Starting phenix.real_space_refine on Wed Nov 20 05:12:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4f_45184/11_2024/9c4f_45184.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4f_45184/11_2024/9c4f_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4f_45184/11_2024/9c4f_45184.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4f_45184/11_2024/9c4f_45184.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4f_45184/11_2024/9c4f_45184.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9c4f_45184/11_2024/9c4f_45184.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.050 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 13753 2.51 5 N 3649 2.21 5 O 4078 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 21560 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4021 Number of conformers: 1 Conformer: "" Number of residues, atoms: 517, 4021 Classifications: {'peptide': 517} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 43, 'TRANS': 472} Chain breaks: 4 Chain: "I" Number of atoms: 1455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1455 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 7, 'TRANS': 181} Restraints were copied for chains: B, C, D, E Time building chain proxies: 12.53, per 1000 atoms: 0.58 Number of scatterers: 21560 At special positions: 0 Unit cell: (204.12, 174.96, 147.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 4078 8.00 N 3649 7.00 C 13753 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.94 Conformation dependent library (CDL) restraints added in 3.1 seconds 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5032 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 72 sheets defined 13.8% alpha, 31.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.41 Creating SS restraints... Processing helix chain 'A' and resid 3 through 7 Processing helix chain 'A' and resid 94 through 99 removed outlier: 4.123A pdb=" N PHE A 98 " --> pdb=" O ALA A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 111 Processing helix chain 'A' and resid 196 through 199 removed outlier: 3.673A pdb=" N GLY A 199 " --> pdb=" O GLY A 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 196 through 199' Processing helix chain 'A' and resid 213 through 217 Processing helix chain 'A' and resid 248 through 252 removed outlier: 3.798A pdb=" N MET A 252 " --> pdb=" O PHE A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 284 Processing helix chain 'A' and resid 377 through 382 Processing helix chain 'A' and resid 524 through 528 removed outlier: 3.509A pdb=" N THR A 528 " --> pdb=" O PRO A 525 " (cutoff:3.500A) Processing helix chain 'A' and resid 532 through 536 Processing helix chain 'B' and resid 3 through 7 Processing helix chain 'B' and resid 94 through 99 removed outlier: 4.124A pdb=" N PHE B 98 " --> pdb=" O ALA B 94 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 111 Processing helix chain 'B' and resid 196 through 199 removed outlier: 3.673A pdb=" N GLY B 199 " --> pdb=" O GLY B 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 196 through 199' Processing helix chain 'B' and resid 213 through 217 Processing helix chain 'B' and resid 248 through 252 removed outlier: 3.797A pdb=" N MET B 252 " --> pdb=" O PHE B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 284 Processing helix chain 'B' and resid 377 through 382 Processing helix chain 'B' and resid 524 through 528 removed outlier: 3.508A pdb=" N THR B 528 " --> pdb=" O PRO B 525 " (cutoff:3.500A) Processing helix chain 'B' and resid 532 through 536 Processing helix chain 'E' and resid 3 through 7 Processing helix chain 'E' and resid 94 through 99 removed outlier: 4.123A pdb=" N PHE E 98 " --> pdb=" O ALA E 94 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 111 Processing helix chain 'E' and resid 196 through 199 removed outlier: 3.672A pdb=" N GLY E 199 " --> pdb=" O GLY E 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 196 through 199' Processing helix chain 'E' and resid 213 through 217 Processing helix chain 'E' and resid 248 through 252 removed outlier: 3.798A pdb=" N MET E 252 " --> pdb=" O PHE E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 280 through 284 Processing helix chain 'E' and resid 377 through 382 Processing helix chain 'E' and resid 524 through 528 removed outlier: 3.509A pdb=" N THR E 528 " --> pdb=" O PRO E 525 " (cutoff:3.500A) Processing helix chain 'E' and resid 532 through 536 Processing helix chain 'C' and resid 3 through 7 Processing helix chain 'C' and resid 94 through 99 removed outlier: 4.124A pdb=" N PHE C 98 " --> pdb=" O ALA C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 111 Processing helix chain 'C' and resid 196 through 199 removed outlier: 3.673A pdb=" N GLY C 199 " --> pdb=" O GLY C 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 196 through 199' Processing helix chain 'C' and resid 213 through 217 Processing helix chain 'C' and resid 248 through 252 removed outlier: 3.797A pdb=" N MET C 252 " --> pdb=" O PHE C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 284 Processing helix chain 'C' and resid 377 through 382 Processing helix chain 'C' and resid 524 through 528 removed outlier: 3.509A pdb=" N THR C 528 " --> pdb=" O PRO C 525 " (cutoff:3.500A) Processing helix chain 'C' and resid 532 through 536 Processing helix chain 'D' and resid 3 through 7 Processing helix chain 'D' and resid 94 through 99 removed outlier: 4.123A pdb=" N PHE D 98 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 111 Processing helix chain 'D' and resid 196 through 199 removed outlier: 3.673A pdb=" N GLY D 199 " --> pdb=" O GLY D 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 196 through 199' Processing helix chain 'D' and resid 213 through 217 Processing helix chain 'D' and resid 248 through 252 removed outlier: 3.798A pdb=" N MET D 252 " --> pdb=" O PHE D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 284 Processing helix chain 'D' and resid 377 through 382 Processing helix chain 'D' and resid 524 through 528 removed outlier: 3.509A pdb=" N THR D 528 " --> pdb=" O PRO D 525 " (cutoff:3.500A) Processing helix chain 'D' and resid 532 through 536 Processing helix chain 'I' and resid 282 through 286 removed outlier: 3.529A pdb=" N SER I 286 " --> pdb=" O GLY I 283 " (cutoff:3.500A) Processing helix chain 'I' and resid 287 through 303 Processing helix chain 'I' and resid 330 through 344 Processing helix chain 'I' and resid 351 through 365 Processing helix chain 'I' and resid 366 through 368 No H-bonds generated for 'chain 'I' and resid 366 through 368' Processing helix chain 'I' and resid 394 through 407 Processing helix chain 'I' and resid 422 through 432 Processing helix chain 'I' and resid 445 through 458 removed outlier: 3.559A pdb=" N GLU I 456 " --> pdb=" O ASP I 452 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL I 457 " --> pdb=" O PHE I 453 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 28 through 31 removed outlier: 6.444A pdb=" N TYR E 481 " --> pdb=" O VAL E 128 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL E 128 " --> pdb=" O TYR E 481 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N VAL E 483 " --> pdb=" O ILE E 126 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE E 126 " --> pdb=" O VAL E 483 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LYS E 493 " --> pdb=" O PRO E 116 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY E 495 " --> pdb=" O ILE E 114 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE E 114 " --> pdb=" O GLY E 495 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 228 through 233 removed outlier: 8.837A pdb=" N SER A 10 " --> pdb=" O VAL E 139 " (cutoff:3.500A) removed outlier: 9.200A pdb=" N VAL E 141 " --> pdb=" O SER A 10 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLY A 12 " --> pdb=" O VAL E 141 " (cutoff:3.500A) removed outlier: 8.731A pdb=" N ASP E 143 " --> pdb=" O GLY A 12 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 22 through 25 removed outlier: 5.995A pdb=" N ILE E 460 " --> pdb=" O PRO E 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 22 through 25 removed outlier: 5.995A pdb=" N ILE E 460 " --> pdb=" O PRO E 86 " (cutoff:3.500A) removed outlier: 7.253A pdb=" N TYR E 83 " --> pdb=" O THR E 188 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR E 188 " --> pdb=" O TYR E 83 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N THR E 85 " --> pdb=" O TYR E 186 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N TYR E 186 " --> pdb=" O THR E 85 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N TRP E 87 " --> pdb=" O TYR E 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.444A pdb=" N TYR A 481 " --> pdb=" O VAL A 128 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL A 128 " --> pdb=" O TYR A 481 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL A 483 " --> pdb=" O ILE A 126 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE A 126 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LYS A 493 " --> pdb=" O PRO A 