I 358 MET cc_start: 0.7780 (mmp) cc_final: 0.7348 (mmp) outliers start: 52 outliers final: 35 residues processed: 692 average time/residue: 0.3863 time to fit residues: 395.1562 Evaluate side-chains 710 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 665 time to evaluate : 2.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 173 GLU Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 382 LYS Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 489 THR Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 274 ARG Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 540 LYS Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 274 ARG Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 435 ASP Chi-restraints excluded: chain C residue 543 GLU Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 133 ASP Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 341 ASP Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 490 MET Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain I residue 383 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 214 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 175 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 179 optimal weight: 2.9990 chunk 233 optimal weight: 8.9990 chunk 253 optimal weight: 9.9990 chunk 237 optimal weight: 5.9990 chunk 66 optimal weight: 0.9990 chunk 68 optimal weight: 0.8980 chunk 211 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 552 HIS ** E 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 GLN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS D 376 ASN ** D 421 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 = 0.3353 r_free = 0.3353 target = 0.109531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.091030 restraints weight = 35901.202| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 2.15 r_work: 0.2955 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2815 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.4260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 22196 Z= 0.319 Angle : 0.581 9.725 30252 Z= 0.293 Chirality : 0.042 0.243 3258 Planarity : 0.005 0.101 3942 Dihedral : 4.699 21.846 2967 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.95 % Favored : 98.02 % Rotamer: Outliers : 2.25 % Allowed : 15.41 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.15), residues: 2722 helix: -0.19 (0.36), residues: 218 sheet: -0.02 (0.19), residues: 638 loop : -0.34 (0.13), residues: 1866 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 177 HIS 0.005 0.001 HIS C 53 PHE 0.020 0.002 PHE C 374 TYR 0.031 0.002 TYR C 250 ARG 0.009 0.001 ARG B 148 =============================================================================== Job complete usr+sys time: 14671.57 seconds wall clock time: 261 minutes 22.82 seconds (15682.82 seconds total)