Starting phenix.real_space_refine on Tue Mar 19 03:54:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8s_20691/03_2024/6u8s_20691_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8s_20691/03_2024/6u8s_20691.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8s_20691/03_2024/6u8s_20691.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8s_20691/03_2024/6u8s_20691.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8s_20691/03_2024/6u8s_20691_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6u8s_20691/03_2024/6u8s_20691_updated.pdb" } resolution = 3.14 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= 0.054 sd= 2.057 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: 0.06s 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: 11.65, per 1000 atoms: 0.50 Number of scatterers: 23080 At special positions: 0 Unit cell: (122.85, 122.85, 118.65, 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: 9.18 Conformation dependent library (CDL) restraints added in 3.9 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: 128 helices and 32 sheets defined 35.1% alpha, 9.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.53 Creating SS restraints... Processing helix chain 'A' and resid 2 through 5 No H-bonds generated for 'chain 'A' and resid 2 through 5' Processing helix chain 'A' and resid 20 through 24 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 83 Processing helix chain 'A' and resid 97 through 108 removed outlier: 3.612A pdb=" N LYS A 108 " --> pdb=" O VAL A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 254 through 266 removed outlier: 3.688A pdb=" N LYS A 257 " --> pdb=" O GLU A 254 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP A 261 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing helix chain 'A' and resid 281 through 293 removed outlier: 3.700A pdb=" N ASP A 292 " --> pdb=" O LYS A 288 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS A 293 " --> pdb=" O TYR A 289 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 314 Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 343 through 356 removed outlier: 3.849A pdb=" N SER A 351 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 379 Processing helix chain 'A' and resid 417 through 419 No H-bonds generated for 'chain 'A' and resid 417 through 419' 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 484 Processing helix chain 'A' and resid 495 through 501 Processing helix chain 'B' and resid 2 through 5 No H-bonds generated for 'chain 'B' and resid 2 through 5' Processing helix chain 'B' and resid 20 through 24 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 83 Processing helix chain 'B' and resid 97 through 108 removed outlier: 3.613A pdb=" N LYS B 108 " --> pdb=" O VAL B 104 " (cutoff:3.500A) Processing helix chain 'B' and resid 254 through 266 removed outlier: 3.688A pdb=" N LYS B 257 " --> pdb=" O GLU B 254 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP B 261 " --> pdb=" O TYR B 258 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 293 removed outlier: 3.701A pdb=" N ASP B 292 " --> pdb=" O LYS B 288 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS B 293 " --> pdb=" O TYR B 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 314 Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 343 through 356 removed outlier: 3.849A pdb=" N SER B 351 " --> pdb=" O VAL B 347 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 370 through 379 Processing helix chain 'B' and resid 417 through 419 No H-bonds generated for 'chain 'B' and resid 417 through 419' 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 484 Processing helix chain 'B' and resid 495 through 501 Processing helix chain 'C' and resid 2 through 5 No H-bonds generated for 'chain 'C' and resid 2 through 5' Processing helix chain 'C' and resid 20 through 24 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 83 Processing helix chain 'C' and resid 97 through 108 removed outlier: 3.612A pdb=" N LYS C 108 " --> pdb=" O VAL C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 254 through 266 removed outlier: 3.688A pdb=" N LYS C 257 " --> pdb=" O GLU C 254 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N ASP C 261 " --> pdb=" O TYR C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 281 through 293 removed outlier: 3.700A pdb=" N ASP C 292 " --> pdb=" O LYS C 288 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LYS C 293 " --> pdb=" O TYR C 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 314 Processing helix chain 'C' and resid 333 through 337 Processing helix chain 'C' and resid 343 through 356 removed outlier: 3.848A pdb=" N SER C 351 " --> pdb=" O VAL C 347 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 370 through 379 Processing helix chain 'C' and resid 417 through 419 No H-bonds generated for 'chain 'C' and resid 417 through 419' 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 484 Processing helix chain 'C' and resid 495 through 501 Processing helix chain 'D' and resid 2 through 5 No H-bonds generated for 'chain 'D' and resid 2 through 5' Processing helix chain 'D' and resid 20 through 24 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 83 Processing helix chain 'D' and resid 97 through 108 removed outlier: 3.612A pdb=" N LYS D 108 " --> pdb=" O VAL D 104 " (cutoff:3.500A) Processing helix chain 'D' and resid 254 through 266 removed outlier: 3.688A pdb=" N LYS D 257 " --> pdb=" O GLU D 254 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP D 261 " --> pdb=" O TYR D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 281 through 293 removed outlier: 3.700A pdb=" N ASP D 292 " --> pdb=" O LYS D 288 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS D 293 " --> pdb=" O TYR D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 314 Processing helix chain 'D' and resid 333 through 337 Processing helix chain 'D' and resid 343 through 356 removed outlier: 3.849A pdb=" N SER D 351 " --> pdb=" O VAL D 347 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 370 through 379 Processing helix chain 'D' and resid 417 through 419 No H-bonds generated for 'chain 'D' and resid 417 through 419' 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 484 Processing helix chain 'D' and resid 495 through 501 Processing helix chain 'E' and resid 2 through 5 No H-bonds generated for 'chain 'E' and resid 2 through 5' Processing helix chain 'E' and resid 20 through 24 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 83 Processing helix chain 'E' and resid 97 through 108 removed outlier: 3.613A pdb=" N LYS E 108 " --> pdb=" O VAL E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 266 removed outlier: 3.688A pdb=" N LYS E 257 " --> pdb=" O GLU E 254 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASP E 261 " --> pdb=" O TYR E 258 " (cutoff:3.500A) Processing helix chain 'E' and resid 281 through 293 removed outlier: 3.701A pdb=" N ASP E 292 " --> pdb=" O LYS E 288 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS E 293 " --> pdb=" O TYR E 289 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 314 Processing helix chain 'E' and resid 333 through 337 Processing helix chain 'E' and resid 343 through 356 removed outlier: 3.848A pdb=" N SER E 351 " --> pdb=" O VAL E 347 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 370 through 379 Processing helix chain 'E' and resid 417 through 419 No H-bonds generated for 'chain 'E' and resid 417 through 419' 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 484 Processing helix chain 'E' and resid 495 through 501 Processing helix chain 'F' and resid 2 through 5 No H-bonds generated for 'chain 'F' and resid 2 through 5' Processing helix chain 'F' and resid 20 through 24 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 83 Processing helix chain 'F' and resid 97 through 108 removed outlier: 3.613A pdb=" N LYS F 108 " --> pdb=" O VAL F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 254 through 266 removed outlier: 3.688A pdb=" N LYS F 257 " --> pdb=" O GLU F 254 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASP F 261 " --> pdb=" O TYR F 258 " (cutoff:3.500A) Processing helix chain 'F' and resid 281 through 293 removed outlier: 3.700A pdb=" N ASP F 292 " --> pdb=" O LYS F 288 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS F 293 " --> pdb=" O TYR F 289 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 314 Processing helix chain 'F' and resid 333 through 337 Processing helix chain 'F' and resid 343 through 356 removed outlier: 3.849A pdb=" N SER F 351 " --> pdb=" O VAL F 347 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ARG F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 370 through 379 Processing helix chain 'F' and resid 417 through 419 No H-bonds generated for 'chain 'F' and resid 417 through 419' 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 484 Processing helix chain 'F' and resid 495 through 501 Processing helix chain 'G' and resid 2 through 5 No H-bonds generated for 'chain 'G' and resid 2 through 5' Processing helix chain 'G' and resid 20 through 24 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 83 Processing helix chain 'G' and resid 97 through 108 removed outlier: 3.613A pdb=" N LYS G 108 " --> pdb=" O VAL G 104 " (cutoff:3.500A) Processing helix chain 'G' and resid 254 through 266 removed outlier: 3.688A pdb=" N LYS G 257 " --> pdb=" O GLU G 254 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ASP G 261 " --> pdb=" O TYR G 258 " (cutoff:3.500A) Processing helix chain 'G' and resid 281 through 293 removed outlier: 3.700A pdb=" N ASP G 292 " --> pdb=" O LYS G 288 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS G 293 " --> pdb=" O TYR G 289 " (cutoff:3.500A) Processing helix chain 'G' and resid 307 through 314 Processing helix chain 'G' and resid 333 through 337 Processing helix chain 'G' and resid 343 through 356 removed outlier: 3.849A pdb=" N SER G 351 " --> pdb=" O VAL G 347 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 370 through 379 Processing helix chain 'G' and resid 417 through 419 No H-bonds generated for 'chain 'G' and resid 417 through 419' 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 484 Processing helix chain 'G' and resid 495 through 501 Processing helix chain 'H' and resid 2 through 5 No H-bonds generated for 'chain 'H' and resid 2 through 5' Processing helix chain 'H' and resid 20 through 24 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 83 Processing helix chain 'H' and resid 97 through 108 removed outlier: 3.613A pdb=" N LYS H 108 " --> pdb=" O VAL H 104 " (cutoff:3.500A) Processing helix chain 'H' and resid 254 through 266 removed outlier: 3.688A pdb=" N LYS H 257 " --> pdb=" O GLU H 254 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N ASP H 261 " --> pdb=" O TYR H 258 " (cutoff:3.500A) Processing helix chain 'H' and resid 281 through 293 removed outlier: 3.700A pdb=" N ASP H 292 " --> pdb=" O LYS H 288 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS H 293 " --> pdb=" O TYR H 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 314 Processing helix chain 'H' and resid 333 through 337 Processing helix chain 'H' and resid 343 through 356 removed outlier: 3.848A pdb=" N SER H 351 " --> pdb=" O VAL H 347 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ARG H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 370 through 379 Processing helix chain 'H' and resid 417 through 419 No H-bonds generated for 'chain 'H' and resid 417 through 419' 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 484 Processing helix chain 'H' and resid 495 through 501 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: 5.964A pdb=" N VAL A 384 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR A 383 " --> pdb=" O VAL A 361 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 248 through 250 removed outlier: 6.636A pdb=" N GLN A 298 " --> pdb=" O VAL A 271 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU A 273 " --> pdb=" O GLN A 298 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE A 300 " --> pdb=" O LEU A 273 " (cutoff:3.500A) 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: 5.964A pdb=" N VAL B 384 " --> pdb=" O VAL B 66 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR B 383 " --> pdb=" O VAL B 361 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 248 through 250 removed outlier: 6.636A pdb=" N GLN B 298 " --> pdb=" O VAL B 271 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU B 273 " --> pdb=" O GLN B 298 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE B 300 " --> pdb=" O LEU B 273 " (cutoff:3.500A) 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: 5.963A pdb=" N VAL C 384 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR C 383 " --> pdb=" O VAL C 361 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 248 through 250 removed outlier: 6.637A pdb=" N GLN C 298 " --> pdb=" O VAL C 271 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU C 273 " --> pdb=" O GLN C 298 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE C 300 " --> pdb=" O LEU C 273 " (cutoff:3.500A) 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: 5.964A pdb=" N VAL D 384 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR D 383 " --> pdb=" O VAL D 361 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 248 through 250 removed outlier: 6.636A pdb=" N GLN D 298 " --> pdb=" O VAL D 271 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU D 273 " --> pdb=" O GLN D 298 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE D 300 " --> pdb=" O LEU D 273 " (cutoff:3.500A) 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: 5.963A pdb=" N VAL E 384 " --> pdb=" O VAL E 66 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR E 383 " --> pdb=" O VAL E 361 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 248 through 250 removed outlier: 6.636A pdb=" N GLN E 298 " --> pdb=" O VAL E 271 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LEU E 273 " --> pdb=" O GLN E 298 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE E 300 " --> pdb=" O LEU E 273 " (cutoff:3.500A) 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: 5.963A pdb=" N VAL F 384 " --> pdb=" O VAL F 66 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N THR F 383 " --> pdb=" O VAL F 361 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 248 through 250 removed outlier: 6.637A pdb=" N GLN F 298 " --> pdb=" O VAL F 271 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU F 273 " --> pdb=" O GLN F 298 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE F 300 " --> pdb=" O LEU F 273 " (cutoff:3.500A) 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: 5.964A pdb=" N VAL G 384 " --> pdb=" O VAL G 66 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR G 383 " --> pdb=" O VAL G 361 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 248 through 250 removed outlier: 6.637A pdb=" N GLN G 298 " --> pdb=" O VAL G 271 " (cutoff:3.500A) removed outlier: 7.456A pdb=" N LEU G 273 " --> pdb=" O GLN G 298 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N ILE G 300 " --> pdb=" O LEU G 273 " (cutoff:3.500A) 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: 5.964A pdb=" N VAL H 384 " --> pdb=" O VAL H 66 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N THR H 383 " --> pdb=" O VAL H 361 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 248 through 250 removed outlier: 6.637A pdb=" N GLN H 298 " --> pdb=" O VAL H 271 " (cutoff:3.500A) removed outlier: 7.457A pdb=" N LEU H 273 " --> pdb=" O GLN H 298 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE H 300 " --> pdb=" O LEU H 273 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 401 through 403 672 hydrogen bonds defined for protein. 1752 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: 7.42 Time building geometry restraints manager: 9.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.29: 3824 1.29 - 1.42: 5738 1.42 - 1.55: 13554 1.55 - 1.68: 124 1.68 - 1.80: 240 Bond restraints: 23480 Sorted by residual: bond pdb=" C3D NAD E 602 " pdb=" C4D NAD E 602 " ideal model delta sigma weight residual 1.531 1.301 0.230 2.00e-02 2.50e+03 1.33e+02 bond pdb=" C3D NAD G 602 " pdb=" C4D NAD G 602 " ideal model delta sigma weight residual 1.531 1.301 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C3D NAD H 602 " pdb=" C4D NAD H 602 " ideal model delta sigma weight residual 1.531 1.301 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C3D NAD C 602 " pdb=" C4D NAD C 602 " ideal model delta sigma weight residual 1.531 1.301 0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C3D NAD D 602 " pdb=" C4D NAD D 602 " ideal model delta sigma weight residual 1.531 1.301 0.230 2.00e-02 2.50e+03 1.32e+02 ... (remaining 23475 not shown) Histogram of bond angle deviations from ideal: 96.61 - 104.96: 426 104.96 - 113.31: 12922 113.31 - 121.66: 13384 121.66 - 130.01: 4932 130.01 - 138.36: 128 Bond angle restraints: 31792 Sorted by residual: angle pdb=" N1A NAD A 602 " pdb=" C6A NAD A 602 " pdb=" N6A NAD A 602 " ideal model delta sigma weight residual 119.35 102.99 16.36 3.00e+00 1.11e-01 2.97e+01 angle pdb=" N1A NAD E 602 " pdb=" C6A NAD E 602 " pdb=" N6A NAD E 602 " ideal model delta sigma weight residual 119.35 103.00 16.35 3.00e+00 1.11e-01 2.97e+01 angle pdb=" N1A NAD D 602 " pdb=" C6A NAD D 602 " pdb=" N6A NAD D 602 " ideal model delta sigma weight residual 119.35 103.00 16.35 3.00e+00 1.11e-01 2.97e+01 angle pdb=" N1A NAD C 602 " pdb=" C6A NAD C 602 " pdb=" N6A NAD C 602 " ideal model delta sigma weight residual 119.35 103.00 16.35 3.00e+00 1.11e-01 2.97e+01 angle pdb=" N1A NAD B 602 " pdb=" C6A NAD B 602 " pdb=" N6A NAD B 602 " ideal model delta sigma weight residual 119.35 103.00 16.35 3.00e+00 1.11e-01 2.97e+01 ... (remaining 31787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.68: 12916 17.68 - 35.36: 812 35.36 - 53.04: 408 53.04 - 70.72: 88 70.72 - 88.41: 24 Dihedral angle restraints: 14248 sinusoidal: 5744 harmonic: 8504 Sorted by residual: dihedral pdb=" CA LEU B 235 " pdb=" C LEU B 235 " pdb=" N ALA B 236 " pdb=" CA ALA B 236 " ideal model delta harmonic sigma weight residual -180.00 -157.62 -22.38 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LEU F 235 " pdb=" C LEU F 235 " pdb=" N ALA F 236 " pdb=" CA ALA F 236 " ideal model delta harmonic sigma weight residual -180.00 -157.65 -22.35 0 5.00e+00 4.00e-02 2.00e+01 dihedral pdb=" CA LEU H 235 " pdb=" C LEU H 235 " pdb=" N ALA H 236 " pdb=" CA ALA H 236 " ideal model delta harmonic sigma weight residual 180.00 -157.67 -22.33 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 14245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 2755 0.071 - 0.142: 785 0.142 - 0.212: 92 0.212 - 0.283: 8 0.283 - 0.354: 16 Chirality restraints: 3656 Sorted by residual: chirality pdb=" C3B NAD H 602 " pdb=" C2B NAD H 602 " pdb=" C4B NAD H 602 " pdb=" O3B NAD H 602 " both_signs ideal model delta sigma weight residual False -2.71 -2.36 -0.35 2.00e-01 2.50e+01 3.13e+00 chirality pdb=" C3B NAD B 602 " pdb=" C2B NAD B 602 " pdb=" C4B NAD B 602 " pdb=" O3B NAD B 602 " both_signs ideal model delta sigma weight residual False -2.71 -2.36 -0.35 2.00e-01 2.50e+01 3.11e+00 chirality pdb=" C3B NAD D 602 " pdb=" C2B NAD D 602 " pdb=" C4B NAD D 602 " pdb=" O3B NAD D 602 " both_signs ideal model delta sigma weight residual False -2.71 -2.36 -0.35 2.00e-01 2.50e+01 3.11e+00 ... (remaining 3653 not shown) Planarity restraints: 4000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR H 63 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.10e+00 pdb=" N PRO H 64 " 0.098 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 D 63 " 0.037 5.00e-02 4.00e+02 5.64e-02 5.10e+00 pdb=" N PRO D 64 " -0.098 5.00e-02 4.00e+02 pdb=" CA PRO D 64 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO D 64 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 63 " 0.037 5.00e-02 4.00e+02 5.63e-02 5.07e+00 pdb=" N PRO A 64 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 64 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 64 " 0.031 5.00e-02 4.00e+02 ... (remaining 3997 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 6185 2.79 - 3.31: 21367 3.31 - 3.84: 40784 3.84 - 4.37: 47800 4.37 - 4.90: 79165 Nonbonded interactions: 195301 Sorted by model distance: nonbonded pdb=" O SER F 327 " pdb=" OG SER F 327 " model vdw 2.257 2.440 nonbonded pdb=" O SER H 327 " pdb=" OG SER H 327 " model vdw 2.257 2.440 nonbonded pdb=" O SER G 327 " pdb=" OG SER G 327 " model vdw 2.257 2.440 nonbonded pdb=" O SER E 327 " pdb=" OG SER E 327 " model vdw 2.257 2.440 nonbonded pdb=" O SER D 327 " pdb=" OG SER D 327 " model vdw 2.258 2.440 ... (remaining 195296 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 7.920 Check model and map are aligned: 0.330 Set scattering table: 0.210 Process input model: 60.000 Find NCS groups from input model: 1.600 Set up NCS constraints: 0.180 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 75.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 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 : 0.012 0.230 23480 Z= 0.816 Angle : 1.357 16.360 31792 Z= 0.677 Chirality : 0.066 0.354 3656 Planarity : 0.007 0.056 4000 Dihedral : 15.528 88.405 8856 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 9.06 % Allowed : 8.05 % Favored : 82.89 % 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: -4.07 (0.12), residues: 2960 helix: -3.47 (0.10), residues: 1064 sheet: -2.58 (0.18), residues: 456 loop : -1.97 (0.15), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS G 92 PHE 0.019 0.003 PHE B 401 TYR 0.019 0.003 TYR H 484 ARG 0.024 0.002 ARG C 407 *********************** 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 1478 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1262 time to evaluate : 2.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8607 (m-30) cc_final: 0.8120 (m-30) REVERT: A 42 ILE cc_start: 0.8958 (pp) cc_final: 0.8739 (pt) REVERT: A 105 ARG cc_start: 0.9037 (mtm110) cc_final: 0.8677 (mtm110) REVERT: A 109 LYS cc_start: 0.9327 (mttp) cc_final: 0.9037 (mttt) REVERT: A 275 SER cc_start: 0.9145 (t) cc_final: 0.8857 (t) REVERT: A 276 SER cc_start: 0.8619 (p) cc_final: 0.8362 (p) REVERT: A 285 ASN cc_start: 0.9359 (m-40) cc_final: 0.9009 (m-40) REVERT: A 352 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8551 (tm-30) REVERT: A 395 GLU cc_start: 0.8753 (mp0) cc_final: 0.7955 (mp0) REVERT: A 399 GLU cc_start: 0.8555 (pm20) cc_final: 0.8294 (pm20) REVERT: A 404 ASP cc_start: 0.8922 (t0) cc_final: 0.8599 (t0) REVERT: B 25 ASN cc_start: 0.9039 (m110) cc_final: 0.8822 (p0) REVERT: B 28 ASP cc_start: 0.8633 (m-30) cc_final: 0.8182 (m-30) REVERT: B 50 ASP cc_start: 0.8853 (t70) cc_final: 0.8577 (t70) REVERT: B 105 ARG cc_start: 0.9104 (mtm110) cc_final: 0.8763 (mtm110) REVERT: B 106 LYS cc_start: 0.9576 (mtpt) cc_final: 0.9173 (mtpp) REVERT: B 109 LYS cc_start: 0.9364 (mttp) cc_final: 0.9106 (mttt) REVERT: B 274 ASP cc_start: 0.8815 (t0) cc_final: 0.8562 (t0) REVERT: B 276 SER cc_start: 0.8583 (p) cc_final: 0.8343 (p) REVERT: B 281 ILE cc_start: 0.9093 (tp) cc_final: 0.8879 (tp) REVERT: B 285 ASN cc_start: 0.9345 (m-40) cc_final: 0.9143 (m-40) REVERT: B 313 LEU cc_start: 0.9393 (mt) cc_final: 0.9130 (mp) REVERT: B 352 GLU cc_start: 0.9020 (tm-30) cc_final: 0.8602 (tm-30) REVERT: B 395 GLU cc_start: 0.8812 (mp0) cc_final: 0.8116 (mp0) REVERT: B 399 GLU cc_start: 0.8567 (pm20) cc_final: 0.8336 (pm20) REVERT: B 400 TYR cc_start: 0.8116 (m-80) cc_final: 0.7864 (m-80) REVERT: B 404 ASP cc_start: 0.8929 (t0) cc_final: 0.8588 (t0) REVERT: C 28 ASP cc_start: 0.8626 (m-30) cc_final: 0.8172 (m-30) REVERT: C 50 ASP cc_start: 0.8882 (t70) cc_final: 0.8667 (t70) REVERT: C 93 HIS cc_start: 0.9315 (p-80) cc_final: 0.9064 (p90) REVERT: C 105 ARG cc_start: 0.9010 (mtm110) cc_final: 0.8809 (mtm110) REVERT: C 109 LYS cc_start: 0.9343 (mttp) cc_final: 0.8537 (tptt) REVERT: C 259 ARG cc_start: 0.9026 (mtp85) cc_final: 0.8702 (ttm-80) REVERT: C 276 SER cc_start: 0.8550 (p) cc_final: 0.8259 (p) REVERT: C 284 ILE cc_start: 0.9259 (OUTLIER) cc_final: 0.9057 (pp) REVERT: C 285 ASN cc_start: 0.9364 (m-40) cc_final: 0.9021 (m-40) REVERT: C 352 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8517 (tm-30) REVERT: C 395 GLU cc_start: 0.8717 (mp0) cc_final: 0.7976 (mp0) REVERT: C 399 GLU cc_start: 0.8520 (pm20) cc_final: 0.8273 (pm20) REVERT: C 404 ASP cc_start: 0.8926 (t0) cc_final: 0.8574 (t0) REVERT: D 28 ASP cc_start: 0.8619 (m-30) cc_final: 0.8136 (m-30) REVERT: D 42 ILE cc_start: 0.9050 (pp) cc_final: 0.8841 (pt) REVERT: D 50 ASP cc_start: 0.8855 (t70) cc_final: 0.8601 (t70) REVERT: D 84 LEU cc_start: 0.8648 (mm) cc_final: 0.8332 (tp) REVERT: D 106 LYS cc_start: 0.9634 (mtpt) cc_final: 0.9247 (mtpp) REVERT: D 108 LYS cc_start: 0.9548 (OUTLIER) cc_final: 0.9337 (mttm) REVERT: D 109 LYS cc_start: 0.9352 (mttp) cc_final: 0.8715 (tptt) REVERT: D 275 SER cc_start: 0.9145 (t) cc_final: 0.8847 (t) REVERT: D 276 SER cc_start: 0.8599 (p) cc_final: 0.8301 (p) REVERT: D 285 ASN cc_start: 0.9375 (m-40) cc_final: 0.9038 (m-40) REVERT: D 352 GLU cc_start: 0.8960 (tm-30) cc_final: 0.8519 (tm-30) REVERT: D 368 GLN cc_start: 0.9008 (mt0) cc_final: 0.8514 (mp10) REVERT: D 395 GLU cc_start: 0.8841 (mp0) cc_final: 0.8082 (mp0) REVERT: D 399 GLU cc_start: 0.8541 (pm20) cc_final: 0.8272 (pm20) REVERT: D 400 TYR cc_start: 0.8114 (m-80) cc_final: 0.7626 (m-80) REVERT: D 404 ASP cc_start: 