116 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY A 495 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE A 114 " --> pdb=" O GLY A 495 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 228 through 233 removed outlier: 7.440A pdb=" N VAL A 139 " --> pdb=" O SER B 10 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY B 12 " --> pdb=" O VAL A 139 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 55 through 57 removed outlier: 7.252A pdb=" N TYR A 83 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR A 188 " --> pdb=" O TYR A 83 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N THR A 85 " --> pdb=" O TYR A 186 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N TYR A 186 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N TRP A 87 " --> pdb=" O TYR A 184 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 55 through 57 removed outlier: 5.995A pdb=" N ILE A 460 " --> pdb=" O PRO A 86 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 191 through 194 Processing sheet with id=AB1, first strand: chain 'A' and resid 244 through 245 removed outlier: 6.707A pdb=" N GLY A 244 " --> pdb=" O HIS A 552 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'A' and resid 262 through 266 removed outlier: 6.469A pdb=" N LYS A 272 " --> pdb=" O ASP A 265 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 289 through 290 removed outlier: 6.369A pdb=" N MET A 289 " --> pdb=" O VAL A 414 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'A' and resid 317 through 321 removed outlier: 6.595A pdb=" N THR A 324 " --> pdb=" O THR A 320 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 338 through 341 Processing sheet with id=AB6, first strand: chain 'A' and resid 356 through 357 Processing sheet with id=AB7, first strand: chain 'A' and resid 374 through 375 removed outlier: 6.497A pdb=" N PHE A 374 " --> pdb=" O LEU A 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AB9, first strand: chain 'A' and resid 427 through 429 removed outlier: 6.049A pdb=" N SER A 428 " --> pdb=" O LEU A 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'A' and resid 477 through 478 removed outlier: 6.398A pdb=" N THR A 477 " --> pdb=" O THR C 11 " (cutoff:3.500A) removed outlier: 7.266A pdb=" N ALA C 13 " --> pdb=" O THR A 477 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N VAL B 139 " --> pdb=" O SER C 10 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY C 12 " --> pdb=" O VAL B 139 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 28 through 31 removed outlier: 6.443A pdb=" N TYR B 481 " --> pdb=" O VAL B 128 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL B 128 " --> pdb=" O TYR B 481 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL B 483 " --> pdb=" O ILE B 126 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE B 126 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LYS B 493 " --> pdb=" O PRO B 116 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY B 495 " --> pdb=" O ILE B 114 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE B 114 " --> pdb=" O GLY B 495 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 55 through 57 removed outlier: 7.252A pdb=" N TYR B 83 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR B 188 " --> pdb=" O TYR B 83 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N THR B 85 " --> pdb=" O TYR B 186 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N TYR B 186 " --> pdb=" O THR B 85 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N TRP B 87 " --> pdb=" O TYR B 184 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 55 through 57 removed outlier: 5.995A pdb=" N ILE B 460 " --> pdb=" O PRO B 86 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 191 through 194 Processing sheet with id=AC6, first strand: chain 'B' and resid 244 through 245 removed outlier: 6.707A pdb=" N GLY B 244 " --> pdb=" O HIS B 552 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC6 Processing sheet with id=AC7, first strand: chain 'B' and resid 262 through 266 removed outlier: 6.469A pdb=" N LYS B 272 " --> pdb=" O ASP B 265 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 289 through 290 removed outlier: 6.370A pdb=" N MET B 289 " --> pdb=" O VAL B 414 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 317 through 321 removed outlier: 6.595A pdb=" N THR B 324 " --> pdb=" O THR B 320 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 338 through 341 Processing sheet with id=AD2, first strand: chain 'B' and resid 356 through 357 Processing sheet with id=AD3, first strand: chain 'B' and resid 374 through 375 removed outlier: 6.497A pdb=" N PHE B 374 " --> pdb=" O LEU B 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 Processing sheet with id=AD4, first strand: chain 'B' and resid 391 through 392 Processing sheet with id=AD5, first strand: chain 'B' and resid 427 through 429 removed outlier: 6.050A pdb=" N SER B 428 " --> pdb=" O LEU B 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'B' and resid 477 through 478 removed outlier: 6.398A pdb=" N THR B 477 " --> pdb=" O THR D 11 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ALA D 13 " --> pdb=" O THR B 477 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N VAL C 139 " --> pdb=" O SER D 10 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N GLY D 12 " --> pdb=" O VAL C 139 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.444A pdb=" N TYR C 481 " --> pdb=" O VAL C 128 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL C 128 " --> pdb=" O TYR C 481 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL C 483 " --> pdb=" O ILE C 126 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE C 126 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N LYS C 493 " --> pdb=" O PRO C 116 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLY C 495 " --> pdb=" O ILE C 114 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE C 114 " --> pdb=" O GLY C 495 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 477 through 478 removed outlier: 8.837A pdb=" N SER E 10 " --> pdb=" O VAL D 139 " (cutoff:3.500A) removed outlier: 9.201A pdb=" N VAL D 141 " --> pdb=" O SER E 10 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N GLY E 12 " --> pdb=" O VAL D 141 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N ASP D 143 " --> pdb=" O GLY E 12 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 28 through 31 removed outlier: 6.443A pdb=" N TYR D 481 " --> pdb=" O VAL D 128 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N VAL D 128 " --> pdb=" O TYR D 481 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL D 483 " --> pdb=" O ILE D 126 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE D 126 " --> pdb=" O VAL D 483 " (cutoff:3.500A) removed outlier: 5.155A pdb=" N LYS D 493 " --> pdb=" O PRO D 116 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLY D 495 " --> pdb=" O ILE D 114 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE D 114 " --> pdb=" O GLY D 495 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'E' and resid 22 through 25 removed outlier: 5.995A pdb=" N ILE D 460 " --> pdb=" O PRO D 86 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'E' and resid 22 through 25 removed outlier: 5.995A pdb=" N ILE D 460 " --> pdb=" O PRO D 86 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N TYR D 83 " --> pdb=" O THR D 188 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N THR D 188 " --> pdb=" O TYR D 83 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N THR D 85 " --> pdb=" O TYR D 186 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N TYR D 186 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N TRP D 87 " --> pdb=" O TYR D 184 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'E' and resid 191 through 194 Processing sheet with id=AE4, first strand: chain 'E' and resid 244 through 245 removed outlier: 6.708A pdb=" N GLY E 244 " --> pdb=" O HIS E 552 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'E' and resid 262 through 266 removed outlier: 6.469A pdb=" N LYS E 272 " --> pdb=" O ASP E 265 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 289 through 290 removed outlier: 6.370A pdb=" N MET E 289 " --> pdb=" O VAL E 414 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'E' and resid 317 through 321 removed outlier: 6.595A pdb=" N THR E 324 " --> pdb=" O THR E 320 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'E' and resid 338 through 341 Processing sheet with id=AE9, first strand: chain 'E' and resid 356 through 357 Processing sheet with id=AF1, first strand: chain 'E' and resid 374 through 375 removed outlier: 6.497A pdb=" N PHE E 374 " --> pdb=" O LEU E 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF1 Processing sheet with id=AF2, first strand: chain 'E' and resid 391 through 392 Processing sheet with id=AF3, first strand: chain 'E' and resid 427 through 429 removed outlier: 6.050A pdb=" N SER E 428 " --> pdb=" O LEU E 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF3 Processing sheet with id=AF4, first