Starting phenix.real_space_refine on Tue Mar 19 03:50:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ua5_20706/03_2024/6ua5_20706_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ua5_20706/03_2024/6ua5_20706.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ua5_20706/03_2024/6ua5_20706.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ua5_20706/03_2024/6ua5_20706.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ua5_20706/03_2024/6ua5_20706_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ua5_20706/03_2024/6ua5_20706_updated.pdb" } resolution = 3.79 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.102 sd= 3.978 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 24 5.49 5 S 144 5.16 5 C 14512 2.51 5 N 3920 2.21 5 O 4480 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 356": "NH1" <-> "NH2" Residue "A ARG 407": "NH1" <-> "NH2" Residue "A ARG 412": "NH1" <-> "NH2" Residue "A ARG 512": "NH1" <-> "NH2" Residue "B ARG 356": "NH1" <-> "NH2" Residue "B ARG 407": "NH1" <-> "NH2" Residue "B ARG 412": "NH1" <-> "NH2" Residue "B ARG 512": "NH1" <-> "NH2" Residue "C ARG 356": "NH1" <-> "NH2" Residue "C ARG 407": "NH1" <-> "NH2" Residue "C ARG 412": "NH1" <-> "NH2" Residue "C ARG 512": "NH1" <-> "NH2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "D ARG 407": "NH1" <-> "NH2" Residue "D ARG 412": "NH1" <-> "NH2" Residue "D ARG 512": "NH1" <-> "NH2" Residue "E ARG 356": "NH1" <-> "NH2" Residue "E ARG 407": "NH1" <-> "NH2" Residue "E ARG 412": "NH1" <-> "NH2" Residue "E ARG 512": "NH1" <-> "NH2" Residue "F ARG 356": "NH1" <-> "NH2" Residue "F ARG 407": "NH1" <-> "NH2" Residue "F ARG 412": "NH1" <-> "NH2" Residue "F ARG 512": "NH1" <-> "NH2" Residue "G ARG 356": "NH1" <-> "NH2" Residue "G ARG 407": "NH1" <-> "NH2" Residue "G ARG 412": "NH1" <-> "NH2" Residue "G ARG 512": "NH1" <-> "NH2" Residue "H ARG 356": "NH1" <-> "NH2" Residue "H ARG 407": "NH1" <-> "NH2" Residue "H ARG 412": "NH1" <-> "NH2" Residue "H ARG 512": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 23080 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "B" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "C" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "D" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "E" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "F" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "G" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "H" Number of atoms: 2818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2818 Classifications: {'peptide': 376} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 363} Chain breaks: 2 Chain: "A" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "B" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "C" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "D" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "E" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "F" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "G" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Chain: "H" Number of atoms: 67 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 67 Unusual residues: {'NAD': 1} Classifications: {'RNA': 1, 'undetermined': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 1} Time building chain proxies: 11.81, per 1000 atoms: 0.51 Number of scatterers: 23080 At special positions: 0 Unit cell: (124.95, 124.95, 120.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 144 16.00 P 24 15.00 O 4480 8.00 N 3920 7.00 C 14512 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 - 3.50 Amino acid : False - 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=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.95 Conformation dependent library (CDL) restraints added in 3.6 seconds 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5392 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 112 helices and 32 sheets defined 31.9% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.74 Creating SS restraints... Processing helix chain 'A' and resid 20 through 23 No H-bonds generated for 'chain 'A' and resid 20 through 23' Processing helix chain 'A' and resid 32 through 34 No H-bonds generated for 'chain 'A' and resid 32 through 34' Processing helix chain 'A' and resid 76 through 85 Processing helix chain 'A' and resid 97 through 109 removed outlier: 3.603A pdb=" N LYS A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 266 removed outlier: 4.335A pdb=" N ASP A 261 " --> pdb=" O TYR A 258 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 262 " --> pdb=" O ARG A 259 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 290 Processing helix chain 'A' and resid 307 through 314 removed outlier: 4.216A pdb=" N ASN A 312 " --> pdb=" O ALA A 308 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU A 313 " --> pdb=" O GLN A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 336 No H-bonds generated for 'chain 'A' and resid 333 through 336' Processing helix chain 'A' and resid 346 through 357 removed outlier: 4.117A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE A 357 " --> pdb=" O TYR A 353 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 378 Processing helix chain 'A' and resid 453 through 455 No H-bonds generated for 'chain 'A' and resid 453 through 455' Processing helix chain 'A' and resid 457 through 471 Processing helix chain 'A' and resid 476 through 485 Processing helix chain 'A' and resid 495 through 501 removed outlier: 3.781A pdb=" N GLU A 500 " --> pdb=" O SER A 496 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 23 No H-bonds generated for 'chain 'B' and resid 20 through 23' Processing helix chain 'B' and resid 32 through 34 No H-bonds generated for 'chain 'B' and resid 32 through 34' Processing helix chain 'B' and resid 76 through 85 Processing helix chain 'B' and resid 97 through 109 removed outlier: 3.604A pdb=" N LYS B 109 " --> pdb=" O ARG B 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 266 removed outlier: 4.335A pdb=" N ASP B 261 " --> pdb=" O TYR B 258 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU B 262 " --> pdb=" O ARG B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 290 Processing helix chain 'B' and resid 307 through 314 removed outlier: 4.216A pdb=" N ASN B 312 " --> pdb=" O ALA B 308 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU B 313 " --> pdb=" O GLN B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 333 through 336 No H-bonds generated for 'chain 'B' and resid 333 through 336' Processing helix chain 'B' and resid 346 through 357 removed outlier: 4.116A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE B 357 " --> pdb=" O TYR B 353 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 378 Processing helix chain 'B' and resid 453 through 455 No H-bonds generated for 'chain 'B' and resid 453 through 455' Processing helix chain 'B' and resid 457 through 471 Processing helix chain 'B' and resid 476 through 485 Processing helix chain 'B' and resid 495 through 501 removed outlier: 3.780A pdb=" N GLU B 500 " --> pdb=" O SER B 496 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 23 No H-bonds generated for 'chain 'C' and resid 20 through 23' Processing helix chain 'C' and resid 32 through 34 No H-bonds generated for 'chain 'C' and resid 32 through 34' Processing helix chain 'C' and resid 76 through 85 Processing helix chain 'C' and resid 97 through 109 removed outlier: 3.604A pdb=" N LYS C 109 " --> pdb=" O ARG C 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 266 removed outlier: 4.334A pdb=" N ASP C 261 " --> pdb=" O TYR C 258 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU C 262 " --> pdb=" O ARG C 259 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 290 Processing helix chain 'C' and resid 307 through 314 removed outlier: 4.217A pdb=" N ASN C 312 " --> pdb=" O ALA C 308 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU C 313 " --> pdb=" O GLN C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 333 through 336 No H-bonds generated for 'chain 'C' and resid 333 through 336' Processing helix chain 'C' and resid 346 through 357 removed outlier: 4.117A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE C 357 " --> pdb=" O TYR C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 371 through 378 Processing helix chain 'C' and resid 453 through 455 No H-bonds generated for 'chain 'C' and resid 453 through 455' Processing helix chain 'C' and resid 457 through 471 Processing helix chain 'C' and resid 476 through 485 Processing helix chain 'C' and resid 495 through 501 removed outlier: 3.780A pdb=" N GLU C 500 " --> pdb=" O SER C 496 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 23 No H-bonds generated for 'chain 'D' and resid 20 through 23' Processing helix chain 'D' and resid 32 through 34 No H-bonds generated for 'chain 'D' and resid 32 through 34' Processing helix chain 'D' and resid 76 through 85 Processing helix chain 'D' and resid 97 through 109 removed outlier: 3.604A pdb=" N LYS D 109 " --> pdb=" O ARG D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 266 removed outlier: 4.334A pdb=" N ASP D 261 " --> pdb=" O TYR D 258 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU D 262 " --> pdb=" O ARG D 259 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 290 Processing helix chain 'D' and resid 307 through 314 removed outlier: 4.217A pdb=" N ASN D 312 " --> pdb=" O ALA D 308 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU D 313 " --> pdb=" O GLN D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 333 through 336 No H-bonds generated for 'chain 'D' and resid 333 through 336' Processing helix chain 'D' and resid 346 through 357 removed outlier: 4.117A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N PHE D 357 " --> pdb=" O TYR D 353 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 378 Processing helix chain 'D' and resid 453 through 455 No H-bonds generated for 'chain 'D' and resid 453 through 455' Processing helix chain 'D' and resid 457 through 471 Processing helix chain 'D' and resid 476 through 485 Processing helix chain 'D' and resid 495 through 501 removed outlier: 3.781A pdb=" N GLU D 500 " --> pdb=" O SER D 496 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 23 No H-bonds generated for 'chain 'E' and resid 20 through 23' Processing helix chain 'E' and resid 32 through 34 No H-bonds generated for 'chain 'E' and resid 32 through 34' Processing helix chain 'E' and resid 76 through 85 Processing helix chain 'E' and resid 97 through 109 removed outlier: 3.604A pdb=" N LYS E 109 " --> pdb=" O ARG E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 266 removed outlier: 4.334A pdb=" N ASP E 261 " --> pdb=" O TYR E 258 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU E 262 " --> pdb=" O ARG E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 290 Processing helix chain 'E' and resid 307 through 314 removed outlier: 4.217A pdb=" N ASN E 312 " --> pdb=" O ALA E 308 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU E 313 " --> pdb=" O GLN E 309 " (cutoff:3.500A) Processing helix chain 'E' and resid 333 through 336 No H-bonds generated for 'chain 'E' and resid 333 through 336' Processing helix chain 'E' and resid 346 through 357 removed outlier: 4.117A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE E 357 " --> pdb=" O TYR E 353 " (cutoff:3.500A) Processing helix chain 'E' and resid 371 through 378 Processing helix chain 'E' and resid 453 through 455 No H-bonds generated for 'chain 'E' and resid 453 through 455' Processing helix chain 'E' and resid 457 through 471 Processing helix chain 'E' and resid 476 through 485 Processing helix chain 'E' and resid 495 through 501 removed outlier: 3.781A pdb=" N GLU E 500 " --> pdb=" O SER E 496 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 23 No H-bonds generated for 'chain 'F' and resid 20 through 23' Processing helix chain 'F' and resid 32 through 34 No H-bonds generated for 'chain 'F' and resid 32 through 34' Processing helix chain 'F' and resid 76 through 85 Processing helix chain 'F' and resid 97 through 109 removed outlier: 3.604A pdb=" N LYS F 109 " --> pdb=" O ARG F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 266 removed outlier: 4.334A pdb=" N ASP F 261 " --> pdb=" O TYR F 258 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU F 262 " --> pdb=" O ARG