Starting phenix.real_space_refine on Thu Sep 18 22:49:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9c4f_45184/09_2025/9c4f_45184.cif Found real_map, /net/cci-nas-00/data/ceres_data/9c4f_45184/09_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_45184/09_2025/9c4f_45184.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9c4f_45184/09_2025/9c4f_45184.map" model { file = "/net/cci-nas-00/data/ceres_data/9c4f_45184/09_2025/9c4f_45184.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9c4f_45184/09_2025/9c4f_45184.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.68, per 1000 atoms: 0.17 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: 1.82 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 1.2 microseconds 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: 0.93 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: 5.75 Time building geometry restraints manager: 2.50 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: 12.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 21.580 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.480 ------------------------------------------------------------------------------- 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= 0.278 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.017 0.003 ARG C 502 TYR 0.081 0.005 TYR I 423 PHE 0.092 0.004 PHE I 453 TRP 0.101 0.004 TRP I 322 HIS 0.010 0.002 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00531 (22196) covalent geometry : angle 0.81744 (30252) hydrogen bonds : bond 0.19596 ( 548) hydrogen bonds : angle 8.39123 ( 1443) *********************** 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 : 0.699 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: 0.6168 (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: 0.8021 (mpt180) REVERT: B 53 HIS cc_start: 0.7484 (p90) cc_final: 0.7092 (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: 0.7304 (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: 0.7654 (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: 0.6876 (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: 0.6407 (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: 0.1582 time to fit residues: 172.0098 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 : 0.708 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.7980 chunk 215 optimal weight: 0.5980 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 0.0000 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 0.8980 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.6980 overall best weight: 0.5984 ------------------------------------------------------------------------------- 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 193 ASN ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN A 335 GLN A 385 GLN A 425 GLN A 451 GLN A 513 HIS 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 ** E 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 432 ASN I 274 ASN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.113163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.093902 restraints weight = 36138.280| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.19 r_work: 0.3018 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 22196 Z= 0.131 Angle : 0.607 9.646 30252 Z= 0.312 Chirality : 0.043 0.280 3258 Planarity : 0.004 0.124 3942 Dihedral : 6.138 53.384 2977 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.14 % Favored : 98.82 % Rotamer: Outliers : 2.04 % Allowed : 7.60 % Favored : 90.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.18 (0.15), residues: 2722 helix: 0.44 (0.38), residues: 183 sheet: 0.19 (0.19), residues: 668 loop : -0.25 (0.13), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG I 439 TYR 0.017 0.001 TYR D 159 PHE 0.019 0.002 PHE I 315 TRP 0.022 0.002 TRP C 545 HIS 0.010 0.001 HIS D 53 Details of bonding type rmsd covalent geometry : bond 0.00293 (22196) covalent geometry : angle 0.60658 (30252) hydrogen bonds : bond 0.04036 ( 548) hydrogen bonds : angle 6.44606 ( 1443) *********************** 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 699 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 651 time to evaluate : 0.734 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: 0.8494 (t) cc_final: 0.8098 (m) REVERT: A 53 HIS cc_start: 0.8205 (p-80) cc_final: 0.7961 (p90) REVERT: A 109 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7586 (mt-10) REVERT: A 130 ASP cc_start: 0.7538 (m-30) cc_final: 0.7337 (m-30) REVERT: A 207 GLU cc_start: 0.5808 (tm-30) cc_final: 0.3587 (tm-30) REVERT: A 215 GLU cc_start: 0.8213 (mp0) cc_final: 0.7397 (mp0) REVERT: A 240 GLU cc_start: 0.8079 (tp30) cc_final: 0.7759 (tp30) REVERT: A 259 SER cc_start: 0.8803 (m) cc_final: 0.8377 (p) REVERT: A 295 ASN cc_start: 0.7974 (t0) cc_final: 0.7600 (t0) REVERT: A 384 LEU cc_start: 0.8800 (mt) cc_final: 0.8462 (mt) REVERT: A 434 ASP cc_start: 0.8277 (m-30) cc_final: 0.8013 (p0) REVERT: A 435 ASP cc_start: 0.6238 (p0) cc_final: 0.6022 (p0) REVERT: A 540 LYS cc_start: 0.8371 (mttt) cc_final: 0.8014 (mttm) REVERT: A 546 THR cc_start: 0.8456 (p) cc_final: 0.8044 (t) REVERT: B 24 MET cc_start: 0.8356 (mmm) cc_final: 0.7893 (tpp) REVERT: B 53 HIS cc_start: 0.7912 (p90) cc_final: 0.7539 (p-80) REVERT: B 55 LYS cc_start: 0.8691 (mttt) cc_final: 0.8448 (mttt) REVERT: B 91 ASP cc_start: 0.7885 (t0) cc_final: 0.7671 (t0) REVERT: B 110 ASN cc_start: 0.8462 (m-40) cc_final: 0.8182 (m110) REVERT: B 130 ASP cc_start: 0.7938 (m-30) cc_final: 0.7650 (m-30) REVERT: B 134 LYS cc_start: 0.8626 (tttt) cc_final: 0.8390 (ttpp) REVERT: B 154 ASP cc_start: 0.7644 (t0) cc_final: 0.7327 (t0) REVERT: B 156 GLU cc_start: 0.8050 (mt-10) cc_final: 0.7832 (mt-10) REVERT: B 177 TRP cc_start: 0.8791 (m-10) cc_final: 0.8584 (m-10) REVERT: B 215 GLU cc_start: 0.8128 (mp0) cc_final: 0.7814 (mp0) REVERT: B 230 MET cc_start: 0.8212 (tmm) cc_final: 0.7827 (tmm) REVERT: B 253 TYR cc_start: 0.8940 (p90) cc_final: 0.8735 (p90) REVERT: B 295 ASN cc_start: 0.7895 (t0) cc_final: 0.7474 (t0) REVERT: B 296 SER cc_start: 0.8777 (t) cc_final: 0.8439 (t) REVERT: B 329 ARG cc_start: 0.8616 (mtt90) cc_final: 0.8000 (mtt-85) REVERT: B 356 GLN cc_start: 0.8237 (mp-120) cc_final: 0.7944 (mp10) REVERT: B 374 PHE cc_start: 0.8582 (m-80) cc_final: 0.8018 (m-80) REVERT: B 435 ASP cc_start: 0.8267 (t0) cc_final: 0.7125 (p0) REVERT: B 498 LYS cc_start: 0.8670 (ttmt) cc_final: 0.8308 (mmmm) REVERT: B 523 TYR cc_start: 0.8896 (p90) cc_final: 0.8289 (p90) REVERT: B 524 ASP cc_start: 0.8590 (t0) cc_final: 0.8190 (t0) REVERT: B 539 GLU cc_start: 0.7996 (tt0) cc_final: 0.7512 (tt0) REVERT: B 543 GLU cc_start: 0.8071 (mt-10) cc_final: 0.7862 (tt0) REVERT: B 550 ARG cc_start: 0.8164 (mtt-85) cc_final: 0.7937 (mtt-85) REVERT: E 91 ASP cc_start: 0.7628 (t0) cc_final: 0.7410 (t0) REVERT: E 129 LYS cc_start: 0.8193 (mttp) cc_final: 0.7941 (mttp) REVERT: E 130 ASP cc_start: 0.7769 (m-30) cc_final: 0.7490 (m-30) REVERT: E 154 ASP cc_start: 0.8410 (t0) cc_final: 0.7961 (t0) REVERT: E 161 TYR cc_start: 0.8410 (t80) cc_final: 0.8164 (t80) REVERT: E 193 ASN cc_start: 0.8071 (t0) cc_final: 0.7444 (t0) REVERT: E 202 LYS cc_start: 0.8738 (mttt) cc_final: 0.8515 (mttt) REVERT: E 215 GLU cc_start: 0.8240 (mp0) cc_final: 0.7369 (mp0) REVERT: E 295 ASN cc_start: 0.8410 (t0) cc_final: 0.7777 (t0) REVERT: E 382 LYS cc_start: 0.8288 (mtmt) cc_final: 0.8084 (ptmt) REVERT: E 432 ASN cc_start: 0.8270 (p0) cc_final: 0.7948 (p0) REVERT: E 510 TYR cc_start: 0.8295 (m-80) cc_final: 0.7619 (m-80) REVERT: C 103 GLU cc_start: 0.7791 (mt-10) cc_final: 0.7334 (mt-10) REVERT: C 143 ASP cc_start: 0.7424 (m-30) cc_final: 0.7169 (m-30) REVERT: C 154 ASP cc_start: 0.7951 (t0) cc_final: 0.7353 (t0) REVERT: C 180 PHE cc_start: 0.8478 (m-80) cc_final: 0.7994 (m-80) REVERT: C 191 ASP cc_start: 0.7818 (m-30) cc_final: 0.7580 (m-30) REVERT: C 193 ASN cc_start: 0.7587 (t0) cc_final: 0.7263 (t0) REVERT: C 194 THR cc_start: 0.7983 (m) cc_final: 0.7688 (m) REVERT: C 200 ASP cc_start: 0.6824 (m-30) cc_final: 0.6464 (m-30) REVERT: C 295 ASN cc_start: 0.7928 (t0) cc_final: 0.7471 (t0) REVERT: C 356 GLN cc_start: 0.8261 (mp-120) cc_final: 0.8024 (mp10) REVERT: C 371 VAL cc_start: 0.8972 (t) cc_final: 0.8602 (p) REVERT: C 374 PHE cc_start: 0.8502 (m-80) cc_final: 0.8174 (m-80) REVERT: C 521 VAL cc_start: 0.8662 (t) cc_final: 0.8294 (p) REVERT: C 546 THR cc_start: 0.8344 (p) cc_final: 0.8133 (p) REVERT: D 21 VAL cc_start: 0.8739 (t) cc_final: 0.8382 (m) REVERT: D 58 SER cc_start: 0.8360 (t) cc_final: 0.7684 (p) REVERT: D 103 GLU cc_start: 0.7934 (mt-10) cc_final: 0.7728 (mt-10) REVERT: D 130 ASP cc_start: 0.7738 (m-30) cc_final: 0.7454 (m-30) REVERT: D 154 ASP cc_start: 0.8049 (t0) cc_final: 0.7770 (t0) REVERT: D 156 GLU cc_start: 0.8262 (mt-10) cc_final: 0.8037 (mp0) REVERT: D 168 ASP cc_start: 0.7879 (t0) cc_final: 0.7637 (t0) REVERT: D 203 LYS cc_start: 0.8551 (ttmm) cc_final: 0.8288 (ttmm) REVERT: D 215 GLU cc_start: 0.8362 (mp0) cc_final: 0.7496 (mp0) REVERT: D 242 LEU cc_start: 0.8488 (mt) cc_final: 0.8224 (mp) REVERT: D 253 TYR cc_start: 0.8650 (p90) cc_final: 0.8203 (p90) REVERT: D 289 MET cc_start: 0.8669 (mmm) cc_final: 0.8352 (mmt) REVERT: D 341 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7741 (m-30) REVERT: D 382 LYS cc_start: 0.8443 (mtmt) cc_final: 0.8138 (mtmt) REVERT: D 389 MET cc_start: 0.8611 (mmm) cc_final: 0.8357 (mmm) REVERT: D 523 TYR cc_start: 0.8585 (p90) cc_final: 0.8036 (p90) REVERT: D 539 GLU cc_start: 0.7911 (tt0) cc_final: 0.7564 (tt0) REVERT: I 358 MET cc_start: 0.7020 (mmp) cc_final: 0.6660 (mmp) outliers start: 48 outliers final: 28 residues processed: 667 average time/residue: 0.1716 time to fit residues: 171.3210 Evaluate side-chains 639 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 610 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 193 ASN Chi-restraints excluded: chain A residue 275 SER 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 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 91 optimal weight: 3.9990 chunk 231 optimal weight: 2.9990 chunk 108 optimal weight: 0.9980 chunk 80 optimal weight: 8.9990 chunk 49 optimal weight: 9.9990 chunk 78 optimal weight: 5.9990 chunk 223 optimal weight: 3.9990 chunk 142 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 252 optimal weight: 4.