strand: chain 'C' and resid 55 through 57 removed outlier: 7.253A pdb=" N TYR C 83 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N THR C 188 " --> pdb=" O TYR C 83 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N THR C 85 " --> pdb=" O TYR C 186 " (cutoff:3.500A) removed outlier: 8.177A pdb=" N TYR C 186 " --> pdb=" O THR C 85 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N TRP C 87 " --> pdb=" O TYR C 184 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 55 through 57 removed outlier: 5.995A pdb=" N ILE C 460 " --> pdb=" O PRO C 86 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 191 through 194 Processing sheet with id=AF7, first strand: chain 'C' and resid 244 through 245 removed outlier: 6.707A pdb=" N GLY C 244 " --> pdb=" O HIS C 552 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'C' and resid 262 through 266 removed outlier: 6.469A pdb=" N LYS C 272 " --> pdb=" O ASP C 265 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'C' and resid 289 through 290 removed outlier: 6.370A pdb=" N MET C 289 " --> pdb=" O VAL C 414 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF9 Processing sheet with id=AG1, first strand: chain 'C' and resid 317 through 321 removed outlier: 6.595A pdb=" N THR C 324 " --> pdb=" O THR C 320 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'C' and resid 338 through 341 Processing sheet with id=AG3, first strand: chain 'C' and resid 356 through 357 Processing sheet with id=AG4, first strand: chain 'C' and resid 374 through 375 removed outlier: 6.497A pdb=" N PHE C 374 " --> pdb=" O LEU C 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG4 Processing sheet with id=AG5, first strand: chain 'C' and resid 391 through 392 Processing sheet with id=AG6, first strand: chain 'C' and resid 427 through 429 removed outlier: 6.049A pdb=" N SER C 428 " --> pdb=" O LEU C 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'D' and resid 191 through 194 Processing sheet with id=AG8, first strand: chain 'D' and resid 244 through 245 removed outlier: 6.708A pdb=" N GLY D 244 " --> pdb=" O HIS D 552 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'D' and resid 262 through 266 removed outlier: 6.469A pdb=" N LYS D 272 " --> pdb=" O ASP D 265 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'D' and resid 289 through 290 removed outlier: 6.370A pdb=" N MET D 289 " --> pdb=" O VAL D 414 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH1 Processing sheet with id=AH2, first strand: chain 'D' and resid 317 through 321 removed outlier: 6.595A pdb=" N THR D 324 " --> pdb=" O THR D 320 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'D' and resid 338 through 341 Processing sheet with id=AH4, first strand: chain 'D' and resid 356 through 357 Processing sheet with id=AH5, first strand: chain 'D' and resid 374 through 375 removed outlier: 6.498A pdb=" N PHE D 374 " --> pdb=" O LEU D 544 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH5 Processing sheet with id=AH6, first strand: chain 'D' and resid 391 through 392 Processing sheet with id=AH7, first strand: chain 'D' and resid 427 through 429 removed outlier: 6.049A pdb=" N SER D 428 " --> pdb=" O LEU D 449 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH7 Processing sheet with id=AH8, first strand: chain 'I' and resid 319 through 321 Processing sheet with id=AH9, first strand: chain 'I' and resid 319 through 321 removed outlier: 6.025A pdb=" N LYS I 273 " --> pdb=" O GLN I 309 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N ASN I 311 " --> pdb=" O LYS I 273 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL I 275 " --> pdb=" O ASN I 311 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE I 313 " --> pdb=" O VAL I 275 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N PHE I 277 " --> pdb=" O ILE I 313 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N PHE I 315 " --> pdb=" O PHE I 277 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE I 279 " --> pdb=" O PHE I 315 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N SER I 378 " --> pdb=" O SER I 411 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N PHE I 413 " --> pdb=" O SER I 378 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE I 380 " --> pdb=" O PHE I 413 " (cutoff:3.500A) removed outlier: 7.799A pdb=" N LEU I 415 " --> pdb=" O ILE I 380 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N LEU I 382 " --> pdb=" O LEU I 415 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N PHE I 417 " --> pdb=" O LEU I 382 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR I 384 " --> pdb=" O PHE I 417 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N ARG I 438 " --> pdb=" O LEU I 412 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS I 414 " --> pdb=" O ARG I 438 " (cutoff:3.500A) removed outlier: 7.214A pdb=" N ILE I 440 " --> pdb=" O CYS I 414 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N GLY I 416 " --> pdb=" O ILE I 440 " (cutoff:3.500A) 590 hydrogen bonds defined for protein. 1443 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.19 Time building geometry restraints manager: 5.76 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: 8.150 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: 0.030 Extract box with map and model: 0.950 Check model and map are aligned: 0.160 Set scattering table: 0.210 Process input model: 48.950 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 22196 Z= 0.356 Angle : 0.817 15.911 30252 Z= 0.494 Chirality : 0.050 0.306 3258 Planarity : 0.008 0.140 3942 Dihedral : 13.074 88.853 8015 Min Nonbonded Distance : 1.661 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.07 % Allowed : 2.53 % Favored : 97.39 % Rotamer: Outliers : 0.30 % Allowed : 0.55 % Favored : 99.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.14), residues: 2722 helix: -0.43 (0.39), residues: 175 sheet: 0.53 (0.19), residues: 676 loop : -0.79 (0.12), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.101 0.004 TRP I 322 HIS 0.010 0.002 HIS B 216 PHE 0.092 0.004 PHE I 453 TYR 0.081 0.005 TYR I 423 ARG 0.017 0.003 ARG C 502 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 734 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 727 time to evaluate : 2.435 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 SER cc_start: 0.7725 (m) cc_final: 0.7406 (m) REVERT: A 53 HIS cc_start: 0.7672 (p90) cc_final: 0.7126 (p-80) REVERT: A 215 GLU cc_start: 0.6949 (mp0) cc_final: 0.6167 (mp0) REVERT: A 229 THR cc_start: 0.8347 (m) cc_final: 0.8054 (p) REVERT: A 295 ASN cc_start: 0.7520 (t0) cc_final: 0.7274 (t0) REVERT: A 384 LEU cc_start: 0.8210 (mt) cc_final: 0.7885 (mt) REVERT: A 546 THR cc_start: 0.7973 (p) cc_final: 0.7745 (t) REVERT: B 32 SER cc_start: 0.8314 (p) cc_final: 0.8051 (t) REVERT: B 42 ARG cc_start: 0.8431 (mmt-90) cc_final: 0.8022 (mpt180) REVERT: B 53 HIS cc_start: 0.7484 (p90) cc_final: 0.7093 (p-80) REVERT: B 110 ASN cc_start: 0.7798 (m-40) cc_final: 0.7585 (m110) REVERT: B 156 GLU cc_start: 0.7512 (mt-10) cc_final: 0.7303 (mt-10) REVERT: B 329 ARG cc_start: 0.8011 (mtt90) cc_final: 0.7712 (mtt180) REVERT: B 378 LYS cc_start: 0.7995 (pttm) cc_final: 0.7769 (ptmm) REVERT: B 498 LYS cc_start: 0.8453 (ttmt) cc_final: 0.8205 (mmmm) REVERT: B 523 TYR cc_start: 0.8737 (p90) cc_final: 0.8535 (p90) REVERT: B 524 ASP cc_start: 0.7858 (t0) cc_final: 0.7653 (t0) REVERT: E 24 MET cc_start: 0.7181 (mmm) cc_final: 0.6809 (mmm) REVERT: E 91 ASP cc_start: 0.6755 (t0) cc_final: 0.6474 (t0) REVERT: E 143 ASP cc_start: 0.6932 (m-30) cc_final: 0.6670 (m-30) REVERT: E 193 ASN cc_start: 0.7143 (t0) cc_final: 0.6851 (t0) REVERT: E 215 GLU cc_start: 0.7148 (mp0) cc_final: 0.6477 (mp0) REVERT: E 230 MET cc_start: 0.6878 (tmm) cc_final: 0.6651 (tmm) REVERT: E 295 ASN cc_start: 0.7735 (t0) cc_final: 0.7442 (t0) REVERT: E 432 ASN cc_start: 0.7931 (p0) cc_final: 0.7622 (p0) REVERT: E 510 TYR cc_start: 0.7879 (m-80) cc_final: 0.7494 (m-80) REVERT: C 154 ASP cc_start: 0.7179 (t0) cc_final: 0.6830 (t0) REVERT: C 180 PHE cc_start: 0.7615 (m-80) cc_final: 0.7205 (m-80) REVERT: C 287 ASN cc_start: 0.7086 (m-40) cc_final: 0.6818 (m110) REVERT: C 295 ASN cc_start: 0.7168 (t0) cc_final: 0.6877 (t0) REVERT: C 371 VAL cc_start: 0.9104 (t) cc_final: 0.8865 (p) REVERT: C 428 SER cc_start: 0.8087 (t) cc_final: 0.7882 (t) REVERT: D 24 MET cc_start: 0.7830 (mmm) cc_final: 0.7526 (mmm) REVERT: D 80 ILE cc_start: 0.8432 (pt) cc_final: 0.8216 (pt) REVERT: D 103 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6795 (mt-10) REVERT: D 130 ASP cc_start: 0.6638 (m-30) cc_final: 0.6408 (m-30) REVERT: D 154 ASP cc_start: 0.7304 (t0) cc_final: 0.6979 (t0) REVERT: D 168 ASP cc_start: 0.7308 (t0) cc_final: 0.7088 (t0) REVERT: D 287 ASN cc_start: 0.7228 (m-40) cc_final: 0.7022 (m110) REVERT: D 417 ARG cc_start: 0.7751 (mtm-85) cc_final: 0.7516 (mtm-85) outliers start: 7 outliers final: 5 residues processed: 731 average time/residue: 0.4016 time to fit residues: 436.8058 Evaluate side-chains 608 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 