0.8879 (t0) cc_final: 0.8576 (t0) REVERT: E 28 ASP cc_start: 0.8644 (m-30) cc_final: 0.8180 (m-30) REVERT: E 91 ILE cc_start: 0.8356 (mp) cc_final: 0.8154 (mp) REVERT: E 105 ARG cc_start: 0.9009 (mtm110) cc_final: 0.8796 (mtm110) REVERT: E 109 LYS cc_start: 0.9325 (mttp) cc_final: 0.8559 (tptt) REVERT: E 276 SER cc_start: 0.8599 (p) cc_final: 0.8354 (p) REVERT: E 285 ASN cc_start: 0.9343 (m-40) cc_final: 0.9004 (m-40) REVERT: E 352 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8496 (tm-30) REVERT: E 368 GLN cc_start: 0.9006 (mt0) cc_final: 0.8425 (mp10) REVERT: E 395 GLU cc_start: 0.8722 (mp0) cc_final: 0.7922 (mp0) REVERT: E 399 GLU cc_start: 0.8591 (pm20) cc_final: 0.8315 (pm20) REVERT: E 404 ASP cc_start: 0.8968 (t0) cc_final: 0.8624 (t0) REVERT: E 482 MET cc_start: 0.8964 (mtp) cc_final: 0.8705 (mtp) REVERT: F 28 ASP cc_start: 0.8611 (m-30) cc_final: 0.8112 (m-30) REVERT: F 50 ASP cc_start: 0.8882 (t70) cc_final: 0.8629 (t70) REVERT: F 84 LEU cc_start: 0.8760 (mm) cc_final: 0.8407 (tp) REVERT: F 98 GLU cc_start: 0.9347 (mp0) cc_final: 0.9106 (mp0) REVERT: F 108 LYS cc_start: 0.9564 (OUTLIER) cc_final: 0.9351 (mttm) REVERT: F 109 LYS cc_start: 0.9356 (mttp) cc_final: 0.9095 (mttm) REVERT: F 276 SER cc_start: 0.8565 (p) cc_final: 0.8326 (p) REVERT: F 281 ILE cc_start: 0.9082 (tp) cc_final: 0.8713 (tp) REVERT: F 285 ASN cc_start: 0.9296 (m-40) cc_final: 0.8982 (m110) REVERT: F 352 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8662 (tm-30) REVERT: F 368 GLN cc_start: 0.8986 (mt0) cc_final: 0.8453 (mp10) REVERT: F 395 GLU cc_start: 0.8842 (mp0) cc_final: 0.8137 (mp0) REVERT: F 399 GLU cc_start: 0.8650 (pm20) cc_final: 0.8330 (pm20) REVERT: F 404 ASP cc_start: 0.8959 (t0) cc_final: 0.8649 (t0) REVERT: F 482 MET cc_start: 0.8900 (mtp) cc_final: 0.8635 (mtp) REVERT: G 28 ASP cc_start: 0.8672 (m-30) cc_final: 0.8218 (m-30) REVERT: G 50 ASP cc_start: 0.8817 (t70) cc_final: 0.8577 (t0) REVERT: G 93 HIS cc_start: 0.9352 (p-80) cc_final: 0.9128 (p90) REVERT: G 98 GLU cc_start: 0.9286 (mp0) cc_final: 0.9051 (mp0) REVERT: G 108 LYS cc_start: 0.9630 (OUTLIER) cc_final: 0.9406 (mttm) REVERT: G 109 LYS cc_start: 0.9314 (mttp) cc_final: 0.8811 (tptt) REVERT: G 261 ASP cc_start: 0.9392 (p0) cc_final: 0.9154 (p0) REVERT: G 275 SER cc_start: 0.9061 (t) cc_final: 0.8741 (t) REVERT: G 276 SER cc_start: 0.8709 (p) cc_final: 0.8431 (p) REVERT: G 281 ILE cc_start: 0.9291 (tp) cc_final: 0.8928 (tp) REVERT: G 285 ASN cc_start: 0.9335 (m-40) cc_final: 0.8961 (m-40) REVERT: G 352 GLU cc_start: 0.8935 (tm-30) cc_final: 0.8486 (tm-30) REVERT: G 395 GLU cc_start: 0.8755 (mp0) cc_final: 0.7978 (mp0) REVERT: G 399 GLU cc_start: 0.8459 (pm20) cc_final: 0.8211 (pm20) REVERT: G 404 ASP cc_start: 0.8977 (t0) cc_final: 0.8606 (t0) REVERT: G 482 MET cc_start: 0.9001 (mtp) cc_final: 0.8758 (mtp) REVERT: H 25 ASN cc_start: 0.9057 (m110) cc_final: 0.8830 (p0) REVERT: H 28 ASP cc_start: 0.8708 (m-30) cc_final: 0.8264 (m-30) REVERT: H 50 ASP cc_start: 0.8832 (t70) cc_final: 0.8563 (t70) REVERT: H 84 LEU cc_start: 0.8553 (mm) cc_final: 0.8239 (tp) REVERT: H 98 GLU cc_start: 0.9370 (mp0) cc_final: 0.9124 (mp0) REVERT: H 105 ARG cc_start: 0.9143 (mtm110) cc_final: 0.8810 (mtm110) REVERT: H 106 LYS cc_start: 0.9586 (mtpt) cc_final: 0.9221 (mtpp) REVERT: H 109 LYS cc_start: 0.9339 (mttp) cc_final: 0.9109 (mttt) REVERT: H 274 ASP cc_start: 0.8788 (t0) cc_final: 0.8547 (t0) REVERT: H 276 SER cc_start: 0.8614 (p) cc_final: 0.8276 (p) REVERT: H 281 ILE cc_start: 0.9197 (tp) cc_final: 0.8989 (tp) REVERT: H 285 ASN cc_start: 0.9406 (m-40) cc_final: 0.9184 (m110) REVERT: H 352 GLU cc_start: 0.9047 (tm-30) cc_final: 0.8654 (tm-30) REVERT: H 395 GLU cc_start: 0.8790 (mp0) cc_final: 0.8073 (mp0) REVERT: H 399 GLU cc_start: 0.8502 (pm20) cc_final: 0.8277 (pm20) REVERT: H 400 TYR cc_start: 0.8104 (m-80) cc_final: 0.7875 (m-80) REVERT: H 404 ASP cc_start: 0.8928 (t0) cc_final: 0.8582 (t0) REVERT: H 482 MET cc_start: 0.8871 (mtp) cc_final: 0.8605 (mtp) outliers start: 216 outliers final: 108 residues processed: 1332 average time/residue: 0.3284 time to fit residues: 683.8143 Evaluate side-chains 1053 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 941 time to evaluate : 2.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 66 VAL Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 78 MET Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 254 GLU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 386 MET Chi-restraints excluded: chain A residue 479 VAL Chi-restraints excluded: chain A residue 505 SER Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 56 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 250 ILE Chi-restraints excluded: chain B residue 254 GLU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 290 ILE Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 386 MET Chi-restraints excluded: chain B residue 479 VAL Chi-restraints excluded: chain B residue 505 SER Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 284 ILE Chi-restraints excluded: chain C residue 290 ILE Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 386 MET Chi-restraints excluded: chain C residue 479 VAL Chi-restraints excluded: chain C residue 505 SER Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 51 LEU 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 108 LYS Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 254 GLU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 290 ILE Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 386 MET Chi-restraints excluded: chain D residue 479 VAL Chi-restraints excluded: chain D residue 505 SER Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 254 GLU Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 290 ILE Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 386 MET Chi-restraints excluded: chain E residue 479 VAL Chi-restraints excluded: chain E residue 505 SER Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 108 LYS Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 254 GLU Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 290 ILE Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 386 MET Chi-restraints excluded: chain F residue 479 VAL Chi-restraints excluded: chain F residue 505 SER Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 254 GLU Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 290 ILE Chi-restraints excluded: chain G residue 327 SER Chi-restraints excluded: chain G residue 386 MET Chi-restraints excluded: chain G residue 479 VAL Chi-restraints excluded: chain G residue 505 SER Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 78 MET Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 254 GLU Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 290 ILE Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 386 MET Chi-restraints excluded: chain H residue 479 VAL Chi-restraints excluded: chain H residue 505 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 249 optimal weight: 2.9990 chunk 224 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 76 optimal weight: 2.9990 chunk 151 optimal weight: 0.8980 chunk 119 optimal weight: 0.7980 chunk 232 optimal weight: 0.3980 chunk 89 optimal weight: 0.9980 chunk 141 optimal weight: 1.9990 chunk 172 optimal weight: 0.5980 chunk 268 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 25 ASN A 48 GLN A 93 HIS A 243 GLN A 277 GLN A 285 ASN A 303 ASN A 309 GLN A 312 ASN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 22 GLN B 25 ASN B 48 GLN B 243 GLN B 277 GLN B 285 ASN B 303 ASN B 309 GLN B 312 ASN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 22 GLN C 25 ASN C 48 GLN C 243 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN D 25 ASN D 48 GLN D 93 HIS D 243 GLN D 277 GLN D 285 ASN D 303 ASN D 309 GLN D 312 ASN ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 GLN E 25 ASN E 48 GLN E 93 HIS E 243 GLN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 ASN ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN F 48 GLN F 93 HIS F 243 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 ASN F 303 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN F 441 GLN ** F 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 22 GLN G 48 GLN G 243 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 ASN G 303 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 498 GLN H 22 GLN H 25 ASN H 48 GLN H 93 HIS H 243 GLN ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 285 ASN H 303 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 312 ASN ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 64 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 23480 Z= 0.232 Angle : 0.677 8.362 31792 Z= 0.340 Chirality : 0.045 0.170 3656 Planarity : 0.005 0.045 4000 Dihedral : 12.906 89.515 3925 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 13.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 7.38 % Allowed : 19.25 % Favored : 73.36 % 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: -3.09 (0.13), residues: 2960 helix: -2.22 (0.13), residues: 1048 sheet: -2.56 (0.19), residues: 456 loop : -1.61 (0.15), residues: 1456 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS B 253 PHE 0.015 0.001 PHE A 24 TYR 0.019 0.002 TYR D 411 ARG 0.007 0.001 ARG F 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 1222 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 1046 time to evaluate : 2.705 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8642 (m-30) cc_final: 0.8300 (m-30) REVERT: A 50 ASP cc_start: 0.8952 (t0) cc_final: 0.8727 (t0) REVERT: A 51 LEU cc_start: 0.9394 (OUTLIER) cc_final: 0.9100 (pp) REVERT: A 58 LYS cc_start: 0.9302 (mmtp) cc_final: 0.9038 (mmmm) REVERT: A 98 GLU cc_start: 0.9415 (mp0) cc_final: 0.9205 (mp0) REVERT: A 105 ARG cc_start: 0.8981 (mtm110) cc_final: 0.8754 (mtm110) REVERT: A 109 LYS cc_start: 0.9294 (mttp) cc_final: 0.8624 (tptt) REVERT: A 239 ASP cc_start: 0.7904 (OUTLIER) cc_final: 0.7267 (p0) REVERT: A 275 SER cc_start: 0.9111 (t) cc_final: 0.8886 (t) REVERT: A 276 SER cc_start: 0.8442 (p) cc_final: 0.8171 (p) REVERT: A 281 ILE cc_start: 0.9034 (tp) cc_final: 0.8367 (tp) REVERT: A 285 ASN cc_start: 0.9336 (m110) cc_final: 0.8950 (m-40) REVERT: A 352 GLU cc_start: 0.8928 (tm-30) cc_final: 0.8605 (tm-30) REVERT: A 355 ARG cc_start: 0.9522 (ptm-80) cc_final: 0.9082 (ptm-80) REVERT: A 362 ILE cc_start: 0.8377 (mt) cc_final: 0.8137 (mt) REVERT: A 368 GLN cc_start: 0.9040 (mt0) cc_final: 0.8582 (mp10) REVERT: A 395 GLU cc_start: 0.8500 (mp0) cc_final: 0.8100 (mp0) REVERT: A 399 GLU cc_start: 0.8519 (pm20) cc_final: 0.8266 (mp0) REVERT: A 400 TYR cc_start: 0.8205 (m-80) cc_final: 0.6954 (m-10) REVERT: A 404 ASP cc_start: 0.8825 (t0) cc_final: 0.8480 (t0) REVERT: A 407 ARG cc_start: 0.8773 (ttt-90) cc_final: 0.7679 (ttt-90) REVERT: A 449 ASP cc_start: 0.9190 (p0) cc_final: 0.8773 (p0) REVERT: A 461 ILE cc_start: 0.9109 (pp) cc_final: 0.8813 (mt) REVERT: A 482 MET cc_start: 0.9107 (mtp) cc_final: 0.8733 (mtp) REVERT: A 512 ARG cc_start: 0.7845 (ttm-80) cc_final: 0.7581 (ptm160) REVERT: B 25 ASN cc_start: 0.9004 (m-40) cc_final: 0.8779 (p0) REVERT: B 28 ASP cc_start: 0.8657 (m-30) cc_final: 0.8306 (m-30) REVERT: B 58 LYS cc_start: 0.9393 (mmtp) cc_final: 0.9142 (mmmm) REVERT: B 105 ARG cc_start: 0.9039 (mtm110) cc_final: 0.8819 (mtm110) REVERT: B 109 LYS cc_start: 0.9334 (mttp) cc_final: 0.9020 (mttm) REVERT: B 239 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7319 (p0) REVERT: B 276 SER cc_start: 0.8568 (p) cc_final: 0.8270 (p) REVERT: B 281 ILE cc_start: 0.8947 (tp) cc_final: 0.8331 (tt) REVERT: B 285 ASN cc_start: 0.9329 (m110) cc_final: 0.8947 (m-40) REVERT: B 352 GLU cc_start: 0.8949 (tm-30) cc_final: 0.8620 (tm-30) REVERT: B 355 ARG cc_start: 0.9508 (ptm-80) cc_final: 0.9069 (ptm-80) REVERT: B 368 GLN cc_start: 0.8955 (mt0) cc_final: 0.8432 (mp10) REVERT: B 395 GLU cc_start: 0.8567 (mp0) cc_final: 0.8210 (mp0) REVERT: B 399 GLU cc_start: 0.8545 (pm20) cc_final: 0.8312 (mp0) REVERT: B 404 ASP cc_start: 0.8887 (t0) cc_final: 0.8593 (t0) REVERT: B 461 ILE cc_start: 0.9152 (pp) cc_final: 0.8922 (pp) REVERT: B 482 MET cc_start: 0.9017 (mtp) cc_final: 0.8705 (mtp) REVERT: B 512 ARG cc_start: 0.7919 (ttm-80) cc_final: 0.7662 (ptm160) REVERT: C 28 ASP cc_start: 0.8694 (m-30) cc_final: 0.8349 (m-30) REVERT: C 50 ASP cc_start: 0.8865 (t70) cc_final: 0.8653 (t0) REVERT: C 58 LYS cc_start: 0.9289 (mmtp) cc_final: 0.9070 (mmmm) REVERT: C 98 GLU cc_start: 0.9389 (mp0) cc_final: 0.9171 (mp0) REVERT: C 109 LYS cc_start: 0.9295 (mttp) cc_final: 0.8976 (mttm) REVERT: C 239 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7484 (p0) REVERT: C 276 SER cc_start: 0.8373 (p) cc_final: 0.8071 (p) REVERT: C 281 ILE cc_start: 