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 455 GLN ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 195 GLN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN ** B 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 HIS C 155 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 ASN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 385 GLN C 425 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.112302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.094036 restraints weight = 35209.901| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 2.02 r_work: 0.2958 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.2820 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 22196 Z= 0.277 Angle : 0.621 8.629 30252 Z= 0.322 Chirality : 0.045 0.287 3258 Planarity : 0.005 0.121 3942 Dihedral : 5.866 54.184 2975 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.40 % Favored : 98.57 % Rotamer: Outliers : 2.76 % Allowed : 10.36 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.15), residues: 2722 helix: 0.62 (0.39), residues: 183 sheet: 0.12 (0.19), residues: 638 loop : -0.27 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 373 TYR 0.019 0.002 TYR C 422 PHE 0.023 0.002 PHE B 219 TRP 0.020 0.002 TRP B 25 HIS 0.035 0.002 HIS E 53 Details of bonding type rmsd covalent geometry : bond 0.00621 (22196) covalent geometry : angle 0.62072 (30252) hydrogen bonds : bond 0.04490 ( 548) hydrogen bonds : angle 6.23735 ( 1443) *********************** 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 737 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 672 time to evaluate : 0.837 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 24 MET cc_start: 0.8395 (mmm) cc_final: 0.7912 (mmm) REVERT: A 53 HIS cc_start: 0.8117 (p-80) cc_final: 0.7881 (p90) REVERT: A 76 THR cc_start: 0.8781 (p) cc_final: 0.8568 (p) REVERT: A 124 SER cc_start: 0.8611 (m) cc_final: 0.8272 (p) REVERT: A 134 LYS cc_start: 0.8858 (ttpp) cc_final: 0.8508 (ttpp) REVERT: A 207 GLU cc_start: 0.6563 (tm-30) cc_final: 0.4440 (tm-30) REVERT: A 240 GLU cc_start: 0.8084 (tp30) cc_final: 0.7752 (tp30) REVERT: A 257 TYR cc_start: 0.8863 (m-80) cc_final: 0.8657 (m-80) REVERT: A 259 SER cc_start: 0.8963 (m) cc_final: 0.8705 (p) REVERT: A 295 ASN cc_start: 0.7963 (t0) cc_final: 0.7618 (t0) REVERT: A 434 ASP cc_start: 0.8197 (m-30) cc_final: 0.7939 (p0) REVERT: A 435 ASP cc_start: 0.6784 (p0) cc_final: 0.6493 (p0) REVERT: A 486 MET cc_start: 0.8519 (OUTLIER) cc_final: 0.8285 (ptm) REVERT: A 540 LYS cc_start: 0.8476 (mttt) cc_final: 0.8067 (mttm) REVERT: A 546 THR cc_start: 0.8623 (p) cc_final: 0.8212 (t) REVERT: B 8 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7360 (mt-10) REVERT: B 51 GLU cc_start: 0.7396 (tt0) cc_final: 0.6762 (tt0) REVERT: B 53 HIS cc_start: 0.7791 (p90) cc_final: 0.7346 (p90) REVERT: B 55 LYS cc_start: 0.8710 (mttt) cc_final: 0.8479 (mttt) REVERT: B 110 ASN cc_start: 0.8402 (m-40) cc_final: 0.8107 (m110) REVERT: B 130 ASP cc_start: 0.8022 (m-30) cc_final: 0.7691 (m-30) REVERT: B 134 LYS cc_start: 0.8710 (tttt) cc_final: 0.8329 (ttpp) REVERT: B 154 ASP cc_start: 0.7581 (t0) cc_final: 0.7155 (t0) REVERT: B 157 TYR cc_start: 0.8336 (m-80) cc_final: 0.7790 (m-80) REVERT: B 203 LYS cc_start: 0.8504 (tttt) cc_final: 0.8246 (ttmt) REVERT: B 215 GLU cc_start: 0.8077 (mp0) cc_final: 0.7792 (mp0) REVERT: B 230 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7616 (tmm) REVERT: B 294 VAL cc_start: 0.8592 (t) cc_final: 0.8359 (p) REVERT: B 296 SER cc_start: 0.8830 (t) cc_final: 0.8354 (p) REVERT: B 300 LYS cc_start: 0.7466 (mptt) cc_final: 0.7093 (mmtt) REVERT: B 344 LYS cc_start: 0.7109 (tttp) cc_final: 0.5924 (tttp) REVERT: B 374 PHE cc_start: 0.8481 (m-80) cc_final: 0.8276 (m-80) REVERT: B 377 GLU cc_start: 0.7188 (mm-30) cc_final: 0.6872 (mm-30) REVERT: B 497 ARG cc_start: 0.8352 (mtm-85) cc_final: 0.8138 (mtm110) REVERT: B 523 TYR cc_start: 0.8932 (p90) cc_final: 0.8331 (p90) REVERT: B 524 ASP cc_start: 0.8631 (t0) cc_final: 0.8182 (t0) REVERT: B 543 GLU cc_start: 0.8022 (mt-10) cc_final: 0.7738 (tt0) REVERT: B 546 THR cc_start: 0.8296 (OUTLIER) cc_final: 0.7967 (t) REVERT: B 550 ARG cc_start: 0.8450 (mtt-85) cc_final: 0.8129 (mtt180) REVERT: E 55 LYS cc_start: 0.8586 (mtmt) cc_final: 0.8246 (mtmt) REVERT: E 91 ASP cc_start: 0.7620 (t0) cc_final: 0.7374 (t70) REVERT: E 129 LYS cc_start: 0.8273 (mttp) cc_final: 0.8002 (mttp) REVERT: E 130 ASP cc_start: 0.7770 (m-30) cc_final: 0.7442 (m-30) REVERT: E 133 ASP cc_start: 0.8053 (m-30) cc_final: 0.7715 (m-30) REVERT: E 193 ASN cc_start: 0.8162 (t0) cc_final: 0.7600 (t0) REVERT: E 202 LYS cc_start: 0.8761 (mttt) cc_final: 0.8519 (mttt) REVERT: E 215 GLU cc_start: 0.8316 (mp0) cc_final: 0.7231 (mp0) REVERT: E 272 LYS cc_start: 0.8147 (mmtt) cc_final: 0.7791 (mmtt) REVERT: E 294 VAL cc_start: 0.8749 (t) cc_final: 0.8434 (p) REVERT: E 295 ASN cc_start: 0.8379 (t0) cc_final: 0.7617 (t0) REVERT: E 423 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7963 (mt-10) REVERT: E 432 ASN cc_start: 0.8299 (p0) cc_final: 0.7935 (p0) REVERT: E 540 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8402 (mtpt) REVERT: E 543 GLU cc_start: 0.8052 (tt0) cc_final: 0.7834 (tt0) REVERT: C 51 GLU cc_start: 0.8001 (tt0) cc_final: 0.7704 (tt0) REVERT: C 103 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7081 (mt-10) REVERT: C 154 ASP cc_start: 0.8052 (t0) cc_final: 0.7493 (t0) REVERT: C 158 LYS cc_start: 0.6007 (tptp) cc_final: 0.5462 (tttp) REVERT: C 191 ASP cc_start: 0.7768 (m-30) cc_final: 0.7534 (m-30) REVERT: C 192 VAL cc_start: 0.8720 (t) cc_final: 0.8432 (p) REVERT: C 193 ASN cc_start: 0.7782 (t0) cc_final: 0.7449 (t0) REVERT: C 220 GLN cc_start: 0.8258 (mt0) cc_final: 0.8050 (mt0) REVERT: C 230 MET cc_start: 0.8337 (tmm) cc_final: 0.8103 (tmm) REVERT: C 294 VAL cc_start: 0.8624 (t) cc_final: 0.8305 (p) REVERT: C 295 ASN cc_start: 0.8001 (t0) cc_final: 0.7657 (t0) REVERT: C 296 SER cc_start: 0.8911 (t) cc_final: 0.8694 (t) REVERT: C 329 ARG cc_start: 0.8007 (mtt90) cc_final: 0.7739 (mtt-85) REVERT: C 371 VAL cc_start: 0.8996 (t) cc_final: 0.8676 (p) REVERT: C 374 PHE cc_start: 0.8562 (m-80) cc_final: 0.8269 (m-80) REVERT: C 414 VAL cc_start: 0.8642 (t) cc_final: 0.8255 (m) REVERT: C 471 LYS cc_start: 0.8276 (mmtt) cc_final: 0.7807 (mmtt) REVERT: C 521 VAL cc_start: 0.8638 (t) cc_final: 0.8326 (p) REVERT: C 524 ASP cc_start: 0.8110 (t0) cc_final: 0.7778 (t0) REVERT: C 546 THR cc_start: 0.8385 (p) cc_final: 0.8178 (p) REVERT: D 21 VAL cc_start: 0.8788 (t) cc_final: 0.8455 (m) REVERT: D 49 ASP cc_start: 0.8492 (t0) cc_final: 0.8186 (t0) REVERT: D 51 GLU cc_start: 0.7731 (tt0) cc_final: 0.7431 (tt0) REVERT: D 58 SER cc_start: 0.8323 (t) cc_final: 0.7796 (p) REVERT: D 135 THR cc_start: 0.8636 (m) cc_final: 0.8349 (t) REVERT: D 151 MET cc_start: 0.8456 (ttp) cc_final: 0.8175 (ttp) REVERT: D 168 ASP cc_start: 0.8041 (t0) cc_final: 0.7742 (t0) REVERT: D 203 LYS cc_start: 0.8601 (ttmm) cc_final: 0.8293 (ttmm) REVERT: D 207 GLU cc_start: 0.5932 (tm-30) cc_final: 0.5381 (tm-30) REVERT: D 215 GLU cc_start: 0.8367 (mp0) cc_final: 0.7494 (mp0) REVERT: D 293 LEU cc_start: 0.8845 (mp) cc_final: 0.8610 (mm) REVERT: D 341 ASP cc_start: 0.8101 (OUTLIER) cc_final: 0.7790 (m-30) REVERT: D 346 VAL cc_start: 0.8792 (t) cc_final: 0.8524 (p) REVERT: D 382 LYS cc_start: 0.8696 (mtmt) cc_final: 0.8396 (mtmt) REVERT: D 435 ASP cc_start: 0.8132 (t0) cc_final: 0.7575 (p0) REVERT: D 521 VAL cc_start: 0.8497 (t) cc_final: 0.8201 (p) REVERT: D 524 ASP cc_start: 0.8101 (t0) cc_final: 0.7608 (t0) REVERT: I 271 MET cc_start: 0.5512 (pmm) cc_final: 0.5052 (pmm) REVERT: I 338 ARG cc_start: 0.7403 (ttp80) cc_final: 0.7178 (ttp80) REVERT: I 358 MET cc_start: 0.7358 (mmp) cc_final: 0.6912 (mmp) outliers start: 65 outliers final: 45 residues processed: 693 average time/residue: 0.1566 time to fit residues: 163.3435 Evaluate side-chains 696 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 646 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 230 MET Chi-restraints excluded: chain A residue 275 SER 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 2 THR Chi-restraints excluded: chain B residue 21 VAL 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 298 SER Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 38 CYS Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 201 SER 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 C residue 77 ILE Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 188 THR Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 423 GLU Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 142 THR 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 406 GLU Chi-restraints excluded: chain D residue 477 THR 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 35 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 163 optimal weight: 4.9990 chunk 60 optimal weight: 0.8980 chunk 130 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 115 optimal weight: 2.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 ASN ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 52 HIS ** B 195 GLN ** 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 513 HIS C 106 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 ASN C 356 GLN C 380 GLN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS D 380 GLN ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 432 ASN ** D 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.108399 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.089617 restraints weight = 36195.610| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.16 r_work: 0.2928 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.3463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.082 22196 Z= 0.268 Angle : 0.589 8.619 30252 Z= 0.304 Chirality : 0.044 0.280 3258 Planarity : 0.005 0.119 3942 Dihedral : 5.528 55.543 2973 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.76 % Favored : 98.20 % Rotamer: Outliers : 2.85 % Allowed : 11.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.36 (0.15), residues: 2722 helix: 0.35 (0.38), residues: 183 sheet: -0.03 (0.19), residues: 638 loop : -0.34 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 417 TYR 0.017 0.002 TYR B 159 PHE 0.022 0.002 PHE B 219 TRP 0.016 0.002 TRP B 25 HIS 0.007 0.001 HIS B 536 Details of bonding type rmsd covalent geometry : bond 0.00592 (22196) covalent geometry : angle 0.58926 (30252) hydrogen bonds : bond 0.03926 ( 548) hydrogen bonds : angle 6.15960 ( 1443) *********************** 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 732 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 665 time to evaluate : 0.831 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: 0.8537 (t) cc_final: 0.8100 (m) REVERT: A 24 MET cc_start: 0.8332 (mmm) cc_final: 0.7872 (mmm) REVERT: A 76 THR cc_start: 0.8779 (p) cc_final: 0.8553 (p) REVERT: A 124 SER cc_start: 0.8592 (m) cc_final: 0.8280 (p) REVERT: A 197 ILE cc_start: 0.8612 (OUTLIER) cc_final: 0.8376 (mt) REVERT: A 207 GLU cc_start: 0.6823 (tm-30) cc_final: 0.4172 (tt0) REVERT: A 240 GLU cc_start: 0.8207 (tp30) cc_final: 0.7867 (tp30) REVERT: A 295 ASN cc_start: 0.8012 (t0) cc_final: 0.7648 (t0) REVERT: A 434 ASP cc_start: 0.8218 (m-30) cc_final: 0.7828 (p0) REVERT: A 435 ASP cc_start: 0.6648 (p0) cc_final: 0.6375 (p0) REVERT: A 486 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.8280 (ptm) REVERT: A 507 PRO cc_start: 0.8900 (Cg_exo) cc_final: 0.8615 (Cg_endo) REVERT: A 540 LYS cc_start: 0.8519 (mttt) cc_final: 0.8139 (mttm) REVERT: A 546 THR cc_start: 0.8676 (p) cc_final: 0.8291 (t) REVERT: B 51 GLU cc_start: 0.7414 (tt0) cc_final: 0.6816 (tt0) REVERT: B 53 HIS cc_start: 0.7882 (p90) cc_final: 0.7407 (p90) REVERT: B 55 LYS cc_start: 0.8677 (mttt) cc_final: 0.8467 (mttt) REVERT: B 110 ASN cc_start: 0.8371 (m-40) cc_final: 0.8052 (m110) REVERT: B 130 ASP cc_start: 0.8039 (m-30) cc_final: 0.7679 (m-30) REVERT: B 134 LYS cc_start: 0.8738 (tttt) cc_final: 0.8265 (ttpp) REVERT: B 154 ASP cc_start: 0.7622 (t0) cc_final: 0.7243 (t0) REVERT: B 157 TYR cc_start: 0.8302 (m-80) cc_final: 0.7633 (m-80) REVERT: B 215 GLU cc_start: 0.8102 (mp0) cc_final: 0.7769 (mp0) REVERT: B 230 MET cc_start: 0.8108 (tmm) cc_final: 0.7702 (tmm) REVERT: B 294 VAL cc_start: 0.8619 (t) cc_final: 0.8395 (p) REVERT: B 296 SER cc_start: 0.8754 (t) cc_final: 0.8219 (p) REVERT: B 329 ARG cc_start: 0.8589 (mtt90) cc_final: 0.8100 (mtt-85) REVERT: B 376 ASN cc_start: 0.8248 (t0) cc_final: 0.7862 (t0) REVERT: B 377 GLU cc_start: 0.7180 (mm-30) cc_final: 0.6856 (mm-30) REVERT: B 389 MET cc_start: 0.8544 (tpp) cc_final: 0.8180 (tpt) REVERT: B 407 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8722 (ttm170) REVERT: B 523 TYR cc_start: 0.8878 (p90) cc_final: 0.8455 (p90) REVERT: B 524 ASP cc_start: 0.8647 (t0) cc_final: 0.8143 (t0) REVERT: B 539 GLU cc_start: 0.8115 (tt0) cc_final: 0.7749 (tt0) REVERT: B 543 GLU cc_start: 0.8035 (mt-10) cc_final: 0.7752 (tt0) REVERT: B 546 THR cc_start: 0.8291 (p) cc_final: 0.7980 (t) REVERT: B 554 LEU cc_start: 0.7347 (OUTLIER) cc_final: 0.7017 (mp) REVERT: E 81 MET cc_start: 0.8683 (tmm) cc_final: 0.8272 (ttp) REVERT: E 129 LYS cc_start: 0.8327 (mttp) cc_final: 0.7908 (mtpp) REVERT: E 130 ASP cc_start: 0.7781 (m-30) cc_final: 0.7507 (m-30) REVERT: E 193 ASN cc_start: 0.8292 (t0) cc_final: 0.7869 (t0) REVERT: E 202 LYS cc_start: 0.8744 (mttt) cc_final: 0.8475 (mttt) REVERT: E 215 GLU cc_start: 0.8270 (mp0) cc_final: 0.7257 (mp0) REVERT: E 294 VAL cc_start: 0.8753 (t) cc_final: 0.8386 (p) REVERT: E 295 ASN cc_start: 0.8415 (t0) cc_final: 0.7657 (t0) REVERT: E 382 LYS cc_start: 0.8405 (mtpt) cc_final: 0.8065 (mtmt) REVERT: E 389 MET cc_start: 0.8636 (tpp) cc_final: 0.8219 (tpt) REVERT: E 423 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7922 (mt-10) REVERT: E 490 MET cc_start: 0.8462 (tpp) cc_final: 0.8217 (ttm) REVERT: E 540 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8429 (mtpt) REVERT: E 543 GLU cc_start: 0.8057 (tt0) cc_final: 0.7837 (tt0) REVERT: E 554 LEU cc_start: 0.7170 (OUTLIER) cc_final: 0.6879 (mp) REVERT: C 21 VAL cc_start: 0.8642 (t) cc_final: 0.8339 (m) REVERT: C 51 GLU cc_start: 0.8084 (tt0) cc_final: 0.7717 (tt0) REVERT: C 55 LYS cc_start: 0.8635 (mtmm) cc_final: 0.8430 (mtmm) REVERT: C 103 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7085 (mt-10) REVERT: C 154 ASP cc_start: 0.7985 (t0) cc_final: 0.7460 (t0) REVERT: C 158 LYS cc_start: 0.6004 (tptp) cc_final: 0.5444 (tttp) REVERT: C 191 ASP cc_start: 0.7821 (m-30) cc_final: 0.7564 (m-30) REVERT: C 192 VAL cc_start: 0.8718 (t) cc_final: 0.8448 (p) REVERT: C 193 ASN cc_start: 0.7826 (t0) cc_final: 0.7479 (t0) REVERT: C 204 LEU cc_start: 0.8299 (mt) cc_final: 0.8057 (mm) REVERT: C 207 GLU cc_start: 0.5912 (tm-30) cc_final: 0.4478 (tm-30) REVERT: C 220 GLN cc_start: 0.8308 (mt0) cc_final: 0.8071 (mt0) REVERT: C 230 MET cc_start: 0.8360 (tmm) cc_final: 0.8109 (tmm) REVERT: C 294 VAL cc_start: 0.8590 (t) cc_final: 0.8330 (p) REVERT: C 295 ASN cc_start: 0.8226 (t0) cc_final: 0.7827 (t0) REVERT: C 296 SER cc_start: 0.8955 (t) cc_final: 0.8547 (p) REVERT: C 329 ARG cc_start: 0.8023 (mtt90) cc_final: 0.7742 (mtt-85) REVERT: C 347 THR cc_start: 0.8816 (m) cc_final: 0.8588 (p) REVERT: C 371 VAL cc_start: 0.8939 (t) cc_final: 0.8601 (p) REVERT: C 374 PHE cc_start: 0.8603 (m-80) cc_final: 0.8345 (m-80) REVERT: C 414 VAL cc_start: 0.8697 (t) cc_final: 0.8369 (m) REVERT: C 435 ASP cc_start: 0.6280 (OUTLIER) cc_final: 0.5761 (t70) REVERT: C 471 LYS cc_start: 0.8326 (mmtt) cc_final: 0.7840 (mmtt) REVERT: C 521 VAL cc_start: 0.8638 (t) cc_final: 0.8355 (p) REVERT: C 524 ASP cc_start: 0.8190 (t0) cc_final: 0.7777 (t0) REVERT: C 534 HIS cc_start: 0.8014 (m-70) cc_final: 0.7718 (m-70) REVERT: C 543 GLU cc_start: 0.8077 (mt-10) cc_final: 0.7785 (tt0) REVERT: C 546 THR cc_start: 0.8433 (p) cc_final: 0.8027 (m) REVERT: D 21 VAL cc_start: 0.8705 (t) cc_final: 0.8371 (m) REVERT: D 24 MET cc_start: 0.8541 (mmm) cc_final: 0.7810 (mmm) REVERT: D 49 ASP cc_start: 0.8502 (t0) cc_final: 0.8192 (t0) REVERT: D 51 GLU cc_start: 0.7743 (tt0) cc_final: 0.7410 (tt0) REVERT: D 55 LYS cc_start: 0.8862 (mttp) cc_final: 0.8504 (mttp) REVERT: D 58 SER cc_start: 0.8350 (t) cc_final: 0.7869 (p) REVERT: D 103 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7797 (mt-10) REVERT: D 135 THR cc_start: 0.8621 (m) cc_final: 0.8405 (t) REVERT: D 151 MET cc_start: 0.8449 (ttp) cc_final: 0.8186 (ttp) REVERT: D 168 ASP cc_start: 0.8130 (t0) cc_final: 0.7880 (t0) REVERT: D 192 VAL cc_start: 0.8916 (t) cc_final: 0.8699 (p) REVERT: D 201 SER cc_start: 0.8233 (OUTLIER) cc_final: 0.7966 (m) REVERT: D 203 LYS cc_start: 0.8570 (ttmm) cc_final: 0.8317 (ttmm) REVERT: D 207 GLU cc_start: 0.5985 (tm-30) cc_final: 0.5033 (tm-30) REVERT: D 215 GLU cc_start: 0.8382 (mp0) cc_final: 0.7560 (mp0) REVERT: D 341 ASP cc_start: 0.8122 (OUTLIER) cc_final: 0.7774 (m-30) REVERT: D 382 LYS cc_start: 0.8766 (mtmt) cc_final: 0.8448 (mtmt) REVERT: D 435 ASP cc_start: 0.8103 (t0) cc_final: 0.7606 (p0) REVERT: I 271 MET cc_start: 0.5260 (pmm) cc_final: 0.4802 (pmm) REVERT: I 357 LEU cc_start: 0.8371 (mt) cc_final: 0.8103 (mt) REVERT: I 358 MET cc_start: 0.7572 (mmp) cc_final: 0.7073 (mmp) outliers start: 67 outliers final: 42 residues processed: 687 average time/residue: 0.1568 time to fit residues: 161.4240 Evaluate side-chains 695 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 644 time to evaluate : 0.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 27 GLU 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 2 THR 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 274 ARG Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 407 ARG Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 38 CYS Chi-restraints excluded: chain E residue 201 SER 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 540 LYS Chi-restraints excluded: chain E residue 554 LEU 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 188 THR 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 434 ASP 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 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 294 VAL 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 546 THR Chi-restraints excluded: chain I residue 399 GLN 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 157 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 114 optimal weight: 0.9990 chunk 87 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 141 optimal weight: 0.7980 chunk 236 optimal weight: 3.9990 chunk 211 optimal weight: 4.9990 chunk 164 optimal weight: 5.9990 chunk 212 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** 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 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 53 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 ASN C 356 GLN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 552 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.112820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.094931 restraints weight = 34934.170| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 2.02 r_work: 0.2986 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 moved from start: 0.3607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 22196 Z= 0.160 Angle : 0.539 8.502 30252 Z= 0.276 Chirality : 0.041 0.277 3258 Planarity : 0.005 0.118 3942 Dihedral : 5.032 55.611 2969 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.54 % Favored : 98.42 % Rotamer: Outliers : 2.76 % Allowed : 12.91 % Favored : 84.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.15), residues: 2722 helix: 0.52 (0.39), residues: 183 sheet: -0.05 (0.19), residues: 638 loop : -0.29 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 417 TYR 0.014 0.001 TYR A 523 PHE 0.025 0.002 PHE B 374 TRP 0.012 0.001 TRP B 25 HIS 0.006 0.001 HIS C 517 Details of bonding type rmsd covalent geometry : bond 0.00357 (22196) covalent geometry : angle 0.53894 (30252) hydrogen bonds : bond 0.03466 ( 548) hydrogen bonds : angle 5.97605 ( 1443) *********************** 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 733 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 668 time to evaluate : 0.609 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: A 21 VAL cc_start: 0.8528 (t) cc_final: 0.8105 (m) REVERT: A 24 MET cc_start: 0.8266 (mmm) cc_final: 0.7802 (mmm) REVERT: A 76 THR cc_start: 0.8785 (p) cc_final: 0.8555 (p) REVERT: A 124 SER cc_start: 0.8631 (m) cc_final: 0.8325 (p) REVERT: A 197 ILE cc_start: 0.8586 (OUTLIER) cc_final: 0.8342 (mt) REVERT: A 207 GLU cc_start: 0.6666 (tm-30) cc_final: 0.4374 (tt0) REVERT: A 240 GLU cc_start: 0.8195 (tp30) cc_final: 0.7866 (tp30) REVERT: A 295 ASN cc_start: 0.7980 (t0) cc_final: 0.7630 (t0) REVERT: A 296 SER cc_start: 0.8594 (t) cc_final: 0.8077 (p) REVERT: A 389 MET cc_start: 0.8504 (tpp) cc_final: 0.8184 (ttm) REVERT: A 434 ASP cc_start: 0.8177 (m-30) cc_final: 0.7793 (p0) REVERT: A 435 ASP cc_start: 0.6244 (p0) cc_final: 0.5986 (p0) REVERT: A 486 MET cc_start: 0.8490 (OUTLIER) cc_final: 0.8270 (ptm) REVERT: A 540 LYS cc_start: 0.8527 (mttt) cc_final: 0.8086 (mttm) REVERT: A 546 THR cc_start: 0.8649 (p) cc_final: 0.8273 (t) REVERT: B 8 GLU cc_start: 0.7993 (mt-10) cc_final: 0.7450 (mt-10) REVERT: B 51 GLU cc_start: 0.7349 (tt0) cc_final: 0.6744 (tt0) REVERT: B 53 HIS cc_start: 0.7879 (p90) cc_final: 0.7375 (p90) REVERT: B 110 ASN cc_start: 0.8345 (m-40) cc_final: 0.7948 (m110) REVERT: B 130 ASP cc_start: 0.7966 (m-30) cc_final: 0.7622 (m-30) REVERT: B 134 LYS cc_start: 0.8694 (tttt) cc_final: 0.8285 (ttpp) REVERT: B 154 ASP cc_start: 0.7623 (t0) cc_final: 0.7291 (t0) REVERT: B 157 TYR cc_start: 0.8331 (m-80) cc_final: 0.7660 (m-80) REVERT: B 215 GLU cc_start: 0.8071 (mp0) cc_final: 0.7701 (mp0) REVERT: B 230 MET cc_start: 0.8057 (OUTLIER) cc_final: 0.7669 (tmm) REVERT: B 296 SER cc_start: 0.8709 (t) cc_final: 0.8146 (p) REVERT: B 376 ASN cc_start: 0.8197 (t0) cc_final: 0.7831 (t0) REVERT: B 435 ASP cc_start: 0.8441 (t0) cc_final: 0.7610 (p0) REVERT: B 523 TYR cc_start: 0.8834 (p90) cc_final: 0.8587 (p90) REVERT: B 524 ASP cc_start: 0.8665 (t0) cc_final: 0.8161 (t0) REVERT: B 532 GLN cc_start: 0.8172 (mm-40) cc_final: 0.7711 (mm-40) REVERT: B 539 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7621 (tt0) REVERT: B 543 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7592 (tt0) REVERT: B 546 THR cc_start: 0.8279 (p) cc_final: 0.7976 (t) REVERT: B 554 LEU cc_start: 0.7262 (OUTLIER) cc_final: 0.6988 (mp) REVERT: E 19 ASN cc_start: 0.8638 (t0) cc_final: 0.8383 (t0) REVERT: E 81 MET cc_start: 0.8661 (tmm) cc_final: 0.8269 (ttp) REVERT: E 117 ASP cc_start: 0.7906 (t0) cc_final: 0.7673 (t0) REVERT: E 120 THR cc_start: 0.8451 (m) cc_final: 0.8158 (t) REVERT: E 130 ASP cc_start: 0.7768 (m-30) cc_final: 0.7494 (m-30) REVERT: E 193 ASN cc_start: 0.8198 (t0) cc_final: 0.7708 (t0) REVERT: E 202 LYS cc_start: 0.8728 (mttt) cc_final: 0.8442 (mttt) REVERT: E 215 GLU cc_start: 0.8253 (mp0) cc_final: 0.7341 (mp0) REVERT: E 294 VAL cc_start: 0.8722 (t) cc_final: 0.8363 (p) REVERT: E 