603 time to evaluate : 2.689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain C residue 265 ASP Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain I residue 443 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 114 optimal weight: 7.9990 chunk 70 optimal weight: 1.9990 chunk 139 optimal weight: 0.0570 chunk 110 optimal weight: 0.9980 chunk 213 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 130 optimal weight: 1.9990 chunk 159 optimal weight: 3.9990 chunk 247 optimal weight: 3.9990 overall best weight: 1.2102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN A 53 HIS A 155 HIS ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN A 335 GLN A 385 GLN A 451 GLN A 513 HIS ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 533 HIS B 195 GLN ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN B 335 GLN B 380 GLN B 385 GLN B 425 GLN B 513 HIS B 534 HIS E 155 HIS E 216 HIS E 385 GLN C 5 ASN C 155 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 286 GLN C 335 GLN C 380 GLN ** C 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN D 5 ASN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 335 GLN D 380 GLN D 385 GLN ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 432 ASN I 274 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 22196 Z= 0.266 Angle : 0.616 9.264 30252 Z= 0.319 Chirality : 0.044 0.286 3258 Planarity : 0.004 0.123 3942 Dihedral : 6.237 53.757 2977 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.10 % Favored : 98.86 % Rotamer: Outliers : 2.04 % Allowed : 7.56 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.15), residues: 2722 helix: 0.39 (0.38), residues: 183 sheet: 0.22 (0.19), residues: 668 loop : -0.28 (0.13), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 545 HIS 0.008 0.001 HIS D 53 PHE 0.020 0.002 PHE I 315 TYR 0.017 0.002 TYR D 159 ARG 0.006 0.001 ARG I 439 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5444 Ramachandran restraints generated. 2722 Oldfield, 0 Emsley, 2722 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 650 time to evaluate : 2.634 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 207 GLU cc_start: 0.5476 (tm-30) cc_final: 0.4223 (tm-30) REVERT: A 215 GLU cc_start: 0.7389 (mp0) cc_final: 0.6739 (mp0) REVERT: A 240 GLU cc_start: 0.7314 (tp30) cc_final: 0.7032 (tp30) REVERT: A 295 ASN cc_start: 0.7398 (t0) cc_final: 0.7154 (t0) REVERT: A 384 LEU cc_start: 0.8310 (mt) cc_final: 0.7968 (mt) REVERT: A 486 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.7060 (ptm) REVERT: A 546 THR cc_start: 0.8053 (p) cc_final: 0.7761 (t) REVERT: B 24 MET cc_start: 0.7587 (mmm) cc_final: 0.7352 (tpp) REVERT: B 32 SER cc_start: 0.8327 (p) cc_final: 0.8121 (t) REVERT: B 154 ASP cc_start: 0.6717 (t0) cc_final: 0.6479 (t0) REVERT: B 374 PHE cc_start: 0.7860 (m-80) cc_final: 0.7579 (m-80) REVERT: B 523 TYR cc_start: 0.8713 (p90) cc_final: 0.8402 (p90) REVERT: E 91 ASP cc_start: 0.6979 (t0) cc_final: 0.6646 (t0) REVERT: E 193 ASN cc_start: 0.7425 (t0) cc_final: 0.7035 (t0) REVERT: E 215 GLU cc_start: 0.7570 (mp0) cc_final: 0.6864 (mp0) REVERT: E 295 ASN cc_start: 0.7869 (t0) cc_final: 0.7491 (t0) REVERT: E 432 ASN cc_start: 0.7898 (p0) cc_final: 0.7591 (p0) REVERT: E 510 TYR cc_start: 0.7892 (m-80) cc_final: 0.7384 (m-80) REVERT: C 180 PHE cc_start: 0.7711 (m-80) cc_final: 0.7390 (m-80) REVERT: C 194 THR cc_start: 0.7912 (m) cc_final: 0.7603 (m) REVERT: C 295 ASN cc_start: 0.7233 (t0) cc_final: 0.7004 (t0) REVERT: C 440 GLN cc_start: 0.7609 (mp10) cc_final: 0.7366 (mp10) REVERT: C 521 VAL cc_start: 0.8635 (t) cc_final: 0.8299 (p) REVERT: D 24 MET cc_start: 0.8083 (mmm) cc_final: 0.7160 (mmm) REVERT: D 58 SER cc_start: 0.7998 (t) cc_final: 0.7459 (p) REVERT: D 103 GLU cc_start: 0.6996 (mt-10) cc_final: 0.6778 (mt-10) REVERT: D 154 ASP cc_start: 0.7263 (t0) cc_final: 0.6822 (t70) REVERT: D 203 LYS cc_start: 0.8026 (ttmm) cc_final: 0.7782 (ttmm) REVERT: D 215 GLU cc_start: 0.7777 (mp0) cc_final: 0.7183 (mp0) REVERT: D 242 LEU cc_start: 0.7980 (mt) cc_final: 0.7771 (mp) REVERT: D 289 MET cc_start: 0.8126 (mmm) cc_final: 0.7890 (mmt) REVERT: D 389 MET cc_start: 0.7565 (mmm) cc_final: 0.7364 (mmm) REVERT: D 461 LEU cc_start: 0.8091 (tp) cc_final: 0.7868 (tp) outliers start: 48 outliers final: 29 residues processed: 669 average time/residue: 0.3792 time to fit residues: 378.0566 Evaluate side-chains 632 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 602 time to evaluate : 2.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 391 THR Chi-restraints excluded: chain A residue 486 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain E residue 6 SER Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 75 CYS Chi-restraints excluded: chain E residue 192 VAL Chi-restraints excluded: chain E residue 201 SER Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 265 ASP Chi-restraints excluded: chain E residue 274 ARG Chi-restraints excluded: chain E residue 459 LYS Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 176 ILE Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 265 ASP Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 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 137 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 206 optimal weight: 6.9990 chunk 168 optimal weight: 2.9990 chunk 68 optimal weight: 0.1980 chunk 248 optimal weight: 0.9990 chunk 268 optimal weight: 0.5980 chunk 221 optimal weight: 1.9990 chunk 246 optimal weight: 0.8980 chunk 84 optimal weight: 0.0770 chunk 199 optimal weight: 0.8980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 287 ASN B 5 ASN B 53 HIS ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN B 356 GLN C 155 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 GLN C 287 ASN C 356 GLN C 380 GLN ** C 385 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 425 GLN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 22196 Z= 0.173 Angle : 0.550 8.700 30252 Z= 0.281 Chirality : 0.041 0.288 3258 Planarity : 0.004 0.121 3942 Dihedral : 5.524 53.451 2975 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.36 % Favored : 98.60 % Rotamer: Outliers : 2.46 % Allowed : 10.83 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.15), residues: 2722 helix: 0.75 (0.39), residues: 183 sheet: 0.12 (0.19), residues: 668 loop : -0.15 (0.13), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 545 HIS 0.007 0.001 HIS B 53 PHE 0.016 0.001 PHE I 315 TYR 0.015 0.001 TYR D 523 ARG 0.006 0.000 ARG C 417 *********************** 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 709 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 651 time to evaluate : 2.123 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: 0.7686 (mmm) cc_final: 0.7214 (mmm) REVERT: A 203 LYS cc_start: 0.8083 (ttmt) cc_final: 0.7843 (ttmt) REVERT: A 207 GLU cc_start: 0.5549 (tm-30) cc_final: 0.4173 (tm-30) REVERT: A 215 GLU cc_start: 0.7359 (mp0) cc_final: 0.6638 (mp0) REVERT: A 240 GLU cc_start: 0.7343 (tp30) cc_final: 0.7066 (tp30) REVERT: A 295 ASN cc_start: 0.7425 (t0) cc_final: 0.7191 (t0) REVERT: A 384 LEU cc_start: 0.8317 (mt) cc_final: 0.7971 (mt) REVERT: B 32 SER cc_start: 0.8318 (p) cc_final: 0.8086 (t) REVERT: B 42 ARG cc_start: 0.8407 (mmt-90) cc_final: 0.8004 (mpt180) REVERT: B 154 ASP cc_start: 0.6655 (t0) cc_final: 0.6429 (t0) REVERT: B 215 GLU cc_start: 0.7245 (mp0) cc_final: 0.7013 (mp0) REVERT: B 329 ARG cc_start: 0.8118 (mtt90) cc_final: 0.7657 (mtt-85) REVERT: B 344 LYS cc_start: 0.7375 (tttp) cc_final: 0.6818 (ttmm) REVERT: B 374 PHE cc_start: 0.7815 (m-80) cc_final: 0.7541 (m-80) REVERT: E 24 MET cc_start: 0.7162 (mmm) cc_final: 0.6928 (tpp) REVERT: E 91 ASP cc_start: 0.6881 (t0) cc_final: 0.6636 (t0) REVERT: E 161 TYR cc_start: 0.7733 (t80) cc_final: 0.7500 (t80) REVERT: E 193 ASN cc_start: 0.7491 (t0) cc_final: 0.7122 (t0) REVERT: E 215 GLU cc_start: 0.7517 (mp0) cc_final: 0.6765 (mp0) REVERT: E 295 ASN cc_start: 0.7847 (t0) cc_final: 0.7495 (t0) REVERT: E 432 ASN cc_start: 0.7790 (p0) cc_final: 0.7476 (p0) REVERT: C 133 ASP cc_start: 0.7639 (m-30) cc_final: 0.7296 (m-30) REVERT: C 207 GLU cc_start: 0.5169 (tm-30) cc_final: 0.4610 (tm-30) REVERT: C 295 ASN cc_start: 0.7160 (t0) cc_final: 0.6952 (t0) REVERT: C 521 VAL cc_start: 0.8483 (t) cc_final: 0.8175 (p) REVERT: D 45 LEU cc_start: 0.8006 (tt) cc_final: 0.7742 (tt) REVERT: D 58 SER cc_start: 0.7947 (t) cc_final: 0.7607 (p) REVERT: D 103 GLU cc_start: 0.6997 (mt-10) cc_final: 0.6746 (mt-10) REVERT: D 203 LYS cc_start: 0.8074 (ttmm) cc_final: 0.7781 (ttmm) REVERT: D 215 GLU cc_start: 0.7730 (mp0) cc_final: 0.7222 (mp0) REVERT: D 242 LEU cc_start: 0.8030 (mt) cc_final: 0.7740 (mp) REVERT: D 461 LEU cc_start: 0.8113 (tp) cc_final: 0.7861 (tp) REVERT: D 523 TYR cc_start: 0.8387 (p90) cc_final: 0.8127 (p90) outliers start: 58 outliers final: 37 residues processed: 667 average time/residue: 0.3907 time to fit residues: 383.8587 Evaluate side-chains 647 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 610 time to evaluate : 2.548 ------------------------------------------------------------------------------- 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 38 CYS Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 265 ASP Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 283 ILE Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain B residue 274 ARG 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 230 MET Chi-restraints excluded: chain E residue 265 ASP 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 C residue 27 GLU Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 434 ASP Chi-restraints excluded: chain C residue 476 THR Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 133 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 317 SER Chi-restraints excluded: chain D residue 477 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 0.7980 chunk 186 optimal weight: 7.9990 chunk 128 optimal weight: 7.9990 chunk 27 optimal weight: 0.0870 chunk 118 optimal weight: 2.9990 chunk 166 optimal weight: 7.9990 chunk 249 optimal weight: 6.9990 chunk 263 optimal weight: 20.0000 chunk 130 optimal weight: 3.9990 chunk 236 optimal weight: 2.9990 chunk 71 optimal weight: 5.9990 overall best weight: 2.