F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 290 Processing helix chain 'F' and resid 307 through 314 removed outlier: 4.217A pdb=" N ASN F 312 " --> pdb=" O ALA F 308 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU F 313 " --> pdb=" O GLN F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 333 through 336 No H-bonds generated for 'chain 'F' and resid 333 through 336' Processing helix chain 'F' and resid 346 through 357 removed outlier: 4.117A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE F 357 " --> pdb=" O TYR F 353 " (cutoff:3.500A) Processing helix chain 'F' and resid 371 through 378 Processing helix chain 'F' and resid 453 through 455 No H-bonds generated for 'chain 'F' and resid 453 through 455' Processing helix chain 'F' and resid 457 through 471 Processing helix chain 'F' and resid 476 through 485 Processing helix chain 'F' and resid 495 through 501 removed outlier: 3.781A pdb=" N GLU F 500 " --> pdb=" O SER F 496 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 23 No H-bonds generated for 'chain 'G' and resid 20 through 23' Processing helix chain 'G' and resid 32 through 34 No H-bonds generated for 'chain 'G' and resid 32 through 34' Processing helix chain 'G' and resid 76 through 85 Processing helix chain 'G' and resid 97 through 109 removed outlier: 3.604A pdb=" N LYS G 109 " --> pdb=" O ARG G 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 266 removed outlier: 4.334A pdb=" N ASP G 261 " --> pdb=" O TYR G 258 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU G 262 " --> pdb=" O ARG G 259 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 290 Processing helix chain 'G' and resid 307 through 314 removed outlier: 4.217A pdb=" N ASN G 312 " --> pdb=" O ALA G 308 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU G 313 " --> pdb=" O GLN G 309 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 336 No H-bonds generated for 'chain 'G' and resid 333 through 336' Processing helix chain 'G' and resid 346 through 357 removed outlier: 4.117A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N PHE G 357 " --> pdb=" O TYR G 353 " (cutoff:3.500A) Processing helix chain 'G' and resid 371 through 378 Processing helix chain 'G' and resid 453 through 455 No H-bonds generated for 'chain 'G' and resid 453 through 455' Processing helix chain 'G' and resid 457 through 471 Processing helix chain 'G' and resid 476 through 485 Processing helix chain 'G' and resid 495 through 501 removed outlier: 3.781A pdb=" N GLU G 500 " --> pdb=" O SER G 496 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 23 No H-bonds generated for 'chain 'H' and resid 20 through 23' Processing helix chain 'H' and resid 32 through 34 No H-bonds generated for 'chain 'H' and resid 32 through 34' Processing helix chain 'H' and resid 76 through 85 Processing helix chain 'H' and resid 97 through 109 removed outlier: 3.604A pdb=" N LYS H 109 " --> pdb=" O ARG H 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 266 removed outlier: 4.334A pdb=" N ASP H 261 " --> pdb=" O TYR H 258 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU H 262 " --> pdb=" O ARG H 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 290 Processing helix chain 'H' and resid 307 through 314 removed outlier: 4.217A pdb=" N ASN H 312 " --> pdb=" O ALA H 308 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LEU H 313 " --> pdb=" O GLN H 309 " (cutoff:3.500A) Processing helix chain 'H' and resid 333 through 336 No H-bonds generated for 'chain 'H' and resid 333 through 336' Processing helix chain 'H' and resid 346 through 357 removed outlier: 4.117A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N PHE H 357 " --> pdb=" O TYR H 353 " (cutoff:3.500A) Processing helix chain 'H' and resid 371 through 378 Processing helix chain 'H' and resid 453 through 455 No H-bonds generated for 'chain 'H' and resid 453 through 455' Processing helix chain 'H' and resid 457 through 471 Processing helix chain 'H' and resid 476 through 485 Processing helix chain 'H' and resid 495 through 501 removed outlier: 3.780A pdb=" N GLU H 500 " --> pdb=" O SER H 496 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 35 through 37 Processing sheet with id= B, first strand: chain 'A' and resid 65 through 67 removed outlier: 6.160A pdb=" N VAL A 384 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR A 383 " --> pdb=" O VAL A 361 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU A 321 " --> pdb=" O ILE A 362 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASP A 364 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL A 323 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 247 through 250 removed outlier: 6.432A pdb=" N VAL A 270 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE A 250 " --> pdb=" O VAL A 270 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL A 272 " --> pdb=" O ILE A 250 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N GLN A 298 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE A 300 " --> pdb=" O LEU A 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 401 through 403 Processing sheet with id= E, first strand: chain 'B' and resid 35 through 37 Processing sheet with id= F, first strand: chain 'B' and resid 65 through 67 removed outlier: 6.160A pdb=" N VAL B 384 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR B 383 " --> pdb=" O VAL B 361 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU B 321 " --> pdb=" O ILE B 362 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N ASP B 364 " --> pdb=" O LEU B 321 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL B 323 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 247 through 250 removed outlier: 6.432A pdb=" N VAL B 270 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE B 250 " --> pdb=" O VAL B 270 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL B 272 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLN B 298 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= G Processing sheet with id= H, first strand: chain 'B' and resid 401 through 403 Processing sheet with id= I, first strand: chain 'C' and resid 35 through 37 Processing sheet with id= J, first strand: chain 'C' and resid 65 through 67 removed outlier: 6.160A pdb=" N VAL C 384 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR C 383 " --> pdb=" O VAL C 361 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU C 321 " --> pdb=" O ILE C 362 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ASP C 364 " --> pdb=" O LEU C 321 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL C 323 " --> pdb=" O ASP C 364 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 247 through 250 removed outlier: 6.432A pdb=" N VAL C 270 " --> pdb=" O ALA C 248 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE C 250 " --> pdb=" O VAL C 270 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL C 272 " --> pdb=" O ILE C 250 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLN C 298 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= K Processing sheet with id= L, first strand: chain 'C' and resid 401 through 403 Processing sheet with id= M, first strand: chain 'D' and resid 35 through 37 Processing sheet with id= N, first strand: chain 'D' and resid 65 through 67 removed outlier: 6.160A pdb=" N VAL D 384 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR D 383 " --> pdb=" O VAL D 361 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU D 321 " --> pdb=" O ILE D 362 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ASP D 364 " --> pdb=" O LEU D 321 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL D 323 " --> pdb=" O ASP D 364 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 247 through 250 removed outlier: 6.432A pdb=" N VAL D 270 " --> pdb=" O ALA D 248 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE D 250 " --> pdb=" O VAL D 270 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL D 272 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLN D 298 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'D' and resid 401 through 403 Processing sheet with id= Q, first strand: chain 'E' and resid 35 through 37 Processing sheet with id= R, first strand: chain 'E' and resid 65 through 67 removed outlier: 6.161A pdb=" N VAL E 384 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR E 383 " --> pdb=" O VAL E 361 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N LEU E 321 " --> pdb=" O ILE E 362 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ASP E 364 " --> pdb=" O LEU E 321 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL E 323 " --> pdb=" O ASP E 364 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 247 through 250 removed outlier: 6.432A pdb=" N VAL E 270 " --> pdb=" O ALA E 248 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N ILE E 250 " --> pdb=" O VAL E 270 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL E 272 " --> pdb=" O ILE E 250 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLN E 298 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'E' and resid 401 through 403 Processing sheet with id= U, first strand: chain 'F' and resid 35 through 37 Processing sheet with id= V, first strand: chain 'F' and resid 65 through 67 removed outlier: 6.161A pdb=" N VAL F 384 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR F 383 " --> pdb=" O VAL F 361 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU F 321 " --> pdb=" O ILE F 362 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ASP F 364 " --> pdb=" O LEU F 321 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL F 323 " --> pdb=" O ASP F 364 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 247 through 250 removed outlier: 6.432A pdb=" N VAL F 270 " --> pdb=" O ALA F 248 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE F 250 " --> pdb=" O VAL F 270 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL F 272 " --> pdb=" O ILE F 250 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLN F 298 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= W Processing sheet with id= X, first strand: chain 'F' and resid 401 through 403 Processing sheet with id= Y, first strand: chain 'G' and resid 35 through 37 Processing sheet with id= Z, first strand: chain 'G' and resid 65 through 67 removed outlier: 6.161A pdb=" N VAL G 384 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N THR G 383 " --> pdb=" O VAL G 361 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU G 321 " --> pdb=" O ILE G 362 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ASP G 364 " --> pdb=" O LEU G 321 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL G 323 " --> pdb=" O ASP G 364 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 247 through 250 removed outlier: 6.432A pdb=" N VAL G 270 " --> pdb=" O ALA G 248 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE G 250 " --> pdb=" O VAL G 270 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N VAL G 272 " --> pdb=" O ILE G 250 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLN G 298 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AA Processing sheet with id= AB, first strand: chain 'G' and resid 401 through 403 Processing sheet with id= AC, first strand: chain 'H' and resid 35 through 37 Processing sheet with id= AD, first strand: chain 'H' and resid 65 through 67 removed outlier: 6.160A pdb=" N VAL H 384 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N THR H 383 " --> pdb=" O VAL H 361 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU H 321 " --> pdb=" O ILE H 362 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ASP H 364 " --> pdb=" O LEU H 321 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL H 323 " --> pdb=" O ASP H 364 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 247 through 250 removed outlier: 6.432A pdb=" N VAL H 270 " --> pdb=" O ALA H 248 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N ILE H 250 " --> pdb=" O VAL H 270 " (cutoff:3.500A) removed outlier: 5.999A pdb=" N VAL H 272 " --> pdb=" O ILE H 250 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLN H 298 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) No H-bonds generated for sheet with id= AE Processing sheet with id= AF, first strand: chain 'H' and resid 401 through 403 568 hydrogen bonds defined for protein. 