295 ASN cc_start: 0.8396 (t0) cc_final: 0.7637 (t0) REVERT: E 347 THR cc_start: 0.8500 (m) cc_final: 0.8229 (p) REVERT: E 382 LYS cc_start: 0.8399 (mtpt) cc_final: 0.8059 (mtmt) REVERT: E 389 MET cc_start: 0.8543 (tpp) cc_final: 0.8164 (tpt) REVERT: E 423 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7909 (mt-10) REVERT: E 427 TRP cc_start: 0.8669 (p90) cc_final: 0.8381 (p90) REVERT: E 490 MET cc_start: 0.8418 (tpp) cc_final: 0.8207 (ttm) REVERT: E 540 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8406 (mtpt) REVERT: E 543 GLU cc_start: 0.8005 (tt0) cc_final: 0.7772 (tt0) REVERT: E 554 LEU cc_start: 0.7109 (OUTLIER) cc_final: 0.6884 (mp) REVERT: C 21 VAL cc_start: 0.8633 (t) cc_final: 0.8357 (m) REVERT: C 55 LYS cc_start: 0.8617 (mtmm) cc_final: 0.8400 (mtmm) REVERT: C 103 GLU cc_start: 0.7804 (mt-10) cc_final: 0.7100 (mt-10) REVERT: C 154 ASP cc_start: 0.8038 (t0) cc_final: 0.7518 (t0) REVERT: C 158 LYS cc_start: 0.6001 (tptp) cc_final: 0.5408 (tttp) REVERT: C 177 TRP cc_start: 0.8747 (m-10) cc_final: 0.8537 (m-10) REVERT: C 191 ASP cc_start: 0.7803 (m-30) cc_final: 0.7566 (m-30) REVERT: C 192 VAL cc_start: 0.8721 (t) cc_final: 0.8444 (p) REVERT: C 193 ASN cc_start: 0.7801 (t0) cc_final: 0.7463 (t0) REVERT: C 204 LEU cc_start: 0.8248 (mt) cc_final: 0.8018 (mm) REVERT: C 207 GLU cc_start: 0.5870 (tm-30) cc_final: 0.4315 (tm-30) REVERT: C 215 GLU cc_start: 0.8210 (mp0) cc_final: 0.7911 (mp0) REVERT: C 220 GLN cc_start: 0.8274 (mt0) cc_final: 0.8028 (mt0) REVERT: C 230 MET cc_start: 0.8260 (tmm) cc_final: 0.8055 (tmm) REVERT: C 294 VAL cc_start: 0.8620 (t) cc_final: 0.8357 (p) REVERT: C 295 ASN cc_start: 0.8214 (t0) cc_final: 0.7865 (t0) REVERT: C 329 ARG cc_start: 0.7982 (mtt90) cc_final: 0.7501 (mtt-85) REVERT: C 347 THR cc_start: 0.8793 (m) cc_final: 0.8546 (p) REVERT: C 371 VAL cc_start: 0.8930 (t) cc_final: 0.8582 (p) REVERT: C 374 PHE cc_start: 0.8590 (m-80) cc_final: 0.8270 (m-80) REVERT: C 414 VAL cc_start: 0.8717 (t) cc_final: 0.8375 (m) REVERT: C 471 LYS cc_start: 0.8327 (mmtt) cc_final: 0.7869 (mmtt) REVERT: C 521 VAL cc_start: 0.8616 (t) cc_final: 0.8342 (p) REVERT: C 524 ASP cc_start: 0.8209 (t0) cc_final: 0.7757 (t0) REVERT: C 534 HIS cc_start: 0.7945 (m-70) cc_final: 0.7642 (m-70) REVERT: C 546 THR cc_start: 0.8437 (p) cc_final: 0.8068 (m) REVERT: D 21 VAL cc_start: 0.8735 (t) cc_final: 0.8409 (m) REVERT: D 24 MET cc_start: 0.8501 (mmm) cc_final: 0.7805 (mmm) REVERT: D 49 ASP cc_start: 0.8490 (t0) cc_final: 0.8183 (t0) REVERT: D 51 GLU cc_start: 0.7770 (tt0) cc_final: 0.7442 (tt0) REVERT: D 55 LYS cc_start: 0.8820 (mttp) cc_final: 0.8461 (mttp) REVERT: D 58 SER cc_start: 0.8352 (t) cc_final: 0.7866 (p) REVERT: D 103 GLU cc_start: 0.7999 (mt-10) cc_final: 0.7728 (mt-10) REVERT: D 134 LYS cc_start: 0.8815 (ttpp) cc_final: 0.8240 (ttpp) REVERT: D 151 MET cc_start: 0.8432 (ttp) cc_final: 0.8162 (ttp) REVERT: D 168 ASP cc_start: 0.8055 (t0) cc_final: 0.7793 (t0) REVERT: D 192 VAL cc_start: 0.8865 (t) cc_final: 0.8627 (p) REVERT: D 201 SER cc_start: 0.8247 (p) cc_final: 0.7941 (m) REVERT: D 203 LYS cc_start: 0.8487 (ttmm) cc_final: 0.8245 (ttmm) REVERT: D 207 GLU cc_start: 0.5951 (tm-30) cc_final: 0.4356 (tm-30) REVERT: D 215 GLU cc_start: 0.8321 (mp0) cc_final: 0.7494 (mp0) REVERT: D 341 ASP cc_start: 0.8057 (OUTLIER) cc_final: 0.7766 (m-30) REVERT: D 346 VAL cc_start: 0.8785 (t) cc_final: 0.8502 (p) REVERT: D 382 LYS cc_start: 0.8728 (mtmt) cc_final: 0.8438 (mtmt) REVERT: D 389 MET cc_start: 0.8512 (mmm) cc_final: 0.8118 (tpt) REVERT: D 435 ASP cc_start: 0.7985 (t0) cc_final: 0.7496 (p0) REVERT: I 271 MET cc_start: 0.5189 (pmm) cc_final: 0.4730 (pmm) REVERT: I 338 ARG cc_start: 0.7318 (ttp80) cc_final: 0.7091 (ttp80) REVERT: I 357 LEU cc_start: 0.8326 (mt) cc_final: 0.8044 (mt) REVERT: I 358 MET cc_start: 0.7561 (mmp) cc_final: 0.7120 (mmp) outliers start: 65 outliers final: 43 residues processed: 691 average time/residue: 0.1494 time to fit residues: 155.4885 Evaluate side-chains 706 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 655 time to evaluate : 0.656 ------------------------------------------------------------------------------- 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 113 SER Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 548 LYS Chi-restraints excluded: chain B residue 2 THR 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 230 MET Chi-restraints excluded: chain B residue 314 THR 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 38 CYS Chi-restraints excluded: chain E residue 201 SER 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 379 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 76 THR Chi-restraints excluded: chain C residue 102 LEU 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 434 ASP 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 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 406 GLU Chi-restraints excluded: chain D residue 477 THR Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain I residue 399 GLN 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 203 optimal weight: 1.9990 chunk 95 optimal weight: 2.9990 chunk 181 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 127 optimal weight: 10.0000 chunk 266 optimal weight: 8.9990 chunk 183 optimal weight: 3.9990 chunk 92 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 160 optimal weight: 4.9990 chunk 147 optimal weight: 0.0470 overall best weight: 1.9684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 ASN ** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 43 GLN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 ASN C 380 GLN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS D 284 GLN ** D 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 367 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.111294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.092989 restraints weight = 35188.557| |-----------------------------------------------------------------------------| r_work (start): 0.3089 rms_B_bonded: 2.07 r_work: 0.2986 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 22196 Z= 0.236 Angle : 0.568 8.388 30252 Z= 0.290 Chirality : 0.043 0.271 3258 Planarity : 0.005 0.116 3942 Dihedral : 5.073 55.600 2969 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.91 % Favored : 98.05 % Rotamer: Outliers : 3.06 % Allowed : 13.29 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.37 (0.15), residues: 2722 helix: 0.51 (0.39), residues: 183 sheet: -0.06 (0.19), residues: 638 loop : -0.35 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 417 TYR 0.015 0.002 TYR C 337 PHE 0.018 0.002 PHE B 219 TRP 0.013 0.001 TRP B 25 HIS 0.005 0.001 HIS B 536 Details of bonding type rmsd covalent geometry : bond 0.00524 (22196) covalent geometry : angle 0.56763 (30252) hydrogen bonds : bond 0.03693 ( 548) hydrogen bonds : angle 6.02104 ( 1443) *********************** 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 735 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 663 time to evaluate : 0.645 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: A 21 VAL cc_start: 0.8544 (t) cc_final: 0.8101 (m) REVERT: A 22 LYS cc_start: 0.8227 (mttt) cc_final: 0.7849 (mttt) REVERT: A 24 MET cc_start: 0.8313 (mmm) cc_final: 0.7842 (mmm) REVERT: A 124 SER cc_start: 0.8626 (m) cc_final: 0.8334 (p) REVERT: A 197 ILE cc_start: 0.8589 (OUTLIER) cc_final: 0.8346 (mt) REVERT: A 207 GLU cc_start: 0.6841 (tm-30) cc_final: 0.4414 (tt0) REVERT: A 240 GLU cc_start: 0.8226 (tp30) cc_final: 0.7895 (tp30) REVERT: A 295 ASN cc_start: 0.8023 (t0) cc_final: 0.7473 (t0) REVERT: A 296 SER cc_start: 0.8605 (t) cc_final: 0.8111 (p) REVERT: A 434 ASP cc_start: 0.8185 (m-30) cc_final: 0.7793 (p0) REVERT: A 435 ASP cc_start: 0.6236 (p0) cc_final: 0.5987 (p0) REVERT: A 486 MET cc_start: 0.8532 (OUTLIER) cc_final: 0.8295 (ptm) REVERT: A 540 LYS cc_start: 0.8539 (mttt) cc_final: 0.8134 (mttt) REVERT: A 546 THR cc_start: 0.8654 (p) cc_final: 0.8292 (t) REVERT: B 8 GLU cc_start: 0.7963 (mt-10) cc_final: 0.7438 (mt-10) REVERT: B 24 MET cc_start: 0.8210 (mmm) cc_final: 0.7938 (tpp) REVERT: B 51 GLU cc_start: 0.7397 (tt0) cc_final: 0.6734 (tt0) REVERT: B 53 HIS cc_start: 0.7855 (p90) cc_final: 0.7390 (p90) REVERT: B 110 ASN cc_start: 0.8333 (m-40) cc_final: 0.8003 (m110) REVERT: B 130 ASP cc_start: 0.7974 (m-30) cc_final: 0.7608 (m-30) REVERT: B 134 LYS cc_start: 0.8671 (tttt) cc_final: 0.8213 (ttpp) REVERT: B 154 ASP cc_start: 0.7628 (t0) cc_final: 0.7292 (t0) REVERT: B 215 GLU cc_start: 0.8086 (mp0) cc_final: 0.7709 (mp0) REVERT: B 230 MET cc_start: 0.8044 (OUTLIER) cc_final: 0.7665 (tmm) REVERT: B 296 SER cc_start: 0.8693 (t) cc_final: 0.8122 (p) REVERT: B 329 ARG cc_start: 0.8584 (mtt90) cc_final: 0.8100 (mtt-85) REVERT: B 376 ASN cc_start: 0.8216 (t0) cc_final: 0.7831 (t0) REVERT: B 377 GLU cc_start: 0.7230 (mm-30) cc_final: 0.6803 (mm-30) REVERT: B 435 ASP cc_start: 0.8432 (t0) cc_final: 0.7592 (p0) REVERT: B 523 TYR cc_start: 0.8838 (p90) cc_final: 0.8638 (p90) REVERT: B 524 ASP cc_start: 0.8630 (t0) cc_final: 0.8151 (t0) REVERT: B 532 GLN cc_start: 0.8103 (mm-40) cc_final: 0.7672 (mm-40) REVERT: B 539 GLU cc_start: 0.8061 (OUTLIER) cc_final: 0.7699 (tt0) REVERT: B 543 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7621 (tt0) REVERT: B 546 THR cc_start: 0.8367 (p) cc_final: 0.8046 (t) REVERT: B 554 LEU cc_start: 0.7338 (OUTLIER) cc_final: 0.7031 (mp) REVERT: E 81 MET cc_start: 0.8641 (tmm) cc_final: 0.8277 (ttp) REVERT: E 117 ASP cc_start: 0.7921 (t0) cc_final: 0.7671 (t0) REVERT: E 120 THR cc_start: 0.8480 (m) cc_final: 0.8198 (t) REVERT: E 129 LYS cc_start: 0.8311 (mttm) cc_final: 0.8001 (mttp) REVERT: E 130 ASP cc_start: 0.7717 (m-30) cc_final: 0.7463 (m-30) REVERT: E 193 ASN cc_start: 0.8259 (t0) cc_final: 0.7868 (t0) REVERT: E 202 LYS cc_start: 0.8706 (mttt) cc_final: 0.8417 (mttt) REVERT: E 215 GLU cc_start: 0.8203 (mp0) cc_final: 0.7272 (mp0) REVERT: E 294 VAL cc_start: 0.8733 (t) cc_final: 0.8393 (p) REVERT: E 389 MET cc_start: 0.8549 (tpp) cc_final: 0.8169 (tpt) REVERT: E 423 GLU cc_start: 0.8234 (mt-10) cc_final: 0.7986 (mt-10) REVERT: E 490 MET cc_start: 0.8432 (tpp) cc_final: 0.8197 (ttm) REVERT: E 540 LYS cc_start: 0.8650 (OUTLIER) cc_final: 0.8383 (mtpt) REVERT: E 543 GLU cc_start: 0.8001 (tt0) cc_final: 0.7785 (tt0) REVERT: E 550 ARG cc_start: 0.8338 (mtt90) cc_final: 0.8137 (mtt180) REVERT: E 554 LEU cc_start: 0.7195 (OUTLIER) cc_final: 0.6953 (mp) REVERT: C 5 ASN cc_start: 0.8097 (m-40) cc_final: 0.7776 (m-40) REVERT: C 21 VAL cc_start: 0.8681 (t) cc_final: 0.8379 (m) REVERT: C 51 GLU cc_start: 0.8013 (tt0) cc_final: 0.7641 (tt0) REVERT: C 55 LYS cc_start: 0.8631 (mtmm) cc_final: 0.8406 (mtmm) REVERT: C 103 GLU cc_start: 0.7815 (mt-10) cc_final: 0.7021 (mt-10) REVERT: C 143 ASP cc_start: 0.7259 (m-30) cc_final: 0.6927 (m-30) REVERT: C 151 MET cc_start: 0.8412 (ttm) cc_final: 0.8181 (ttp) REVERT: C 154 ASP cc_start: 0.8029 (t0) cc_final: 0.7522 (t0) REVERT: C 158 LYS cc_start: 0.5755 (tptp) cc_final: 0.5112 (tttp) REVERT: C 191 ASP cc_start: 0.7818 (m-30) cc_final: 0.7571 (m-30) REVERT: C 192 VAL cc_start: 0.8743 (t) cc_final: 