0.9002 (tp) cc_final: 0.8763 (tt) REVERT: C 285 ASN cc_start: 0.9346 (m-40) cc_final: 0.9141 (m-40) REVERT: C 368 GLN cc_start: 0.8992 (mt0) cc_final: 0.8531 (mp10) REVERT: C 395 GLU cc_start: 0.8482 (mp0) cc_final: 0.8097 (mp0) REVERT: C 399 GLU cc_start: 0.8517 (pm20) cc_final: 0.8262 (mp0) REVERT: C 400 TYR cc_start: 0.8205 (m-80) cc_final: 0.7623 (m-10) REVERT: C 404 ASP cc_start: 0.8900 (t0) cc_final: 0.8606 (t0) REVERT: C 407 ARG cc_start: 0.8744 (ttt-90) cc_final: 0.8081 (ttt-90) REVERT: C 449 ASP cc_start: 0.9126 (p0) cc_final: 0.8847 (p0) REVERT: C 482 MET cc_start: 0.9096 (mtp) cc_final: 0.8713 (mtp) REVERT: D 28 ASP cc_start: 0.8664 (m-30) cc_final: 0.8265 (m-30) REVERT: D 58 LYS cc_start: 0.9378 (mmtp) cc_final: 0.9166 (mmmm) REVERT: D 105 ARG cc_start: 0.9084 (mtm110) cc_final: 0.8688 (mtm110) REVERT: D 239 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7532 (p0) REVERT: D 275 SER cc_start: 0.9092 (t) cc_final: 0.8869 (t) REVERT: D 276 SER cc_start: 0.8374 (p) cc_final: 0.8153 (p) REVERT: D 281 ILE cc_start: 0.8973 (tp) cc_final: 0.8350 (tt) REVERT: D 285 ASN cc_start: 0.9315 (m110) cc_final: 0.8954 (m-40) REVERT: D 352 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8558 (tm-30) REVERT: D 355 ARG cc_start: 0.9494 (ptm-80) cc_final: 0.9087 (ptm-80) REVERT: D 362 ILE cc_start: 0.8535 (mt) cc_final: 0.8323 (mt) REVERT: D 385 MET cc_start: 0.8902 (ttm) cc_final: 0.8464 (ttp) REVERT: D 395 GLU cc_start: 0.8603 (mp0) cc_final: 0.8178 (mp0) REVERT: D 399 GLU cc_start: 0.8569 (pm20) cc_final: 0.8259 (pm20) REVERT: D 404 ASP cc_start: 0.8787 (t0) cc_final: 0.8456 (t0) REVERT: D 461 ILE cc_start: 0.9128 (pp) cc_final: 0.8892 (pp) REVERT: D 482 MET cc_start: 0.9012 (mtp) cc_final: 0.8704 (mtp) REVERT: E 28 ASP cc_start: 0.8713 (m-30) cc_final: 0.8309 (m-30) REVERT: E 51 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9166 (pp) REVERT: E 105 ARG cc_start: 0.8983 (mtm110) cc_final: 0.8758 (mtm110) REVERT: E 109 LYS cc_start: 0.9275 (mttp) cc_final: 0.8601 (tptt) REVERT: E 276 SER cc_start: 0.8382 (p) cc_final: 0.8046 (p) REVERT: E 281 ILE cc_start: 0.8927 (tp) cc_final: 0.8481 (tt) REVERT: E 285 ASN cc_start: 0.9291 (m-40) cc_final: 0.9017 (m-40) REVERT: E 299 VAL cc_start: 0.9441 (m) cc_final: 0.9239 (p) REVERT: E 352 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8609 (tm-30) REVERT: E 355 ARG cc_start: 0.9520 (ptm-80) cc_final: 0.9137 (ptm-80) REVERT: E 386 MET cc_start: 0.8952 (mtm) cc_final: 0.8542 (mtm) REVERT: E 395 GLU cc_start: 0.8496 (mp0) cc_final: 0.7964 (mp0) REVERT: E 399 GLU cc_start: 0.8564 (pm20) cc_final: 0.8297 (pm20) REVERT: E 400 TYR cc_start: 0.8199 (m-80) cc_final: 0.7936 (m-10) REVERT: E 404 ASP cc_start: 0.8924 (t0) cc_final: 0.8667 (t70) REVERT: E 482 MET cc_start: 0.8992 (mtp) cc_final: 0.8684 (mtp) REVERT: E 512 ARG cc_start: 0.7856 (ttm-80) cc_final: 0.7536 (ttm-80) REVERT: F 28 ASP cc_start: 0.8661 (m-30) cc_final: 0.8275 (m-30) REVERT: F 105 ARG cc_start: 0.9070 (mtm110) cc_final: 0.8682 (mtm110) REVERT: F 239 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7513 (p0) REVERT: F 276 SER cc_start: 0.8459 (p) cc_final: 0.8230 (p) REVERT: F 281 ILE cc_start: 0.9029 (tp) cc_final: 0.8730 (tt) REVERT: F 285 ASN cc_start: 0.9296 (m110) cc_final: 0.9037 (m110) REVERT: F 352 GLU cc_start: 0.8849 (tm-30) cc_final: 0.8576 (tm-30) REVERT: F 395 GLU cc_start: 0.8687 (mp0) cc_final: 0.8086 (mp0) REVERT: F 399 GLU cc_start: 0.8648 (pm20) cc_final: 0.8325 (pm20) REVERT: F 400 TYR cc_start: 0.8109 (m-80) cc_final: 0.7819 (m-80) REVERT: F 404 ASP cc_start: 0.8919 (t0) cc_final: 0.8649 (t0) REVERT: F 461 ILE cc_start: 0.9136 (pp) cc_final: 0.8926 (pp) REVERT: F 482 MET cc_start: 0.8945 (mtp) cc_final: 0.8602 (mtp) REVERT: F 512 ARG cc_start: 0.7794 (ttm-80) cc_final: 0.7299 (ptm160) REVERT: G 28 ASP cc_start: 0.8740 (m-30) cc_final: 0.8433 (m-30) REVERT: G 51 LEU cc_start: 0.9450 (OUTLIER) cc_final: 0.9197 (pp) REVERT: G 58 LYS cc_start: 0.9305 (mmtp) cc_final: 0.9007 (mmmm) REVERT: G 105 ARG cc_start: 0.8982 (mtm110) cc_final: 0.8317 (mtm110) REVERT: G 106 LYS cc_start: 0.9560 (mtpt) cc_final: 0.9342 (ttpt) REVERT: G 108 LYS cc_start: 0.9613 (OUTLIER) cc_final: 0.9401 (mttm) REVERT: G 239 ASP cc_start: 0.8349 (OUTLIER) cc_final: 0.7162 (p0) REVERT: G 275 SER cc_start: 0.9026 (t) cc_final: 0.8771 (t) REVERT: G 276 SER cc_start: 0.8393 (p) cc_final: 0.8182 (p) REVERT: G 281 ILE cc_start: 0.9180 (tp) cc_final: 0.8505 (tp) REVERT: G 285 ASN cc_start: 0.9321 (m110) cc_final: 0.8937 (m-40) REVERT: G 352 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8583 (tm-30) REVERT: G 355 ARG cc_start: 0.9504 (ptm-80) cc_final: 0.9100 (ptm-80) REVERT: G 395 GLU cc_start: 0.8589 (mp0) cc_final: 0.8089 (mp0) REVERT: G 399 GLU cc_start: 0.8463 (pm20) cc_final: 0.8169 (pm20) REVERT: G 404 ASP cc_start: 0.8886 (t0) cc_final: 0.8575 (t70) REVERT: G 482 MET cc_start: 0.9010 (mtp) cc_final: 0.8699 (mtp) REVERT: G 512 ARG cc_start: 0.7663 (ttm-80) cc_final: 0.7450 (ptm160) REVERT: H 28 ASP cc_start: 0.8755 (m-30) cc_final: 0.8370 (m-30) REVERT: H 51 LEU cc_start: 0.9406 (OUTLIER) cc_final: 0.9104 (pp) REVERT: H 58 LYS cc_start: 0.9403 (mmtp) cc_final: 0.9145 (mmmm) REVERT: H 105 ARG cc_start: 0.9098 (mtm110) cc_final: 0.8702 (mtm110) REVERT: H 109 LYS cc_start: 0.9313 (mttp) cc_final: 0.9066 (mttt) REVERT: H 256 ASP cc_start: 0.9137 (m-30) cc_final: 0.8925 (p0) REVERT: H 276 SER cc_start: 0.8452 (p) cc_final: 0.8184 (p) REVERT: H 281 ILE cc_start: 0.9030 (tp) cc_final: 0.8464 (tp) REVERT: H 285 ASN cc_start: 0.9379 (m110) cc_final: 0.9019 (m-40) REVERT: H 286 MET cc_start: 0.9410 (tpp) cc_final: 0.8771 (tpp) REVERT: H 299 VAL cc_start: 0.9331 (m) cc_final: 0.9109 (p) REVERT: H 352 GLU cc_start: 0.8990 (tm-30) cc_final: 0.8671 (tm-30) REVERT: H 355 ARG cc_start: 0.9495 (ptm-80) cc_final: 0.9079 (ptm-80) REVERT: H 395 GLU cc_start: 0.8550 (mp0) cc_final: 0.8211 (mp0) REVERT: H 399 GLU cc_start: 0.8484 (pm20) cc_final: 0.8244 (pm20) REVERT: H 404 ASP cc_start: 0.8848 (t0) cc_final: 0.8507 (t0) REVERT: H 461 ILE cc_start: 0.9045 (pp) cc_final: 0.8715 (mt) REVERT: H 482 MET cc_start: 0.8963 (mtp) cc_final: 0.8714 (mtp) outliers start: 176 outliers final: 79 residues processed: 1111 average time/residue: 0.3253 time to fit residues: 562.1386 Evaluate side-chains 1018 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 928 time to evaluate : 2.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 49 VAL Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 239 ASP Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 239 ASP Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 260 LEU Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 239 ASP Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 239 ASP Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 260 LEU Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 49 VAL Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 239 ASP Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 260 LEU Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 108 LYS Chi-restraints excluded: chain G residue 239 ASP Chi-restraints excluded: chain G residue 245 LEU Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 296 ASN Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 49 VAL Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 239 ASP Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 260 LEU Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 149 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 223 optimal weight: 0.6980 chunk 183 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 269 optimal weight: 3.9990 chunk 290 optimal weight: 5.9990 chunk 239 optimal weight: 3.9990 chunk 267 optimal weight: 1.9990 chunk 91 optimal weight: 0.3980 chunk 216 optimal weight: 3.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 GLN A 312 ASN ** A 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN B 22 GLN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN C 22 GLN ** C 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 22 GLN ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 GLN ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 ASN ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN F 469 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 ASN ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 441 GLN ** G 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 GLN ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 334 GLN ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.3022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 23480 Z= 0.324 Angle : 0.667 7.852 31792 Z= 0.339 Chirality : 0.046 0.166 3656 Planarity : 0.004 0.042 4000 Dihedral : 11.493 89.542 3799 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 7.09 % Allowed : 20.72 % Favored : 72.19 % 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: -2.48 (0.14), residues: 2960 helix: -1.63 (0.14), residues: 1072 sheet: -2.33 (0.22), residues: 408 loop : -1.33 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 454 PHE 0.012 0.001 PHE D 401 TYR 0.020 0.002 TYR D 400 ARG 0.011 0.001 ARG F 407 *********************** 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 1122 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 953 time to evaluate : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8658 (m-30) cc_final: 0.8325 (m-30) REVERT: A 51 LEU cc_start: 0.9377 (OUTLIER) cc_final: 0.8977 (pp) REVERT: A 105 ARG cc_start: 0.9026 (mtm110) cc_final: 0.8585 (mtm110) REVERT: A 109 LYS cc_start: 0.9315 (mttp) cc_final: 0.9103 (mptt) REVERT: A 276 SER cc_start: 0.8755 (p) cc_final: 0.8452 (p) REVERT: A 352 GLU cc_start: 0.9041 (tm-30) cc_final: 0.8753 (tm-30) REVERT: A 385 MET cc_start: 0.8918 (ttm) cc_final: 0.8693 (ttm) REVERT: A 395 GLU cc_start: 0.8672 (mp0) cc_final: 0.8130 (mp0) REVERT: A 404 ASP cc_start: 0.8909 (t0) cc_final: 0.8571 (t70) REVERT: A 406 ILE cc_start: 0.9097 (mp) cc_final: 0.8797 (mp) REVERT: A 414 MET cc_start: 0.9442 (mpt) cc_final: 0.9173 (mpt) REVERT: A 482 MET cc_start: 0.9097 (mtp) cc_final: 0.8800 (mtp) REVERT: B 28 ASP cc_start: 0.8688 (m-30) cc_final: 0.8360 (m-30) REVERT: B 51 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9075 (pp) REVERT: B 58 LYS cc_start: 0.9425 (mmtp) cc_final: 0.9051 (mmmm) REVERT: B 105 ARG cc_start: 0.9094 (mtm110) cc_final: 0.8751 (mtm110) REVERT: B 109 LYS cc_start: 0.9339 (mttp) cc_final: 0.8984 (mttt) REVERT: B 276 SER cc_start: 0.8857 (p) cc_final: 0.8625 (p) REVERT: B 352 GLU cc_start: 0.9066 (tm-30) cc_final: 0.8763 (tm-30) REVERT: B 385 MET cc_start: 0.8830 (ttm) cc_final: 0.8585 (ttm) REVERT: B 395 GLU cc_start: 0.8736 (mp0) cc_final: 0.8223 (mp0) REVERT: B 399 GLU cc_start: 0.8613 (pm20) cc_final: 0.8324 (pm20) REVERT: B 404 ASP cc_start: 0.8941 (t0) cc_final: 0.8661 (t0) REVERT: B 414 MET cc_start: 0.9462 (mpt) cc_final: 0.9238 (mpt) REVERT: C 28 ASP cc_start: 0.8716 (m-30) cc_final: 0.8414 (m-30) REVERT: C 51 LEU cc_start: 0.9412 (OUTLIER) cc_final: 0.9081 (pp) REVERT: C 105 ARG cc_start: 0.9055 (mtm110) cc_final: 0.8632 (mtm110) REVERT: C 109 LYS cc_start: 0.9294 (mttp) cc_final: 0.9060 (mptt) REVERT: C 276 SER cc_start: 0.8543 (p) cc_final: 0.8187 (p) REVERT: C 352 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8734 (tm-30) REVERT: C 385 MET cc_start: 0.8870 (ttm) cc_final: 0.8613 (ttm) REVERT: C 395 GLU cc_start: 0.8688 (mp0) cc_final: 0.8265 (mp0) REVERT: C 404 ASP cc_start: 0.8959 (t0) cc_final: 0.8698 (t70) REVERT: C 414 MET cc_start: 0.9423 (mpt) cc_final: 0.9160 (mpt) REVERT: C 438 LYS cc_start: 0.8329 (mmtt) cc_final: 0.7958 (mmtm) REVERT: C 482 MET cc_start: 0.9083 (mtp) cc_final: 0.8783 (mtp) REVERT: D 28 ASP cc_start: 0.8660 (m-30) cc_final: 0.8319 (m-30) REVERT: D 51 LEU cc_start: 0.9357 (OUTLIER) cc_final: 0.8987 (pp) REVERT: D 58 LYS cc_start: 0.9420 (mmtp) cc_final: 0.9080 (mmmm) REVERT: D 105 ARG cc_start: 0.9027 (mtm110) cc_final: 0.8767 (mtm110) REVERT: D 109 LYS cc_start: 0.9352 (mttt) cc_final: 0.9064 (mttt) REVERT: D 276 SER cc_start: 0.8738 (p) cc_final: 0.8453 (p) REVERT: D 319 ASP cc_start: 0.8570 (m-30) cc_final: 0.8322 (m-30) REVERT: D 385 MET cc_start: 0.8962 (ttm) cc_final: 0.8464 (ttm) REVERT: D 395 GLU cc_start: 0.8761 (mp0) cc_final: 0.8223 (mp0) REVERT: D 399 GLU cc_start: 0.8631 (pm20) cc_final: 0.8343 (pm20) REVERT: D 404 ASP cc_start: 0.8877 (t0) cc_final: 0.8543 (t0) REVERT: D 414 MET cc_start: 0.9454 (mpt) cc_final: 0.9246 (mpt) REVERT: D 438 LYS cc_start: 0.8384 (mmtt) cc_final: 0.8000 (mmtm) REVERT: E 28 ASP cc_start: 0.8736 (m-30) cc_final: 0.8408 (m-30) REVERT: E 51 LEU cc_start: 0.9443 (OUTLIER) cc_final: 0.9078 (pp) REVERT: E 105 ARG cc_start: 0.9023 (mtm110) cc_final: 0.8799 (mtm110) REVERT: E 109 LYS cc_start: 0.9324 (mttp) cc_final: 0.8934 (tmtt) REVERT: E 276 SER cc_start: 0.8726 (p) cc_final: 0.8411 (p) REVERT: E 352 GLU cc_start: 0.9005 (tm-30) cc_final: 0.8724 (tm-30) REVERT: E 385 MET cc_start: 0.8731 (ttm) cc_final: 0.8505 (ttm) REVERT: E 386 MET cc_start: 0.8863 (mtm) cc_final: 0.8382 (mtm) REVERT: E 395 GLU cc_start: 0.8670 (mp0) cc_final: 0.8222 (mp0) REVERT: E 399 GLU cc_start: 0.8670 (pm20) cc_final: 0.8386 (pm20) REVERT: E 404 ASP cc_start: 0.8979 (t0) cc_final: 0.8735 (t70) REVERT: E 414 MET cc_start: 0.9411 (mpt) cc_final: 0.9194 (mpt) REVERT: F 28 ASP cc_start: 0.8757 (m-30) cc_final: 0.8452 (m-30) REVERT: F 51 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9062 (pp) REVERT: F 78 MET cc_start: 0.8677 (OUTLIER) cc_final: 0.8463 (ttm) REVERT: F 105 ARG cc_start: 0.9049 (mtm110) cc_final: 0.8494 (mtm110) REVERT: F 109 LYS cc_start: 0.9379 (mttt) cc_final: 0.9044 (mttt) REVERT: F 276 SER cc_start: 0.8572 (p) cc_final: 0.8237 (p) REVERT: F 279 ASN cc_start: 0.8825 (t0) cc_final: 0.7679 (t0) REVERT: F 285 ASN cc_start: 0.9345 (m110) cc_final: 0.9135 (m-40) REVERT: F 352 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8753 (tm-30) REVERT: F 355 ARG cc_start: 0.9284 (ptm-80) cc_final: 0.9037 (ptm-80) REVERT: F 395 GLU cc_start: 0.8762 (mp0) cc_final: 0.8161 (mp0) REVERT: F 399 GLU cc_start: 0.8705 (pm20) cc_final: 0.8393 (pm20) REVERT: F 404 ASP cc_start: 0.8969 (t0) cc_final: 0.8724 (t70) REVERT: F 414 MET cc_start: 0.9418 (mpt) cc_final: 0.9176 (mpt) REVERT: G 28 ASP cc_start: 0.8787 (m-30) cc_final: 0.8547 (m-30) REVERT: G 51 LEU cc_start: 0.9454 (OUTLIER) cc_final: 0.9120 (pp) REVERT: G 275 SER cc_start: 0.9040 (t) cc_final: 0.8817 (t) REVERT: G 276 SER cc_start: 0.8658 (p) cc_final: 0.8365 (p) REVERT: G 285 ASN cc_start: 0.9332 (m110) cc_final: 0.9094 (m-40) REVERT: G 352 GLU cc_start: 0.9024 (tm-30) cc_final: 0.8756 (tm-30) REVERT: G 355 ARG cc_start: 0.9482 (ptm-80) cc_final: 0.9252 (ptm-80) REVERT: G 385 MET cc_start: 0.8728 (ttm) cc_final: 0.8395 (ttm) REVERT: G 395 GLU cc_start: 0.8679 (mp0) cc_final: 0.8166 (mp0) REVERT: G 399 GLU cc_start: 0.8539 (pm20) cc_final: 0.8232 (pm20) REVERT: G 404 ASP cc_start: 0.8991 (t0) cc_final: 0.8669 (t70) REVERT: G 414 MET cc_start: 0.9449 (mpt) cc_final: 0.9207 (mpt) REVERT: G 455 LYS cc_start: 0.8879 (mppt) cc_final: 0.8590 (mppt) REVERT: G 510 GLU cc_start: 0.7678 (tp30) cc_final: 0.7437 (tp30) REVERT: H 28 ASP cc_start: 0.8780 (m-30) cc_final: 0.8530 (m-30) REVERT: H 51 LEU cc_start: 0.9324 (OUTLIER) cc_final: 0.8969 (pp) REVERT: H 66 VAL cc_start: 0.7783 (OUTLIER) cc_final: 0.7530 (p) REVERT: H 105 ARG cc_start: 0.9102 (mtm110) cc_final: 0.8756 (mtm110) REVERT: H 276 SER cc_start: 0.8683 (p) cc_final: 0.8336 (p) REVERT: H 286 MET cc_start: 0.9503 (tpp) cc_final: 0.9231 (tpp) REVERT: H 352 GLU cc_start: 0.9114 (tm-30) cc_final: 0.8849 (tm-30) REVERT: H 385 MET cc_start: 0.8705 (ttm) cc_final: 0.8367 (ttm) REVERT: H 395 GLU cc_start: 0.8697 (mp0) cc_final: 0.8165 (mp0) REVERT: H 399 GLU cc_start: 0.8550 (pm20) cc_final: 0.8307 (pm20) REVERT: H 400 TYR cc_start: 0.8152 (m-80) cc_final: 0.7461 (m-10) REVERT: H 404 ASP cc_start: 0.8939 (t0) cc_final: 0.8641 (t0) REVERT: H 407 ARG cc_start: 0.8823 (ttt-90) cc_final: 0.8253 (ttt-90) REVERT: H 414 MET cc_start: 0.9420 (mpt) cc_final: 0.9209 (mpt) outliers start: 169 outliers final: 109 residues processed: 1016 average time/residue: 0.3246 time to fit residues: 515.8044 Evaluate side-chains 991 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 872 time to evaluate : 2.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 260 LEU Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 255 ASP Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 499 VAL Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 74 THR Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 73 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 56 THR Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 78 MET Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 417 LEU 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 51 LEU Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 73 VAL Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 296 ASN Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 499 VAL Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 74 THR Chi-restraints excluded: chain H residue 250 ILE Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 499 VAL Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 266 optimal weight: 0.9980 chunk 202 optimal weight: 0.8980 chunk 139 optimal weight: 5.9990 chunk 29 optimal weight: 5.9990 chunk 128 optimal weight: 0.0570 chunk 180 optimal weight: 3.9990 chunk 270 optimal weight: 5.9990 chunk 286 optimal weight: 0.7980 chunk 141 optimal weight: 3.9990 chunk 256 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN ** B 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 469 GLN C 100 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 303 ASN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN C 334 GLN ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 312 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 23480 Z= 0.220 Angle : 0.628 9.450 31792 Z= 0.315 Chirality : 0.045 0.151 3656 Planarity : 0.004 0.037 4000 Dihedral : 10.909 89.900 3786 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 5.91 % Allowed : 23.49 % Favored : 70.60 % 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: -2.05 (0.14), residues: 2960 helix: -1.35 (0.15), residues: 1048 sheet: -2.42 (0.24), residues: 320 loop : -1.03 (0.15), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 92 PHE 0.013 0.001 PHE A 401 TYR 0.017 0.001 TYR H 258 ARG 0.011 0.001 ARG F 407 *********************** 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 1102 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 961 time to evaluate : 2.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8591 (m-30) cc_final: 0.8319 (m-30) REVERT: A 51 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.8963 (pp) REVERT: A 105 ARG cc_start: 0.8953 (mtm110) cc_final: 0.8728 (mtm110) REVERT: A 276 SER cc_start: 0.8704 (p) cc_final: 0.8402 (p) REVERT: A 335 GLU cc_start: 0.8430 (tm-30) cc_final: 0.7640 (tm-30) REVERT: A 352 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8705 (tm-30) REVERT: A 355 ARG cc_start: 0.9449 (ptm-80) cc_final: 0.9211 (ptm-80) REVERT: A 385 MET cc_start: 0.8810 (ttm) cc_final: 0.8500 (ttm) REVERT: A 395 GLU cc_start: 0.8658 (mp0) cc_final: 0.8122 (mp0) REVERT: A 399 GLU cc_start: 0.8537 (pm20) cc_final: 0.8331 (mp0) REVERT: A 404 ASP cc_start: 0.8907 (t0) cc_final: 0.8690 (t70) REVERT: A 409 LYS cc_start: 0.8666 (ttmp) cc_final: 0.8122 (ttmt) REVERT: A 482 MET cc_start: 0.9093 (mtp) cc_final: 0.8877 (mtp) REVERT: B 25 ASN cc_start: 0.9067 (m-40) cc_final: 0.8772 (p0) REVERT: B 28 ASP cc_start: 0.8615 (m-30) cc_final: 0.8325 (m-30) REVERT: B 51 LEU cc_start: 0.9370 (OUTLIER) cc_final: 0.9125 (pp) REVERT: B 276 SER cc_start: 0.8697 (p) cc_final: 0.8390 (p) REVERT: B 335 GLU cc_start: 0.8572 (tm-30) cc_final: 0.7773 (tm-30) REVERT: B 355 ARG cc_start: 0.9418 (ptm-80) cc_final: 0.9205 (ptm-80) REVERT: B 379 LEU cc_start: 0.9319 (mt) cc_final: 0.9058 (mt) REVERT: B 385 MET cc_start: 0.8780 (ttm) cc_final: 0.8554 (ttm) REVERT: B 395 GLU cc_start: 0.8710 (mp0) cc_final: 0.8144 (mp0) REVERT: B 399 GLU cc_start: 0.8625 (pm20) cc_final: 0.8394 (pm20) REVERT: B 404 ASP cc_start: 0.8896 (t0) cc_final: 0.8615 (t0) REVERT: C 28 ASP cc_start: 0.8636 (m-30) cc_final: 0.8362 (m-30) REVERT: C 51 LEU cc_start: 0.9396 (OUTLIER) cc_final: 0.9082 (pp) REVERT: C 78 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7830 (ptm) REVERT: C 105 ARG cc_start: 0.8957 (mtm110) cc_final: 0.8462 (mtm110) REVERT: C 109 LYS cc_start: 0.9322 (mttp) cc_final: 0.9057 (mptt) REVERT: C 276 SER cc_start: 0.8385 (p) cc_final: 0.8061 (p) REVERT: C 279 ASN cc_start: 0.8655 (t0) cc_final: 0.7654 (t0) REVERT: C 335 GLU cc_start: 0.8503 (tm-30) cc_final: 0.7700 (tm-30) REVERT: C 352 GLU cc_start: 0.9052 (tm-30) cc_final: 0.8675 (tm-30) REVERT: C 385 MET cc_start: 0.8815 (ttm) cc_final: 0.8561 (ttm) REVERT: C 386 MET cc_start: 0.9177 (mtm) cc_final: 0.8823 (mtp) REVERT: C 395 GLU cc_start: 0.8630 (mp0) cc_final: 0.8191 (mp0) REVERT: C 399 GLU cc_start: 0.8532 (pm20) cc_final: 0.8311 (mp0) REVERT: C 400 TYR cc_start: 0.7894 (m-10) cc_final: 0.7331 (m-10) REVERT: C 404 ASP cc_start: 0.8914 (t0) cc_final: 0.8657 (t70) REVERT: C 409 LYS cc_start: 0.8746 (ttmp) cc_final: 0.8267 (ttmt) REVERT: C 438 LYS cc_start: 0.8401 (mmtt) cc_final: 0.8035 (mmtm) REVERT: D 28 ASP cc_start: 0.8680 (m-30) cc_final: 0.8365 (m-30) REVERT: D 51 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9142 (pp) REVERT: D 58 LYS cc_start: 0.9385 (mmtp) cc_final: 0.9047 (mmmm) REVERT: D 105 ARG cc_start: 0.9051 (mtm110) cc_final: 0.8757 (mtm110) REVERT: D 109 LYS cc_start: 0.9358 (mttt) cc_final: 0.9151 (mttt) REVERT: D 276 SER cc_start: 0.8674 (p) cc_final: 0.8394 (p) REVERT: D 319 ASP cc_start: 0.8515 (m-30) cc_final: 0.8238 (m-30) REVERT: D 335 GLU cc_start: 0.8572 (tm-30) cc_final: 0.7788 (tm-30) REVERT: D 352 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8677 (tm-30) REVERT: D 355 ARG cc_start: 0.9394 (ptm-80) cc_final: 0.9172 (ptm-80) REVERT: D 385 MET cc_start: 0.8933 (ttm) cc_final: 0.8484 (ttm) REVERT: D 395 GLU cc_start: 0.8729 (mp0) cc_final: 0.8198 (mp0) REVERT: D 399 GLU cc_start: 0.8598 (pm20) cc_final: 0.8378 (pm20) REVERT: D 404 ASP cc_start: 0.8881 (t0) cc_final: 0.8604 (t0) REVERT: D 407 ARG cc_start: 0.8965 (ttt90) cc_final: 0.8744 (ttt90) REVERT: D 438 LYS cc_start: 0.8406 (mmtt) cc_final: 0.8037 (mmtm) REVERT: E 28 ASP cc_start: 0.8675 (m-30) cc_final: 0.8375 (m-30) REVERT: E 51 LEU cc_start: 0.9393 (OUTLIER) cc_final: 0.9050 (pp) REVERT: E 105 ARG cc_start: 0.8951 (mtm110) cc_final: 0.8711 (mtm110) REVERT: E 109 LYS cc_start: 0.9321 (mttp) cc_final: 0.8937 (tmtt) REVERT: E 276 SER cc_start: 0.8620 (p) cc_final: 0.8323 (p) REVERT: E 352 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8736 (tm-30) REVERT: E 386 MET cc_start: 0.8891 (mtm) cc_final: 0.8429 (mtm) REVERT: E 395 GLU cc_start: 0.8642 (mp0) cc_final: 0.8178 (mp0) REVERT: E 399 GLU cc_start: 0.8602 (pm20) cc_final: 0.8326 (pm20) REVERT: E 404 ASP cc_start: 0.9002 (t0) cc_final: 0.8763 (t70) REVERT: E 409 LYS cc_start: 0.8691 (ttmp) cc_final: 0.8102 (tttt) REVERT: F 28 ASP cc_start: 0.8705 (m-30) cc_final: 0.8452 (m-30) REVERT: F 51 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.8943 (pp) REVERT: F 105 ARG cc_start: 0.9048 (mtm110) cc_final: 0.8536 (mtm110) REVERT: F 109 LYS cc_start: 0.9404 (mttt) cc_final: 0.9083 (mttt) REVERT: F 276 SER cc_start: 0.8142 (p) cc_final: 0.7801 (p) REVERT: F 279 ASN cc_start: 0.8963 (t0) cc_final: 0.7864 (t0) REVERT: F 352 GLU cc_start: 0.9030 (tm-30) cc_final: 0.8752 (tm-30) REVERT: F 393 THR cc_start: 0.9182 (p) cc_final: 0.8330 (p) REVERT: F 395 GLU cc_start: 0.8698 (mp0) cc_final: 0.8010 (mp0) REVERT: F 399 GLU cc_start: 0.8704 (pm20) cc_final: 0.8420 (pm20) REVERT: F 404 ASP cc_start: 0.8972 (t0) cc_final: 0.8715 (t70) REVERT: G 28 ASP cc_start: 0.8786 (m-30) cc_final: 0.8584 (m-30) REVERT: G 51 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8971 (pp) REVERT: G 80 ILE cc_start: 0.9322 (pp) cc_final: 0.9094 (pp) REVERT: G 84 LEU cc_start: 0.8544 (OUTLIER) cc_final: 0.8143 (mm) REVERT: G 276 SER cc_start: 0.8482 (p) cc_final: 0.8151 (p) REVERT: G 352 GLU cc_start: 0.9052 (tm-30) cc_final: 0.8748 (tm-30) REVERT: G 355 ARG cc_start: 0.9415 (ptm-80) cc_final: 0.9188 (ptm-80) REVERT: G 385 MET cc_start: 0.8758 (ttm) cc_final: 0.8488 (ttm) REVERT: G 395 GLU cc_start: 0.8665 (mp0) cc_final: 0.8172 (mp0) REVERT: G 399 GLU cc_start: 0.8534 (pm20) cc_final: 0.8255 (pm20) REVERT: G 404 ASP cc_start: 0.8999 (t0) cc_final: 0.8711 (t70) REVERT: G 455 LYS cc_start: 0.8932 (mppt) cc_final: 0.8603 (mppt) REVERT: G 510 GLU cc_start: 0.7643 (tp30) cc_final: 0.7407 (tp30) REVERT: H 28 ASP cc_start: 0.8727 (m-30) cc_final: 0.8455 (m-30) REVERT: H 51 LEU cc_start: 0.9290 (OUTLIER) cc_final: 0.8890 (pp) REVERT: H 105 ARG cc_start: 0.9026 (mtm110) cc_final: 0.8708 (mtm110) REVERT: H 258 TYR cc_start: 0.8947 (t80) cc_final: 0.8746 (t80) REVERT: H 276 SER cc_start: 0.8657 (p) cc_final: 0.8387 (p) REVERT: H 286 MET cc_start: 0.9522 (tpp) cc_final: 0.9248 (tpp) REVERT: H 335 GLU cc_start: 0.8617 (tm-30) cc_final: 0.7855 (tm-30) REVERT: H 352 GLU cc_start: 0.9085 (tm-30) cc_final: 0.8810 (tm-30) REVERT: H 355 ARG cc_start: 0.9400 (ptm-80) cc_final: 0.9185 (ptm-80) REVERT: H 395 GLU cc_start: 0.8701 (mp0) cc_final: 0.8103 (mp0) REVERT: H 399 GLU cc_start: 0.8566 (pm20) cc_final: 0.8279 (pm20) REVERT: H 404 ASP cc_start: 0.8919 (t0) cc_final: 0.8622 (t0) REVERT: H 512 ARG cc_start: 0.8019 (ttm-80) cc_final: 0.7569 (ptm160) outliers start: 141 outliers final: 96 residues processed: 1016 average time/residue: 0.3297 time to fit residues: 523.5296 Evaluate side-chains 1005 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 899 time to evaluate : 2.834 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 469 GLN Chi-restraints excluded: chain B residue 51 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 327 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 78 MET Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 327 SER Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 74 THR Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 327 SER Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 269 ASP Chi-restraints excluded: chain G residue 296 ASN Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 327 SER Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 238 optimal weight: 0.9990 chunk 162 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 213 optimal weight: 0.6980 chunk 118 optimal weight: 0.6980 chunk 244 optimal weight: 0.9990 chunk 197 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 146 optimal weight: 1.9990 chunk 256 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 GLN B 343 GLN B 469 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN C 334 GLN ** C 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 343 GLN ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 312 ASN ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 343 GLN ** H 469 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7832 moved from start: 0.3509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 23480 Z= 0.233 Angle : 0.624 9.168 31792 Z= 0.315 Chirality : 0.045 0.158 3656 Planarity : 0.004 0.037 4000 Dihedral : 10.403 89.053 3780 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 16.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 6.88 % Allowed : 25.13 % Favored : 67.99 % 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: -1.93 (0.15), residues: 2960 helix: -1.17 (0.15), residues: 1056 sheet: -2.47 (0.25), residues: 320 loop : -0.99 (0.15), residues: 1584 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 92 PHE 0.012 0.001 PHE B 401 TYR 0.020 0.001 TYR F 258 ARG 0.009 0.001 ARG B 105 *********************** 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 1114 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 164 poor density : 950 time to evaluate : 2.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8591 (m-30) cc_final: 0.8356 (m-30) REVERT: A 51 LEU cc_start: 0.9362 (OUTLIER) cc_final: 0.9007 (pp) REVERT: A 109 LYS cc_start: 0.9589 (mmmt) cc_final: 0.9047 (tptt) REVERT: A 276 SER cc_start: 0.8639 (p) cc_final: 0.8311 (p) REVERT: A 335 GLU cc_start: 0.8452 (tm-30) cc_final: 0.7719 (tm-30) REVERT: A 352 GLU cc_start: 0.9052 (tm-30) cc_final: 0.8715 (tm-30) REVERT: A 355 ARG cc_start: 0.9429 (ptm-80) cc_final: 0.9014 (ptm-80) REVERT: A 385 MET cc_start: 0.8808 (ttm) cc_final: 0.8432 (ttm) REVERT: A 395 GLU cc_start: 0.8729 (mp0) cc_final: 0.8228 (mp0) REVERT: A 399 GLU cc_start: 0.8568 (pm20) cc_final: 0.8271 (mp0) REVERT: A 404 ASP cc_start: 0.8979 (t0) cc_final: 0.8779 (t70) REVERT: A 409 LYS cc_start: 0.8706 (ttmp) cc_final: 0.8386 (ttmt) REVERT: B 28 ASP cc_start: 0.8605 (m-30) cc_final: 0.8348 (m-30) REVERT: B 256 ASP cc_start: 0.9299 (m-30) cc_final: 0.8981 (p0) REVERT: B 335 GLU cc_start: 0.8601 (tm-30) cc_final: 0.7870 (tm-30) REVERT: B 352 GLU cc_start: 0.9067 (tm-30) cc_final: 0.8700 (tm-30) REVERT: B 355 ARG cc_start: 0.9399 (ptm-80) cc_final: 0.9016 (ptm-80) REVERT: B 395 GLU cc_start: 0.8778 (mp0) cc_final: 0.8218 (mp0) REVERT: B 399 GLU cc_start: 0.8688 (pm20) cc_final: 0.8423 (pm20) REVERT: B 404 ASP cc_start: 0.8934 (t0) cc_final: 0.8671 (t0) REVERT: C 28 ASP cc_start: 0.8631 (m-30) cc_final: 0.8393 (m-30) REVERT: C 51 LEU cc_start: 0.9404 (OUTLIER) cc_final: 0.9131 (pp) REVERT: C 105 ARG cc_start: 0.8980 (mtm110) cc_final: 0.8467 (mtm110) REVERT: C 109 LYS cc_start: 0.9336 (mttp) cc_final: 0.9055 (mptt) REVERT: C 276 SER cc_start: 0.8269 (p) cc_final: 0.7915 (p) REVERT: C 279 ASN cc_start: 0.8728 (t0) cc_final: 0.8130 (t0) REVERT: C 335 GLU cc_start: 0.8516 (tm-30) cc_final: 0.7769 (tm-30) REVERT: C 352 GLU cc_start: 0.9073 (tm-30) cc_final: 0.8706 (tm-30) REVERT: C 385 MET cc_start: 0.8805 (ttm) cc_final: 0.8575 (ttm) REVERT: C 395 GLU cc_start: 0.8697 (mp0) cc_final: 0.8235 (mp0) REVERT: C 404 ASP cc_start: 0.8955 (t0) cc_final: 0.8716 (t70) REVERT: C 407 ARG cc_start: 0.8997 (ttt90) cc_final: 0.8790 (ttt90) REVERT: C 409 LYS cc_start: 0.8802 (ttmp) cc_final: 0.8448 (ttmt) REVERT: C 438 LYS cc_start: 0.8430 (mmtt) cc_final: 0.8097 (mmtm) REVERT: D 28 ASP cc_start: 0.8636 (m-30) cc_final: 0.8389 (m-30) REVERT: D 51 LEU cc_start: 0.9480 (OUTLIER) cc_final: 0.9176 (pp) REVERT: D 84 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8291 (tp) REVERT: D 105 ARG cc_start: 0.9047 (mtm110) cc_final: 0.8575 (mtm110) REVERT: D 109 LYS cc_start: 0.9407 (mttt) cc_final: 0.9112 (mttt) REVERT: D 276 SER cc_start: 0.8610 (p) cc_final: 0.8321 (p) REVERT: D 335 GLU cc_start: 0.8579 (tm-30) cc_final: 0.7878 (tm-30) REVERT: D 395 GLU cc_start: 0.8772 (mp0) cc_final: 0.8182 (mp0) REVERT: D 399 GLU cc_start: 0.8687 (pm20) cc_final: 0.8387 (pm20) REVERT: D 404 ASP cc_start: 0.8892 (t0) cc_final: 0.8633 (t0) REVERT: D 407 ARG cc_start: 0.8916 (ttt90) cc_final: 0.8688 (ttt90) REVERT: D 409 LYS cc_start: 0.8750 (ttmp) cc_final: 0.8217 (tttt) REVERT: D 438 LYS cc_start: 0.8407 (mmtt) cc_final: 0.8040 (mmtm) REVERT: E 28 ASP cc_start: 0.8674 (m-30) cc_final: 0.8407 (m-30) REVERT: E 51 LEU cc_start: 0.9378 (OUTLIER) cc_final: 0.9082 (pp) REVERT: E 105 ARG cc_start: 0.8957 (mtm110) cc_final: 0.8714 (mtm110) REVERT: E 109 LYS cc_start: 0.9361 (mttp) cc_final: 0.8961 (tmtt) REVERT: E 258 TYR cc_start: 0.8949 (t80) cc_final: 0.8737 (t80) REVERT: E 276 SER cc_start: 0.8565 (p) cc_final: 0.8272 (p) REVERT: E 322 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7194 (ptm160) REVERT: E 352 GLU cc_start: 0.9031 (tm-30) cc_final: 0.8729 (tm-30) REVERT: E 385 MET cc_start: 0.8492 (ttm) cc_final: 0.7994 (ttm) REVERT: E 386 MET cc_start: 0.8891 (mtm) cc_final: 0.8424 (mtm) REVERT: E 395 GLU cc_start: 0.8713 (mp0) cc_final: 0.8233 (mp0) REVERT: E 399 GLU cc_start: 0.8639 (pm20) cc_final: 0.8382 (pm20) REVERT: E 400 TYR cc_start: 0.7818 (m-10) cc_final: 0.7337 (m-10) REVERT: E 404 ASP cc_start: 0.8987 (t0) cc_final: 0.8765 (t70) REVERT: E 407 ARG cc_start: 0.8848 (ttt90) cc_final: 0.8612 (ttt90) REVERT: E 409 LYS cc_start: 0.8736 (ttmp) cc_final: 0.8304 (tttt) REVERT: F 28 ASP cc_start: 0.8702 (m-30) cc_final: 0.8464 (m-30) REVERT: F 51 LEU cc_start: 0.9340 (OUTLIER) cc_final: 0.9028 (pp) REVERT: F 80 ILE cc_start: 0.9350 (pp) cc_final: 0.9136 (pp) REVERT: F 84 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8150 (mm) REVERT: F 105 ARG cc_start: 0.9009 (mtm110) cc_final: 0.8756 (mtm110) REVERT: F 276 SER cc_start: 0.8121 (p) cc_final: 0.7789 (p) REVERT: F 279 ASN cc_start: 0.9007 (t0) cc_final: 0.7888 (t0) REVERT: F 352 GLU cc_start: 0.9042 (tm-30) cc_final: 0.8733 (tm-30) REVERT: F 355 ARG cc_start: 0.9193 (ptm-80) cc_final: 0.8912 (ptm-80) REVERT: F 393 THR cc_start: 0.9217 (p) cc_final: 0.8386 (p) REVERT: F 395 GLU cc_start: 0.8701 (mp0) cc_final: 0.8020 (mp0) REVERT: F 399 GLU cc_start: 0.8715 (pm20) cc_final: 0.8434 (pm20) REVERT: F 404 ASP cc_start: 0.8930 (t0) cc_final: 0.8707 (t70) REVERT: G 51 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8932 (pp) REVERT: G 80 ILE cc_start: 0.9375 (pp) cc_final: 0.9142 (pp) REVERT: G 84 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8229 (mm) REVERT: G 276 SER cc_start: 0.8484 (p) cc_final: 0.8127 (p) REVERT: G 352 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8749 (tm-30) REVERT: G 355 ARG cc_start: 0.9400 (ptm-80) cc_final: 0.9023 (ptm-80) REVERT: G 395 GLU cc_start: 0.8726 (mp0) cc_final: 0.8218 (mp0) REVERT: G 404 ASP cc_start: 0.9002 (t0) cc_final: 0.8701 (t70) REVERT: G 409 LYS cc_start: 0.8854 (ttmp) cc_final: 0.8036 (tttt) REVERT: G 510 GLU cc_start: 0.7652 (tp30) cc_final: 0.7420 (tp30) REVERT: H 28 ASP cc_start: 0.8732 (m-30) cc_final: 0.8506 (m-30) REVERT: H 51 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.8991 (pp) REVERT: H 105 ARG cc_start: 0.8984 (mtm110) cc_final: 0.8677 (mtm110) REVERT: H 258 TYR cc_start: 0.8980 (t80) cc_final: 0.8744 (t80) REVERT: H 276 SER cc_start: 0.8630 (p) cc_final: 0.8275 (p) REVERT: H 286 MET cc_start: 0.9503 (tpp) cc_final: 0.9206 (tpp) REVERT: H 335 GLU cc_start: 0.8618 (tm-30) cc_final: 0.7871 (tm-30) REVERT: H 352 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8818 (tm-30) REVERT: H 355 ARG cc_start: 0.9388 (ptm-80) cc_final: 0.9043 (ptm-80) REVERT: H 395 GLU cc_start: 0.8717 (mp0) cc_final: 0.8116 (mp0) REVERT: H 399 GLU cc_start: 0.8560 (pm20) cc_final: 0.8348 (pm20) REVERT: H 404 ASP cc_start: 0.8926 (t0) cc_final: 0.8629 (t0) REVERT: H 409 LYS cc_start: 0.8657 (ttmp) cc_final: 0.7916 (tttt) REVERT: H 512 ARG cc_start: 0.7953 (ttm-80) cc_final: 0.7697 (ptm160) outliers start: 164 outliers final: 117 residues processed: 1023 average time/residue: 0.3380 time to fit residues: 536.8086 Evaluate side-chains 1031 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 903 time to evaluate : 2.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 255 ASP Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 388 SER Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 485 SER Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 471 ILE Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 63 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 322 ARG Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain E residue 500 GLU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 417 LEU 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 7 SER Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 63 THR Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 235 LEU Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 296 ASN Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 325 MET Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 471 ILE Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 96 optimal weight: 0.9980 chunk 257 optimal weight: 2.9990 chunk 56 optimal weight: 0.7980 chunk 167 optimal weight: 0.0970 chunk 70 optimal weight: 4.9990 chunk 286 optimal weight: 0.0040 chunk 237 optimal weight: 5.9990 chunk 132 optimal weight: 0.6980 chunk 23 optimal weight: 1.9990 chunk 94 optimal weight: 3.9990 chunk 150 optimal weight: 2.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN B 303 ASN ** B 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN C 469 GLN D 100 GLN D 285 ASN D 303 ASN ** D 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 469 GLN ** E 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 469 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 285 ASN F 303 ASN ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 285 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 469 GLN ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 303 ASN ** H 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 469 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.3716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23480 Z= 0.193 Angle : 0.627 8.489 31792 Z= 0.312 Chirality : 0.044 0.155 3656 Planarity : 0.004 0.037 4000 Dihedral : 9.827 86.983 3775 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 6.17 % Allowed : 26.68 % Favored : 67.16 % 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: -1.90 (0.15), residues: 2960 helix: -1.19 (0.15), residues: 1048 sheet: -2.60 (0.24), residues: 336 loop : -0.88 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.000 HIS D 92 PHE 0.014 0.001 PHE B 24 TYR 0.017 0.001 TYR D 411 ARG 0.012 0.001 ARG A 407 *********************** 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 1128 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 981 time to evaluate : 2.