1464 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: 6.69 Time building geometry restraints manager: 9.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 3848 1.30 - 1.43: 5812 1.43 - 1.56: 13468 1.56 - 1.68: 112 1.68 - 1.81: 240 Bond restraints: 23480 Sorted by residual: bond pdb=" C3D NAD D 602 " pdb=" C4D NAD D 602 " ideal model delta sigma weight residual 1.531 1.296 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C3D NAD E 602 " pdb=" C4D NAD E 602 " ideal model delta sigma weight residual 1.531 1.296 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C3D NAD A 602 " pdb=" C4D NAD A 602 " ideal model delta sigma weight residual 1.531 1.296 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C3D NAD G 602 " pdb=" C4D NAD G 602 " ideal model delta sigma weight residual 1.531 1.296 0.235 2.00e-02 2.50e+03 1.38e+02 bond pdb=" C3D NAD C 602 " pdb=" C4D NAD C 602 " ideal model delta sigma weight residual 1.531 1.297 0.234 2.00e-02 2.50e+03 1.37e+02 ... (remaining 23475 not shown) Histogram of bond angle deviations from ideal: 97.77 - 105.62: 544 105.62 - 113.47: 13027 113.47 - 121.32: 12423 121.32 - 129.17: 5670 129.17 - 137.02: 128 Bond angle restraints: 31792 Sorted by residual: angle pdb=" CB GLU C 103 " pdb=" CG GLU C 103 " pdb=" CD GLU C 103 " ideal model delta sigma weight residual 112.60 122.68 -10.08 1.70e+00 3.46e-01 3.52e+01 angle pdb=" CB GLU G 103 " pdb=" CG GLU G 103 " pdb=" CD GLU G 103 " ideal model delta sigma weight residual 112.60 122.67 -10.07 1.70e+00 3.46e-01 3.51e+01 angle pdb=" CB GLU D 103 " pdb=" CG GLU D 103 " pdb=" CD GLU D 103 " ideal model delta sigma weight residual 112.60 122.66 -10.06 1.70e+00 3.46e-01 3.50e+01 angle pdb=" CB GLU B 103 " pdb=" CG GLU B 103 " pdb=" CD GLU B 103 " ideal model delta sigma weight residual 112.60 122.65 -10.05 1.70e+00 3.46e-01 3.49e+01 angle pdb=" CB GLU E 103 " pdb=" CG GLU E 103 " pdb=" CD GLU E 103 " ideal model delta sigma weight residual 112.60 122.64 -10.04 1.70e+00 3.46e-01 3.49e+01 ... (remaining 31787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.11: 12775 17.11 - 34.23: 945 34.23 - 51.34: 372 51.34 - 68.46: 136 68.46 - 85.57: 20 Dihedral angle restraints: 14248 sinusoidal: 5744 harmonic: 8504 Sorted by residual: dihedral pdb=" CA THR C 45 " pdb=" C THR C 45 " pdb=" N ALA C 46 " pdb=" CA ALA C 46 " ideal model delta harmonic sigma weight residual -180.00 -154.54 -25.46 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA THR H 45 " pdb=" C THR H 45 " pdb=" N ALA H 46 " pdb=" CA ALA H 46 " ideal model delta harmonic sigma weight residual 180.00 -154.61 -25.39 0 5.00e+00 4.00e-02 2.58e+01 dihedral pdb=" CA THR F 45 " pdb=" C THR F 45 " pdb=" N ALA F 46 " pdb=" CA ALA F 46 " ideal model delta harmonic sigma weight residual -180.00 -154.62 -25.38 0 5.00e+00 4.00e-02 2.58e+01 ... (remaining 14245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2516 0.067 - 0.134: 873 0.134 - 0.201: 218 0.201 - 0.268: 22 0.268 - 0.335: 27 Chirality restraints: 3656 Sorted by residual: chirality pdb=" CB VAL E 304 " pdb=" CA VAL E 304 " pdb=" CG1 VAL E 304 " pdb=" CG2 VAL E 304 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.81e+00 chirality pdb=" CB VAL D 304 " pdb=" CA VAL D 304 " pdb=" CG1 VAL D 304 " pdb=" CG2 VAL D 304 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.79e+00 chirality pdb=" CB VAL H 304 " pdb=" CA VAL H 304 " pdb=" CG1 VAL H 304 " pdb=" CG2 VAL H 304 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.78e+00 ... (remaining 3653 not shown) Planarity restraints: 4000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR H 63 " -0.038 5.00e-02 4.00e+02 5.78e-02 5.35e+00 pdb=" N PRO H 64 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO H 64 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO H 64 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR C 63 " 0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO C 64 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR E 63 " -0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO E 64 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO E 64 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO E 64 " -0.032 5.00e-02 4.00e+02 ... (remaining 3997 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 2973 2.73 - 3.28: 22340 3.28 - 3.82: 40376 3.82 - 4.36: 47824 4.36 - 4.90: 79421 Nonbonded interactions: 192934 Sorted by model distance: nonbonded pdb=" O GLY E 40 " pdb=" NE2 GLN F 277 " model vdw 2.192 2.520 nonbonded pdb=" O GLY F 40 " pdb=" NE2 GLN G 277 " model vdw 2.246 2.520 nonbonded pdb=" OG SER F 496 " pdb=" NE2 GLN G 498 " model vdw 2.250 2.520 nonbonded pdb=" OG SER E 496 " pdb=" NE2 GLN F 498 " model vdw 2.251 2.520 nonbonded pdb=" OG SER A 496 " pdb=" NE2 GLN B 498 " model vdw 2.263 2.520 ... (remaining 192929 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.710 Check model and map are aligned: 0.350 Set scattering table: 0.210 Process input model: 58.940 Find NCS groups from input model: 1.700 Set up NCS constraints: 0.160 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 70.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 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 : 0.014 0.235 23480 Z= 0.941 Angle : 1.503 16.046 31792 Z= 0.766 Chirality : 0.074 0.335 3656 Planarity : 0.007 0.058 4000 Dihedral : 15.754 85.571 8856 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 8.52 % Allowed : 9.94 % Favored : 81.54 % Cbeta Deviations : 0.30 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -4.43 (0.13), residues: 2960 helix: -3.82 (0.08), residues: 1120 sheet: -2.67 (0.24), residues: 400 loop : -2.13 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS A 92 PHE 0.022 0.004 PHE A 401 TYR 0.031 0.003 TYR F 12 ARG 0.014 0.002 ARG G 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1123 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 920 time to evaluate : 2.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 HIS cc_start: 0.8632 (p90) cc_final: 0.8330 (p-80) REVERT: A 102 ASN cc_start: 0.8390 (t0) cc_final: 0.7732 (t0) REVERT: A 254 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.7642 (tt0) REVERT: A 259 ARG cc_start: 0.8691 (ttm-80) cc_final: 0.8151 (ttm170) REVERT: A 274 ASP cc_start: 0.8673 (t0) cc_final: 0.8376 (t70) REVERT: A 315 ASP cc_start: 0.7280 (OUTLIER) cc_final: 0.7063 (m-30) REVERT: A 327 SER cc_start: 0.8695 (p) cc_final: 0.8159 (p) REVERT: A 359 VAL cc_start: 0.9365 (t) cc_final: 0.9010 (p) REVERT: A 386 MET cc_start: 0.8600 (mtm) cc_final: 0.8388 (mtm) REVERT: A 395 GLU cc_start: 0.8775 (mp0) cc_final: 0.8525 (mp0) REVERT: A 461 ILE cc_start: 0.9076 (pt) cc_final: 0.8618 (mt) REVERT: A 483 MET cc_start: 0.9226 (tmm) cc_final: 0.8744 (tmm) REVERT: B 32 TYR cc_start: 0.8655 (m-80) cc_final: 0.8426 (m-80) REVERT: B 92 HIS cc_start: 0.8702 (p90) cc_final: 0.8384 (p-80) REVERT: B 102 ASN cc_start: 0.8587 (t0) cc_final: 0.7940 (t0) REVERT: B 254 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.7615 (tt0) REVERT: B 259 ARG cc_start: 0.8708 (ttm-80) cc_final: 0.8199 (ttm170) REVERT: B 274 ASP cc_start: 0.8723 (t0) cc_final: 0.8334 (t70) REVERT: B 315 ASP cc_start: 0.7214 (OUTLIER) cc_final: 0.7000 (m-30) REVERT: B 359 VAL cc_start: 0.9310 (t) cc_final: 0.8947 (p) REVERT: B 386 MET cc_start: 0.8626 (mtm) cc_final: 0.8410 (mtm) REVERT: B 483 MET cc_start: 0.9222 (tmm) cc_final: 0.8776 (tmm) REVERT: C 56 THR cc_start: 0.9014 (OUTLIER) cc_final: 0.8804 (p) REVERT: C 78 MET cc_start: 0.8127 (OUTLIER) cc_final: 0.7867 (ttp) REVERT: C 92 HIS cc_start: 0.8610 (p90) cc_final: 0.8249 (p-80) REVERT: C 102 ASN cc_start: 0.8547 (t0) cc_final: 0.7875 (t0) REVERT: C 254 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.7759 (tt0) REVERT: C 274 ASP cc_start: 0.8708 (t0) cc_final: 0.8425 (t70) REVERT: C 296 ASN cc_start: 0.8687 (p0) cc_final: 0.8341 (p0) REVERT: C 327 SER cc_start: 0.8719 (p) cc_final: 0.8179 (p) REVERT: C 386 MET cc_start: 0.8684 (mtm) cc_final: 0.8446 (mtm) REVERT: C 395 GLU cc_start: 0.8760 (mp0) cc_final: 0.8547 (mp0) REVERT: C 483 MET cc_start: 0.9260 (tmm) cc_final: 0.8742 (tmm) REVERT: D 50 ASP cc_start: 0.8242 (t0) cc_final: 0.8024 (t0) REVERT: D 56 THR cc_start: 0.9047 (OUTLIER) cc_final: 0.8764 (p) REVERT: D 92 HIS cc_start: 0.8743 (p90) cc_final: 0.8379 (p-80) REVERT: D 102 ASN cc_start: 0.8692 (t0) cc_final: 0.8068 (t0) REVERT: D 254 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7740 (tt0) REVERT: D 274 ASP cc_start: 0.8732 (t0) cc_final: 0.8360 (t70) REVERT: D 283 GLN cc_start: 0.9027 (tt0) cc_final: 0.8816 (tt0) REVERT: D 296 ASN cc_start: 0.8668 (p0) cc_final: 0.8353 (p0) REVERT: D 386 MET cc_start: 0.8695 (mtm) cc_final: 0.8412 (mtm) REVERT: D 483 MET cc_start: 0.9226 (tmm) cc_final: 0.8779 (tmm) REVERT: E 78 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7759 (ttp) REVERT: E 92 HIS cc_start: 0.8470 (p90) cc_final: 0.8131 (p-80) REVERT: E 102 ASN cc_start: 0.8478 (t0) cc_final: 0.7799 (t0) REVERT: E 254 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.7663 (tt0) REVERT: E 259 ARG cc_start: 0.8688 (ttm-80) cc_final: 0.8059 (ttm170) REVERT: E 315 ASP cc_start: 0.7126 (OUTLIER) cc_final: 0.6911 (m-30) REVERT: E 327 SER cc_start: 0.8865 (p) cc_final: 0.8382 (p) REVERT: E 386 MET cc_start: 0.8580 (mtm) cc_final: 0.8334 (mtm) REVERT: E 395 GLU cc_start: 0.8806 (mp0) cc_final: 0.8517 (mp0) REVERT: E 461 ILE cc_start: 0.9087 (pt) cc_final: 0.8615 (mt) REVERT: E 483 MET cc_start: 0.9248 (tmm) cc_final: 0.8733 (tmm) REVERT: E 510 GLU cc_start: 0.7023 (tm-30) cc_final: 0.6693 (tm-30) REVERT: F 92 HIS cc_start: 0.8575 (p90) cc_final: 0.8159 (p-80) REVERT: F 100 GLN cc_start: 0.9468 (OUTLIER) cc_final: 0.9246 (mt0) REVERT: F 102 ASN cc_start: 0.8792 (t0) cc_final: 0.8179 (t0) REVERT: F 254 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7493 (tt0) REVERT: F 285 ASN cc_start: 0.8842 (m110) cc_final: 0.8523 (m110) REVERT: F 315 ASP cc_start: 0.7166 (OUTLIER) cc_final: 0.6911 (m-30) REVERT: F 327 SER cc_start: 0.8834 (p) cc_final: 0.8297 (p) REVERT: F 386 MET cc_start: 0.8736 (mtm) cc_final: 0.8477 (mtm) REVERT: F 483 MET cc_start: 0.9249 (tmm) cc_final: 0.8770 (tmm) REVERT: G 32 TYR cc_start: 0.8660 (m-80) cc_final: 0.8401 (m-80) REVERT: G 92 HIS cc_start: 0.8601 (p90) cc_final: 0.8314 (p-80) REVERT: G 102 ASN cc_start: 0.8473 (t0) cc_final: 0.7786 (t0) REVERT: G 254 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.7673 (tt0) REVERT: G 259 ARG cc_start: 0.8656 (ttm-80) cc_final: 0.8112 (ttm170) REVERT: G 274 ASP cc_start: 0.8719 (t0) cc_final: 0.8404 (t70) REVERT: G 296 ASN cc_start: 0.8747 (p0) cc_final: 0.8424 (p0) REVERT: G 315 ASP cc_start: 0.7335 (OUTLIER) cc_final: 0.7122 (m-30) REVERT: G 327 SER cc_start: 0.8800 (p) cc_final: 0.8275 (p) REVERT: G 359 VAL cc_start: 0.9359 (t) cc_final: 0.9024 (p) REVERT: G 386 MET cc_start: 0.8638 (mtm) cc_final: 0.8414 (mtm) REVERT: G 483 MET cc_start: 0.9208 (tmm) cc_final: 0.8766 (tmm) REVERT: H 92 HIS cc_start: 0.8766 (p90) cc_final: 0.8417 (p-80) REVERT: H 102 ASN cc_start: 0.8666 (t0) cc_final: 0.8018 (t0) REVERT: H 254 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: H 259 ARG cc_start: 0.8719 (ttm-80) cc_final: 0.8222 (ttm170) REVERT: H 274 ASP cc_start: 0.8758 (t0) cc_final: 0.8317 (t70) REVERT: H 296 ASN cc_start: 0.8623 (p0) cc_final: 0.8327 (p0) REVERT: H 315 ASP cc_start: 0.7278 (OUTLIER) cc_final: 0.7046 (m-30) REVERT: H 359 VAL cc_start: 0.9357 (t) cc_final: 0.8988 (p) REVERT: H 386 MET cc_start: 0.8692 (mtm) cc_final: 0.8415 (mtm) REVERT: H 483 MET cc_start: 0.9208 (tmm) cc_final: 0.8801 (tmm) outliers start: 203 outliers final: 94 residues processed: 991 average time/residue: 0.3311 time to fit residues: 511.7465 Evaluate side-chains 803 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 690 time to evaluate : 2.