0.8474 (p) REVERT: C 193 ASN cc_start: 0.7834 (t0) cc_final: 0.7519 (t0) REVERT: C 204 LEU cc_start: 0.8251 (mt) cc_final: 0.8014 (mm) REVERT: C 207 GLU cc_start: 0.5839 (tm-30) cc_final: 0.4158 (tm-30) REVERT: C 215 GLU cc_start: 0.8232 (mp0) cc_final: 0.7944 (mp0) REVERT: C 230 MET cc_start: 0.8238 (tmm) cc_final: 0.8028 (tmm) REVERT: C 294 VAL cc_start: 0.8699 (t) cc_final: 0.8391 (p) REVERT: C 295 ASN cc_start: 0.8271 (t0) cc_final: 0.7898 (t0) REVERT: C 371 VAL cc_start: 0.8957 (t) cc_final: 0.8637 (p) REVERT: C 374 PHE cc_start: 0.8592 (m-80) cc_final: 0.8262 (m-80) REVERT: C 414 VAL cc_start: 0.8727 (t) cc_final: 0.8392 (m) REVERT: C 471 LYS cc_start: 0.8403 (mmtt) cc_final: 0.7935 (mmtt) REVERT: C 521 VAL cc_start: 0.8619 (t) cc_final: 0.8352 (p) REVERT: C 524 ASP cc_start: 0.8246 (t0) cc_final: 0.7726 (t0) REVERT: C 534 HIS cc_start: 0.7983 (m-70) cc_final: 0.7669 (m-70) REVERT: C 542 GLU cc_start: 0.7984 (pt0) cc_final: 0.7783 (pt0) REVERT: C 546 THR cc_start: 0.8403 (p) cc_final: 0.8066 (m) REVERT: D 21 VAL cc_start: 0.8768 (t) cc_final: 0.8473 (m) REVERT: D 24 MET cc_start: 0.8509 (mmm) cc_final: 0.7841 (mmm) REVERT: D 49 ASP cc_start: 0.8490 (t0) cc_final: 0.8185 (t0) REVERT: D 51 GLU cc_start: 0.7653 (tt0) cc_final: 0.7350 (tt0) REVERT: D 55 LYS cc_start: 0.8820 (mttp) cc_final: 0.8464 (mttp) REVERT: D 58 SER cc_start: 0.8362 (t) cc_final: 0.8106 (p) REVERT: D 103 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7726 (mt-10) REVERT: D 151 MET cc_start: 0.8430 (ttp) cc_final: 0.8160 (ttp) REVERT: D 168 ASP cc_start: 0.8101 (t0) cc_final: 0.7827 (t0) REVERT: D 192 VAL cc_start: 0.8876 (t) cc_final: 0.8655 (p) REVERT: D 201 SER cc_start: 0.8279 (p) cc_final: 0.7982 (m) REVERT: D 203 LYS cc_start: 0.8437 (ttmm) cc_final: 0.8214 (ttmm) REVERT: D 207 GLU cc_start: 0.5726 (tm-30) cc_final: 0.4314 (tm-30) REVERT: D 215 GLU cc_start: 0.8343 (mp0) cc_final: 0.7551 (mp0) REVERT: D 341 ASP cc_start: 0.8086 (OUTLIER) cc_final: 0.7780 (m-30) REVERT: D 346 VAL cc_start: 0.8850 (t) cc_final: 0.8577 (p) REVERT: D 382 LYS cc_start: 0.8722 (mtmt) cc_final: 0.8373 (mtmt) REVERT: D 435 ASP cc_start: 0.8005 (t0) cc_final: 0.7532 (p0) REVERT: I 271 MET cc_start: 0.5154 (pmm) cc_final: 0.4659 (pmm) REVERT: I 358 MET cc_start: 0.7578 (mmp) cc_final: 0.7206 (mmp) outliers start: 72 outliers final: 52 residues processed: 682 average time/residue: 0.1492 time to fit residues: 152.0451 Evaluate side-chains 714 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 653 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 53 HIS Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 152 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 A residue 548 LYS Chi-restraints excluded: chain B residue 2 THR 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 230 MET Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 539 GLU 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 38 CYS 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 379 GLU 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 27 GLU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 133 ASP 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 434 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 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 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 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 20 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 178 optimal weight: 0.0870 chunk 77 optimal weight: 9.9990 chunk 169 optimal weight: 0.0770 chunk 128 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 200 optimal weight: 0.0010 chunk 31 optimal weight: 0.5980 chunk 191 optimal weight: 7.9990 chunk 166 optimal weight: 0.8980 overall best weight: 0.3322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 53 HIS E 517 HIS C 43 GLN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 451 GLN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 GLN D 380 GLN ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.113589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.095445 restraints weight = 35050.742| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.08 r_work: 0.2997 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.3928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.074 22196 Z= 0.098 Angle : 0.516 8.268 30252 Z= 0.262 Chirality : 0.040 0.269 3258 Planarity : 0.005 0.112 3942 Dihedral : 4.674 55.371 2969 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.36 % Favored : 98.60 % Rotamer: Outliers : 2.42 % Allowed : 14.82 % Favored : 82.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.15), residues: 2722 helix: 0.59 (0.39), residues: 183 sheet: -0.02 (0.20), residues: 613 loop : -0.25 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 417 TYR 0.013 0.001 TYR A 523 PHE 0.016 0.001 PHE I 315 TRP 0.015 0.001 TRP D 87 HIS 0.005 0.001 HIS A 339 Details of bonding type rmsd covalent geometry : bond 0.00220 (22196) covalent geometry : angle 0.51617 (30252) hydrogen bonds : bond 0.03019 ( 548) hydrogen bonds : angle 5.76206 ( 1443) *********************** 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 735 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 678 time to evaluate : 0.782 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: A 21 VAL cc_start: 0.8485 (t) cc_final: 0.8064 (m) REVERT: A 55 LYS cc_start: 0.8326 (mtpp) cc_final: 0.8123 (mtpp) REVERT: A 124 SER cc_start: 0.8638 (m) cc_final: 0.8309 (p) REVERT: A 197 ILE cc_start: 0.8576 (OUTLIER) cc_final: 0.8268 (mt) REVERT: A 207 GLU cc_start: 0.6761 (tm-30) cc_final: 0.3713 (tt0) REVERT: A 222 LEU cc_start: 0.8339 (mt) cc_final: 0.8078 (mp) REVERT: A 240 GLU cc_start: 0.8221 (tp30) cc_final: 0.7900 (tp30) REVERT: A 251 GLU cc_start: 0.6072 (tm-30) cc_final: 0.5833 (tm-30) REVERT: A 295 ASN cc_start: 0.8000 (t0) cc_final: 0.7640 (t0) REVERT: A 377 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7246 (mm-30) REVERT: A 382 LYS cc_start: 0.8288 (mtpt) cc_final: 0.7942 (ptpt) REVERT: A 434 ASP cc_start: 0.8119 (m-30) cc_final: 0.7679 (p0) REVERT: A 435 ASP cc_start: 0.5965 (p0) cc_final: 0.5758 (p0) REVERT: A 486 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.8263 (ptm) REVERT: A 540 LYS cc_start: 0.8452 (mttt) cc_final: 0.8035 (mttt) REVERT: A 546 THR cc_start: 0.8562 (p) cc_final: 0.8221 (t) REVERT: B 8 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7323 (mt-10) REVERT: B 24 MET cc_start: 0.8100 (mmm) cc_final: 0.7759 (tpp) REVERT: B 51 GLU cc_start: 0.7439 (tt0) cc_final: 0.6585 (tt0) REVERT: B 53 HIS cc_start: 0.7829 (p90) cc_final: 0.7136 (p-80) REVERT: B 110 ASN cc_start: 0.8229 (m-40) cc_final: 0.7827 (m110) REVERT: B 130 ASP cc_start: 0.7978 (m-30) cc_final: 0.7615 (m-30) REVERT: B 134 LYS cc_start: 0.8506 (tttt) cc_final: 0.8050 (ttpp) REVERT: B 154 ASP cc_start: 0.7651 (t0) cc_final: 0.7289 (t0) REVERT: B 203 LYS cc_start: 0.8546 (tttt) cc_final: 0.8190 (ttmm) REVERT: B 215 GLU cc_start: 0.8027 (mp0) cc_final: 0.7586 (mp0) REVERT: B 230 MET cc_start: 0.8191 (tmm) cc_final: 0.7761 (tmm) REVERT: B 273 PHE cc_start: 0.7977 (m-80) cc_final: 0.7746 (m-80) REVERT: B 329 ARG cc_start: 0.8522 (mtt90) cc_final: 0.8083 (mtt-85) REVERT: B 376 ASN cc_start: 0.8159 (t0) cc_final: 0.7699 (t0) REVERT: B 433 LEU cc_start: 0.8593 (mt) cc_final: 0.8313 (mm) REVERT: B 435 ASP cc_start: 0.8407 (t0) cc_final: 0.7548 (p0) REVERT: B 510 TYR cc_start: 0.8567 (m-10) cc_final: 0.8241 (m-10) REVERT: B 513 HIS cc_start: 0.8331 (p-80) cc_final: 0.8125 (p-80) REVERT: B 524 ASP cc_start: 0.8590 (t0) cc_final: 0.8100 (t0) REVERT: B 532 GLN cc_start: 0.8037 (mm-40) cc_final: 0.7508 (mm-40) REVERT: B 539 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7735 (tt0) REVERT: B 543 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7543 (tt0) REVERT: B 546 THR cc_start: 0.8312 (p) cc_final: 0.8019 (t) REVERT: B 554 LEU cc_start: 0.7205 (OUTLIER) cc_final: 0.6971 (mp) REVERT: E 18 SER cc_start: 0.8237 (p) cc_final: 0.7921 (m) REVERT: E 19 ASN cc_start: 0.8621 (t0) cc_final: 0.8288 (t0) REVERT: E 81 MET cc_start: 0.8643 (tmm) cc_final: 0.8337 (ttp) REVERT: E 117 ASP cc_start: 0.7787 (t0) cc_final: 0.7516 (t0) REVERT: E 120 THR cc_start: 0.8384 (m) cc_final: 0.8114 (t) REVERT: E 129 LYS cc_start: 0.8273 (mttm) cc_final: 0.7970 (mttp) REVERT: E 130 ASP cc_start: 0.7750 (m-30) cc_final: 0.7486 (m-30) REVERT: E 148 ARG cc_start: 0.8515 (mmt-90) cc_final: 0.8175 (mmt-90) REVERT: E 193 ASN cc_start: 0.8161 (t0) cc_final: 0.7675 (t0) REVERT: E 202 LYS cc_start: 0.8668 (mttt) cc_final: 0.8351 (mttt) REVERT: E 215 GLU cc_start: 0.8163 (mp0) cc_final: 0.7211 (mp0) REVERT: E 257 TYR cc_start: 0.8877 (m-80) cc_final: 0.8542 (m-80) REVERT: E 294 VAL cc_start: 0.8678 (t) cc_final: 0.8338 (p) REVERT: E 347 THR cc_start: 0.8413 (m) cc_final: 0.8104 (p) REVERT: E 382 LYS cc_start: 0.8425 (mtmm) cc_final: 0.8200 (ptmt) REVERT: E 389 MET cc_start: 0.8499 (tpp) cc_final: 0.8130 (tpt) REVERT: E 423 GLU cc_start: 0.8155 (mt-10) cc_final: 0.7874 (mt-10) REVERT: E 427 TRP cc_start: 0.8650 (p90) cc_final: 0.8353 (p90) REVERT: E 540 LYS cc_start: 0.8628 (OUTLIER) cc_final: 0.8347 (mtpt) REVERT: E 543 GLU cc_start: 0.7885 (tt0) cc_final: 0.7659 (tt0) REVERT: C 5 ASN cc_start: 0.7989 (m-40) cc_final: 0.7681 (m-40) REVERT: C 21 VAL cc_start: 0.8597 (t) cc_final: 0.8381 (m) REVERT: C 55 LYS cc_start: 0.8594 (mtmm) cc_final: 0.8367 (mtmm) REVERT: C 151 MET cc_start: 0.8395 (ttm) cc_final: 0.7985 (ttp) REVERT: C 158 LYS cc_start: 0.5864 (tptp) cc_final: 0.5199 (tttp) REVERT: C 191 ASP cc_start: 0.7837 (m-30) cc_final: 0.7573 (m-30) REVERT: C 192 VAL cc_start: 0.8751 (t) cc_final: 0.8460 (p) REVERT: C 193 ASN cc_start: 0.7786 (t0) cc_final: 0.7475 (t0) REVERT: C 204 LEU cc_start: 0.8163 (mt) cc_final: 0.7935 (mm) REVERT: C 215 GLU cc_start: 0.8156 (mp0) cc_final: 0.7888 (mp0) REVERT: C 294 VAL cc_start: 0.8654 (t) cc_final: 0.8301 (p) REVERT: C 295 ASN cc_start: 0.8087 (t0) cc_final: 0.7745 (t0) REVERT: C 371 VAL cc_start: 0.8890 (t) cc_final: 0.8555 (p) REVERT: C 374 PHE cc_start: 0.8489 (m-80) cc_final: 0.8147 (m-80) REVERT: C 414 VAL cc_start: 0.8761 (t) cc_final: 0.8412 (m) REVERT: C 440 GLN cc_start: 0.8351 (mp10) cc_final: 0.7865 (mt0) REVERT: C 471 LYS cc_start: 0.8400 (mmtt) cc_final: 0.7891 (mmtt) REVERT: C 518 LEU cc_start: 0.8756 (mt) cc_final: 0.8551 (mp) REVERT: C 521 VAL cc_start: 0.8563 (t) cc_final: 0.8285 (p) REVERT: C 524 ASP cc_start: 0.8265 (t0) cc_final: 0.7866 (t0) REVERT: C 534 HIS cc_start: 0.7919 (m-70) cc_final: 0.7602 (m-70) REVERT: C 546 THR cc_start: 0.8417 (p) cc_final: 0.8112 (m) REVERT: D 21 VAL cc_start: 0.8738 (t) cc_final: 0.8432 (m) REVERT: D 24 MET cc_start: 0.8314 (mmm) cc_final: 0.7783 (mmm) REVERT: D 49 ASP cc_start: 0.8500 (t0) cc_final: 0.8165 (t0) REVERT: D 51 GLU cc_start: 0.7619 (tt0) cc_final: 0.7372 (tt0) REVERT: D 55 LYS cc_start: 0.8787 (mttp) cc_final: 0.8424 (mttp) REVERT: D 58 SER cc_start: 0.8351 (t) cc_final: 0.8132 (p) REVERT: D 103 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7677 (mt-10) REVERT: D 151 MET cc_start: 0.8356 (ttp) cc_final: 0.8099 (ttp) REVERT: D 168 