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 5 ASN B 53 HIS ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 287 ASN B 380 GLN ** B 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 425 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 552 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 ASN C 356 GLN C 385 GLN ** D 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.3309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 22196 Z= 0.397 Angle : 0.604 8.580 30252 Z= 0.309 Chirality : 0.044 0.274 3258 Planarity : 0.005 0.119 3942 Dihedral : 5.500 53.099 2973 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.65 % Favored : 98.31 % Rotamer: Outliers : 2.89 % Allowed : 11.89 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.15), residues: 2722 helix: 0.63 (0.39), residues: 183 sheet: 0.07 (0.19), residues: 638 loop : -0.27 (0.13), residues: 1901 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 25 HIS 0.010 0.002 HIS D 53 PHE 0.020 0.002 PHE B 492 TYR 0.025 0.002 TYR C 250 ARG 0.007 0.001 ARG E 373 *********************** 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 719 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 651 time to evaluate : 2.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 MET cc_start: 0.7703 (mmm) cc_final: 0.7261 (mmm) REVERT: A 42 ARG cc_start: 0.8170 (mmt-90) cc_final: 0.7862 (mmt-90) REVERT: A 173 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6923 (mt-10) REVERT: A 197 ILE cc_start: 0.8231 (OUTLIER) cc_final: 0.7964 (mt) REVERT: A 207 GLU cc_start: 0.6067 (tm-30) cc_final: 0.4543 (tm-30) REVERT: A 215 GLU cc_start: 0.7403 (mp0) cc_final: 0.6680 (mp0) REVERT: A 240 GLU cc_start: 0.7429 (tp30) cc_final: 0.7192 (tp30) REVERT: A 295 ASN cc_start: 0.7437 (t0) cc_final: 0.7191 (t0) REVERT: A 434 ASP cc_start: 0.4644 (OUTLIER) cc_final: 0.4311 (p0) REVERT: B 32 SER cc_start: 0.8382 (p) cc_final: 0.7793 (t) REVERT: B 154 ASP cc_start: 0.6676 (t0) cc_final: 0.6445 (t0) REVERT: B 157 TYR cc_start: 0.8132 (m-80) cc_final: 0.7555 (m-80) REVERT: B 215 GLU cc_start: 0.7257 (mp0) cc_final: 0.7040 (mp0) REVERT: B 283 ILE cc_start: 0.8494 (pp) cc_final: 0.8271 (pt) REVERT: B 374 PHE cc_start: 0.7885 (m-80) cc_final: 0.7656 (m-80) REVERT: E 81 MET cc_start: 0.7949 (tmm) cc_final: 0.7649 (ttp) REVERT: E 193 ASN cc_start: 0.7606 (t0) cc_final: 0.7260 (t0) REVERT: E 215 GLU cc_start: 0.7548 (mp0) cc_final: 0.6780 (mp0) REVERT: E 295 ASN cc_start: 0.7862 (t0) cc_final: 0.7379 (t0) REVERT: E 540 LYS cc_start: 0.8128 (OUTLIER) cc_final: 0.7892 (mtpt) REVERT: C 207 GLU cc_start: 0.5499 (tm-30) cc_final: 0.4074 (tm-30) REVERT: C 215 GLU cc_start: 0.7576 (mp0) cc_final: 0.6776 (mp0) REVERT: C 229 THR cc_start: 0.8523 (m) cc_final: 0.8177 (p) REVERT: C 295 ASN cc_start: 0.7287 (t0) cc_final: 0.7078 (t0) REVERT: C 329 ARG cc_start: 0.7498 (mtt90) cc_final: 0.7241 (mtt-85) REVERT: C 417 ARG cc_start: 0.8290 (ptp-110) cc_final: 0.7899 (ptp90) REVERT: C 521 VAL cc_start: 0.8571 (t) cc_final: 0.8295 (p) REVERT: D 24 MET cc_start: 0.7916 (mmm) cc_final: 0.7085 (mmm) REVERT: D 58 SER cc_start: 0.7912 (t) cc_final: 0.7623 (p) REVERT: D 103 GLU cc_start: 0.7009 (mt-10) cc_final: 0.6753 (mt-10) REVERT: D 203 LYS cc_start: 0.8071 (ttmm) cc_final: 0.7783 (ttmm) REVERT: D 207 GLU cc_start: 0.5694 (tm-30) cc_final: 0.5255 (tm-30) REVERT: D 215 GLU cc_start: 0.7753 (mp0) cc_final: 0.7339 (mp0) REVERT: D 417 ARG cc_start: 0.7947 (ttm110) cc_final: 0.7711 (mtm110) outliers start: 68 outliers final: 45 residues processed: 671 average time/residue: 0.3851 time to fit residues: 381.3090 Evaluate side-chains 667 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 619 time to evaluate : 2.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 75 CYS Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 84 SER 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 543 GLU 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 55 LYS 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 294 VAL Chi-restraints excluded: chain E residue 344 LYS Chi-restraints excluded: chain E residue 486 MET Chi-restraints excluded: chain E residue 540 LYS Chi-restraints excluded: chain C residue 357 THR 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 546 THR Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 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 346 VAL Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 478 LEU Chi-restraints excluded: chain D residue 546 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 0.6980 chunk 149 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 196 optimal weight: 0.8980 chunk 108 optimal weight: 0.6980 chunk 225 optimal weight: 5.9990 chunk 182 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 134 optimal weight: 0.9980 chunk 236 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN ** 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 53 HIS ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 GLN ** B 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 425 GLN ** E 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 ASN ** C 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 53 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** D 432 ASN D 552 HIS I 399 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7338 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 22196 Z= 0.199 Angle : 0.545 8.563 30252 Z= 0.277 Chirality : 0.041 0.280 3258 Planarity : 0.005 0.117 3942 Dihedral : 4.848 23.037 2967 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.51 % Favored : 98.46 % Rotamer: Outliers : 2.89 % Allowed : 13.63 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.15), residues: 2722 helix: 0.04 (0.35), residues: 213 sheet: 0.09 (0.19), residues: 638 loop : -0.27 (0.13), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 545 HIS 0.006 0.001 HIS B 53 PHE 0.018 0.001 PHE A 40 TYR 0.027 0.001 TYR C 250 ARG 0.006 0.000 ARG D 274 *********************** 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 712 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 644 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8042 (mmt-90) cc_final: 0.7842 (mmt-90) REVERT: A 207 GLU cc_start: 0.5891 (tm-30) cc_final: 0.4287 (tm-30) REVERT: A 215 GLU cc_start: 0.7343 (mp0) cc_final: 0.6609 (mp0) REVERT: A 240 GLU cc_start: 0.7422 (tp30) cc_final: 0.7178 (tp30) REVERT: A 295 ASN cc_start: 0.7339 (t0) cc_final: 0.7131 (t0) REVERT: A 296 SER cc_start: 0.7771 (t) cc_final: 0.7460 (p) REVERT: A 325 ARG cc_start: 0.8044 (mtm180) cc_final: 0.5829 (mtt180) REVERT: B 32 SER cc_start: 0.8398 (p) cc_final: 0.7932 (t) REVERT: B 42 ARG cc_start: 0.8389 (mmt-90) cc_final: 0.8064 (mpt180) REVERT: B 157 TYR cc_start: 0.8068 (m-80) cc_final: 0.7483 (m-80) REVERT: B 215 GLU cc_start: 0.7227 (mp0) cc_final: 0.6956 (mp0) REVERT: B 283 ILE cc_start: 0.8285 (pp) cc_final: 0.8075 (pt) REVERT: B 329 ARG cc_start: 0.8060 (mtt90) cc_final: 0.7608 (mtt-85) REVERT: B 374 PHE cc_start: 0.7835 (m-80) cc_final: 0.7598 (m-80) REVERT: B 407 ARG cc_start: 0.8616 (OUTLIER) cc_final: 0.8359 (ttm170) REVERT: E 81 MET cc_start: 0.7905 (tmm) cc_final: 0.7620 (ttp) REVERT: E 193 ASN cc_start: 0.7567 (t0) cc_final: 0.7249 (t0) REVERT: E 215 GLU cc_start: 0.7447 (mp0) cc_final: 0.6766 (mp0) REVERT: E 389 MET cc_start: 0.7610 (tpp) cc_final: 0.7384 (tpt) REVERT: E 548 LYS cc_start: 0.8495 (mttp) cc_final: 0.8277 (mttp) REVERT: C 215 GLU cc_start: 0.7496 (mp0) cc_final: 0.7282 (mp0) REVERT: C 229 THR cc_start: 0.8140 (m) cc_final: 0.7841 (p) REVERT: C 230 MET cc_start: 0.7140 (ppp) cc_final: 0.6882 (ppp) REVERT: C 295 ASN cc_start: 0.7121 (t0) cc_final: 0.6897 (t0) REVERT: C 374 PHE cc_start: 0.7969 (m-80) cc_final: 0.7751 (m-80) REVERT: C 434 ASP cc_start: 0.4003 (p0) cc_final: 0.3720 (p0) REVERT: C 521 VAL cc_start: 0.8528 (t) cc_final: 0.8239 (p) REVERT: D 24 MET cc_start: 0.7779 (mmm) cc_final: 0.7037 (mmm) REVERT: D 58 SER cc_start: 0.7834 (t) cc_final: 0.7601 (p) REVERT: D 103 GLU cc_start: 0.6938 (mt-10) cc_final: 0.6707 (mt-10) REVERT: D 203 LYS cc_start: 0.8030 (ttmm) cc_final: 0.7749 (ttmm) REVERT: D 207 GLU cc_start: 0.5559 (tm-30) cc_final: 0.5038 (tm-30) REVERT: D 215 GLU cc_start: 0.7695 (mp0) cc_final: 0.7341 (mp0) REVERT: D 242 LEU cc_start: 0.8000 (mt) cc_final: 0.7675 (mp) REVERT: D 274 ARG cc_start: 0.7120 (ptm-80) cc_final: 0.6508 (ptm-80) REVERT: D 286 GLN cc_start: 0.7997 (mm-40) cc_final: 0.7729 (mm-40) outliers start: 68 outliers final: 52 residues processed: 667 average time/residue: 0.3977 time to fit residues: 390.8323 Evaluate side-chains 677 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 624 time to evaluate : 2.