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 103 GLU Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 252 THR Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 304 VAL Chi-restraints excluded: chain A residue 315 ASP Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 491 GLU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 103 GLU Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 252 THR Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 304 VAL Chi-restraints excluded: chain B residue 315 ASP Chi-restraints excluded: chain B residue 370 VAL Chi-restraints excluded: chain B residue 485 SER Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 103 GLU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 304 VAL Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 491 GLU Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain C residue 513 LEU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 78 MET Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 304 VAL Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 485 SER Chi-restraints excluded: chain D residue 491 GLU Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 103 GLU Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 252 THR Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 304 VAL Chi-restraints excluded: chain E residue 315 ASP Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 485 SER Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 53 SER Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 100 GLN Chi-restraints excluded: chain F residue 103 GLU Chi-restraints excluded: chain F residue 235 LEU Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 252 THR Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 304 VAL Chi-restraints excluded: chain F residue 315 ASP Chi-restraints excluded: chain F residue 370 VAL Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 103 GLU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 304 VAL Chi-restraints excluded: chain G residue 315 ASP Chi-restraints excluded: chain G residue 370 VAL Chi-restraints excluded: chain G residue 485 SER Chi-restraints excluded: chain G residue 491 GLU Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 103 GLU Chi-restraints excluded: chain H residue 235 LEU Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 252 THR Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain H residue 304 VAL Chi-restraints excluded: chain H residue 315 ASP Chi-restraints excluded: chain H residue 370 VAL Chi-restraints excluded: chain H residue 485 SER Chi-restraints excluded: chain H residue 491 GLU Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 3.9990 chunk 224 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 151 optimal weight: 4.9990 chunk 119 optimal weight: 0.9980 chunk 232 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 141 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 chunk 268 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 303 ASN ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN A 469 GLN ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 ASN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 GLN B 465 GLN B 469 GLN ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 368 GLN C 465 GLN C 469 GLN ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 298 GLN D 303 ASN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 GLN D 465 GLN ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 469 GLN F 100 GLN F 303 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 GLN F 465 GLN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 368 GLN G 465 GLN G 469 GLN ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 368 GLN H 465 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 23480 Z= 0.250 Angle : 0.684 11.445 31792 Z= 0.349 Chirality : 0.046 0.160 3656 Planarity : 0.005 0.036 4000 Dihedral : 12.852 78.958 3946 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 5.16 % Allowed : 19.88 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -3.26 (0.14), residues: 2960 helix: -2.58 (0.12), residues: 1072 sheet: -2.63 (0.24), residues: 368 loop : -1.60 (0.15), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 92 PHE 0.016 0.002 PHE H 44 TYR 0.018 0.002 TYR G 41 ARG 0.003 0.001 ARG H 407 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 747 time to evaluate : 2.636 Fit side-chains REVERT: A 42 ILE cc_start: 0.8260 (pt) cc_final: 0.7992 (pt) REVERT: A 92 HIS cc_start: 0.8630 (p90) cc_final: 0.8298 (p90) REVERT: A 102 ASN cc_start: 0.8432 (t0) cc_final: 0.7762 (t0) REVERT: A 103 GLU cc_start: 0.8136 (tp30) cc_final: 0.7896 (tp30) REVERT: A 296 ASN cc_start: 0.8572 (p0) cc_final: 0.8236 (p0) REVERT: A 327 SER cc_start: 0.8534 (p) cc_final: 0.8015 (p) REVERT: A 329 SER cc_start: 0.9373 (p) cc_final: 0.9171 (p) REVERT: A 461 ILE cc_start: 0.8824 (pt) cc_final: 0.8586 (mt) REVERT: A 483 MET cc_start: 0.9188 (tmm) cc_final: 0.8797 (tmm) REVERT: A 491 GLU cc_start: 0.8360 (tp30) cc_final: 0.8134 (tp30) REVERT: B 92 HIS cc_start: 0.8728 (p90) cc_final: 0.8313 (p90) REVERT: B 102 ASN cc_start: 0.8667 (t0) cc_final: 0.8020 (t0) REVERT: B 259 ARG cc_start: 0.8860 (ttm-80) cc_final: 0.8570 (tpp80) REVERT: B 274 ASP cc_start: 0.8660 (t0) cc_final: 0.8439 (t70) REVERT: B 327 SER cc_start: 0.8599 (p) cc_final: 0.8047 (p) REVERT: B 461 ILE cc_start: 0.8971 (pt) cc_final: 0.8617 (mt) REVERT: B 483 MET cc_start: 0.9187 (tmm) cc_final: 0.8762 (tmm) REVERT: C 43 ASP cc_start: 0.7895 (m-30) cc_final: 0.7674 (m-30) REVERT: C 92 HIS cc_start: 0.8679 (p90) cc_final: 0.8324 (p90) REVERT: C 102 ASN cc_start: 0.8558 (t0) cc_final: 0.7828 (t0) REVERT: C 103 GLU cc_start: 0.8383 (tp30) cc_final: 0.8147 (tp30) REVERT: C 296 ASN cc_start: 0.8611 (p0) cc_final: 0.8312 (p0) REVERT: C 327 SER cc_start: 0.8534 (p) cc_final: 0.8062 (p) REVERT: C 461 ILE cc_start: 0.9036 (pt) cc_final: 0.8624 (mt) REVERT: C 483 MET cc_start: 0.9219 (tmm) cc_final: 0.8786 (tmm) REVERT: C 491 GLU cc_start: 0.8514 (tp30) cc_final: 0.8270 (tp30) REVERT: D 56 THR cc_start: 0.8939 (OUTLIER) cc_final: 0.8521 (p) REVERT: D 92 HIS cc_start: 0.8754 (p90) cc_final: 0.8335 (p90) REVERT: D 102 ASN cc_start: 0.8729 (t0) cc_final: 0.8054 (t0) REVERT: D 103 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8364 (tp30) REVERT: D 259 ARG cc_start: 0.8838 (ttm-80) cc_final: 0.8593 (tpp80) REVERT: D 274 ASP cc_start: 0.8642 (t0) cc_final: 0.8435 (t70) REVERT: D 296 ASN cc_start: 0.8664 (p0) cc_final: 0.8376 (p0) REVERT: D 327 SER cc_start: 0.8529 (p) cc_final: 0.7920 (p) REVERT: D 395 GLU cc_start: 0.8825 (mp0) cc_final: 0.8481 (mp0) REVERT: D 461 ILE cc_start: 0.8990 (pt) cc_final: 0.8576 (mt) REVERT: D 483 MET cc_start: 0.9213 (tmm) cc_final: 0.8762 (tmm) REVERT: D 491 GLU cc_start: 0.8504 (tp30) cc_final: 0.8285 (tp30) REVERT: E 43 ASP cc_start: 0.7945 (m-30) cc_final: 0.7648 (m-30) REVERT: E 92 HIS cc_start: 0.8639 (p90) cc_final: 0.8269 (p90) REVERT: E 102 ASN cc_start: 0.8513 (t0) cc_final: 0.7765 (t0) REVERT: E 103 GLU cc_start: 0.8203 (tp30) cc_final: 0.7928 (tp30) REVERT: E 281 ILE cc_start: 0.8835 (OUTLIER) cc_final: 0.8630 (mp) REVERT: E 327 SER cc_start: 0.8669 (p) cc_final: 0.8157 (p) REVERT: E 441 GLN cc_start: 0.8720 (mt0) cc_final: 0.8440 (mt0) REVERT: E 483 MET cc_start: 0.9241 (tmm) cc_final: 0.8741 (tmm) REVERT: E 510 GLU cc_start: 0.6998 (tm-30) cc_final: 0.6671 (tm-30) REVERT: F 6 ILE cc_start: 0.9137 (tt) cc_final: 0.8936 (tt) REVERT: F 43 ASP cc_start: 0.7877 (m-30) cc_final: 0.7671 (m-30) REVERT: F 92 HIS cc_start: 0.8602 (p90) cc_final: 0.8051 (p90) REVERT: F 102 ASN cc_start: 0.8859 (t0) cc_final: 0.8264 (t0) REVERT: F 259 ARG cc_start: 0.8816 (ttm-80) cc_final: 0.8517 (tpp80) REVERT: F 285 ASN cc_start: 0.8886 (m110) cc_final: 0.8575 (m110) REVERT: F 296 ASN cc_start: 0.8784 (p0) cc_final: 0.8389 (p0) REVERT: F 319 ASP cc_start: 0.7952 (t0) cc_final: 0.7733 (t0) REVERT: F 327 SER cc_start: 0.8608 (p) cc_final: 0.8116 (p) REVERT: F 461 ILE cc_start: 0.8990 (pt) cc_final: 0.8622 (mt) REVERT: F 483 MET cc_start: 0.9220 (tmm) cc_final: 0.8801 (tmm) REVERT: G 42 ILE cc_start: 0.8069 (pt) cc_final: 0.7818 (pt) REVERT: G 92 HIS cc_start: 0.8729 (p90) cc_final: 0.8331 (p90) REVERT: G 102 ASN cc_start: 0.8503 (t0) cc_final: 0.7803 (t0) REVERT: G 103 GLU cc_start: 0.8143 (tp30) cc_final: 0.7881 (tp30) REVERT: G 259 ARG cc_start: 0.8831 (ttm-80) cc_final: 0.8596 (tpp80) REVERT: G 296 ASN cc_start: 0.8669 (p0) cc_final: 0.8401 (p0) REVERT: G 327 SER cc_start: 0.8580 (p) cc_final: 0.8032 (p) REVERT: G 395 GLU cc_start: 0.8769 (mp0) cc_final: 0.8383 (mp0) REVERT: G 461 ILE cc_start: 0.8925 (pt) cc_final: 0.8496 (mt) REVERT: G 483 MET cc_start: 0.9158 (tmm) cc_final: 0.8688 (tmm) REVERT: G 491 GLU cc_start: 0.8404 (tp30) cc_final: 0.8157 (tp30) REVERT: H 56 THR cc_start: 0.8596 (p) cc_final: 0.8389 (p) REVERT: H 92 HIS cc_start: 0.8724 (p90) cc_final: 0.8308 (p90) REVERT: H 102 ASN cc_start: 0.8691 (t0) cc_final: 0.8029 (t0) REVERT: H 241 LYS cc_start: 0.9334 (tppt) cc_final: 0.9123 (tppt) REVERT: H 259 ARG cc_start: 0.8827 (ttm-80) cc_final: 0.8615 (tpp80) REVERT: H 274 ASP cc_start: 0.8612 (t0) cc_final: 0.8262 (t70) REVERT: H 296 ASN cc_start: 0.8558 (p0) cc_final: 0.8304 (p0) REVERT: H 319 ASP cc_start: 0.7880 (t0) cc_final: 0.7591 (t0) REVERT: H 327 SER cc_start: 0.8514 (p) cc_final: 0.7984 (p) REVERT: H 395 GLU cc_start: 0.8843 (mp0) cc_final: 0.8522 (mp0) REVERT: H 461 ILE cc_start: 0.8893 (pt) cc_final: 0.8474 (mt) REVERT: H 483 MET cc_start: 0.9158 (tmm) cc_final: 0.8715 (tmm) outliers start: 123 outliers final: 69 residues processed: 810 average time/residue: 0.3425 time to fit residues: 441.3986 Evaluate side-chains 732 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 660 time to evaluate : 2.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 235 LEU Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 245 LEU Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 103 GLU Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 488 LEU Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 245 LEU Chi-restraints excluded: chain E residue 274 ASP Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 245 LEU Chi-restraints excluded: chain F residue 274 ASP Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 245 LEU Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 223 optimal weight: 6.9990 chunk 183 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 269 optimal weight: 4.9990 chunk 290 optimal weight: 0.7980 chunk 239 optimal weight: 2.9990 chunk 267 optimal weight: 0.7980 chunk 91 optimal weight: 0.9980 chunk 216 optimal weight: 6.9990 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 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 ASN D 469 GLN E 100 GLN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 469 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 469 GLN ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 469 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23480 Z= 0.208 Angle : 0.625 10.321 31792 Z= 0.315 Chirality : 0.045 0.136 3656 Planarity : 0.004 0.031 4000 Dihedral : 10.769 86.493 3792 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 17.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 4.49 % Allowed : 22.82 % Favored : 72.