ASP cc_start: 0.7990 (t0) cc_final: 0.7748 (t0) REVERT: D 192 VAL cc_start: 0.8801 (t) cc_final: 0.8561 (p) REVERT: D 201 SER cc_start: 0.8183 (p) cc_final: 0.7880 (m) REVERT: D 203 LYS cc_start: 0.8441 (ttmm) cc_final: 0.8202 (ttmm) REVERT: D 215 GLU cc_start: 0.8253 (mp0) cc_final: 0.7464 (mp0) REVERT: D 242 LEU cc_start: 0.8508 (mt) cc_final: 0.8225 (mp) REVERT: D 341 ASP cc_start: 0.8025 (t0) cc_final: 0.7795 (m-30) REVERT: D 343 ASP cc_start: 0.8178 (p0) cc_final: 0.7886 (p0) REVERT: D 346 VAL cc_start: 0.8800 (t) cc_final: 0.8545 (p) REVERT: D 382 LYS cc_start: 0.8714 (mtmt) cc_final: 0.8311 (mtmt) REVERT: D 389 MET cc_start: 0.8473 (mmm) cc_final: 0.8080 (tpt) REVERT: D 435 ASP cc_start: 0.8035 (t0) cc_final: 0.7511 (p0) REVERT: D 447 TRP cc_start: 0.8766 (m-90) cc_final: 0.8319 (m-90) REVERT: D 521 VAL cc_start: 0.8531 (t) cc_final: 0.8245 (p) REVERT: I 271 MET cc_start: 0.4706 (pmm) cc_final: 0.4180 (pmm) REVERT: I 358 MET cc_start: 0.7591 (mmp) cc_final: 0.7224 (mmp) outliers start: 57 outliers final: 42 residues processed: 696 average time/residue: 0.1476 time to fit residues: 154.8567 Evaluate side-chains 707 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 659 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 113 SER 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 406 GLU Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 2 THR 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 192 VAL Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 539 GLU 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 38 CYS Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 134 LYS 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 379 GLU Chi-restraints excluded: chain E residue 406 GLU 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 405 ILE Chi-restraints excluded: chain C residue 420 LEU 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 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 477 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 41 optimal weight: 0.7980 chunk 178 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 97 optimal weight: 2.9990 chunk 184 optimal weight: 0.8980 chunk 146 optimal weight: 5.9990 chunk 226 optimal weight: 1.9990 chunk 173 optimal weight: 3.9990 chunk 264 optimal weight: 7.9990 chunk 245 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 ASN A 388 ASN ** 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** E 53 HIS E 517 HIS C 183 GLN ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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** I 441 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.110000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.091514 restraints weight = 35951.674| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.16 r_work: 0.2965 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.4017 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= 0.175 Angle : 0.543 10.481 30252 Z= 0.273 Chirality : 0.041 0.261 3258 Planarity : 0.005 0.111 3942 Dihedral : 4.627 20.486 2967 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.76 % Favored : 98.20 % Rotamer: Outliers : 2.68 % Allowed : 14.78 % Favored : 82.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.27 (0.15), residues: 2722 helix: 0.61 (0.39), residues: 183 sheet: 0.02 (0.19), residues: 638 loop : -0.30 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 417 TYR 0.014 0.001 TYR A 523 PHE 0.019 0.002 PHE E 57 TRP 0.012 0.001 TRP B 25 HIS 0.005 0.001 HIS B 216 Details of bonding type rmsd covalent geometry : bond 0.00391 (22196) covalent geometry : angle 0.54280 (30252) hydrogen bonds : bond 0.03337 ( 548) hydrogen bonds : angle 5.82201 ( 1443) *********************** 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 728 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 665 time to evaluate : 0.816 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: A 21 VAL cc_start: 0.8520 (t) cc_final: 0.8082 (m) REVERT: A 22 LYS cc_start: 0.8233 (mttt) cc_final: 0.7844 (mttt) REVERT: A 55 LYS cc_start: 0.8366 (mtpp) cc_final: 0.8141 (mtpp) REVERT: A 124 SER cc_start: 0.8560 (m) cc_final: 0.8224 (p) REVERT: A 197 ILE cc_start: 0.8594 (OUTLIER) cc_final: 0.8304 (mt) REVERT: A 207 GLU cc_start: 0.6775 (tm-30) cc_final: 0.4398 (tt0) REVERT: A 227 THR cc_start: 0.7819 (p) cc_final: 0.7609 (p) REVERT: A 240 GLU cc_start: 0.8276 (tp30) cc_final: 0.7954 (tp30) REVERT: A 251 GLU cc_start: 0.6113 (tm-30) cc_final: 0.5859 (tm-30) REVERT: A 284 GLN cc_start: 0.8393 (tp40) cc_final: 0.7741 (tm-30) REVERT: A 295 ASN cc_start: 0.8046 (t0) cc_final: 0.7674 (t0) REVERT: A 377 GLU cc_start: 0.7682 (mm-30) cc_final: 0.7273 (mm-30) REVERT: A 382 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.7877 (ptpt) REVERT: A 434 ASP cc_start: 0.8149 (m-30) cc_final: 0.7711 (p0) REVERT: A 435 ASP cc_start: 0.6155 (p0) cc_final: 0.5899 (p0) REVERT: A 486 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8265 (ptm) REVERT: A 540 LYS cc_start: 0.8444 (mttt) cc_final: 0.8070 (mttt) REVERT: A 546 THR cc_start: 0.8567 (p) cc_final: 0.8226 (t) REVERT: B 8 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7348 (mt-10) REVERT: B 51 GLU cc_start: 0.7461 (tt0) cc_final: 0.6838 (tt0) REVERT: B 53 HIS cc_start: 0.7855 (p90) cc_final: 0.7373 (p90) REVERT: B 110 ASN cc_start: 0.8288 (m-40) cc_final: 0.7896 (m110) REVERT: B 120 THR cc_start: 0.8394 (m) cc_final: 0.8182 (t) REVERT: B 130 ASP cc_start: 0.8017 (m-30) cc_final: 0.7668 (m-30) REVERT: B 134 LYS cc_start: 0.8595 (tttt) cc_final: 0.8132 (ttpp) REVERT: B 154 ASP cc_start: 0.7652 (t0) cc_final: 0.7241 (t0) REVERT: B 193 ASN cc_start: 0.8434 (t0) cc_final: 0.8076 (t0) REVERT: B 215 GLU cc_start: 0.8096 (mp0) cc_final: 0.7696 (mp0) REVERT: B 230 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7785 (tmm) REVERT: B 273 PHE cc_start: 0.8066 (m-80) cc_final: 0.7745 (m-80) REVERT: B 329 ARG cc_start: 0.8644 (mtt90) cc_final: 0.8172 (mtt-85) REVERT: B 376 ASN cc_start: 0.8164 (t0) cc_final: 0.7756 (t0) REVERT: B 435 ASP cc_start: 0.8442 (t0) cc_final: 0.7592 (p0) REVERT: B 510 TYR cc_start: 0.8576 (m-10) cc_final: 0.8267 (m-10) REVERT: B 513 HIS cc_start: 0.8379 (p-80) cc_final: 0.8115 (p-80) REVERT: B 524 ASP cc_start: 0.8568 (t0) cc_final: 0.8123 (t0) REVERT: B 532 GLN cc_start: 0.8042 (mm-40) cc_final: 0.7546 (mm-40) REVERT: B 543 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7639 (tt0) REVERT: B 546 THR cc_start: 0.8378 (p) cc_final: 0.8073 (t) REVERT: B 554 LEU cc_start: 0.7276 (OUTLIER) cc_final: 0.6998 (mp) REVERT: E 18 SER cc_start: 0.8286 (p) cc_final: 0.7888 (m) REVERT: E 19 ASN cc_start: 0.8701 (t0) cc_final: 0.8357 (t0) REVERT: E 81 MET cc_start: 0.8665 (tmm) cc_final: 0.8355 (ttp) REVERT: E 117 ASP cc_start: 0.7843 (t0) cc_final: 0.7596 (t0) REVERT: E 120 THR cc_start: 0.8271 (m) cc_final: 0.7999 (t) REVERT: E 129 LYS cc_start: 0.8327 (mttm) cc_final: 0.8066 (mttp) REVERT: E 130 ASP cc_start: 0.7808 (m-30) cc_final: 0.7539 (m-30) REVERT: E 193 ASN cc_start: 0.8207 (t0) cc_final: 0.7720 (t0) REVERT: E 202 LYS cc_start: 0.8709 (mttt) cc_final: 0.8381 (mttt) REVERT: E 215 GLU cc_start: 0.8224 (mp0) cc_final: 0.7276 (mp0) REVERT: E 257 TYR cc_start: 0.8900 (m-80) cc_final: 0.8678 (m-80) REVERT: E 294 VAL cc_start: 0.8693 (t) cc_final: 0.8352 (p) REVERT: E 423 GLU cc_start: 0.8206 (mt-10) cc_final: 0.7977 (mt-10) REVERT: E 427 TRP cc_start: 0.8648 (p90) cc_final: 0.8357 (p90) REVERT: E 540 LYS cc_start: 0.8672 (OUTLIER) cc_final: 0.8384 (mtpt) REVERT: E 543 GLU cc_start: 0.7853 (tt0) cc_final: 0.7638 (tt0) REVERT: E 554 LEU cc_start: 0.7112 (OUTLIER) cc_final: 0.6911 (mp) REVERT: C 5 ASN cc_start: 0.8063 (m-40) cc_final: 0.7749 (m-40) REVERT: C 55 LYS cc_start: 0.8628 (mtmm) cc_final: 0.8411 (mtmm) REVERT: C 151 MET cc_start: 0.8498 (ttm) cc_final: 0.8171 (ttp) REVERT: C 154 ASP cc_start: 0.8015 (t0) cc_final: 0.7511 (t0) REVERT: C 158 LYS cc_start: 0.5690 (tptp) cc_final: 0.4965 (tttp) REVERT: C 191 ASP cc_start: 0.7851 (m-30) cc_final: 0.7599 (m-30) REVERT: C 192 VAL cc_start: 0.8719 (t) cc_final: 0.8448 (p) REVERT: C 193 ASN cc_start: 0.7835 (t0) cc_final: 0.7521 (t0) REVERT: C 204 LEU cc_start: 0.8212 (mt) cc_final: 0.7977 (mm) REVERT: C 215 GLU cc_start: 0.8232 (mp0) cc_final: 0.7420 (mp0) REVERT: C 231 SER cc_start: 0.8566 (t) cc_final: 0.8169 (p) REVERT: C 294 VAL cc_start: 0.8653 (t) cc_final: 0.8308 (p) REVERT: C 295 ASN cc_start: 0.8082 (t0) cc_final: 0.7731 (t0) REVERT: C 371 VAL cc_start: 0.8922 (t) cc_final: 0.8587 (p) REVERT: C 373 ARG cc_start: 0.8642 (mtp180) cc_final: 0.8424 (mtp180) REVERT: C 374 PHE cc_start: 0.8501 (m-80) cc_final: 0.8190 (m-80) REVERT: C 414 VAL cc_start: 0.8791 (t) cc_final: 0.8448 (m) REVERT: C 435 ASP cc_start: 0.5852 (OUTLIER) cc_final: 0.5326 (t70) REVERT: C 471 LYS cc_start: 0.8456 (mmtt) cc_final: 0.8007 (mmtt) REVERT: C 521 VAL cc_start: 0.8576 (t) cc_final: 0.8304 (p) REVERT: C 524 ASP cc_start: 0.8290 (t0) cc_final: 0.7809 (t0) REVERT: C 534 HIS cc_start: 0.7956 (m-70) cc_final: 0.7646 (m-70) REVERT: C 546 THR cc_start: 0.8390 (p) cc_final: 0.8096 (m) REVERT: D 21 VAL cc_start: 0.8744 (t) cc_final: 0.8440 (m) REVERT: D 49 ASP cc_start: 0.8505 (t0) cc_final: 0.8197 (t0) REVERT: D 51 GLU cc_start: 0.7641 (tt0) cc_final: 0.7337 (tt0) REVERT: D 55 LYS cc_start: 0.8807 (mttp) cc_final: 0.8441 (mttp) REVERT: D 58 SER cc_start: 0.8366 (t) cc_final: 0.8158 (p) REVERT: D 103 GLU cc_start: 0.7988 (mt-10) cc_final: 0.7732 (mt-10) REVERT: D 134 LYS cc_start: 0.8786 (ttpp) cc_final: 0.8251 (ttpp) REVERT: D 151 MET cc_start: 0.8358 (ttp) cc_final: 0.8107 (ttp) REVERT: D 168 ASP cc_start: 0.8071 (t0) cc_final: 0.7807 (t0) REVERT: D 192 VAL cc_start: 0.8834 (t) cc_final: 0.8589 (p) REVERT: D 201 SER cc_start: 0.8232 (p) cc_final: 0.7958 (m) REVERT: D 203 LYS cc_start: 0.8482 (ttmm) cc_final: 0.8237 (ttmm) REVERT: D 215 GLU cc_start: 0.8307 (mp0) cc_final: 0.7460 (mp0) REVERT: D 242 LEU cc_start: 0.8548 (mt) cc_final: 0.8255 (mp) REVERT: D 341 ASP cc_start: 0.8062 (t0) cc_final: 0.7774 (m-30) REVERT: D 346 VAL cc_start: 0.8792 (t) cc_final: 0.8522 (p) REVERT: D 382 LYS cc_start: 0.8772 (mtmt) cc_final: 0.8490 (mtmt) REVERT: D 389 MET cc_start: 0.8572 (mmm) cc_final: 0.8170 (tpt) REVERT: D 435 ASP cc_start: 0.8019 (t0) cc_final: 0.7521 (p0) REVERT: D 521 VAL cc_start: 0.8546 (t) cc_final: 0.8257 (p) REVERT: I 271 MET cc_start: 0.4672 (pmm) cc_final: 0.4127 (pmm) REVERT: I 358 MET cc_start: 0.7659 (mmp) cc_final: 0.7238 (mmp) outliers start: 63 outliers final: 48 residues processed: 684 average time/residue: 0.1614 time to fit residues: 165.1227 Evaluate side-chains 712 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 656 time to evaluate : 0.633 ------------------------------------------------------------------------------- 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 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 382 LYS 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 548 LYS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 2 THR 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 151 MET Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 38 CYS Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain E residue 134 LYS 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 378 LYS Chi-restraints excluded: chain E residue 379 GLU Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 473 MET 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 27 GLU Chi-restraints excluded: chain C residue 76 THR 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 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 133 ASP Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 477 THR 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 256 optimal weight: 0.2980 chunk 269 optimal weight: 0.0980 chunk 101 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 113 optimal weight: 0.9980 chunk 78 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 176 optimal weight: 4.9990 chunk 60 optimal weight: 0.7980 chunk 52 optimal weight: 6.9990 chunk 193 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** 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 E 53 HIS E 517 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.111315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.092920 restraints weight = 35860.590| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.16 r_work: 0.2989 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.072 22196 Z= 0.107 Angle : 0.522 8.721 30252 Z= 0.262 Chirality : 0.040 0.260 3258 Planarity : 0.004 0.107 3942 Dihedral : 4.443 18.478 2967 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.58 % Favored : 98.38 % Rotamer: Outliers : 2.51 % Allowed : 15.46 % Favored : 82.