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 429 LYS Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 407 ARG Chi-restraints excluded: chain B residue 543 GLU 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 55 LYS Chi-restraints excluded: chain E residue 75 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 294 VAL Chi-restraints excluded: chain E residue 344 LYS Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain E residue 459 LYS Chi-restraints excluded: chain E residue 460 ILE 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 188 THR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 546 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 0.9980 chunk 237 optimal weight: 10.0000 chunk 52 optimal weight: 7.9990 chunk 154 optimal weight: 0.6980 chunk 65 optimal weight: 0.0980 chunk 264 optimal weight: 7.9990 chunk 219 optimal weight: 0.7980 chunk 122 optimal weight: 0.5980 chunk 21 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 ASN ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 356 GLN ** B 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 517 HIS ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 287 ASN ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS D 284 GLN ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 22196 Z= 0.178 Angle : 0.531 8.389 30252 Z= 0.269 Chirality : 0.041 0.273 3258 Planarity : 0.004 0.115 3942 Dihedral : 4.647 21.480 2967 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.36 % Favored : 98.60 % Rotamer: Outliers : 2.89 % Allowed : 14.56 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.15), residues: 2722 helix: 0.16 (0.36), residues: 213 sheet: 0.10 (0.19), residues: 638 loop : -0.24 (0.13), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 545 HIS 0.006 0.001 HIS D 53 PHE 0.016 0.001 PHE I 315 TYR 0.026 0.001 TYR C 250 ARG 0.004 0.000 ARG E 373 *********************** 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 704 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 636 time to evaluate : 2.466 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ARG cc_start: 0.8066 (mmt-90) cc_final: 0.7809 (mmt-90) REVERT: A 197 ILE cc_start: 0.8287 (OUTLIER) cc_final: 0.8025 (mt) REVERT: A 207 GLU cc_start: 0.5856 (tm-30) cc_final: 0.3843 (tt0) REVERT: A 215 GLU cc_start: 0.7299 (mp0) cc_final: 0.6614 (mp0) REVERT: A 240 GLU cc_start: 0.7420 (tp30) cc_final: 0.7157 (tp30) REVERT: A 343 ASP cc_start: 0.6908 (p0) cc_final: 0.6686 (p0) REVERT: B 32 SER cc_start: 0.8337 (p) cc_final: 0.7929 (t) REVERT: B 215 GLU cc_start: 0.7209 (mp0) cc_final: 0.6939 (mp0) REVERT: B 374 PHE cc_start: 0.7782 (m-80) cc_final: 0.7576 (m-80) REVERT: B 407 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8262 (ttp-170) REVERT: B 532 GLN cc_start: 0.7368 (mm-40) cc_final: 0.7160 (mm-40) REVERT: E 81 MET cc_start: 0.7863 (tmm) cc_final: 0.7617 (ttp) REVERT: E 129 LYS cc_start: 0.7025 (mttp) cc_final: 0.6816 (mttp) REVERT: E 193 ASN cc_start: 0.7575 (t0) cc_final: 0.7271 (t0) REVERT: E 215 GLU cc_start: 0.7432 (mp0) cc_final: 0.6772 (mp0) REVERT: E 257 TYR cc_start: 0.8555 (m-80) cc_final: 0.8334 (m-80) REVERT: E 389 MET cc_start: 0.7586 (tpp) cc_final: 0.7361 (tpt) REVERT: C 125 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7201 (mm-30) REVERT: C 229 THR cc_start: 0.8016 (m) cc_final: 0.7722 (p) REVERT: C 284 GLN cc_start: 0.7723 (tp40) cc_final: 0.7379 (tm-30) REVERT: C 295 ASN cc_start: 0.7114 (t0) cc_final: 0.6878 (t0) REVERT: C 374 PHE cc_start: 0.7973 (m-80) cc_final: 0.7772 (m-80) REVERT: C 521 VAL cc_start: 0.8501 (t) cc_final: 0.8228 (p) REVERT: D 203 LYS cc_start: 0.8007 (ttmm) cc_final: 0.7763 (ttmm) REVERT: D 207 GLU cc_start: 0.5405 (tm-30) cc_final: 0.4923 (tm-30) REVERT: D 215 GLU cc_start: 0.7670 (mp0) cc_final: 0.7299 (mp0) REVERT: D 242 LEU cc_start: 0.7947 (mt) cc_final: 0.7634 (mp) REVERT: D 274 ARG cc_start: 0.7065 (ptm-80) cc_final: 0.6375 (ptm-80) REVERT: D 286 GLN cc_start: 0.8025 (mm-40) cc_final: 0.7427 (mm-40) outliers start: 68 outliers final: 53 residues processed: 657 average time/residue: 0.3877 time to fit residues: 377.0851 Evaluate side-chains 678 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 623 time to evaluate : 2.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 38 CYS Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 176 ILE Chi-restraints excluded: chain A residue 197 ILE Chi-restraints excluded: chain A residue 204 LEU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 407 ARG Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 543 GLU 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 49 ASP Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 274 ARG Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain E residue 460 ILE 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 294 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 546 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 150 optimal weight: 2.9990 chunk 192 optimal weight: 0.9990 chunk 149 optimal weight: 0.0570 chunk 222 optimal weight: 8.9990 chunk 147 optimal weight: 0.9980 chunk 263 optimal weight: 20.0000 chunk 164 optimal weight: 6.9990 chunk 160 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN A 323 ASN ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 22196 Z= 0.325 Angle : 0.569 8.965 30252 Z= 0.290 Chirality : 0.043 0.269 3258 Planarity : 0.005 0.113 3942 Dihedral : 4.818 22.800 2967 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.69 % Favored : 98.27 % Rotamer: Outliers : 3.06 % Allowed : 14.95 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.15), residues: 2722 helix: 0.12 (0.36), residues: 213 sheet: 0.01 (0.19), residues: 638 loop : -0.31 (0.13), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 25 HIS 0.007 0.001 HIS E 278 PHE 0.018 0.002 PHE B 492 TYR 0.025 0.001 TYR C 250 ARG 0.006 0.001 ARG E 373 *********************** 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 714 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 642 time to evaluate : 2.468 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 42 ARG cc_start: 0.8083 (mmt-90) cc_final: 0.7831 (mmt-90) REVERT: A 197 ILE cc_start: 0.8269 (OUTLIER) cc_final: 0.8003 (mt) REVERT: A 207 GLU cc_start: 0.6065 (tm-30) cc_final: 0.4054 (tt0) REVERT: A 215 GLU cc_start: 0.7370 (mp0) cc_final: 0.6657 (mp0) REVERT: A 240 GLU cc_start: 0.7446 (tp30) cc_final: 0.7199 (tp30) REVERT: A 325 ARG cc_start: 0.8027 (mtm180) cc_final: 0.5846 (mtt180) REVERT: A 343 ASP cc_start: 0.6987 (p0) cc_final: 0.6749 (p0) REVERT: B 32 SER cc_start: 0.8299 (p) cc_final: 0.7881 (t) REVERT: B 215 GLU cc_start: 0.7232 (mp0) cc_final: 0.6966 (mp0) REVERT: B 407 ARG cc_start: 0.8633 (OUTLIER) cc_final: 0.8431 (ttm170) REVERT: B 470 ILE cc_start: 0.7825 (mt) cc_final: 0.7475 (pt) REVERT: B 473 MET cc_start: 0.4608 (mtm) cc_final: 0.4276 (mtm) REVERT: B 532 GLN cc_start: 0.7437 (mm-40) cc_final: 0.7203 (mm-40) REVERT: E 81 MET cc_start: 0.7888 (tmm) cc_final: 0.7672 (ttp) REVERT: E 91 ASP cc_start: 0.6952 (t0) cc_final: 0.6719 (t0) REVERT: E 129 LYS cc_start: 0.7137 (mttp) cc_final: 0.6877 (mttp) REVERT: E 193 ASN cc_start: 0.7626 (t0) cc_final: 0.7387 (t0) REVERT: E 215 GLU cc_start: 0.7476 (mp0) cc_final: 0.6817 (mp0) REVERT: E 325 ARG cc_start: 0.8112 (mtp180) cc_final: 0.6324 (mtt90) REVERT: E 389 MET cc_start: 0.7666 (tpp) cc_final: 0.7428 (tpt) REVERT: C 125 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7212 (mm-30) REVERT: C 284 GLN cc_start: 0.7719 (tp40) cc_final: 0.7367 (tm-30) REVERT: C 295 ASN cc_start: 0.7280 (t0) cc_final: 0.7014 (t0) REVERT: C 376 ASN cc_start: 0.8112 (t0) cc_final: 0.7889 (t0) REVERT: C 521 VAL cc_start: 0.8549 (t) cc_final: 0.8273 (p) REVERT: D 103 GLU cc_start: 0.6979 (mt-10) cc_final: 0.6736 (mt-10) REVERT: D 207 GLU cc_start: 0.5653 (tm-30) cc_final: 0.4909 (tm-30) REVERT: D 215 GLU cc_start: 0.7682 (mp0) cc_final: 0.7310 (mp0) REVERT: D 242 LEU cc_start: 0.7999 (mt) cc_final: 0.7692 (mp) REVERT: D 274 ARG cc_start: 0.7118 (ptm-80) cc_final: 0.6432 (ptm-80) outliers start: 72 outliers final: 61 residues processed: 666 average time/residue: 0.3836 time to fit residues: 377.2685 Evaluate side-chains 688 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 625 time to evaluate : 2.