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -2.99 (0.14), residues: 2960 helix: -2.17 (0.13), residues: 1160 sheet: -2.62 (0.24), residues: 384 loop : -1.46 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 92 PHE 0.015 0.001 PHE D 44 TYR 0.014 0.002 TYR G 41 ARG 0.003 0.000 ARG A 480 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 812 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 705 time to evaluate : 2.296 Fit side-chains REVERT: A 92 HIS cc_start: 0.8647 (p90) cc_final: 0.8242 (p90) REVERT: A 102 ASN cc_start: 0.8548 (t0) cc_final: 0.7876 (t0) REVERT: A 327 SER cc_start: 0.8521 (p) cc_final: 0.8031 (p) REVERT: A 395 GLU cc_start: 0.8760 (mp0) cc_final: 0.8297 (mp0) REVERT: A 461 ILE cc_start: 0.8853 (pt) cc_final: 0.8629 (mt) REVERT: A 483 MET cc_start: 0.9217 (tmm) cc_final: 0.8796 (tmm) REVERT: B 51 LEU cc_start: 0.9127 (tt) cc_final: 0.8416 (tt) REVERT: B 92 HIS cc_start: 0.8708 (p90) cc_final: 0.8287 (p90) REVERT: B 102 ASN cc_start: 0.8752 (t0) cc_final: 0.8092 (t0) REVERT: B 274 ASP cc_start: 0.8748 (t0) cc_final: 0.8476 (t70) REVERT: B 327 SER cc_start: 0.8657 (p) cc_final: 0.8144 (p) REVERT: B 461 ILE cc_start: 0.8914 (pt) cc_final: 0.8617 (mt) REVERT: B 483 MET cc_start: 0.9230 (tmm) cc_final: 0.8818 (tmm) REVERT: C 43 ASP cc_start: 0.7999 (m-30) cc_final: 0.7755 (m-30) REVERT: C 92 HIS cc_start: 0.8669 (p90) cc_final: 0.8307 (p90) REVERT: C 102 ASN cc_start: 0.8611 (t0) cc_final: 0.7876 (t0) REVERT: C 327 SER cc_start: 0.8550 (p) cc_final: 0.8003 (p) REVERT: C 461 ILE cc_start: 0.8960 (pt) cc_final: 0.8681 (mt) REVERT: C 483 MET cc_start: 0.9236 (tmm) cc_final: 0.8806 (tmm) REVERT: D 56 THR cc_start: 0.8758 (OUTLIER) cc_final: 0.8442 (p) REVERT: D 92 HIS cc_start: 0.8736 (p90) cc_final: 0.8320 (p90) REVERT: D 102 ASN cc_start: 0.8771 (t0) cc_final: 0.8089 (t0) REVERT: D 274 ASP cc_start: 0.8711 (t0) cc_final: 0.8316 (t70) REVERT: D 327 SER cc_start: 0.8537 (p) cc_final: 0.7947 (p) REVERT: D 461 ILE cc_start: 0.8895 (pt) cc_final: 0.8578 (mt) REVERT: D 483 MET cc_start: 0.9209 (tmm) cc_final: 0.8709 (tmm) REVERT: E 43 ASP cc_start: 0.8025 (m-30) cc_final: 0.7785 (m-30) REVERT: E 51 LEU cc_start: 0.9152 (tt) cc_final: 0.8505 (tt) REVERT: E 102 ASN cc_start: 0.8558 (t0) cc_final: 0.7838 (t0) REVERT: E 296 ASN cc_start: 0.8619 (p0) cc_final: 0.8334 (p0) REVERT: E 327 SER cc_start: 0.8556 (p) cc_final: 0.8139 (p) REVERT: E 395 GLU cc_start: 0.8786 (mp0) cc_final: 0.8305 (mp0) REVERT: E 441 GLN cc_start: 0.8714 (mt0) cc_final: 0.8462 (mt0) REVERT: F 78 MET cc_start: 0.8085 (OUTLIER) cc_final: 0.7815 (ttp) REVERT: F 92 HIS cc_start: 0.8742 (p90) cc_final: 0.8342 (p90) REVERT: F 102 ASN cc_start: 0.8880 (t0) cc_final: 0.8283 (t0) REVERT: F 285 ASN cc_start: 0.8952 (m110) cc_final: 0.8634 (m110) REVERT: F 296 ASN cc_start: 0.8662 (p0) cc_final: 0.8312 (p0) REVERT: F 319 ASP cc_start: 0.8046 (t0) cc_final: 0.7812 (t0) REVERT: F 327 SER cc_start: 0.8613 (p) cc_final: 0.8156 (p) REVERT: F 461 ILE cc_start: 0.8915 (pt) cc_final: 0.8641 (mt) REVERT: F 483 MET cc_start: 0.9217 (tmm) cc_final: 0.8749 (tmm) REVERT: G 92 HIS cc_start: 0.8629 (p90) cc_final: 0.8198 (p90) REVERT: G 102 ASN cc_start: 0.8534 (t0) cc_final: 0.7835 (t0) REVERT: G 327 SER cc_start: 0.8578 (p) cc_final: 0.8187 (p) REVERT: G 461 ILE cc_start: 0.8870 (pt) cc_final: 0.8573 (mt) REVERT: G 483 MET cc_start: 0.9208 (tmm) cc_final: 0.8732 (tmm) REVERT: H 92 HIS cc_start: 0.8690 (p90) cc_final: 0.8257 (p90) REVERT: H 102 ASN cc_start: 0.8772 (t0) cc_final: 0.8100 (t0) REVERT: H 242 LYS cc_start: 0.8433 (mttp) cc_final: 0.8117 (tppt) REVERT: H 245 LEU cc_start: 0.9006 (mt) cc_final: 0.8788 (mt) REVERT: H 274 ASP cc_start: 0.8713 (t0) cc_final: 0.8225 (t70) REVERT: H 319 ASP cc_start: 0.8143 (t0) cc_final: 0.7914 (t0) REVERT: H 327 SER cc_start: 0.8532 (p) cc_final: 0.7975 (p) REVERT: H 461 ILE cc_start: 0.8835 (pt) cc_final: 0.8524 (mt) REVERT: H 483 MET cc_start: 0.9177 (tmm) cc_final: 0.8697 (tmm) outliers start: 107 outliers final: 74 residues processed: 756 average time/residue: 0.3229 time to fit residues: 383.2006 Evaluate side-chains 740 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 664 time to evaluate : 2.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 453 ILE Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 475 SER Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 475 SER Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 453 ILE Chi-restraints excluded: chain H residue 475 SER Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 3.9990 chunk 202 optimal weight: 4.9990 chunk 139 optimal weight: 9.9990 chunk 29 optimal weight: 0.1980 chunk 128 optimal weight: 0.7980 chunk 180 optimal weight: 4.9990 chunk 270 optimal weight: 5.9990 chunk 286 optimal weight: 0.8980 chunk 141 optimal weight: 0.9990 chunk 256 optimal weight: 0.9980 chunk 77 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 465 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 23480 Z= 0.190 Angle : 0.615 9.043 31792 Z= 0.303 Chirality : 0.044 0.136 3656 Planarity : 0.004 0.031 4000 Dihedral : 9.716 87.613 3761 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 4.95 % Allowed : 25.55 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -2.62 (0.14), residues: 2960 helix: -1.76 (0.13), residues: 1168 sheet: -2.52 (0.25), residues: 384 loop : -1.32 (0.16), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.000 HIS E 92 PHE 0.014 0.001 PHE H 44 TYR 0.018 0.002 TYR D 484 ARG 0.008 0.000 ARG D 355 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 834 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 716 time to evaluate : 2.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 HIS cc_start: 0.8599 (p90) cc_final: 0.8378 (p-80) REVERT: A 102 ASN cc_start: 0.8599 (t0) cc_final: 0.7876 (t0) REVERT: A 327 SER cc_start: 0.8473 (p) cc_final: 0.7998 (p) REVERT: A 395 GLU cc_start: 0.8633 (mp0) cc_final: 0.8417 (mp0) REVERT: A 461 ILE cc_start: 0.8882 (pt) cc_final: 0.8655 (mt) REVERT: B 78 MET cc_start: 0.8124 (OUTLIER) cc_final: 0.7759 (ttm) REVERT: B 92 HIS cc_start: 0.8677 (p90) cc_final: 0.8431 (p-80) REVERT: B 102 ASN cc_start: 0.8761 (t0) cc_final: 0.8106 (t0) REVERT: B 242 LYS cc_start: 0.8385 (mttp) cc_final: 0.8065 (tppt) REVERT: B 259 ARG cc_start: 0.9110 (tpp80) cc_final: 0.8588 (tpp80) REVERT: B 274 ASP cc_start: 0.8810 (t0) cc_final: 0.8342 (t70) REVERT: B 327 SER cc_start: 0.8567 (p) cc_final: 0.8035 (p) REVERT: B 483 MET cc_start: 0.9227 (tmm) cc_final: 0.8826 (tmm) REVERT: B 487 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7796 (mm-30) REVERT: C 43 ASP cc_start: 0.7991 (m-30) cc_final: 0.7738 (m-30) REVERT: C 92 HIS cc_start: 0.8676 (p90) cc_final: 0.8474 (p-80) REVERT: C 102 ASN cc_start: 0.8661 (t0) cc_final: 0.7949 (t0) REVERT: C 327 SER cc_start: 0.8566 (p) cc_final: 0.7959 (p) REVERT: C 461 ILE cc_start: 0.8965 (pt) cc_final: 0.8681 (mt) REVERT: C 483 MET cc_start: 0.9254 (tmm) cc_final: 0.8831 (tmm) REVERT: D 56 THR cc_start: 0.8577 (p) cc_final: 0.8312 (p) REVERT: D 92 HIS cc_start: 0.8685 (p90) cc_final: 0.8453 (p-80) REVERT: D 102 ASN cc_start: 0.8858 (t0) cc_final: 0.8196 (t0) REVERT: D 259 ARG cc_start: 0.9122 (tpp80) cc_final: 0.8896 (tpp80) REVERT: D 274 ASP cc_start: 0.8835 (t0) cc_final: 0.8290 (t70) REVERT: D 327 SER cc_start: 0.8504 (p) cc_final: 0.7981 (p) REVERT: D 461 ILE cc_start: 0.8876 (pt) cc_final: 0.8578 (mt) REVERT: D 483 MET cc_start: 0.9219 (tmm) cc_final: 0.8769 (tmm) REVERT: E 43 ASP cc_start: 0.8114 (m-30) cc_final: 0.7842 (m-30) REVERT: E 78 MET cc_start: 0.8650 (tpp) cc_final: 0.8167 (tpp) REVERT: E 82 MET cc_start: 0.8305 (mtp) cc_final: 0.7929 (mtp) REVERT: E 102 ASN cc_start: 0.8616 (t0) cc_final: 0.7881 (t0) REVERT: E 296 ASN cc_start: 0.8585 (p0) cc_final: 0.8333 (p0) REVERT: E 327 SER cc_start: 0.8530 (p) cc_final: 0.8057 (p) REVERT: E 395 GLU cc_start: 0.8671 (mp0) cc_final: 0.8418 (mp0) REVERT: E 399 GLU cc_start: 0.7935 (pm20) cc_final: 0.7733 (mp0) REVERT: E 441 GLN cc_start: 0.8730 (mt0) cc_final: 0.8528 (mt0) REVERT: E 483 MET cc_start: 0.9175 (tmm) cc_final: 0.8728 (tmm) REVERT: F 78 MET cc_start: 0.8168 (OUTLIER) cc_final: 0.7926 (ttp) REVERT: F 92 HIS cc_start: 0.8656 (p90) cc_final: 0.8447 (p-80) REVERT: F 102 ASN cc_start: 0.8902 (t0) cc_final: 0.8310 (t0) REVERT: F 259 ARG cc_start: 0.8916 (tpp80) cc_final: 0.8457 (tpp80) REVERT: F 285 ASN cc_start: 0.8973 (m110) cc_final: 0.8632 (m110) REVERT: F 296 ASN cc_start: 0.8625 (p0) cc_final: 0.8341 (p0) REVERT: F 319 ASP cc_start: 0.8055 (t0) cc_final: 0.7800 (t0) REVERT: F 327 SER cc_start: 0.8620 (p) cc_final: 0.8160 (p) REVERT: F 395 GLU cc_start: 0.8795 (mp0) cc_final: 0.8489 (mp0) REVERT: F 461 ILE cc_start: 0.8893 (pt) cc_final: 0.8650 (mt) REVERT: F 483 MET cc_start: 0.9238 (tmm) cc_final: 0.8793 (tmm) REVERT: G 92 HIS cc_start: 0.8640 (p90) cc_final: 0.8382 (p-80) REVERT: G 102 ASN cc_start: 0.8639 (t0) cc_final: 0.7935 (t0) REVERT: G 327 SER cc_start: 0.8546 (p) cc_final: 0.8152 (p) REVERT: G 483 MET cc_start: 0.9203 (tmm) cc_final: 0.8759 (tmm) REVERT: H 92 HIS cc_start: 0.8707 (p90) cc_final: 0.8464 (p-80) REVERT: H 102 ASN cc_start: 0.8834 (t0) cc_final: 0.8130 (t0) REVERT: H 108 LYS cc_start: 0.9472 (tppt) cc_final: 0.9245 (mmmt) REVERT: H 242 LYS cc_start: 0.8380 (mttp) cc_final: 0.8053 (tppt) REVERT: H 245 LEU cc_start: 0.8982 (mt) cc_final: 0.8691 (mt) REVERT: H 274 ASP cc_start: 0.8813 (t0) cc_final: 0.8264 (t70) REVERT: H 319 ASP cc_start: 0.8060 (t0) cc_final: 0.7794 (t0) REVERT: H 327 SER cc_start: 0.8522 (p) cc_final: 0.7968 (p) REVERT: H 399 GLU cc_start: 0.8127 (pm20) cc_final: 0.7849 (mp0) REVERT: H 461 ILE cc_start: 0.8791 (pt) cc_final: 0.8496 (mt) REVERT: H 483 MET cc_start: 0.9202 (tmm) cc_final: 0.8741 (tmm) outliers start: 118 outliers final: 74 residues processed: 788 average time/residue: 0.3245 time to fit residues: 401.3178 Evaluate side-chains 753 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 677 time to evaluate : 2.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 499 VAL Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 235 LEU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 457 VAL Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 382 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 238 optimal weight: 3.9990 chunk 162 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 213 optimal weight: 9.9990 chunk 118 optimal weight: 4.9990 chunk 244 optimal weight: 0.5980 chunk 197 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 146 optimal weight: 0.0770 chunk 256 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 469 GLN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 465 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23480 Z= 0.202 Angle : 0.603 7.674 31792 Z= 0.299 Chirality : 0.044 0.145 3656 Planarity : 0.003 0.030 4000 Dihedral : 8.983 87.325 3739 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Rotamer: Outliers : 5.66 % Allowed : 26.01 % Favored : 68.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -2.31 (0.15), residues: 2960 helix: -1.29 (0.14), residues: 1160 sheet: -2.47 (0.25), residues: 384 loop : -1.32 (0.16), residues: 1416 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS E 92 PHE 0.012 0.001 PHE D 44 TYR 0.022 0.002 TYR G 4 ARG 0.004 0.000 ARG H 480 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 868 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 733 time to evaluate : 2.509 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 92 HIS cc_start: 0.8644 (p90) cc_final: 0.8407 (p-80) REVERT: A 102 ASN cc_start: 0.8641 (t0) cc_final: 0.7976 (t0) REVERT: A 327 SER cc_start: 0.8477 (p) cc_final: 0.8018 (p) REVERT: A 441 GLN cc_start: 0.8613 (mt0) cc_final: 0.8171 (mt0) REVERT: A 483 MET cc_start: 0.9196 (tmm) cc_final: 0.8767 (tmm) REVERT: B 78 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7729 (ttm) REVERT: B 92 HIS cc_start: 0.8689 (p90) cc_final: 0.8423 (p-80) REVERT: B 102 ASN cc_start: 0.8794 (t0) cc_final: 0.8109 (t0) REVERT: B 274 ASP cc_start: 0.8843 (t0) cc_final: 0.8604 (t70) REVERT: B 327 SER cc_start: 0.8612 (p) cc_final: 0.8109 (p) REVERT: B 483 MET cc_start: 0.9225 (tmm) cc_final: 0.8848 (tmm) REVERT: C 78 MET cc_start: 0.8713 (tpp) cc_final: 0.8374 (tpp) REVERT: C 92 HIS cc_start: 0.8696 (p90) cc_final: 0.8465 (p-80) REVERT: C 102 ASN cc_start: 0.8702 (t0) cc_final: 0.7969 (t0) REVERT: C 327 SER cc_start: 0.8600 (p) cc_final: 0.8093 (p) REVERT: C 461 ILE cc_start: 0.8947 (pt) cc_final: 0.8700 (mt) REVERT: C 483 MET cc_start: 0.9255 (tmm) cc_final: 0.8838 (tmm) REVERT: D 56 THR cc_start: 0.8641 (p) cc_final: 0.8399 (p) REVERT: D 102 ASN cc_start: 0.9020 (t0) cc_final: 0.8503 (t0) REVERT: D 259 ARG cc_start: 0.9119 (tpp80) cc_final: 0.8900 (tpp80) REVERT: D 274 ASP cc_start: 0.8862 (t70) cc_final: 0.8381 (t70) REVERT: D 327 SER cc_start: 0.8557 (p) cc_final: 0.8054 (p) REVERT: D 461 ILE cc_start: 0.8858 (pt) cc_final: 0.8549 (mt) REVERT: E 43 ASP cc_start: 0.8140 (m-30) cc_final: 0.7850 (m-30) REVERT: E 102 ASN cc_start: 0.8693 (t0) cc_final: 0.7986 (t0) REVERT: E 327 SER cc_start: 0.8571 (p) cc_final: 0.8015 (p) REVERT: E 395 GLU cc_start: 0.8681 (mp0) cc_final: 0.8472 (mp0) REVERT: E 441 GLN cc_start: 0.8740 (mt0) cc_final: 0.8525 (mt0) REVERT: E 483 MET cc_start: 0.9196 (tmm) cc_final: 0.8764 (tmm) REVERT: F 78 MET cc_start: 0.8230 (OUTLIER) cc_final: 0.7961 (ttp) REVERT: F 92 HIS cc_start: 0.8658 (p90) cc_final: 0.8451 (p-80) REVERT: F 102 ASN cc_start: 0.8962 (t0) cc_final: 0.8366 (t0) REVERT: F 259 ARG cc_start: 0.8902 (tpp80) cc_final: 0.8443 (tpp80) REVERT: F 285 ASN cc_start: 0.9030 (m110) cc_final: 0.8632 (m110) REVERT: F 296 ASN cc_start: 0.8582 (p0) cc_final: 0.8344 (p0) REVERT: F 319 ASP cc_start: 0.8181 (t0) cc_final: 0.7883 (t0) REVERT: F 327 SER cc_start: 0.8669 (p) cc_final: 0.8151 (p) REVERT: F 461 ILE cc_start: 0.8904 (pt) cc_final: 0.8643 (mt) REVERT: F 483 MET cc_start: 0.9258 (tmm) cc_final: 0.8830 (tmm) REVERT: F 487 GLU cc_start: 0.8085 (mt-10) cc_final: 0.7805 (mm-30) REVERT: G 78 MET cc_start: 0.8648 (tpp) cc_final: 0.8432 (tpp) REVERT: G 92 HIS cc_start: 0.8636 (p90) cc_final: 0.8395 (p-80) REVERT: G 102 ASN cc_start: 0.8677 (t0) cc_final: 0.7953 (t0) REVERT: G 327 SER cc_start: 0.8569 (p) cc_final: 0.8058 (p) REVERT: G 399 GLU cc_start: 0.7754 (mp0) cc_final: 0.7527 (mp0) REVERT: G 441 GLN cc_start: 0.8734 (mt0) cc_final: 0.8337 (mt0) REVERT: G 483 MET cc_start: 0.9211 (tmm) cc_final: 0.8817 (tmm) REVERT: G 487 GLU cc_start: 0.8102 (mt-10) cc_final: 0.7830 (mm-30) REVERT: H 78 MET cc_start: 0.8685 (tpp) cc_final: 0.8462 (tpp) REVERT: H 92 HIS cc_start: 0.8710 (p90) cc_final: 0.8423 (p-80) REVERT: H 99 PHE cc_start: 0.9180 (t80) cc_final: 0.8787 (t80) REVERT: H 102 ASN cc_start: 0.8833 (t0) cc_final: 0.8170 (t0) REVERT: H 242 LYS cc_start: 0.8429 (mttp) cc_final: 0.8090 (tppt) REVERT: H 274 ASP cc_start: 0.8839 (t0) cc_final: 0.8207 (t70) REVERT: H 319 ASP cc_start: 0.8070 (t0) cc_final: 0.7845 (t0) REVERT: H 327 SER cc_start: 0.8566 (p) cc_final: 0.8089 (p) REVERT: H 399 GLU cc_start: 0.8107 (pm20) cc_final: 0.7877 (mp0) REVERT: H 461 ILE cc_start: 0.8813 (pt) cc_final: 0.8535 (mt) REVERT: H 483 MET cc_start: 0.9208 (tmm) cc_final: 0.8774 (tmm) outliers start: 135 outliers final: 91 residues processed: 816 average time/residue: 0.3235 time to fit residues: 412.6568 Evaluate side-chains 790 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 697 time to evaluate : 2.