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.19 (0.15), residues: 2722 helix: 0.69 (0.39), residues: 183 sheet: 0.03 (0.20), residues: 613 loop : -0.22 (0.13), residues: 1926 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 417 TYR 0.013 0.001 TYR A 523 PHE 0.018 0.001 PHE E 57 TRP 0.012 0.001 TRP D 87 HIS 0.005 0.001 HIS E 53 Details of bonding type rmsd covalent geometry : bond 0.00244 (22196) covalent geometry : angle 0.52173 (30252) hydrogen bonds : bond 0.03000 ( 548) hydrogen bonds : angle 5.69727 ( 1443) *********************** 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 739 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 680 time to evaluate : 0.862 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 21 VAL cc_start: 0.8480 (t) cc_final: 0.8057 (m) REVERT: A 22 LYS cc_start: 0.8207 (mttt) cc_final: 0.7841 (mttt) REVERT: A 55 LYS cc_start: 0.8366 (mtpp) cc_final: 0.8138 (mtpp) REVERT: A 124 SER cc_start: 0.8593 (m) cc_final: 0.8210 (p) REVERT: A 197 ILE cc_start: 0.8563 (OUTLIER) cc_final: 0.8267 (mt) REVERT: A 207 GLU cc_start: 0.6871 (tm-30) cc_final: 0.4441 (tt0) REVERT: A 227 THR cc_start: 0.7693 (p) cc_final: 0.7478 (p) REVERT: A 240 GLU cc_start: 0.8291 (tp30) cc_final: 0.7971 (tp30) REVERT: A 251 GLU cc_start: 0.6100 (tm-30) cc_final: 0.5872 (tm-30) REVERT: A 284 GLN cc_start: 0.8418 (tp40) cc_final: 0.7750 (tm-30) REVERT: A 295 ASN cc_start: 0.8005 (t0) cc_final: 0.7653 (t0) REVERT: A 296 SER cc_start: 0.8586 (t) cc_final: 0.8381 (m) REVERT: A 325 ARG cc_start: 0.8497 (mtm180) cc_final: 0.8273 (mtm180) REVERT: A 382 LYS cc_start: 0.8249 (OUTLIER) cc_final: 0.7926 (ptpt) REVERT: A 384 LEU cc_start: 0.8810 (mt) cc_final: 0.8597 (mt) REVERT: A 434 ASP cc_start: 0.8021 (m-30) cc_final: 0.7647 (p0) REVERT: A 435 ASP cc_start: 0.5940 (p0) cc_final: 0.5634 (p0) REVERT: A 486 MET cc_start: 0.8493 (OUTLIER) cc_final: 0.8236 (ptm) REVERT: A 540 LYS cc_start: 0.8418 (mttt) cc_final: 0.8008 (mttt) REVERT: A 546 THR cc_start: 0.8513 (p) cc_final: 0.8144 (t) REVERT: B 8 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7335 (mt-10) REVERT: B 51 GLU cc_start: 0.7466 (tt0) cc_final: 0.6907 (tt0) REVERT: B 53 HIS cc_start: 0.7884 (p90) cc_final: 0.7449 (p90) REVERT: B 110 ASN cc_start: 0.8185 (m-40) cc_final: 0.7791 (m110) REVERT: B 130 ASP cc_start: 0.8016 (m-30) cc_final: 0.7647 (m-30) REVERT: B 134 LYS cc_start: 0.8499 (tttt) cc_final: 0.8039 (ttpp) REVERT: B 154 ASP cc_start: 0.7662 (t0) cc_final: 0.7229 (t0) REVERT: B 193 ASN cc_start: 0.8416 (t0) cc_final: 0.8070 (t0) REVERT: B 203 LYS cc_start: 0.8549 (tttt) cc_final: 0.8166 (ttmm) REVERT: B 215 GLU cc_start: 0.8055 (mp0) cc_final: 0.7650 (mp0) REVERT: B 230 MET cc_start: 0.8213 (OUTLIER) cc_final: 0.7762 (tmm) REVERT: B 273 PHE cc_start: 0.7995 (m-80) cc_final: 0.7711 (m-80) REVERT: B 329 ARG cc_start: 0.8634 (mtt90) cc_final: 0.8147 (mtt-85) REVERT: B 376 ASN cc_start: 0.8145 (t0) cc_final: 0.7769 (t0) REVERT: B 435 ASP cc_start: 0.8434 (t0) cc_final: 0.7558 (p0) REVERT: B 463 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8552 (mm-40) REVERT: B 510 TYR cc_start: 0.8577 (m-10) cc_final: 0.8219 (m-80) REVERT: B 513 HIS cc_start: 0.8344 (p-80) cc_final: 0.8136 (p-80) REVERT: B 524 ASP cc_start: 0.8528 (t0) cc_final: 0.8024 (t0) REVERT: B 532 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7496 (mm-40) REVERT: B 539 GLU cc_start: 0.8003 (tt0) cc_final: 0.7727 (tt0) REVERT: B 543 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7542 (tt0) REVERT: B 546 THR cc_start: 0.8352 (OUTLIER) cc_final: 0.8069 (t) REVERT: B 554 LEU cc_start: 0.7217 (OUTLIER) cc_final: 0.7002 (mp) REVERT: E 18 SER cc_start: 0.8208 (p) cc_final: 0.7991 (m) REVERT: E 19 ASN cc_start: 0.8627 (t0) cc_final: 0.8291 (t0) REVERT: E 81 MET cc_start: 0.8679 (tmm) cc_final: 0.8389 (ttp) REVERT: E 117 ASP cc_start: 0.7800 (t0) cc_final: 0.7552 (t0) REVERT: E 120 THR cc_start: 0.8207 (m) cc_final: 0.7955 (t) REVERT: E 129 LYS cc_start: 0.8314 (mttm) cc_final: 0.8057 (mttp) REVERT: E 130 ASP cc_start: 0.7796 (m-30) cc_final: 0.7534 (m-30) REVERT: E 193 ASN cc_start: 0.8173 (t0) cc_final: 0.7687 (t0) REVERT: E 202 LYS cc_start: 0.8684 (mttt) cc_final: 0.8356 (mttt) REVERT: E 215 GLU cc_start: 0.8189 (mp0) cc_final: 0.7274 (mp0) REVERT: E 257 TYR cc_start: 0.8891 (m-80) cc_final: 0.8568 (m-80) REVERT: E 294 VAL cc_start: 0.8676 (t) cc_final: 0.8340 (p) REVERT: E 382 LYS cc_start: 0.8326 (mtmm) cc_final: 0.7877 (mtmt) REVERT: E 423 GLU cc_start: 0.8170 (mt-10) cc_final: 0.7920 (mt-10) REVERT: E 427 TRP cc_start: 0.8665 (p90) cc_final: 0.8357 (p90) REVERT: E 490 MET cc_start: 0.8411 (ttm) cc_final: 0.8115 (mtp) REVERT: E 540 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8295 (mtpt) REVERT: E 543 GLU cc_start: 0.7816 (tt0) cc_final: 0.7597 (tt0) REVERT: C 5 ASN cc_start: 0.7992 (m-40) cc_final: 0.7688 (m-40) REVERT: C 21 VAL cc_start: 0.8613 (t) cc_final: 0.8280 (m) REVERT: C 55 LYS cc_start: 0.8613 (mtmm) cc_final: 0.8394 (mtmm) REVERT: C 151 MET cc_start: 0.8479 (ttm) cc_final: 0.8154 (ttp) REVERT: C 154 ASP cc_start: 0.8003 (t0) cc_final: 0.7484 (t0) REVERT: C 158 LYS cc_start: 0.5620 (tptp) cc_final: 0.4896 (tttp) REVERT: C 191 ASP cc_start: 0.7843 (m-30) cc_final: 0.7549 (m-30) REVERT: C 192 VAL cc_start: 0.8749 (t) cc_final: 0.8471 (p) REVERT: C 193 ASN cc_start: 0.7816 (t0) cc_final: 0.7507 (t0) REVERT: C 204 LEU cc_start: 0.8205 (mt) cc_final: 0.7970 (mm) REVERT: C 215 GLU cc_start: 0.8184 (mp0) cc_final: 0.7409 (mp0) REVERT: C 231 SER cc_start: 0.8484 (t) cc_final: 0.8278 (m) REVERT: C 294 VAL cc_start: 0.8649 (t) cc_final: 0.8304 (p) REVERT: C 295 ASN cc_start: 0.8071 (t0) cc_final: 0.7712 (t0) REVERT: C 371 VAL cc_start: 0.8951 (t) cc_final: 0.8587 (p) REVERT: C 373 ARG cc_start: 0.8599 (mtp180) cc_final: 0.8347 (mtp180) REVERT: C 374 PHE cc_start: 0.8483 (m-80) cc_final: 0.8235 (m-80) REVERT: C 414 VAL cc_start: 0.8764 (t) cc_final: 0.8421 (m) REVERT: C 435 ASP cc_start: 0.5805 (OUTLIER) cc_final: 0.5275 (t70) REVERT: C 440 GLN cc_start: 0.8373 (mp10) cc_final: 0.7876 (mt0) REVERT: C 471 LYS cc_start: 0.8441 (mmtt) cc_final: 0.8008 (mmtt) REVERT: C 521 VAL cc_start: 0.8557 (t) cc_final: 0.8275 (p) REVERT: C 524 ASP cc_start: 0.8246 (t0) cc_final: 0.7790 (t0) REVERT: C 534 HIS cc_start: 0.7912 (m-70) cc_final: 0.7603 (m-70) REVERT: C 543 GLU cc_start: 0.7913 (tt0) cc_final: 0.7665 (tt0) REVERT: C 546 THR cc_start: 0.8399 (p) cc_final: 0.8099 (m) REVERT: D 21 VAL cc_start: 0.8735 (t) cc_final: 0.8440 (m) REVERT: D 49 ASP cc_start: 0.8499 (t0) cc_final: 0.8187 (t0) REVERT: D 51 GLU cc_start: 0.7628 (tt0) cc_final: 0.7377 (tt0) REVERT: D 55 LYS cc_start: 0.8761 (mttp) cc_final: 0.8375 (mttp) REVERT: D 58 SER cc_start: 0.8393 (t) cc_final: 0.8164 (p) REVERT: D 103 GLU cc_start: 0.7947 (mt-10) cc_final: 0.7689 (mt-10) REVERT: D 134 LYS cc_start: 0.8794 (ttpp) cc_final: 0.8221 (ttpp) REVERT: D 151 MET cc_start: 0.8340 (ttp) cc_final: 0.8105 (ttp) REVERT: D 168 ASP cc_start: 0.7997 (t0) cc_final: 0.7755 (t0) REVERT: D 192 VAL cc_start: 0.8791 (t) cc_final: 0.8547 (p) REVERT: D 201 SER cc_start: 0.8194 (p) cc_final: 0.7931 (m) REVERT: D 203 LYS cc_start: 0.8465 (ttmm) cc_final: 0.8222 (ttmm) REVERT: D 215 GLU cc_start: 0.8287 (mp0) cc_final: 0.7436 (mp0) REVERT: D 242 LEU cc_start: 0.8514 (mt) cc_final: 0.8234 (mp) REVERT: D 341 ASP cc_start: 0.8049 (t0) cc_final: 0.7809 (m-30) REVERT: D 343 ASP cc_start: 0.8281 (p0) cc_final: 0.8000 (p0) REVERT: D 346 VAL cc_start: 0.8777 (t) cc_final: 0.8533 (p) REVERT: D 382 LYS cc_start: 0.8757 (mtmt) cc_final: 0.8346 (mtmt) REVERT: D 389 MET cc_start: 0.8527 (mmm) cc_final: 0.8156 (tpt) REVERT: D 435 ASP cc_start: 0.7981 (t0) cc_final: 0.7489 (p0) REVERT: D 447 TRP cc_start: 0.8791 (m-90) cc_final: 0.8358 (m-90) REVERT: D 493 LYS cc_start: 0.8443 (mtmt) cc_final: 0.8200 (mtmt) REVERT: D 521 VAL cc_start: 0.8491 (t) cc_final: 0.8211 (p) REVERT: I 271 MET cc_start: 0.4313 (pmm) cc_final: 0.3727 (pmm) REVERT: I 358 MET cc_start: 0.7673 (mmp) cc_final: 0.7268 (mmp) outliers start: 59 outliers final: 44 residues processed: 699 average time/residue: 0.1567 time to fit residues: 164.0958 Evaluate side-chains 723 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 670 time to evaluate : 0.848 ------------------------------------------------------------------------------- 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 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 382 LYS 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 548 LYS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 2 THR 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 151 MET Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 406 GLU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain B residue 554 LEU Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 38 CYS Chi-restraints excluded: chain E residue 76 THR 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 378 LYS Chi-restraints excluded: chain E residue 420 LEU 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 405 ILE Chi-restraints excluded: chain C residue 420 LEU 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 133 ASP Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 477 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 41 optimal weight: 0.6980 chunk 181 optimal weight: 5.9990 chunk 205 optimal weight: 2.9990 chunk 130 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 261 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** 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 53 HIS E 517 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3386 r_free = 0.3386 target = 0.111701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.093596 restraints weight = 35384.469| |-----------------------------------------------------------------------------| r_work (start): 0.3107 rms_B_bonded: 2.07 r_work: 0.3005 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 22196 Z= 0.251 Angle : 0.585 9.165 30252 Z= 0.296 Chirality : 0.043 0.249 3258 Planarity : 0.005 0.105 3942 Dihedral : 4.768 19.762 2967 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.04 % Allowed : 2.06 % Favored : 97.91 % Rotamer: Outliers : 2.29 % Allowed : 15.75 % Favored : 81.