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2 THR Chi-restraints excluded: chain A residue 18 SER Chi-restraints excluded: chain A residue 27 GLU Chi-restraints excluded: chain A residue 113 SER Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 195 GLN 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 434 ASP Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 80 ILE Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 407 ARG Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 55 LYS 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 261 LEU Chi-restraints excluded: chain E residue 274 ARG Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 344 LYS Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 486 MET 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 208 GLU Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 152 LEU Chi-restraints excluded: chain D residue 173 GLU Chi-restraints excluded: chain D residue 176 ILE 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 346 VAL Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 435 ASP Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain D residue 554 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 0.7980 chunk 105 optimal weight: 0.9990 chunk 157 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 51 optimal weight: 7.9990 chunk 50 optimal weight: 3.9990 chunk 167 optimal weight: 1.9990 chunk 179 optimal weight: 9.9990 chunk 130 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 206 optimal weight: 10.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 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** C 53 HIS ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3981 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= 0.293 Angle : 0.574 8.624 30252 Z= 0.291 Chirality : 0.043 0.263 3258 Planarity : 0.005 0.110 3942 Dihedral : 4.802 21.598 2967 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.73 % Favored : 98.24 % Rotamer: Outliers : 3.14 % Allowed : 15.54 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 2722 helix: 0.10 (0.36), residues: 213 sheet: -0.02 (0.19), residues: 638 loop : -0.36 (0.13), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 427 HIS 0.007 0.001 HIS B 53 PHE 0.036 0.002 PHE B 374 TYR 0.023 0.001 TYR C 250 ARG 0.005 0.001 ARG E 373 *********************** 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 714 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 640 time to evaluate : 2.615 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 42 ARG cc_start: 0.8110 (mmt-90) cc_final: 0.7798 (mmt-90) REVERT: A 207 GLU cc_start: 0.6035 (tm-30) cc_final: 0.4082 (tt0) REVERT: A 240 GLU cc_start: 0.7448 (tp30) cc_final: 0.7196 (tp30) REVERT: A 325 ARG cc_start: 0.8064 (mtm180) cc_final: 0.5826 (mtt180) REVERT: A 343 ASP cc_start: 0.7092 (p0) cc_final: 0.6842 (p0) REVERT: A 384 LEU cc_start: 0.8272 (mt) cc_final: 0.8047 (mt) REVERT: B 32 SER cc_start: 0.8282 (p) cc_final: 0.7927 (t) REVERT: B 215 GLU cc_start: 0.7225 (mp0) cc_final: 0.6995 (mp0) REVERT: B 470 ILE cc_start: 0.7807 (mt) cc_final: 0.7535 (pt) REVERT: B 473 MET cc_start: 0.4943 (mtm) cc_final: 0.4479 (mtm) REVERT: E 81 MET cc_start: 0.7879 (tmm) cc_final: 0.7667 (ttp) REVERT: E 91 ASP cc_start: 0.6945 (t0) cc_final: 0.6695 (t0) REVERT: E 129 LYS cc_start: 0.7147 (mttp) cc_final: 0.6864 (mttp) REVERT: E 193 ASN cc_start: 0.7620 (t0) cc_final: 0.7378 (t0) REVERT: E 215 GLU cc_start: 0.7473 (mp0) cc_final: 0.6823 (mp0) REVERT: E 389 MET cc_start: 0.7678 (tpp) cc_final: 0.7452 (tpt) REVERT: C 125 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7216 (mm-30) REVERT: C 154 ASP cc_start: 0.7344 (t0) cc_final: 0.7130 (t0) REVERT: C 215 GLU cc_start: 0.7574 (mp0) cc_final: 0.7341 (mp0) REVERT: C 229 THR cc_start: 0.8221 (m) cc_final: 0.7912 (p) REVERT: C 284 GLN cc_start: 0.7738 (tp40) cc_final: 0.7371 (tm-30) REVERT: C 295 ASN cc_start: 0.7269 (t0) cc_final: 0.6988 (t0) REVERT: C 389 MET cc_start: 0.7615 (mmm) cc_final: 0.7363 (tpt) REVERT: C 521 VAL cc_start: 0.8535 (t) cc_final: 0.8283 (p) REVERT: D 103 GLU cc_start: 0.6955 (mt-10) cc_final: 0.6740 (mt-10) REVERT: D 134 LYS cc_start: 0.8534 (ttpp) cc_final: 0.8312 (tttp) REVERT: D 207 GLU cc_start: 0.5219 (tm-30) cc_final: 0.4661 (tm-30) REVERT: D 215 GLU cc_start: 0.7675 (mp0) cc_final: 0.7330 (mp0) REVERT: D 242 LEU cc_start: 0.8002 (mt) cc_final: 0.7693 (mp) REVERT: D 274 ARG cc_start: 0.7158 (ptm-80) cc_final: 0.6499 (ptm-80) REVERT: I 383 LEU cc_start: 0.5323 (OUTLIER) cc_final: 0.5094 (tp) outliers start: 74 outliers final: 58 residues processed: 666 average time/residue: 0.4105 time to fit residues: 410.4250 Evaluate side-chains 692 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 633 time to evaluate : 2.606 ------------------------------------------------------------------------------- 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 174 LEU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 55 LYS Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 274 ARG Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 344 LYS Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain E residue 460 ILE Chi-restraints excluded: chain E residue 473 MET Chi-restraints excluded: chain E residue 486 MET Chi-restraints excluded: chain C residue 27 GLU Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 150 CYS Chi-restraints excluded: chain D residue 176 ILE 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 346 VAL Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 406 GLU Chi-restraints excluded: chain D residue 435 ASP Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain I residue 383 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 0.8980 chunk 252 optimal weight: 2.9990 chunk 229 optimal weight: 5.9990 chunk 245 optimal weight: 0.4980 chunk 147 optimal weight: 3.9990 chunk 106 optimal weight: 2.9990 chunk 192 optimal weight: 0.6980 chunk 75 optimal weight: 1.9990 chunk 221 optimal weight: 1.9990 chunk 231 optimal weight: 0.0070 chunk 244 optimal weight: 2.9990 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 HIS ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7331 moved from start: 0.4090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 22196 Z= 0.203 Angle : 0.562 8.520 30252 Z= 0.284 Chirality : 0.041 0.257 3258 Planarity : 0.005 0.107 3942 Dihedral : 4.664 23.106 2967 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.65 % Favored : 98.31 % Rotamer: Outliers : 2.72 % Allowed : 16.26 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.15), residues: 2722 helix: 0.05 (0.36), residues: 213 sheet: -0.01 (0.19), residues: 638 loop : -0.35 (0.13), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 427 HIS 0.007 0.001 HIS B 53 PHE 0.034 0.001 PHE B 374 TYR 0.023 0.001 TYR C 250 ARG 0.011 0.000 ARG I 338 *********************** 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 706 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 642 time to evaluate : 2.761 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 42 ARG cc_start: 0.8036 (mmt-90) cc_final: 0.7788 (mmt-90) REVERT: A 197 ILE cc_start: 0.8229 (mt) cc_final: 0.7928 (mt) REVERT: A 207 GLU cc_start: 0.5948 (tm-30) cc_final: 0.4010 (tt0) REVERT: A 240 GLU cc_start: 0.7444 (tp30) cc_final: 0.7190 (tp30) REVERT: A 325 ARG cc_start: 0.8043 (mtm180) cc_final: 0.5814 (mtt180) REVERT: A 343 ASP cc_start: 0.7043 (p0) cc_final: 0.6824 (p0) REVERT: A 384 LEU cc_start: 0.8243 (mt) cc_final: 0.8023 (mt) REVERT: B 32 SER cc_start: 0.8147 (p) cc_final: 0.7824 (t) REVERT: B 215 GLU cc_start: 0.7213 (mp0) cc_final: 0.6953 (mp0) REVERT: B 470 ILE cc_start: 0.7734 (mt) cc_final: 0.7531 (pt) REVERT: B 473 MET cc_start: 0.5001 (mtm) cc_final: 0.4536 (mtm) REVERT: E 81 MET cc_start: 0.7865 (tmm) cc_final: 0.7661 (ttp) REVERT: E 91 ASP cc_start: 0.6919 (t0) cc_final: 0.6668 (t0) REVERT: E 129 LYS cc_start: 0.7143 (mttp) cc_final: 0.6829 (mtpp) REVERT: E 193 ASN cc_start: 0.7599 (t0) cc_final: 0.7354 (t0) REVERT: E 215 GLU cc_start: 0.7418 (mp0) cc_final: 0.6793 (mp0) REVERT: E 257 TYR cc_start: 0.8530 (m-80) cc_final: 0.8315 (m-80) REVERT: E 325 ARG cc_start: 0.8087 (mtp180) cc_final: 0.6310 (mtt90) REVERT: E 389 MET cc_start: 0.7623 (tpp) cc_final: 0.7396 (tpt) REVERT: C 125 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7234 (mm-30) REVERT: C 154 ASP cc_start: 0.7302 (t0) cc_final: 0.7083 (t0) REVERT: C 284 GLN cc_start: 0.7754 (tp40) cc_final: 0.7382 (tm-30) REVERT: C 295 ASN cc_start: 0.7270 (t0) cc_final: 0.6980 (t0) REVERT: C 389 MET cc_start: 0.7609 (mmm) cc_final: 0.7385 (tpt) REVERT: C 521 VAL cc_start: 0.8503 (t) cc_final: 0.8258 (p) REVERT: D 103 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6711 (mt-10) REVERT: D 134 LYS cc_start: 0.8505 (ttpp) cc_final: 0.8303 (tttp) REVERT: D 207 GLU cc_start: 0.5206 (tm-30) cc_final: 0.4660 (tm-30) REVERT: D 215 GLU cc_start: 0.7643 (mp0) cc_final: 0.7268 (mp0) REVERT: D 242 LEU cc_start: 0.7933 (mt) cc_final: 0.7653 (mp) REVERT: D 274 ARG cc_start: 0.7089 (ptm-80) cc_final: 0.6476 (ptm-80) REVERT: D 343 ASP cc_start: 0.7375 (p0) cc_final: 0.7085 (p0) REVERT: I 383 LEU cc_start: 0.5405 (OUTLIER) cc_final: 0.5182 (tp) outliers start: 64 outliers final: 57 residues processed: 662 average time/residue: 0.3902 time to fit residues: 380.4085 Evaluate side-chains 685 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 627 time to evaluate : 2.645 ------------------------------------------------------------------------------- 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 174 LEU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 473 MET Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 55 LYS Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 274 ARG Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 410 MET 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 C residue 27 GLU Chi-restraints excluded: chain C residue 53 HIS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 133 ASP Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 357 THR 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 526 THR Chi-restraints excluded: chain C residue 546 THR Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 435 ASP Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain D residue 554 LEU Chi-restraints excluded: chain I residue 383 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 1.9990 chunk 259 optimal weight: 0.0870 chunk 158 optimal weight: 0.8980 chunk 123 optimal weight: 6.9990 chunk 180 optimal weight: 4.9990 chunk 271 optimal weight: 40.0000 chunk 250 optimal weight: 0.9990 chunk 216 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 167 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 overall best weight: 0.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 195 GLN ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 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** E 517 HIS ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.4180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 22196 Z= 0.199 Angle : 0.561 9.316 30252 Z= 0.284 Chirality : 0.041 0.252 3258 Planarity : 0.005 0.104 3942 Dihedral : 4.592 20.120 2967 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.87 % Favored : 98.09 % Rotamer: Outliers : 2.51 % Allowed : 16.69 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.15), residues: 2722 helix: -0.06 (0.36), residues: 213 sheet: 0.01 (0.19), residues: 638 loop : -0.36 (0.13), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 427 HIS 0.007 0.001 HIS B 53 PHE 0.032 0.002 PHE B 374 TYR 0.021 0.001 TYR C 250 ARG 0.008 0.000 ARG I 338 ********************** 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 714 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 655 time to evaluate : 2.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ILE cc_start: 0.8221 (mt) cc_final: 0.7912 (mt) REVERT: A 207 GLU cc_start: 0.5963 (tm-30) cc_final: 0.4241 (tt0) REVERT: A 240 GLU cc_start: 0.7449 (tp30) cc_final: 0.7197 (tp30) REVERT: A 384 LEU cc_start: 0.8153 (mt) cc_final: 0.7918 (mt) REVERT: B 32 SER cc_start: 0.8083 (p) cc_final: 0.7831 (t) REVERT: B 42 ARG cc_start: 0.8370 (mmt-90) cc_final: 0.8006 (mpt180) REVERT: B 215 GLU cc_start: 0.7199 (mp0) cc_final: 0.6931 (mp0) REVERT: B 273 PHE cc_start: 0.7011 (m-80) cc_final: 0.6775 (m-80) REVERT: B 329 ARG cc_start: 0.8145 (mtt90) cc_final: 0.7709 (mtt-85) REVERT: B 510 TYR cc_start: 0.8031 (m-10) cc_final: 0.7676 (m-10) REVERT: E 81 MET cc_start: 0.7853 (tmm) cc_final: 0.7643 (ttp) REVERT: E 91 ASP cc_start: 0.6907 (t0) cc_final: 0.6649 (t0) REVERT: E 129 LYS cc_start: 0.7154 (mttp) cc_final: 0.6831 (mtpp) REVERT: E 193 ASN cc_start: 0.7598 (t0) cc_final: 0.7362 (t0) REVERT: E 215 GLU cc_start: 0.7418 (mp0) cc_final: 0.6773 (mp0) REVERT: E 257 TYR cc_start: 0.8523 (m-80) cc_final: 0.8311 (m-80) REVERT: E 325 ARG cc_start: 0.8088 (mtp180) cc_final: 0.6317 (mtt90) REVERT: C 125 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7223 (mm-30) REVERT: C 154 ASP cc_start: 0.7326 (t0) cc_final: 0.7122 (t0) REVERT: C 241 ASN cc_start: 0.7773 (t0) cc_final: 0.7518 (t0) REVERT: C 295 ASN cc_start: 0.7252 (t0) cc_final: 0.6967 (t0) REVERT: C 389 MET cc_start: 0.7604 (mmm) cc_final: 0.7382 (tpt) REVERT: C 473 MET cc_start: 0.5901 (mmm) cc_final: 0.5588 (mmm) REVERT: C 521 VAL cc_start: 0.8431 (t) cc_final: 0.8195 (p) REVERT: D 103 GLU cc_start: 0.6911 (mt-10) cc_final: 0.6697 (mt-10) REVERT: D 134 LYS cc_start: 0.8503 (ttpp) cc_final: 0.8292 (tttp) REVERT: D 215 GLU cc_start: 0.7638 (mp0) cc_final: 0.7277 (mp0) REVERT: D 242 LEU cc_start: 0.7912 (mt) cc_final: 0.7650 (mp) REVERT: D 274 ARG cc_start: 0.7065 (ptm-80) cc_final: 0.6473 (ptm-80) REVERT: D 286 GLN cc_start: 0.8010 (mm-40) cc_final: 0.7692 (mm-40) outliers start: 59 outliers final: 52 residues processed: 673 average time/residue: 0.3966 time to fit residues: 394.5981 Evaluate side-chains 681 residues out of total 2355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 629 time to evaluate : 2.525 ------------------------------------------------------------------------------- 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 128 VAL Chi-restraints excluded: chain A residue 174 LEU Chi-restraints excluded: chain A residue 230 MET Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 406 GLU Chi-restraints excluded: chain A residue 434 ASP Chi-restraints excluded: chain A residue 521 VAL Chi-restraints excluded: chain A residue 533 HIS Chi-restraints excluded: chain A residue 554 LEU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 170 LEU Chi-restraints excluded: chain B residue 294 VAL Chi-restraints excluded: chain B residue 314 THR Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 543 GLU Chi-restraints excluded: chain E residue 21 VAL Chi-restraints excluded: chain E residue 27 GLU Chi-restraints excluded: chain E residue 55 LYS Chi-restraints excluded: chain E residue 227 THR Chi-restraints excluded: chain E residue 230 MET Chi-restraints excluded: chain E residue 261 LEU Chi-restraints excluded: chain E residue 274 ARG Chi-restraints excluded: chain E residue 294 VAL Chi-restraints excluded: chain E residue 410 MET Chi-restraints excluded: chain E residue 420 LEU Chi-restraints excluded: chain E residue 473 MET 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 227 THR Chi-restraints excluded: chain C residue 294 VAL Chi-restraints excluded: chain C residue 357 THR Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 420 LEU Chi-restraints excluded: chain C residue 526 THR Chi-restraints excluded: chain D residue 27 GLU Chi-restraints excluded: chain D residue 35 SER Chi-restraints excluded: chain D residue 53 HIS Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 143 ASP Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 283 ILE Chi-restraints excluded: chain D residue 294 VAL Chi-restraints excluded: chain D residue 346 VAL Chi-restraints excluded: chain D residue 378 LYS Chi-restraints excluded: chain D residue 405 ILE Chi-restraints excluded: chain D residue 435 ASP Chi-restraints excluded: chain D residue 546 THR Chi-restraints excluded: chain D residue 554 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 5.9990 chunk 230 optimal weight: 4.9990 chunk 66 optimal weight: 0.0980 chunk 199 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 216 optimal weight: 7.9990 chunk 90 optimal weight: 0.8980 chunk 222 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 517 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 53 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** E 517 HIS ** C 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 281 HIS ** D 421 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.111073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.092705 restraints weight = 35983.071| |-----------------------------------------------------------------------------| r_work (start): 0.3105 rms_B_bonded: 2.15 r_work: 0.3002 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.4257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 22196 Z= 0.247 Angle : 0.577 10.026 30252 Z= 0.291 Chirality : 0.042 0.247 3258 Planarity : 0.005 0.101 3942 Dihedral : 4.663 20.750 2967 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 1.87 % Favored : 98.09 % Rotamer: Outliers : 2.55 % Allowed : 16.73 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.20 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.15), residues: 2722 helix: -0.14 (0.36), residues: 213 sheet: 0.00 (0.19), residues: 638 loop : -0.38 (0.13), residues: 1871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 427 HIS 0.007 0.001 HIS B 53 PHE 0.031 0.002 PHE B 374 TYR 0.022 0.001 TYR C 250 ARG 0.017 0.001 ARG I 338 =============================================================================== Job complete usr+sys time: 7478.37 seconds wall clock time: 135 minutes 46.14 seconds (8146.14 seconds total)