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 457 VAL Chi-restraints excluded: chain G residue 475 SER Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 388 SER Chi-restraints excluded: chain H residue 475 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 0.7980 chunk 257 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 167 optimal weight: 0.5980 chunk 70 optimal weight: 0.8980 chunk 286 optimal weight: 4.9990 chunk 237 optimal weight: 0.9980 chunk 132 optimal weight: 6.9990 chunk 23 optimal weight: 3.9990 chunk 94 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 465 GLN ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 465 GLN E 469 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 GLN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 ASN G 469 GLN H 243 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 23480 Z= 0.202 Angle : 0.606 8.756 31792 Z= 0.302 Chirality : 0.044 0.146 3656 Planarity : 0.003 0.048 4000 Dihedral : 8.685 87.444 3736 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 18.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 5.49 % Allowed : 27.89 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -2.09 (0.15), residues: 2960 helix: -1.02 (0.14), residues: 1168 sheet: -2.42 (0.26), residues: 384 loop : -1.26 (0.17), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.000 HIS D 92 PHE 0.011 0.001 PHE H 44 TYR 0.025 0.002 TYR B 289 ARG 0.004 0.000 ARG D 480 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 866 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 735 time to evaluate : 2.268 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 92 HIS cc_start: 0.8606 (p90) cc_final: 0.8343 (p-80) REVERT: A 102 ASN cc_start: 0.8654 (t0) cc_final: 0.7974 (t0) REVERT: A 327 SER cc_start: 0.8512 (p) cc_final: 0.8007 (p) REVERT: A 441 GLN cc_start: 0.8635 (mt0) cc_final: 0.8210 (mt0) REVERT: A 483 MET cc_start: 0.9191 (tmm) cc_final: 0.8744 (tmm) REVERT: B 78 MET cc_start: 0.8125 (OUTLIER) cc_final: 0.7722 (ttm) REVERT: B 92 HIS cc_start: 0.8664 (p90) cc_final: 0.8380 (p-80) REVERT: B 102 ASN cc_start: 0.8837 (t0) cc_final: 0.8148 (t0) REVERT: B 242 LYS cc_start: 0.8375 (mttp) cc_final: 0.8089 (tppt) REVERT: B 257 LYS cc_start: 0.9508 (mttm) cc_final: 0.9307 (mttp) REVERT: B 259 ARG cc_start: 0.9071 (tpp80) cc_final: 0.8814 (tpp80) REVERT: B 274 ASP cc_start: 0.8855 (t70) cc_final: 0.8429 (t70) REVERT: B 327 SER cc_start: 0.8670 (p) cc_final: 0.8177 (p) REVERT: B 483 MET cc_start: 0.9245 (tmm) cc_final: 0.8855 (tmm) REVERT: C 78 MET cc_start: 0.8721 (tpp) cc_final: 0.8450 (tpp) REVERT: C 92 HIS cc_start: 0.8655 (p90) cc_final: 0.8412 (p-80) REVERT: C 102 ASN cc_start: 0.8728 (t0) cc_final: 0.8014 (t0) REVERT: C 327 SER cc_start: 0.8648 (p) cc_final: 0.8126 (p) REVERT: C 359 VAL cc_start: 0.9436 (t) cc_final: 0.9085 (p) REVERT: C 461 ILE cc_start: 0.8924 (pt) cc_final: 0.8686 (mt) REVERT: D 56 THR cc_start: 0.8672 (p) cc_final: 0.8420 (p) REVERT: D 102 ASN cc_start: 0.9061 (t0) cc_final: 0.8550 (t0) REVERT: D 103 GLU cc_start: 0.9172 (tp30) cc_final: 0.8956 (tp30) REVERT: D 259 ARG cc_start: 0.9126 (tpp80) cc_final: 0.8893 (tpp80) REVERT: D 274 ASP cc_start: 0.8878 (t70) cc_final: 0.8392 (t70) REVERT: D 327 SER cc_start: 0.8612 (p) cc_final: 0.8030 (p) REVERT: D 461 ILE cc_start: 0.8881 (pt) cc_final: 0.8569 (mt) REVERT: D 483 MET cc_start: 0.9269 (tmm) cc_final: 0.8869 (tmm) REVERT: E 75 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7575 (mm-30) REVERT: E 102 ASN cc_start: 0.8686 (t0) cc_final: 0.7985 (t0) REVERT: E 327 SER cc_start: 0.8585 (p) cc_final: 0.8103 (p) REVERT: E 483 MET cc_start: 0.9196 (tmm) cc_final: 0.8758 (tmm) REVERT: F 78 MET cc_start: 0.8251 (OUTLIER) cc_final: 0.7969 (ttp) REVERT: F 92 HIS cc_start: 0.8652 (p90) cc_final: 0.8420 (p-80) REVERT: F 102 ASN cc_start: 0.8972 (t0) cc_final: 0.8382 (t0) REVERT: F 259 ARG cc_start: 0.8909 (tpp80) cc_final: 0.8443 (tpp80) REVERT: F 285 ASN cc_start: 0.9044 (m110) cc_final: 0.8674 (m110) REVERT: F 319 ASP cc_start: 0.8113 (t0) cc_final: 0.7808 (t0) REVERT: F 327 SER cc_start: 0.8689 (p) cc_final: 0.8204 (p) REVERT: F 461 ILE cc_start: 0.8898 (pt) cc_final: 0.8659 (mt) REVERT: F 483 MET cc_start: 0.9261 (tmm) cc_final: 0.8845 (tmm) REVERT: F 487 GLU cc_start: 0.8056 (mt-10) cc_final: 0.7773 (mm-30) REVERT: G 78 MET cc_start: 0.8499 (tpp) cc_final: 0.8264 (tpp) REVERT: G 92 HIS cc_start: 0.8609 (p90) cc_final: 0.8341 (p-80) REVERT: G 102 ASN cc_start: 0.8714 (t0) cc_final: 0.7995 (t0) REVERT: G 327 SER cc_start: 0.8612 (p) cc_final: 0.8054 (p) REVERT: G 441 GLN cc_start: 0.8734 (mt0) cc_final: 0.8346 (mt0) REVERT: G 483 MET cc_start: 0.9227 (tmm) cc_final: 0.8839 (tmm) REVERT: G 487 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7824 (mm-30) REVERT: H 75 GLU cc_start: 0.8052 (mt-10) cc_final: 0.7714 (tp30) REVERT: H 78 MET cc_start: 0.8644 (tpp) cc_final: 0.8343 (tpp) REVERT: H 92 HIS cc_start: 0.8662 (p90) cc_final: 0.8462 (p-80) REVERT: H 99 PHE cc_start: 0.9209 (t80) cc_final: 0.8886 (t80) REVERT: H 102 ASN cc_start: 0.8856 (t0) cc_final: 0.8205 (t0) REVERT: H 242 LYS cc_start: 0.8421 (mttp) cc_final: 0.8111 (tppt) REVERT: H 257 LYS cc_start: 0.9546 (mttm) cc_final: 0.9332 (mttp) REVERT: H 274 ASP cc_start: 0.8893 (t70) cc_final: 0.8252 (t70) REVERT: H 319 ASP cc_start: 0.8057 (t0) cc_final: 0.7795 (t0) REVERT: H 327 SER cc_start: 0.8605 (p) cc_final: 0.8044 (p) REVERT: H 461 ILE cc_start: 0.8792 (pt) cc_final: 0.8513 (mt) REVERT: H 483 MET cc_start: 0.9210 (tmm) cc_final: 0.8786 (tmm) outliers start: 131 outliers final: 104 residues processed: 816 average time/residue: 0.3117 time to fit residues: 400.3329 Evaluate side-chains 805 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 699 time to evaluate : 2.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 78 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 31 THR Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 47 ASP Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain D residue 31 THR Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 31 THR Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 475 SER Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain F residue 475 SER Chi-restraints excluded: chain G residue 31 THR Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 388 SER Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 457 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 475 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 276 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 163 optimal weight: 4.9990 chunk 209 optimal weight: 5.9990 chunk 162 optimal weight: 2.9990 chunk 241 optimal weight: 1.9990 chunk 159 optimal weight: 0.0030 chunk 285 optimal weight: 5.9990 chunk 178 optimal weight: 3.9990 chunk 173 optimal weight: 4.9990 chunk 131 optimal weight: 2.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 309 GLN ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 253 HIS ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN C 309 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 ASN D 469 GLN E 309 GLN E 368 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 309 GLN H 253 HIS H 303 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 469 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.3418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 23480 Z= 0.353 Angle : 0.686 8.296 31792 Z= 0.348 Chirality : 0.047 0.161 3656 Planarity : 0.004 0.048 4000 Dihedral : 9.046 89.867 3736 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 20.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 6.00 % Allowed : 28.52 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -1.89 (0.15), residues: 2960 helix: -0.78 (0.15), residues: 1144 sheet: -2.69 (0.29), residues: 296 loop : -1.23 (0.16), residues: 1520 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS D 92 PHE 0.011 0.002 PHE B 401 TYR 0.025 0.002 TYR C 4 ARG 0.005 0.000 ARG B 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 143 poor density : 707 time to evaluate : 2.722 Fit side-chains revert: symmetry clash REVERT: A 92 HIS cc_start: 0.8804 (p90) cc_final: 0.8342 (p90) REVERT: A 102 ASN cc_start: 0.8666 (t0) cc_final: 0.7939 (t0) REVERT: A 327 SER cc_start: 0.8662 (p) cc_final: 0.8222 (p) REVERT: A 355 ARG cc_start: 0.8905 (ttp-170) cc_final: 0.8663 (ttp-170) REVERT: A 441 GLN cc_start: 0.8759 (mt0) cc_final: 0.8366 (mt0) REVERT: A 483 MET cc_start: 0.9184 (tmm) cc_final: 0.8772 (tmm) REVERT: B 71 ASP cc_start: 0.9019 (p0) cc_final: 0.8708 (p0) REVERT: B 92 HIS cc_start: 0.8690 (p90) cc_final: 0.8117 (p90) REVERT: B 102 ASN cc_start: 0.8832 (t0) cc_final: 0.8155 (t0) REVERT: B 242 LYS cc_start: 0.8380 (mttp) cc_final: 0.8097 (tppt) REVERT: B 257 LYS cc_start: 0.9526 (mttm) cc_final: 0.9240 (mtpp) REVERT: B 274 ASP cc_start: 0.8937 (t70) cc_final: 0.8353 (t70) REVERT: B 289 TYR cc_start: 0.9083 (t80) cc_final: 0.8531 (t80) REVERT: B 327 SER cc_start: 0.8827 (p) cc_final: 0.8404 (p) REVERT: B 359 VAL cc_start: 0.9453 (t) cc_final: 0.9122 (p) REVERT: C 92 HIS cc_start: 0.8822 (p90) cc_final: 0.8335 (p90) REVERT: C 102 ASN cc_start: 0.8747 (t0) cc_final: 0.8050 (t0) REVERT: C 254 GLU cc_start: 0.8705 (pm20) cc_final: 0.8119 (tt0) REVERT: C 327 SER cc_start: 0.8793 (p) cc_final: 0.8334 (p) REVERT: C 359 VAL cc_start: 0.9458 (t) cc_final: 0.9140 (p) REVERT: C 461 ILE cc_start: 0.8949 (pt) cc_final: 0.8674 (mt) REVERT: D 56 THR cc_start: 0.8853 (p) cc_final: 0.8598 (p) REVERT: D 102 ASN cc_start: 0.9037 (t0) cc_final: 0.8504 (t0) REVERT: D 259 ARG cc_start: 0.9088 (tpp80) cc_final: 0.8649 (tpp80) REVERT: D 274 ASP cc_start: 0.8942 (t70) cc_final: 0.8363 (t70) REVERT: D 327 SER cc_start: 0.8781 (p) cc_final: 0.8340 (p) REVERT: D 461 ILE cc_start: 0.8870 (pt) cc_final: 0.8591 (mt) REVERT: D 465 GLN cc_start: 0.8951 (mt0) cc_final: 0.8730 (mt0) REVERT: D 483 MET cc_start: 0.9255 (tmm) cc_final: 0.8885 (tmm) REVERT: E 19 THR cc_start: 0.9282 (OUTLIER) cc_final: 0.9042 (p) REVERT: E 75 GLU cc_start: 0.7967 (mt-10) cc_final: 0.7608 (mm-30) REVERT: E 102 ASN cc_start: 0.8697 (t0) cc_final: 0.7979 (t0) REVERT: E 312 ASN cc_start: 0.9038 (m-40) cc_final: 0.8725 (m-40) REVERT: E 327 SER cc_start: 0.8703 (p) cc_final: 0.8265 (p) REVERT: E 355 ARG cc_start: 0.8965 (ttp-170) cc_final: 0.8696 (ttp-170) REVERT: E 441 GLN cc_start: 0.8784 (mt0) cc_final: 0.8425 (mt0) REVERT: E 483 MET cc_start: 0.9214 (tmm) cc_final: 0.8795 (tmm) REVERT: F 71 ASP cc_start: 0.9123 (p0) cc_final: 0.8806 (p0) REVERT: F 78 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7868 (ttp) REVERT: F 92 HIS cc_start: 0.8727 (p90) cc_final: 0.8192 (p90) REVERT: F 102 ASN cc_start: 0.8939 (t0) cc_final: 0.8309 (t0) REVERT: F 259 ARG cc_start: 0.8984 (tpp80) cc_final: 0.8489 (tpp80) REVERT: F 319 ASP cc_start: 0.7926 (t0) cc_final: 0.7657 (t0) REVERT: F 327 SER cc_start: 0.8802 (p) cc_final: 0.8351 (p) REVERT: F 335 GLU cc_start: 0.8222 (pp20) cc_final: 0.7943 (pp20) REVERT: F 355 ARG cc_start: 0.8910 (ttp-170) cc_final: 0.8634 (ttp-170) REVERT: F 461 ILE cc_start: 0.8960 (pt) cc_final: 0.8649 (mt) REVERT: F 483 MET cc_start: 0.9257 (tmm) cc_final: 0.8849 (tmm) REVERT: F 487 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7930 (mm-30) REVERT: G 71 ASP cc_start: 0.9077 (p0) cc_final: 0.8760 (p0) REVERT: G 92 HIS cc_start: 0.8727 (p90) cc_final: 0.8111 (p90) REVERT: G 102 ASN cc_start: 0.8732 (t0) cc_final: 0.8025 (t0) REVERT: G 327 SER cc_start: 0.8717 (p) cc_final: 0.8253 (p) REVERT: G 355 ARG cc_start: 0.8907 (ttp-170) cc_final: 0.8603 (ttp-170) REVERT: G 483 MET cc_start: 0.9231 (tmm) cc_final: 0.8862 (tmm) REVERT: H 75 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7825 (tp30) REVERT: H 92 HIS cc_start: 0.8812 (p90) cc_final: 0.8385 (p90) REVERT: H 99 PHE cc_start: 0.9207 (t80) cc_final: 0.8827 (t80) REVERT: H 102 ASN cc_start: 0.8843 (t0) cc_final: 0.8211 (t0) REVERT: H 274 ASP cc_start: 0.8995 (t70) cc_final: 0.8366 (t70) REVERT: H 319 ASP cc_start: 0.8144 (t0) cc_final: 0.7844 (t0) REVERT: H 327 SER cc_start: 0.8717 (p) cc_final: 0.8243 (p) REVERT: H 335 GLU cc_start: 0.8256 (pp20) cc_final: 0.7978 (pp20) REVERT: H 461 ILE cc_start: 0.8819 (pt) cc_final: 0.8556 (mt) REVERT: H 483 MET cc_start: 0.9193 (tmm) cc_final: 0.8806 (tmm) outliers start: 143 outliers final: 114 residues processed: 809 average time/residue: 0.3189 time to fit residues: 406.3008 Evaluate side-chains 798 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 116 poor density : 682 time to evaluate : 2.