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.34 (0.15), residues: 2722 helix: 0.53 (0.39), residues: 183 sheet: -0.02 (0.20), residues: 638 loop : -0.34 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 325 TYR 0.029 0.002 TYR C 250 PHE 0.020 0.002 PHE E 57 TRP 0.014 0.001 TRP C 177 HIS 0.006 0.001 HIS B 106 Details of bonding type rmsd covalent geometry : bond 0.00558 (22196) covalent geometry : angle 0.58541 (30252) hydrogen bonds : bond 0.03700 ( 548) hydrogen bonds : angle 5.88557 ( 1443) ********************** 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 719 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 665 time to evaluate : 0.862 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: 0.8543 (t) cc_final: 0.8132 (m) REVERT: A 22 LYS cc_start: 0.8288 (mttt) cc_final: 0.7899 (mttt) REVERT: A 24 MET cc_start: 0.8309 (mmm) cc_final: 0.7851 (mmm) REVERT: A 55 LYS cc_start: 0.8360 (mtpp) cc_final: 0.8134 (mtpp) REVERT: A 124 SER cc_start: 0.8562 (m) cc_final: 0.8213 (p) REVERT: A 197 ILE cc_start: 0.8583 (OUTLIER) cc_final: 0.8286 (mt) REVERT: A 207 GLU cc_start: 0.6840 (tm-30) cc_final: 0.4456 (tt0) REVERT: A 227 THR cc_start: 0.8221 (p) cc_final: 0.7990 (p) REVERT: A 240 GLU cc_start: 0.8309 (tp30) cc_final: 0.7994 (tp30) REVERT: A 251 GLU cc_start: 0.6167 (tm-30) cc_final: 0.5920 (tm-30) REVERT: A 284 GLN cc_start: 0.8417 (tp40) cc_final: 0.7751 (tm-30) REVERT: A 295 ASN cc_start: 0.8060 (t0) cc_final: 0.7695 (t0) REVERT: A 434 ASP cc_start: 0.8147 (m-30) cc_final: 0.7733 (p0) REVERT: A 486 MET cc_start: 0.8489 (OUTLIER) cc_final: 0.8233 (ptm) REVERT: A 540 LYS cc_start: 0.8452 (mttt) cc_final: 0.8085 (mttt) REVERT: A 546 THR cc_start: 0.8539 (p) cc_final: 0.8232 (t) REVERT: B 8 GLU cc_start: 0.7909 (mt-10) cc_final: 0.7369 (mt-10) REVERT: B 51 GLU cc_start: 0.7468 (tt0) cc_final: 0.6876 (tt0) REVERT: B 53 HIS cc_start: 0.7924 (p90) cc_final: 0.7482 (p90) REVERT: B 110 ASN cc_start: 0.8273 (m-40) cc_final: 0.7943 (m110) REVERT: B 130 ASP cc_start: 0.7905 (m-30) cc_final: 0.7547 (m-30) REVERT: B 134 LYS cc_start: 0.8681 (tttt) cc_final: 0.8272 (ttpp) REVERT: B 154 ASP cc_start: 0.7596 (t0) cc_final: 0.7225 (t0) REVERT: B 193 ASN cc_start: 0.8424 (t0) cc_final: 0.8077 (t0) REVERT: B 203 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8265 (ttmt) REVERT: B 215 GLU cc_start: 0.8080 (mp0) cc_final: 0.7709 (mp0) REVERT: B 230 MET cc_start: 0.8102 (OUTLIER) cc_final: 0.7695 (tmm) REVERT: B 273 PHE cc_start: 0.8112 (m-80) cc_final: 0.7848 (m-10) REVERT: B 294 VAL cc_start: 0.8783 (OUTLIER) cc_final: 0.8567 (p) REVERT: B 329 ARG cc_start: 0.8651 (mtt90) cc_final: 0.8298 (mtt180) REVERT: B 376 ASN cc_start: 0.8178 (t0) cc_final: 0.7790 (t0) REVERT: B 435 ASP cc_start: 0.8442 (t0) cc_final: 0.7581 (p0) REVERT: B 510 TYR cc_start: 0.8587 (m-10) cc_final: 0.8219 (m-80) REVERT: B 524 ASP cc_start: 0.8574 (t0) cc_final: 0.8122 (t0) REVERT: B 532 GLN cc_start: 0.8080 (mm-40) cc_final: 0.7628 (mm-40) REVERT: B 539 GLU cc_start: 0.7942 (tt0) cc_final: 0.7633 (tt0) REVERT: B 543 GLU cc_start: 0.7866 (mt-10) cc_final: 0.7506 (tt0) REVERT: B 546 THR cc_start: 0.8371 (OUTLIER) cc_final: 0.8063 (t) REVERT: E 10 SER cc_start: 0.8148 (m) cc_final: 0.7876 (m) REVERT: E 81 MET cc_start: 0.8620 (tmm) cc_final: 0.8301 (ttp) REVERT: E 117 ASP cc_start: 0.7836 (t0) cc_final: 0.7582 (t0) REVERT: E 129 LYS cc_start: 0.8329 (mttm) cc_final: 0.8048 (mttp) REVERT: E 130 ASP cc_start: 0.7791 (m-30) cc_final: 0.7519 (m-30) REVERT: E 193 ASN cc_start: 0.8208 (t0) cc_final: 0.7747 (t0) REVERT: E 202 LYS cc_start: 0.8727 (mttt) cc_final: 0.8407 (mttt) REVERT: E 215 GLU cc_start: 0.8136 (mp0) cc_final: 0.7079 (mp0) REVERT: E 257 TYR cc_start: 0.8884 (m-80) cc_final: 0.8652 (m-80) REVERT: E 294 VAL cc_start: 0.8711 (t) cc_final: 0.8392 (p) REVERT: E 382 LYS cc_start: 0.8363 (mtmm) cc_final: 0.8065 (mtmt) REVERT: E 423 GLU cc_start: 0.8214 (mt-10) cc_final: 0.7955 (mt-10) REVERT: E 427 TRP cc_start: 0.8634 (p90) cc_final: 0.8344 (p90) REVERT: E 490 MET cc_start: 0.8368 (ttm) cc_final: 0.8161 (mtp) REVERT: E 540 LYS cc_start: 0.8671 (OUTLIER) cc_final: 0.8352 (mtpt) REVERT: C 5 ASN cc_start: 0.8095 (m-40) cc_final: 0.7783 (m-40) REVERT: C 34 ASN cc_start: 0.7785 (m-40) cc_final: 0.7461 (m-40) REVERT: C 55 LYS cc_start: 0.8617 (mtmm) cc_final: 0.8403 (mtmm) REVERT: C 103 GLU cc_start: 0.7778 (mt-10) cc_final: 0.7547 (mt-10) REVERT: C 151 MET cc_start: 0.8507 (ttm) cc_final: 0.8192 (ttp) REVERT: C 154 ASP cc_start: 0.8013 (t0) cc_final: 0.7475 (t0) REVERT: C 158 LYS cc_start: 0.5904 (tptp) cc_final: 0.5234 (tttp) REVERT: C 191 ASP cc_start: 0.7829 (m-30) cc_final: 0.7544 (m-30) REVERT: C 192 VAL cc_start: 0.8726 (t) cc_final: 0.8488 (p) REVERT: C 193 ASN cc_start: 0.7854 (t0) cc_final: 0.7558 (t0) REVERT: C 204 LEU cc_start: 0.8296 (mt) cc_final: 0.8058 (mm) REVERT: C 215 GLU cc_start: 0.8226 (mp0) cc_final: 0.7933 (mp0) REVERT: C 230 MET cc_start: 0.8107 (ppp) cc_final: 0.7803 (ppp) REVERT: C 231 SER cc_start: 0.8571 (t) cc_final: 0.8172 (p) REVERT: C 294 VAL cc_start: 0.8676 (t) cc_final: 0.8352 (p) REVERT: C 295 ASN cc_start: 0.8208 (t0) cc_final: 0.7821 (t0) REVERT: C 371 VAL cc_start: 0.9010 (t) cc_final: 0.8690 (p) REVERT: C 374 PHE cc_start: 0.8496 (m-80) cc_final: 0.8211 (m-80) REVERT: C 414 VAL cc_start: 0.8742 (t) cc_final: 0.8408 (m) REVERT: C 435 ASP cc_start: 0.5985 (OUTLIER) cc_final: 0.5477 (t70) REVERT: C 471 LYS cc_start: 0.8551 (mmtt) cc_final: 0.8141 (mmtt) REVERT: C 521 VAL cc_start: 0.8588 (t) cc_final: 0.8320 (p) REVERT: C 524 ASP cc_start: 0.8212 (t0) cc_final: 0.7765 (t0) REVERT: C 534 HIS cc_start: 0.7891 (m-70) cc_final: 0.7603 (m-70) REVERT: C 540 LYS cc_start: 0.8348 (mttt) cc_final: 0.8043 (mttt) REVERT: C 542 GLU cc_start: 0.7958 (pt0) cc_final: 0.7713 (pt0) REVERT: C 543 GLU cc_start: 0.7842 (tt0) cc_final: 0.7610 (tt0) REVERT: C 546 THR cc_start: 0.8399 (p) cc_final: 0.8104 (m) REVERT: D 21 VAL cc_start: 0.8747 (t) cc_final: 0.8435 (m) REVERT: D 49 ASP cc_start: 0.8498 (t0) cc_final: 0.8214 (t0) REVERT: D 51 GLU cc_start: 0.7659 (tt0) cc_final: 0.7360 (tt0) REVERT: D 55 LYS cc_start: 0.8830 (mttp) cc_final: 0.8458 (mttp) REVERT: D 103 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7664 (mt-10) REVERT: D 134 LYS cc_start: 0.8813 (ttpp) cc_final: 0.8282 (ttpp) REVERT: D 151 MET cc_start: 0.8384 (ttp) cc_final: 0.8146 (ttp) REVERT: D 168 ASP cc_start: 0.8057 (t0) cc_final: 0.7797 (t0) REVERT: D 192 VAL cc_start: 0.8844 (t) cc_final: 0.8624 (p) REVERT: D 201 SER cc_start: 0.8255 (p) cc_final: 0.7985 (m) REVERT: D 203 LYS cc_start: 0.8488 (ttmm) cc_final: 0.8262 (ttmm) REVERT: D 215 GLU cc_start: 0.8307 (mp0) cc_final: 0.7488 (mp0) REVERT: D 242 LEU cc_start: 0.8558 (mt) cc_final: 0.8256 (mp) REVERT: D 274 ARG cc_start: 0.7434 (ttp80) cc_final: 0.7219 (ttp-170) REVERT: D 341 ASP cc_start: 0.8109 (t0) cc_final: 0.7808 (m-30) REVERT: D 346 VAL cc_start: 0.8821 (t) cc_final: 0.8591 (p) REVERT: D 382 LYS cc_start: 0.8751 (mtmt) cc_final: 0.8411 (mtmt) REVERT: D 435 ASP cc_start: 0.7964 (t0) cc_final: 0.7511 (p0) REVERT: D 521 VAL cc_start: 0.8557 (t) cc_final: 0.8254 (p) REVERT: I 271 MET cc_start: 0.4303 (pmm) cc_final: 0.3771 (pmm) REVERT: I 358 MET cc_start: 0.7809 (mmp) cc_final: 0.7360 (mmp) outliers start: 54 outliers final: 44 residues processed: 683 average time/residue: 0.1653 time to fit residues: 169.3272 Evaluate side-chains 705 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 653 time to evaluate : 0.805 ------------------------------------------------------------------------------- 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 151 MET Chi-restraints excluded: chain A residue 152 LEU 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 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 533 HIS Chi-restraints excluded: chain A residue 548 LYS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 2 THR 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 151 MET Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 203 LYS Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 546 THR Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 38 CYS Chi-restraints excluded: chain E residue 76 THR 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 420 LEU Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 540 LYS Chi-restraints excluded: chain C residue 76 THR 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 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 133 ASP Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 261 LEU Chi-restraints excluded: chain D residue 477 THR 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 50 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 164 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 194 optimal weight: 0.4980 chunk 93 optimal weight: 0.8980 chunk 147 optimal weight: 0.5980 chunk 86 optimal weight: 3.9990 chunk 66 optimal weight: 0.0020 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 155 HIS ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 517 HIS ** B 195 GLN ** 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 517 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.111130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.092673 restraints weight = 36063.892| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.18 r_work: 0.2983 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.4253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 22196 Z= 0.114 Angle : 0.536 8.686 30252 Z= 0.270 Chirality : 0.041 0.249 3258 Planarity : 0.005 0.102 3942 Dihedral : 4.515 18.255 2967 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.69 % Favored : 98.27 % Rotamer: Outliers : 2.42 % Allowed : 15.71 % Favored : 81.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.29 (0.15), residues: 2722 helix: 0.58 (0.39), residues: 183 sheet: 0.00 (0.20), residues: 638 loop : -0.30 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 338 TYR 0.025 0.001 TYR C 250 PHE 0.018 0.001 PHE E 57 TRP 0.015 0.001 TRP E 87 HIS 0.004 0.001 HIS C 53 Details of bonding type rmsd covalent geometry : bond 0.00260 (22196) covalent geometry : angle 0.53607 (30252) hydrogen bonds : bond 0.03034 ( 548) hydrogen bonds : angle 5.71695 ( 1443) =============================================================================== Job complete usr+sys time: 7164.96 seconds wall clock time: 123 minutes 3.62 seconds (7383.62 seconds total)