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain A residue 475 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 36 LEU Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain B residue 475 SER Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 36 LEU Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain C residue 475 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 337 LEU Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 448 GLN Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 461 ILE Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 475 SER Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 63 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 306 THR Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 388 SER Chi-restraints excluded: chain G residue 437 ILE Chi-restraints excluded: chain G residue 457 VAL Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 337 LEU Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 388 SER Chi-restraints excluded: chain H residue 437 ILE Chi-restraints excluded: chain H residue 475 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 0.8980 chunk 113 optimal weight: 4.9990 chunk 170 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 55 optimal weight: 0.6980 chunk 181 optimal weight: 0.7980 chunk 194 optimal weight: 6.9990 chunk 141 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 chunk 224 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN C 469 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 ASN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7932 moved from start: 0.3600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23480 Z= 0.203 Angle : 0.621 9.528 31792 Z= 0.312 Chirality : 0.044 0.158 3656 Planarity : 0.003 0.044 4000 Dihedral : 8.601 89.598 3735 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 18.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 5.08 % Allowed : 31.38 % Favored : 63.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -1.72 (0.15), residues: 2960 helix: -0.66 (0.15), residues: 1176 sheet: -2.67 (0.30), residues: 296 loop : -1.11 (0.16), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS E 92 PHE 0.011 0.001 PHE D 44 TYR 0.026 0.002 TYR E 4 ARG 0.004 0.000 ARG F 480 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 849 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 728 time to evaluate : 2.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 75 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7478 (tp30) REVERT: A 102 ASN cc_start: 0.8705 (t0) cc_final: 0.7995 (t0) REVERT: A 327 SER cc_start: 0.8561 (p) cc_final: 0.8110 (p) REVERT: A 441 GLN cc_start: 0.8675 (mt0) cc_final: 0.8343 (mt0) REVERT: A 483 MET cc_start: 0.9156 (tmm) cc_final: 0.8722 (tmm) REVERT: B 92 HIS cc_start: 0.8616 (p90) cc_final: 0.8246 (p-80) REVERT: B 102 ASN cc_start: 0.8863 (t0) cc_final: 0.8194 (t0) REVERT: B 242 LYS cc_start: 0.8364 (mttp) cc_final: 0.8075 (tppt) REVERT: B 257 LYS cc_start: 0.9492 (mttm) cc_final: 0.9268 (mtpp) REVERT: B 274 ASP cc_start: 0.8922 (t70) cc_final: 0.8361 (t70) REVERT: B 359 VAL cc_start: 0.9445 (t) cc_final: 0.9125 (p) REVERT: B 483 MET cc_start: 0.9272 (tmm) cc_final: 0.8601 (tmm) REVERT: B 487 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7827 (mm-30) REVERT: C 75 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7513 (tp30) REVERT: C 78 MET cc_start: 0.8614 (tpp) cc_final: 0.8347 (tpp) REVERT: C 102 ASN cc_start: 0.8795 (t0) cc_final: 0.8092 (t0) REVERT: C 254 GLU cc_start: 0.8699 (pm20) cc_final: 0.8133 (tt0) REVERT: C 327 SER cc_start: 0.8714 (p) cc_final: 0.8260 (p) REVERT: D 102 ASN cc_start: 0.9063 (t0) cc_final: 0.8532 (t0) REVERT: D 259 ARG cc_start: 0.9038 (tpp80) cc_final: 0.8794 (tpp80) REVERT: D 274 ASP cc_start: 0.8926 (t70) cc_final: 0.8245 (t70) REVERT: D 327 SER cc_start: 0.8694 (p) cc_final: 0.8201 (p) REVERT: D 461 ILE cc_start: 0.8866 (pt) cc_final: 0.8544 (mt) REVERT: D 483 MET cc_start: 0.9243 (tmm) cc_final: 0.8818 (tmm) REVERT: E 19 THR cc_start: 0.9086 (OUTLIER) cc_final: 0.8860 (p) REVERT: E 75 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7532 (mm-30) REVERT: E 102 ASN cc_start: 0.8678 (t0) cc_final: 0.7971 (t0) REVERT: E 327 SER cc_start: 0.8663 (p) cc_final: 0.8206 (p) REVERT: E 438 LYS cc_start: 0.7310 (mmtt) cc_final: 0.7030 (mmtm) REVERT: E 441 GLN cc_start: 0.8739 (mt0) cc_final: 0.8373 (mt0) REVERT: E 483 MET cc_start: 0.9172 (tmm) cc_final: 0.8740 (tmm) REVERT: F 71 ASP cc_start: 0.9081 (p0) cc_final: 0.8841 (p0) REVERT: F 78 MET cc_start: 0.8147 (OUTLIER) cc_final: 0.7787 (ttp) REVERT: F 92 HIS cc_start: 0.8635 (p90) cc_final: 0.8339 (p-80) REVERT: F 102 ASN cc_start: 0.8962 (t0) cc_final: 0.8374 (t0) REVERT: F 259 ARG cc_start: 0.8925 (tpp80) cc_final: 0.8468 (tpp80) REVERT: F 319 ASP cc_start: 0.8231 (t0) cc_final: 0.7906 (t0) REVERT: F 327 SER cc_start: 0.8786 (p) cc_final: 0.8326 (p) REVERT: F 461 ILE cc_start: 0.8882 (pt) cc_final: 0.8615 (mt) REVERT: F 483 MET cc_start: 0.9259 (tmm) cc_final: 0.8836 (tmm) REVERT: F 487 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7818 (mm-30) REVERT: G 78 MET cc_start: 0.8490 (tpp) cc_final: 0.8255 (tpp) REVERT: G 92 HIS cc_start: 0.8635 (p90) cc_final: 0.8386 (p-80) REVERT: G 102 ASN cc_start: 0.8746 (t0) cc_final: 0.8056 (t0) REVERT: G 327 SER cc_start: 0.8656 (p) cc_final: 0.8188 (p) REVERT: G 441 GLN cc_start: 0.8715 (mt0) cc_final: 0.8398 (mt0) REVERT: G 483 MET cc_start: 0.9223 (tmm) cc_final: 0.8811 (tmm) REVERT: G 487 GLU cc_start: 0.8110 (mt-10) cc_final: 0.7855 (mm-30) REVERT: H 78 MET cc_start: 0.8605 (tpp) cc_final: 0.8358 (tpp) REVERT: H 92 HIS cc_start: 0.8743 (p90) cc_final: 0.8526 (p-80) REVERT: H 99 PHE cc_start: 0.9189 (t80) cc_final: 0.8820 (t80) REVERT: H 102 ASN cc_start: 0.8862 (t0) cc_final: 0.8215 (t0) REVERT: H 274 ASP cc_start: 0.8961 (t70) cc_final: 0.8266 (t70) REVERT: H 319 ASP cc_start: 0.8160 (t0) cc_final: 0.7848 (t0) REVERT: H 327 SER cc_start: 0.8661 (p) cc_final: 0.8183 (p) REVERT: H 461 ILE cc_start: 0.8808 (pt) cc_final: 0.8455 (mt) REVERT: H 483 MET cc_start: 0.9218 (tmm) cc_final: 0.8793 (tmm) outliers start: 121 outliers final: 91 residues processed: 810 average time/residue: 0.3192 time to fit residues: 408.2586 Evaluate side-chains 776 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 683 time to evaluate : 2.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 382 SER Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 337 LEU Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 268 VAL Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain G residue 36 LEU Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 382 SER Chi-restraints excluded: chain G residue 457 VAL Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 388 SER Chi-restraints excluded: chain H residue 437 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 0.0050 chunk 273 optimal weight: 5.9990 chunk 249 optimal weight: 0.6980 chunk 265 optimal weight: 0.8980 chunk 160 optimal weight: 5.9990 chunk 115 optimal weight: 5.9990 chunk 208 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 240 optimal weight: 0.0570 chunk 251 optimal weight: 6.9990 chunk 264 optimal weight: 3.9990 overall best weight: 0.9314 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 ASN ** D 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 ASN D 465 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 23480 Z= 0.215 Angle : 0.627 10.061 31792 Z= 0.315 Chirality : 0.044 0.156 3656 Planarity : 0.004 0.056 4000 Dihedral : 8.347 89.634 3734 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 19.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 4.49 % Allowed : 32.13 % Favored : 63.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -1.63 (0.15), residues: 2960 helix: -0.53 (0.15), residues: 1168 sheet: -2.66 (0.30), residues: 296 loop : -1.10 (0.16), residues: 1496 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS C 92 PHE 0.010 0.001 PHE A 401 TYR 0.034 0.002 TYR H 289 ARG 0.006 0.000 ARG C 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 722 time to evaluate : 2.446 Fit side-chains revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8779 (t0) cc_final: 0.8103 (t0) REVERT: A 327 SER cc_start: 0.8644 (p) cc_final: 0.8209 (p) REVERT: A 441 GLN cc_start: 0.8681 (mt0) cc_final: 0.8357 (mt0) REVERT: A 483 MET cc_start: 0.9214 (tmm) cc_final: 0.8849 (tmm) REVERT: A 491 GLU cc_start: 0.8380 (tp30) cc_final: 0.8032 (tp30) REVERT: B 92 HIS cc_start: 0.8699 (p90) cc_final: 0.8421 (p-80) REVERT: B 102 ASN cc_start: 0.8916 (t0) cc_final: 0.8283 (t0) REVERT: B 242 LYS cc_start: 0.8376 (mttp) cc_final: 0.8078 (tppt) REVERT: B 274 ASP cc_start: 0.8884 (t70) cc_final: 0.8282 (t70) REVERT: B 327 SER cc_start: 0.8742 (p) cc_final: 0.8280 (p) REVERT: B 487 GLU cc_start: 0.8101 (mt-10) cc_final: 0.7809 (mt-10) REVERT: C 78 MET cc_start: 0.8578 (tpp) cc_final: 0.8320 (tpp) REVERT: C 102 ASN cc_start: 0.8827 (t0) cc_final: 0.8144 (t0) REVERT: C 254 GLU cc_start: 0.8666 (pm20) cc_final: 0.8136 (tt0) REVERT: C 327 SER cc_start: 0.8756 (p) cc_final: 0.8313 (p) REVERT: C 438 LYS cc_start: 0.7557 (mmtt) cc_final: 0.7347 (mmtm) REVERT: C 483 MET cc_start: 0.9095 (tmm) cc_final: 0.8882 (tmm) REVERT: D 42 ILE cc_start: 0.8434 (pt) cc_final: 0.8167 (pt) REVERT: D 102 ASN cc_start: 0.9076 (t0) cc_final: 0.8550 (t0) REVERT: D 259 ARG cc_start: 0.9033 (tpp80) cc_final: 0.8781 (tpp80) REVERT: D 274 ASP cc_start: 0.8911 (t70) cc_final: 0.8510 (t70) REVERT: D 327 SER cc_start: 0.8730 (p) cc_final: 0.8279 (p) REVERT: D 461 ILE cc_start: 0.8745 (pt) cc_final: 0.8381 (mt) REVERT: D 465 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.8661 (mm-40) REVERT: D 483 MET cc_start: 0.9242 (tmm) cc_final: 0.8850 (tmm) REVERT: E 19 THR cc_start: 0.9062 (OUTLIER) cc_final: 0.8828 (p) REVERT: E 102 ASN cc_start: 0.8694 (t0) cc_final: 0.7985 (t0) REVERT: E 108 LYS cc_start: 0.9645 (mmmt) cc_final: 0.9373 (mmmt) REVERT: E 254 GLU cc_start: 0.8733 (pm20) cc_final: 0.8146 (tt0) REVERT: E 327 SER cc_start: 0.8722 (p) cc_final: 0.8288 (p) REVERT: E 359 VAL cc_start: 0.9458 (t) cc_final: 0.9114 (p) REVERT: E 438 LYS cc_start: 0.7388 (mmtt) cc_final: 0.7100 (mmtm) REVERT: E 441 GLN cc_start: 0.8734 (mt0) cc_final: 0.8418 (mt0) REVERT: E 483 MET cc_start: 0.9194 (tmm) cc_final: 0.8817 (tmm) REVERT: F 71 ASP cc_start: 0.9052 (p0) cc_final: 0.8827 (p0) REVERT: F 92 HIS cc_start: 0.8641 (p90) cc_final: 0.8323 (p-80) REVERT: F 102 ASN cc_start: 0.8977 (t0) cc_final: 0.8371 (t0) REVERT: F 259 ARG cc_start: 0.8929 (tpp80) cc_final: 0.8472 (tpp80) REVERT: F 285 ASN cc_start: 0.9123 (m110) cc_final: 0.8646 (m110) REVERT: F 319 ASP cc_start: 0.8211 (t0) cc_final: 0.7994 (t0) REVERT: F 461 ILE cc_start: 0.8884 (pt) cc_final: 0.8636 (mt) REVERT: F 483 MET cc_start: 0.9267 (tmm) cc_final: 0.8862 (tmm) REVERT: F 487 GLU cc_start: 0.8059 (mt-10) cc_final: 0.7754 (mm-30) REVERT: G 78 MET cc_start: 0.8507 (tpp) cc_final: 0.8287 (tpp) REVERT: G 102 ASN cc_start: 0.8759 (t0) cc_final: 0.8066 (t0) REVERT: G 327 SER cc_start: 0.8718 (p) cc_final: 0.8273 (p) REVERT: G 438 LYS cc_start: 0.7459 (mmtt) cc_final: 0.7212 (mmtm) REVERT: G 441 GLN cc_start: 0.8729 (mt0) cc_final: 0.8425 (mt0) REVERT: G 483 MET cc_start: 0.9236 (tmm) cc_final: 0.8875 (tmm) REVERT: G 487 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7852 (mm-30) REVERT: G 491 GLU cc_start: 0.8387 (tp30) cc_final: 0.8048 (tp30) REVERT: H 78 MET cc_start: 0.8637 (tpp) cc_final: 0.8412 (tpp) REVERT: H 92 HIS cc_start: 0.8795 (p90) cc_final: 0.8573 (p-80) REVERT: H 102 ASN cc_start: 0.8883 (t0) cc_final: 0.8252 (t0) REVERT: H 274 ASP cc_start: 0.8911 (t70) cc_final: 0.8356 (t70) REVERT: H 319 ASP cc_start: 0.8087 (t0) cc_final: 0.7805 (t0) REVERT: H 327 SER cc_start: 0.8670 (p) cc_final: 0.8209 (p) REVERT: H 359 VAL cc_start: 0.9434 (t) cc_final: 0.9112 (p) REVERT: H 461 ILE cc_start: 0.8796 (pt) cc_final: 0.8500 (mt) REVERT: H 465 GLN cc_start: 0.8863 (mt0) cc_final: 0.8657 (mm-40) outliers start: 107 outliers final: 93 residues processed: 793 average time/residue: 0.3384 time to fit residues: 426.5096 Evaluate side-chains 796 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 701 time to evaluate : 2.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 337 LEU Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 437 ILE Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain D residue 475 SER Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 457 VAL Chi-restraints excluded: chain G residue 475 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 388 SER Chi-restraints excluded: chain H residue 437 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 4.9990 chunk 281 optimal weight: 0.6980 chunk 171 optimal weight: 0.9990 chunk 133 optimal weight: 0.5980 chunk 195 optimal weight: 2.9990 chunk 294 optimal weight: 4.9990 chunk 271 optimal weight: 9.9990 chunk 234 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 181 optimal weight: 4.9990 chunk 143 optimal weight: 1.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 ASN D 465 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 23480 Z= 0.230 Angle : 0.636 9.478 31792 Z= 0.321 Chirality : 0.045 0.159 3656 Planarity : 0.004 0.047 4000 Dihedral : 8.285 89.974 3733 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer: Outliers : 4.36 % Allowed : 32.55 % Favored : 63.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -1.62 (0.15), residues: 2960 helix: -0.51 (0.15), residues: 1176 sheet: -2.39 (0.30), residues: 280 loop : -1.19 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS E 92 PHE 0.013 0.001 PHE F 99 TYR 0.033 0.002 TYR H 484 ARG 0.007 0.001 ARG B 355 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5920 Ramachandran restraints generated. 2960 Oldfield, 0 Emsley, 2960 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 815 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 711 time to evaluate : 2.293 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 ASN cc_start: 0.8769 (t0) cc_final: 0.8087 (t0) REVERT: A 327 SER cc_start: 0.8646 (p) cc_final: 0.8224 (p) REVERT: A 441 GLN cc_start: 0.8697 (mt0) cc_final: 0.8373 (mt0) REVERT: A 483 MET cc_start: 0.9234 (tmm) cc_final: 0.8700 (tmm) REVERT: A 491 GLU cc_start: 0.8399 (tp30) cc_final: 0.8028 (tp30) REVERT: B 92 HIS cc_start: 0.8737 (p90) cc_final: 0.8464 (p-80) REVERT: B 102 ASN cc_start: 0.8930 (t0) cc_final: 0.8303 (t0) REVERT: B 242 LYS cc_start: 0.8392 (mttp) cc_final: 0.8090 (tppt) REVERT: B 274 ASP cc_start: 0.8876 (t70) cc_final: 0.8272 (t70) REVERT: B 327 SER cc_start: 0.8767 (p) cc_final: 0.8308 (p) REVERT: B 487 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7807 (mm-30) REVERT: C 71 ASP cc_start: 0.8458 (p0) cc_final: 0.8256 (p0) REVERT: C 78 MET cc_start: 0.8525 (tpp) cc_final: 0.8297 (tpp) REVERT: C 102 ASN cc_start: 0.8831 (t0) cc_final: 0.8148 (t0) REVERT: C 327 SER cc_start: 0.8782 (p) cc_final: 0.8349 (p) REVERT: C 438 LYS cc_start: 0.7587 (mmtt) cc_final: 0.7367 (mmtm) REVERT: C 483 MET cc_start: 0.9130 (tmm) cc_final: 0.8781 (tmm) REVERT: C 491 GLU cc_start: 0.8275 (tp30) cc_final: 0.7932 (tp30) REVERT: D 42 ILE cc_start: 0.8403 (pt) cc_final: 0.8121 (pt) REVERT: D 102 ASN cc_start: 0.9085 (t0) cc_final: 0.8546 (t0) REVERT: D 259 ARG cc_start: 0.9036 (tpp80) cc_final: 0.8780 (tpp80) REVERT: D 274 ASP cc_start: 0.8924 (t70) cc_final: 0.8523 (t70) REVERT: D 327 SER cc_start: 0.8750 (p) cc_final: 0.8275 (p) REVERT: D 465 GLN cc_start: 0.9028 (OUTLIER) cc_final: 0.8782 (mm-40) REVERT: D 483 MET cc_start: 0.9242 (tmm) cc_final: 0.8862 (tmm) REVERT: E 19 THR cc_start: 0.9071 (OUTLIER) cc_final: 0.8869 (p) REVERT: E 102 ASN cc_start: 0.8706 (t0) cc_final: 0.7993 (t0) REVERT: E 327 SER cc_start: 0.8727 (p) cc_final: 0.8308 (p) REVERT: E 359 VAL cc_start: 0.9465 (t) cc_final: 0.9121 (p) REVERT: E 441 GLN cc_start: 0.8747 (mt0) cc_final: 0.8423 (mt0) REVERT: F 71 ASP cc_start: 0.9055 (p0) cc_final: 0.8826 (p0) REVERT: F 92 HIS cc_start: 0.8673 (p90) cc_final: 0.8330 (p-80) REVERT: F 102 ASN cc_start: 0.8971 (t0) cc_final: 0.8368 (t0) REVERT: F 259 ARG cc_start: 0.8944 (tpp80) cc_final: 0.8482 (tpp80) REVERT: F 285 ASN cc_start: 0.9118 (m110) cc_final: 0.8650 (m110) REVERT: F 319 ASP cc_start: 0.8180 (t0) cc_final: 0.7964 (t0) REVERT: F 461 ILE cc_start: 0.8905 (pt) cc_final: 0.8639 (mt) REVERT: F 487 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7745 (mm-30) REVERT: G 78 MET cc_start: 0.8505 (tpp) cc_final: 0.8277 (tpp) REVERT: G 102 ASN cc_start: 0.8759 (t0) cc_final: 0.8077 (t0) REVERT: G 327 SER cc_start: 0.8713 (p) cc_final: 0.8280 (p) REVERT: G 359 VAL cc_start: 0.9465 (t) cc_final: 0.9155 (p) REVERT: G 438 LYS cc_start: 0.7537 (mmtt) cc_final: 0.7296 (mmtm) REVERT: G 441 GLN cc_start: 0.8729 (mt0) cc_final: 0.8437 (mt0) REVERT: G 487 GLU cc_start: 0.8114 (mt-10) cc_final: 0.7853 (mm-30) REVERT: G 491 GLU cc_start: 0.8406 (tp30) cc_final: 0.8046 (tp30) REVERT: H 92 HIS cc_start: 0.8785 (p90) cc_final: 0.8469 (p-80) REVERT: H 102 ASN cc_start: 0.9075 (t0) cc_final: 0.8567 (t0) REVERT: H 254 GLU cc_start: 0.8963 (pm20) cc_final: 0.8454 (tt0) REVERT: H 274 ASP cc_start: 0.8893 (t70) cc_final: 0.8342 (t70) REVERT: H 319 ASP cc_start: 0.8287 (t0) cc_final: 0.7871 (t0) REVERT: H 327 SER cc_start: 0.8669 (p) cc_final: 0.8221 (p) REVERT: H 359 VAL cc_start: 0.9437 (t) cc_final: 0.9145 (p) REVERT: H 461 ILE cc_start: 0.8794 (pt) cc_final: 0.8497 (mt) REVERT: H 483 MET cc_start: 0.9210 (tmm) cc_final: 0.8685 (tmm) REVERT: H 487 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7895 (mm-30) outliers start: 104 outliers final: 94 residues processed: 781 average time/residue: 0.3240 time to fit residues: 397.3670 Evaluate side-chains 791 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 695 time to evaluate : 2.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 36 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 63 THR Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 306 THR Chi-restraints excluded: chain A residue 337 LEU Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 351 SER Chi-restraints excluded: chain A residue 457 VAL Chi-restraints excluded: chain B residue 47 ASP Chi-restraints excluded: chain B residue 63 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 382 SER Chi-restraints excluded: chain B residue 457 VAL Chi-restraints excluded: chain C residue 19 THR Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 263 LEU Chi-restraints excluded: chain C residue 271 VAL Chi-restraints excluded: chain C residue 275 SER Chi-restraints excluded: chain C residue 306 THR Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 382 SER Chi-restraints excluded: chain C residue 437 ILE Chi-restraints excluded: chain C residue 457 VAL Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 47 ASP Chi-restraints excluded: chain D residue 63 THR Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 275 SER Chi-restraints excluded: chain D residue 280 SER Chi-restraints excluded: chain D residue 281 ILE Chi-restraints excluded: chain D residue 306 THR Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 382 SER Chi-restraints excluded: chain D residue 465 GLN Chi-restraints excluded: chain E residue 19 THR Chi-restraints excluded: chain E residue 36 LEU Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 71 ASP Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 263 LEU Chi-restraints excluded: chain E residue 271 VAL Chi-restraints excluded: chain E residue 275 SER Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 337 LEU Chi-restraints excluded: chain E residue 351 SER Chi-restraints excluded: chain E residue 382 SER Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 457 VAL Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain E residue 513 LEU Chi-restraints excluded: chain F residue 36 LEU Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 47 ASP Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 263 LEU Chi-restraints excluded: chain F residue 271 VAL Chi-restraints excluded: chain F residue 275 SER Chi-restraints excluded: chain F residue 281 ILE Chi-restraints excluded: chain F residue 306 THR Chi-restraints excluded: chain F residue 351 SER Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 457 VAL Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain G residue 47 ASP Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 271 VAL Chi-restraints excluded: chain G residue 275 SER Chi-restraints excluded: chain G residue 281 ILE Chi-restraints excluded: chain G residue 337 LEU Chi-restraints excluded: chain G residue 351 SER Chi-restraints excluded: chain G residue 457 VAL Chi-restraints excluded: chain G residue 475 SER Chi-restraints excluded: chain H residue 36 LEU Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 47 ASP Chi-restraints excluded: chain H residue 63 THR Chi-restraints excluded: chain H residue 275 SER Chi-restraints excluded: chain H residue 306 THR Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 382 SER Chi-restraints excluded: chain H residue 437 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 186 optimal weight: 0.9990 chunk 250 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 216 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 65 optimal weight: 7.9990 chunk 235 optimal weight: 4.9990 chunk 98 optimal weight: 0.0470 chunk 241 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 overall best weight: 0.6480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 469 GLN D 298 GLN ** D 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 ASN D 465 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 469 GLN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 465 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.149233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.124195 restraints weight = 32828.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.129003 restraints weight = 17216.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.132340 restraints weight = 10861.493| |-----------------------------------------------------------------------------| r_work (final): 0.3422 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7835 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 23480 Z= 0.194 Angle : 0.630 10.737 31792 Z= 0.315 Chirality : 0.044 0.159 3656 Planarity : 0.004 0.046 4000 Dihedral : 8.091 89.784 3733 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 18.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 4.11 % Allowed : 32.84 % Favored : 63.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.28 % 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: -1.57 (0.15), residues: 2960 helix: -0.46 (0.15), residues: 1176 sheet: -2.39 (0.30), residues: 280 loop : -1.16 (0.16), residues: 1504 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS A 92 PHE 0.013 0.001 PHE F 99 TYR 0.028 0.002 TYR B 4 ARG 0.006 0.001 ARG C 355 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6445.66 seconds wall clock time: 116 minutes 16.96 seconds (6976.96 seconds total)