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8564 (m-30) cc_final: 0.8346 (m-30) REVERT: A 51 LEU cc_start: 0.9333 (OUTLIER) cc_final: 0.8955 (pp) REVERT: A 109 LYS cc_start: 0.9604 (mmmt) cc_final: 0.9074 (tptt) REVERT: A 276 SER cc_start: 0.8534 (p) cc_final: 0.8246 (p) REVERT: A 335 GLU cc_start: 0.8450 (tm-30) cc_final: 0.7660 (tm-30) REVERT: A 352 GLU cc_start: 0.9028 (tm-30) cc_final: 0.8659 (tm-30) REVERT: A 355 ARG cc_start: 0.9392 (ptm-80) cc_final: 0.9167 (ptm-80) REVERT: A 385 MET cc_start: 0.8754 (ttm) cc_final: 0.8408 (ttm) REVERT: A 395 GLU cc_start: 0.8777 (mp0) cc_final: 0.8209 (mp0) REVERT: A 409 LYS cc_start: 0.8749 (ttmp) cc_final: 0.8391 (ttmt) REVERT: B 25 ASN cc_start: 0.9094 (m-40) cc_final: 0.8737 (p0) REVERT: B 28 ASP cc_start: 0.8581 (m-30) cc_final: 0.8342 (m-30) REVERT: B 256 ASP cc_start: 0.9288 (m-30) cc_final: 0.8696 (p0) REVERT: B 335 GLU cc_start: 0.8601 (tm-30) cc_final: 0.7813 (tm-30) REVERT: B 352 GLU cc_start: 0.9069 (tm-30) cc_final: 0.8788 (tm-30) REVERT: B 395 GLU cc_start: 0.8785 (mp0) cc_final: 0.8300 (mp0) REVERT: B 404 ASP cc_start: 0.8936 (t0) cc_final: 0.8701 (t70) REVERT: B 510 GLU cc_start: 0.7952 (tp30) cc_final: 0.7655 (tp30) REVERT: C 28 ASP cc_start: 0.8605 (m-30) cc_final: 0.8388 (m-30) REVERT: C 51 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8878 (pp) REVERT: C 105 ARG cc_start: 0.8982 (mtm110) cc_final: 0.8473 (mtm110) REVERT: C 109 LYS cc_start: 0.9333 (mttp) cc_final: 0.9113 (mttt) REVERT: C 276 SER cc_start: 0.8007 (p) cc_final: 0.7573 (p) REVERT: C 279 ASN cc_start: 0.8789 (t0) cc_final: 0.8244 (t0) REVERT: C 335 GLU cc_start: 0.8535 (tm-30) cc_final: 0.7717 (tm-30) REVERT: C 352 GLU cc_start: 0.9037 (tm-30) cc_final: 0.8672 (tm-30) REVERT: C 385 MET cc_start: 0.8809 (ttm) cc_final: 0.8576 (ttm) REVERT: C 395 GLU cc_start: 0.8673 (mp0) cc_final: 0.8054 (mp0) REVERT: C 400 TYR cc_start: 0.7857 (m-10) cc_final: 0.7643 (m-10) REVERT: C 404 ASP cc_start: 0.8959 (t0) cc_final: 0.8736 (t70) REVERT: C 407 ARG cc_start: 0.8949 (ttt90) cc_final: 0.8726 (ttt90) REVERT: C 409 LYS cc_start: 0.8754 (ttmp) cc_final: 0.8418 (ttmt) REVERT: C 438 LYS cc_start: 0.8474 (mmtt) cc_final: 0.8159 (mmtm) REVERT: C 510 GLU cc_start: 0.7753 (tp30) cc_final: 0.7447 (tp30) REVERT: D 28 ASP cc_start: 0.8626 (m-30) cc_final: 0.8398 (m-30) REVERT: D 51 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.8972 (pp) REVERT: D 105 ARG cc_start: 0.9018 (mtm110) cc_final: 0.8609 (mtm110) REVERT: D 109 LYS cc_start: 0.9429 (mttt) cc_final: 0.9163 (mttt) REVERT: D 276 SER cc_start: 0.8513 (p) cc_final: 0.8293 (p) REVERT: D 335 GLU cc_start: 0.8572 (tm-30) cc_final: 0.7809 (tm-30) REVERT: D 352 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8783 (tm-30) REVERT: D 395 GLU cc_start: 0.8783 (mp0) cc_final: 0.8094 (mp0) REVERT: D 399 GLU cc_start: 0.8634 (pm20) cc_final: 0.8361 (pm20) REVERT: D 400 TYR cc_start: 0.8046 (m-10) cc_final: 0.7506 (m-10) REVERT: D 404 ASP cc_start: 0.8904 (t0) cc_final: 0.8665 (t70) REVERT: D 407 ARG cc_start: 0.8950 (ttt90) cc_final: 0.8749 (ttt90) REVERT: D 409 LYS cc_start: 0.8703 (ttmp) cc_final: 0.8169 (tttt) REVERT: D 438 LYS cc_start: 0.8436 (mmtt) cc_final: 0.8116 (mmtm) REVERT: E 28 ASP cc_start: 0.8664 (m-30) cc_final: 0.8444 (m-30) REVERT: E 51 LEU cc_start: 0.9230 (OUTLIER) cc_final: 0.8977 (pp) REVERT: E 105 ARG cc_start: 0.8898 (mtm110) cc_final: 0.8685 (mtm110) REVERT: E 109 LYS cc_start: 0.9357 (mttp) cc_final: 0.9058 (mtmm) REVERT: E 259 ARG cc_start: 0.9356 (ttm-80) cc_final: 0.9041 (ttm170) REVERT: E 276 SER cc_start: 0.8386 (p) cc_final: 0.8068 (p) REVERT: E 352 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8727 (tm-30) REVERT: E 355 ARG cc_start: 0.9181 (ptm-80) cc_final: 0.8903 (ptm-80) REVERT: E 386 MET cc_start: 0.8924 (mtm) cc_final: 0.8439 (mtm) REVERT: E 395 GLU cc_start: 0.8736 (mp0) cc_final: 0.8020 (mp0) REVERT: E 399 GLU cc_start: 0.8627 (pm20) cc_final: 0.8381 (pm20) REVERT: E 404 ASP cc_start: 0.8980 (t0) cc_final: 0.8747 (t70) REVERT: E 409 LYS cc_start: 0.8800 (ttmp) cc_final: 0.8340 (tttt) REVERT: F 28 ASP cc_start: 0.8673 (m-30) cc_final: 0.8463 (m-30) REVERT: F 51 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9069 (pp) REVERT: F 105 ARG cc_start: 0.8998 (mtm110) cc_final: 0.8753 (mtm110) REVERT: F 109 LYS cc_start: 0.9403 (mttt) cc_final: 0.9094 (mttt) REVERT: F 259 ARG cc_start: 0.9389 (ttm-80) cc_final: 0.9103 (ttt-90) REVERT: F 276 SER cc_start: 0.7897 (p) cc_final: 0.7557 (p) REVERT: F 279 ASN cc_start: 0.9032 (t0) cc_final: 0.7931 (t0) REVERT: F 352 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8689 (tm-30) REVERT: F 355 ARG cc_start: 0.9158 (ptm-80) cc_final: 0.8883 (ptm-80) REVERT: F 395 GLU cc_start: 0.8684 (mp0) cc_final: 0.7979 (mp0) REVERT: F 399 GLU cc_start: 0.8720 (pm20) cc_final: 0.8435 (pm20) REVERT: F 400 TYR cc_start: 0.8099 (m-80) cc_final: 0.7645 (m-10) REVERT: F 404 ASP cc_start: 0.8911 (t0) cc_final: 0.8676 (t70) REVERT: F 407 ARG cc_start: 0.9086 (ttt90) cc_final: 0.8717 (ttt90) REVERT: G 51 LEU cc_start: 0.9320 (OUTLIER) cc_final: 0.9041 (pp) REVERT: G 276 SER cc_start: 0.8326 (p) cc_final: 0.7920 (p) REVERT: G 322 ARG cc_start: 0.8036 (OUTLIER) cc_final: 0.7766 (ptm160) REVERT: G 335 GLU cc_start: 0.8575 (tm-30) cc_final: 0.7738 (tm-30) REVERT: G 352 GLU cc_start: 0.9029 (tm-30) cc_final: 0.8701 (tm-30) REVERT: G 385 MET cc_start: 0.8558 (ttm) cc_final: 0.8072 (ttm) REVERT: G 395 GLU cc_start: 0.8725 (mp0) cc_final: 0.8052 (mp0) REVERT: G 404 ASP cc_start: 0.9025 (t0) cc_final: 0.8741 (t70) REVERT: G 409 LYS cc_start: 0.8824 (ttmp) cc_final: 0.8361 (ttmt) REVERT: G 510 GLU cc_start: 0.7713 (tp30) cc_final: 0.7298 (tp30) REVERT: H 28 ASP cc_start: 0.8710 (m-30) cc_final: 0.8501 (m-30) REVERT: H 51 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.9018 (pp) REVERT: H 84 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8072 (mm) REVERT: H 258 TYR cc_start: 0.9013 (t80) cc_final: 0.8774 (t80) REVERT: H 276 SER cc_start: 0.8488 (p) cc_final: 0.8207 (p) REVERT: H 286 MET cc_start: 0.9488 (tpp) cc_final: 0.9161 (tpp) REVERT: H 335 GLU cc_start: 0.8608 (tm-30) cc_final: 0.7866 (tm-30) REVERT: H 385 MET cc_start: 0.8595 (ttm) cc_final: 0.8213 (ttm) REVERT: H 395 GLU cc_start: 0.8719 (mp0) cc_final: 0.8205 (mp0) REVERT: H 399 GLU cc_start: 0.8590 (pm20) cc_final: 0.8301 (pm20) REVERT: H 404 ASP cc_start: 0.8938 (t0) cc_final: 0.8640 (t0) REVERT: H 409 LYS cc_start: 0.8693 (ttmp) cc_final: 0.8294 (ttmt) REVERT: H 438 LYS cc_start: 0.8131 (mmtt) cc_final: 0.7850 (mmtm) REVERT: H 512 ARG cc_start: 0.7944 (ttm-80) cc_final: 0.7731 (ptm160) outliers start: 147 outliers final: 104 residues processed: 1042 average time/residue: 0.3283 time to fit residues: 531.4844 Evaluate side-chains 1046 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 933 time to evaluate : 2.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 269 ASP Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 73 VAL Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 385 MET Chi-restraints excluded: chain F residue 417 LEU 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 51 LEU Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 296 ASN Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 322 ARG Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 513 LEU 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: 3.9990 chunk 163 optimal weight: 0.3980 chunk 209 optimal weight: 0.5980 chunk 162 optimal weight: 0.9990 chunk 241 optimal weight: 0.0870 chunk 159 optimal weight: 4.9990 chunk 285 optimal weight: 4.9990 chunk 178 optimal weight: 3.9990 chunk 173 optimal weight: 0.5980 chunk 131 optimal weight: 5.9990 overall best weight: 0.5360 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 498 GLN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 285 ASN ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN C 334 GLN C 469 GLN D 469 GLN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 303 ASN ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 469 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN ** F 368 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 285 ASN ** 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 285 ASN H 309 GLN H 469 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.3875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23480 Z= 0.198 Angle : 0.644 9.698 31792 Z= 0.319 Chirality : 0.045 0.168 3656 Planarity : 0.004 0.040 4000 Dihedral : 9.395 85.180 3774 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer: Outliers : 6.12 % Allowed : 28.06 % Favored : 65.81 % 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: -1.79 (0.15), residues: 2960 helix: -1.15 (0.15), residues: 1048 sheet: -2.47 (0.25), residues: 336 loop : -0.78 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS A 92 PHE 0.012 0.001 PHE A 401 TYR 0.024 0.001 TYR B 258 ARG 0.014 0.001 ARG B 105 *********************** 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 1130 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 984 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 ASP cc_start: 0.8550 (m-30) cc_final: 0.8342 (m-30) REVERT: A 51 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9015 (pp) REVERT: A 108 LYS cc_start: 0.9544 (mttm) cc_final: 0.9324 (tppp) REVERT: A 109 LYS cc_start: 0.9579 (mmmt) cc_final: 0.9044 (tptt) REVERT: A 256 ASP cc_start: 0.9224 (m-30) cc_final: 0.8917 (p0) REVERT: A 276 SER cc_start: 0.8506 (p) cc_final: 0.8130 (p) REVERT: A 335 GLU cc_start: 0.8491 (tm-30) cc_final: 0.7694 (tm-30) REVERT: A 352 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8776 (tm-30) REVERT: A 385 MET cc_start: 0.8641 (ttm) cc_final: 0.8222 (ttm) REVERT: A 395 GLU cc_start: 0.8827 (mp0) cc_final: 0.8119 (mp0) REVERT: A 406 ILE cc_start: 0.9238 (mm) cc_final: 0.8889 (mp) REVERT: A 409 LYS cc_start: 0.8761 (ttmp) cc_final: 0.8467 (ttmt) REVERT: A 510 GLU cc_start: 0.7712 (tp30) cc_final: 0.7463 (tp30) REVERT: A 512 ARG cc_start: 0.7827 (ttm-80) cc_final: 0.7426 (ttm-80) REVERT: B 25 ASN cc_start: 0.9099 (m-40) cc_final: 0.8723 (p0) REVERT: B 28 ASP cc_start: 0.8546 (m-30) cc_final: 0.8338 (m-30) REVERT: B 105 ARG cc_start: 0.8864 (mtm110) cc_final: 0.8531 (mtm110) REVERT: B 256 ASP cc_start: 0.9262 (m-30) cc_final: 0.8522 (p0) REVERT: B 259 ARG cc_start: 0.9454 (ttm-80) cc_final: 0.9075 (ttm170) REVERT: B 335 GLU cc_start: 0.8605 (tm-30) cc_final: 0.7811 (tm-30) REVERT: B 352 GLU cc_start: 0.9133 (tm-30) cc_final: 0.8758 (tm-30) REVERT: B 395 GLU cc_start: 0.8833 (mp0) cc_final: 0.8323 (mp0) REVERT: B 404 ASP cc_start: 0.8955 (t0) cc_final: 0.8733 (t70) REVERT: B 406 ILE cc_start: 0.9106 (mp) cc_final: 0.8877 (mp) REVERT: B 438 LYS cc_start: 0.8297 (mmtt) cc_final: 0.8027 (mtpt) REVERT: B 510 GLU cc_start: 0.8084 (tp30) cc_final: 0.7755 (tp30) REVERT: C 21 GLN cc_start: 0.8819 (pt0) cc_final: 0.8560 (tt0) REVERT: C 28 ASP cc_start: 0.8613 (m-30) cc_final: 0.8410 (m-30) REVERT: C 51 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.8911 (pp) REVERT: C 105 ARG cc_start: 0.8988 (mtm110) cc_final: 0.8473 (mtm110) REVERT: C 109 LYS cc_start: 0.9349 (mttp) cc_final: 0.9109 (mttt) REVERT: C 256 ASP cc_start: 0.9184 (m-30) cc_final: 0.8904 (p0) REVERT: C 276 SER cc_start: 0.7799 (p) cc_final: 0.7429 (p) REVERT: C 279 ASN cc_start: 0.8879 (t0) cc_final: 0.8346 (t0) REVERT: C 332 ILE cc_start: 0.8853 (OUTLIER) cc_final: 0.8452 (pp) REVERT: C 335 GLU cc_start: 0.8521 (tm-30) cc_final: 0.7687 (tm-30) REVERT: C 352 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8646 (tm-30) REVERT: C 385 MET cc_start: 0.8747 (ttm) cc_final: 0.8518 (ttm) REVERT: C 395 GLU cc_start: 0.8639 (mp0) cc_final: 0.8353 (mp0) REVERT: C 404 ASP cc_start: 0.8950 (t0) cc_final: 0.8742 (t70) REVERT: C 409 LYS cc_start: 0.8790 (ttmp) cc_final: 0.8518 (ttmt) REVERT: C 438 LYS cc_start: 0.8553 (mmtt) cc_final: 0.8216 (mmtm) REVERT: C 510 GLU cc_start: 0.7755 (tp30) cc_final: 0.7448 (tp30) REVERT: D 28 ASP cc_start: 0.8617 (m-30) cc_final: 0.8405 (m-30) REVERT: D 51 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9041 (pp) REVERT: D 105 ARG cc_start: 0.9030 (mtm110) cc_final: 0.8684 (mtm110) REVERT: D 109 LYS cc_start: 0.9436 (mttt) cc_final: 0.9052 (mttm) REVERT: D 276 SER cc_start: 0.8412 (p) cc_final: 0.8096 (p) REVERT: D 332 ILE cc_start: 0.8887 (OUTLIER) cc_final: 0.8357 (pp) REVERT: D 335 GLU cc_start: 0.8557 (tm-30) cc_final: 0.7738 (tm-30) REVERT: D 352 GLU cc_start: 0.9124 (tm-30) cc_final: 0.8776 (tm-30) REVERT: D 395 GLU cc_start: 0.8776 (mp0) cc_final: 0.8358 (mp0) REVERT: D 399 GLU cc_start: 0.8661 (pm20) cc_final: 0.8363 (mp0) REVERT: D 400 TYR cc_start: 0.7910 (m-10) cc_final: 0.6764 (m-10) REVERT: D 404 ASP cc_start: 0.8917 (t0) cc_final: 0.8676 (t0) REVERT: D 407 ARG cc_start: 0.8991 (ttt90) cc_final: 0.8587 (ttt-90) REVERT: D 409 LYS cc_start: 0.8749 (ttmp) cc_final: 0.8296 (tttt) REVERT: D 438 LYS cc_start: 0.8518 (mmtt) cc_final: 0.8177 (mmtm) REVERT: E 51 LEU cc_start: 0.9195 (OUTLIER) cc_final: 0.8962 (pp) REVERT: E 105 ARG cc_start: 0.8863 (mtm110) cc_final: 0.8642 (mtm110) REVERT: E 256 ASP cc_start: 0.9174 (m-30) cc_final: 0.8918 (p0) REVERT: E 276 SER cc_start: 0.8285 (p) cc_final: 0.7903 (p) REVERT: E 335 GLU cc_start: 0.8580 (tm-30) cc_final: 0.7805 (tm-30) REVERT: E 352 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8732 (tm-30) REVERT: E 355 ARG cc_start: 0.9181 (ptm-80) cc_final: 0.8902 (ptm-80) REVERT: E 386 MET cc_start: 0.8934 (mtm) cc_final: 0.8451 (mtm) REVERT: E 395 GLU cc_start: 0.8722 (mp0) cc_final: 0.8334 (mp0) REVERT: E 404 ASP cc_start: 0.8994 (t0) cc_final: 0.8788 (t70) REVERT: E 512 ARG cc_start: 0.7915 (ttm-80) cc_final: 0.7492 (ttm-80) REVERT: F 51 LEU cc_start: 0.9198 (OUTLIER) cc_final: 0.8938 (pp) REVERT: F 105 ARG cc_start: 0.9011 (mtm110) cc_final: 0.8591 (mtm110) REVERT: F 109 LYS cc_start: 0.9392 (mttt) cc_final: 0.9082 (mttt) REVERT: F 259 ARG cc_start: 0.9376 (ttm-80) cc_final: 0.9115 (ttt-90) REVERT: F 276 SER cc_start: 0.7842 (p) cc_final: 0.7506 (p) REVERT: F 279 ASN cc_start: 0.9049 (t0) cc_final: 0.7944 (t0) REVERT: F 285 ASN cc_start: 0.8995 (m-40) cc_final: 0.8786 (m-40) REVERT: F 335 GLU cc_start: 0.8628 (tm-30) cc_final: 0.7857 (tm-30) REVERT: F 352 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8695 (tm-30) REVERT: F 355 ARG cc_start: 0.9186 (ptm-80) cc_final: 0.8902 (ptm-80) REVERT: F 385 MET cc_start: 0.8644 (ttm) cc_final: 0.8226 (ttm) REVERT: F 393 THR cc_start: 0.8915 (OUTLIER) cc_final: 0.8388 (m) REVERT: F 395 GLU cc_start: 0.8681 (mp0) cc_final: 0.8023 (mp0) REVERT: F 399 GLU cc_start: 0.8730 (pm20) cc_final: 0.8481 (pm20) REVERT: F 400 TYR cc_start: 0.8017 (m-80) cc_final: 0.7635 (m-10) REVERT: F 404 ASP cc_start: 0.8923 (t0) cc_final: 0.8704 (t70) REVERT: F 407 ARG cc_start: 0.9090 (ttt90) cc_final: 0.8735 (ttt90) REVERT: G 21 GLN cc_start: 0.8620 (tt0) cc_final: 0.8394 (tt0) REVERT: G 51 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8920 (pp) REVERT: G 276 SER cc_start: 0.8248 (p) cc_final: 0.7921 (p) REVERT: G 332 ILE cc_start: 0.8858 (OUTLIER) cc_final: 0.8385 (pp) REVERT: G 335 GLU cc_start: 0.8552 (tm-30) cc_final: 0.7656 (tm-30) REVERT: G 352 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8703 (tm-30) REVERT: G 355 ARG cc_start: 0.9220 (ptm-80) cc_final: 0.8793 (ptm-80) REVERT: G 395 GLU cc_start: 0.8671 (mp0) cc_final: 0.8347 (mp0) REVERT: G 404 ASP cc_start: 0.9035 (t0) cc_final: 0.8757 (t70) REVERT: G 409 LYS cc_start: 0.8828 (ttmp) cc_final: 0.8468 (ttmt) REVERT: G 510 GLU cc_start: 0.7805 (tp30) cc_final: 0.7368 (tp30) REVERT: H 51 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8970 (pp) REVERT: H 84 LEU cc_start: 0.8483 (OUTLIER) cc_final: 0.8193 (tp) REVERT: H 105 ARG cc_start: 0.8938 (mtm110) cc_final: 0.8681 (mtm110) REVERT: H 109 LYS cc_start: 0.9402 (mttt) cc_final: 0.9075 (mttt) REVERT: H 256 ASP cc_start: 0.9258 (m-30) cc_final: 0.9020 (p0) REVERT: H 258 TYR cc_start: 0.9051 (t80) cc_final: 0.8808 (t80) REVERT: H 276 SER cc_start: 0.8439 (p) cc_final: 0.8046 (p) REVERT: H 286 MET cc_start: 0.9500 (tpp) cc_final: 0.8788 (tpp) REVERT: H 332 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8534 (pp) REVERT: H 335 GLU cc_start: 0.8619 (tm-30) cc_final: 0.7785 (tm-30) REVERT: H 385 MET cc_start: 0.8638 (ttm) cc_final: 0.8242 (ttm) REVERT: H 395 GLU cc_start: 0.8786 (mp0) cc_final: 0.8268 (mp0) REVERT: H 399 GLU cc_start: 0.8617 (pm20) cc_final: 0.8363 (pm20) REVERT: H 404 ASP cc_start: 0.8935 (t0) cc_final: 0.8681 (t70) REVERT: H 409 LYS cc_start: 0.8715 (ttmp) cc_final: 0.8067 (tttt) REVERT: H 438 LYS cc_start: 0.8307 (mmtt) cc_final: 0.8038 (mmtm) REVERT: H 512 ARG cc_start: 0.7952 (ttm-80) cc_final: 0.7728 (ptm160) outliers start: 146 outliers final: 112 residues processed: 1041 average time/residue: 0.3283 time to fit residues: 534.7861 Evaluate side-chains 1082 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 957 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 250 ILE Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 65 LEU Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 56 THR Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 250 ILE Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 469 GLN Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 65 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 281 ILE Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 467 SER 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 51 LEU Chi-restraints excluded: chain F residue 65 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 471 ILE Chi-restraints excluded: chain F residue 500 GLU Chi-restraints excluded: chain F residue 513 LEU Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 65 LEU Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 296 ASN Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 73 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 255 ASP Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 176 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 170 optimal weight: 0.3980 chunk 85 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 181 optimal weight: 1.9990 chunk 194 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 224 optimal weight: 0.6980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 498 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 285 ASN ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 334 GLN D 469 GLN D 498 GLN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 469 GLN ** F 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 303 ASN ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 285 ASN ** H 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 23480 Z= 0.248 Angle : 0.669 10.503 31792 Z= 0.333 Chirality : 0.046 0.170 3656 Planarity : 0.004 0.041 4000 Dihedral : 9.172 84.704 3771 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 17.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 6.50 % Allowed : 28.44 % Favored : 65.06 % 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: -1.79 (0.15), residues: 2960 helix: -1.18 (0.15), residues: 1048 sheet: -2.41 (0.25), residues: 336 loop : -0.77 (0.16), residues: 1576 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS E 92 PHE 0.011 0.001 PHE B 24 TYR 0.022 0.001 TYR E 258 ARG 0.012 0.001 ARG B 105 *********************** 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 1115 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 155 poor density : 960 time to evaluate : 2.643 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 51 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8901 (pp) REVERT: A 84 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8155 (mm) REVERT: A 108 LYS cc_start: 0.9529 (OUTLIER) cc_final: 0.9316 (tppp) REVERT: A 109 LYS cc_start: 0.9568 (mmmt) cc_final: 0.9129 (tptt) REVERT: A 276 SER cc_start: 0.8543 (p) cc_final: 0.8245 (p) REVERT: A 335 GLU cc_start: 0.8496 (tm-30) cc_final: 0.7679 (tm-30) REVERT: A 352 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8798 (tm-30) REVERT: A 385 MET cc_start: 0.8685 (ttm) cc_final: 0.8389 (ttm) REVERT: A 395 GLU cc_start: 0.8851 (mp0) cc_final: 0.8317 (mp0) REVERT: A 399 GLU cc_start: 0.8460 (mp0) cc_final: 0.8206 (mp0) REVERT: A 406 ILE cc_start: 0.9237 (mm) cc_final: 0.8892 (mp) REVERT: A 407 ARG cc_start: 0.9072 (ttt90) cc_final: 0.8803 (ttt90) REVERT: A 409 LYS cc_start: 0.8687 (ttmp) cc_final: 0.8427 (ttmt) REVERT: A 510 GLU cc_start: 0.7710 (tp30) cc_final: 0.7347 (tp30) REVERT: A 512 ARG cc_start: 0.7869 (ttm-80) cc_final: 0.7436 (ttm-80) REVERT: B 21 GLN cc_start: 0.8888 (OUTLIER) cc_final: 0.8408 (tm-30) REVERT: B 105 ARG cc_start: 0.8840 (mtm110) cc_final: 0.8468 (mtm110) REVERT: B 335 GLU cc_start: 0.8606 (tm-30) cc_final: 0.7795 (tm-30) REVERT: B 352 GLU cc_start: 0.9154 (tm-30) cc_final: 0.8822 (tm-30) REVERT: B 395 GLU cc_start: 0.8852 (mp0) cc_final: 0.8304 (mp0) REVERT: B 404 ASP cc_start: 0.8981 (t0) cc_final: 0.8756 (t70) REVERT: B 406 ILE cc_start: 0.9101 (mp) cc_final: 0.8831 (mp) REVERT: B 410 LYS cc_start: 0.8743 (ptmm) cc_final: 0.8513 (ptmt) REVERT: B 469 GLN cc_start: 0.8853 (OUTLIER) cc_final: 0.8611 (tt0) REVERT: B 510 GLU cc_start: 0.8098 (tp30) cc_final: 0.7788 (tp30) REVERT: B 512 ARG cc_start: 0.8298 (ptm160) cc_final: 0.8044 (ptm160) REVERT: C 21 GLN cc_start: 0.8890 (pt0) cc_final: 0.8622 (tt0) REVERT: C 51 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8918 (pp) REVERT: C 84 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8359 (tp) REVERT: C 105 ARG cc_start: 0.8966 (mtm110) cc_final: 0.8436 (mtm110) REVERT: C 109 LYS cc_start: 0.9301 (mttp) cc_final: 0.9079 (mptt) REVERT: C 276 SER cc_start: 0.8024 (p) cc_final: 0.7676 (p) REVERT: C 279 ASN cc_start: 0.8906 (t0) cc_final: 0.8351 (t0) REVERT: C 332 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8548 (pp) REVERT: C 335 GLU cc_start: 0.8503 (tm-30) cc_final: 0.7640 (tm-30) REVERT: C 352 GLU cc_start: 0.9048 (tm-30) cc_final: 0.8698 (tm-30) REVERT: C 385 MET cc_start: 0.8762 (ttm) cc_final: 0.8477 (ttm) REVERT: C 395 GLU cc_start: 0.8768 (mp0) cc_final: 0.8424 (mp0) REVERT: C 404 ASP cc_start: 0.8969 (t0) cc_final: 0.8764 (t70) REVERT: C 409 LYS cc_start: 0.8776 (tttp) cc_final: 0.8551 (ttmt) REVERT: C 510 GLU cc_start: 0.7753 (tp30) cc_final: 0.7438 (tp30) REVERT: D 21 GLN cc_start: 0.8843 (pt0) cc_final: 0.8442 (tm-30) REVERT: D 50 ASP cc_start: 0.8996 (t0) cc_final: 0.8670 (t70) REVERT: D 51 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.8905 (pp) REVERT: D 84 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8247 (tp) REVERT: D 105 ARG cc_start: 0.9060 (mtm110) cc_final: 0.8641 (mtm110) REVERT: D 256 ASP cc_start: 0.9295 (m-30) cc_final: 0.8831 (p0) REVERT: D 276 SER cc_start: 0.8410 (p) cc_final: 0.8111 (p) REVERT: D 332 ILE cc_start: 0.8937 (OUTLIER) cc_final: 0.8419 (pp) REVERT: D 335 GLU cc_start: 0.8560 (tm-30) cc_final: 0.7728 (tm-30) REVERT: D 352 GLU cc_start: 0.9166 (tm-30) cc_final: 0.8822 (tm-30) REVERT: D 395 GLU cc_start: 0.8884 (mp0) cc_final: 0.8443 (mp0) REVERT: D 399 GLU cc_start: 0.8697 (pm20) cc_final: 0.8416 (mp0) REVERT: D 400 TYR cc_start: 0.7912 (m-10) cc_final: 0.6658 (m-10) REVERT: D 404 ASP cc_start: 0.8963 (t0) cc_final: 0.8719 (t0) REVERT: D 407 ARG cc_start: 0.9033 (ttt90) cc_final: 0.8463 (ttt-90) REVERT: D 409 LYS cc_start: 0.8757 (ttmp) cc_final: 0.8309 (tttt) REVERT: D 438 LYS cc_start: 0.8557 (mmtt) cc_final: 0.8220 (mmtm) REVERT: D 449 ASP cc_start: 0.9139 (p0) cc_final: 0.8686 (p0) REVERT: D 510 GLU cc_start: 0.7898 (tp30) cc_final: 0.7557 (tp30) REVERT: E 21 GLN cc_start: 0.8836 (OUTLIER) cc_final: 0.8315 (tm-30) REVERT: E 51 LEU cc_start: 0.9249 (OUTLIER) cc_final: 0.9006 (pp) REVERT: E 105 ARG cc_start: 0.8893 (mtm110) cc_final: 0.8628 (mtm110) REVERT: E 109 LYS cc_start: 0.9444 (mttp) cc_final: 0.8949 (tmtt) REVERT: E 276 SER cc_start: 0.8456 (p) cc_final: 0.8162 (p) REVERT: E 335 GLU cc_start: 0.8587 (tm-30) cc_final: 0.7782 (tm-30) REVERT: E 352 GLU cc_start: 0.9053 (tm-30) cc_final: 0.8753 (tm-30) REVERT: E 379 LEU cc_start: 0.9370 (mt) cc_final: 0.9158 (mt) REVERT: E 385 MET cc_start: 0.8441 (ttm) cc_final: 0.8033 (ttm) REVERT: E 386 MET cc_start: 0.8920 (mtm) cc_final: 0.8457 (mtm) REVERT: E 395 GLU cc_start: 0.8765 (mp0) cc_final: 0.8376 (mp0) REVERT: E 404 ASP cc_start: 0.9029 (t0) cc_final: 0.8818 (t70) REVERT: E 510 GLU cc_start: 0.7774 (tp30) cc_final: 0.7559 (tp30) REVERT: E 512 ARG cc_start: 0.7910 (ttm-80) cc_final: 0.7489 (ttm-80) REVERT: F 21 GLN cc_start: 0.8795 (pt0) cc_final: 0.8454 (tm-30) REVERT: F 51 LEU cc_start: 0.9216 (OUTLIER) cc_final: 0.8961 (pp) REVERT: F 84 LEU cc_start: 0.8557 (OUTLIER) cc_final: 0.8272 (tp) REVERT: F 105 ARG cc_start: 0.9053 (mtm110) cc_final: 0.8680 (mtm110) REVERT: F 108 LYS cc_start: 0.9436 (tppp) cc_final: 0.9214 (mmtp) REVERT: F 109 LYS cc_start: 0.9437 (mttt) cc_final: 0.9175 (mttt) REVERT: F 276 SER cc_start: 0.8068 (p) cc_final: 0.7741 (p) REVERT: F 279 ASN cc_start: 0.9064 (t0) cc_final: 0.8706 (t0) REVERT: F 352 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8727 (tm-30) REVERT: F 355 ARG cc_start: 0.9188 (ptm-80) cc_final: 0.8890 (ptm-80) REVERT: F 385 MET cc_start: 0.8654 (ttm) cc_final: 0.8232 (ttm) REVERT: F 393 THR cc_start: 0.9079 (OUTLIER) cc_final: 0.8612 (m) REVERT: F 395 GLU cc_start: 0.8776 (mp0) cc_final: 0.8132 (mp0) REVERT: F 399 GLU cc_start: 0.8754 (pm20) cc_final: 0.8520 (pm20) REVERT: F 404 ASP cc_start: 0.8953 (t0) cc_final: 0.8723 (t0) REVERT: G 51 LEU cc_start: 0.9260 (OUTLIER) cc_final: 0.8943 (pp) REVERT: G 84 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8082 (mm) REVERT: G 276 SER cc_start: 0.8387 (p) cc_final: 0.8059 (p) REVERT: G 332 ILE cc_start: 0.8906 (OUTLIER) cc_final: 0.8452 (pp) REVERT: G 335 GLU cc_start: 0.8535 (tm-30) cc_final: 0.7632 (tm-30) REVERT: G 352 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8723 (tm-30) REVERT: G 355 ARG cc_start: 0.9225 (ptm-80) cc_final: 0.8814 (ptm-80) REVERT: G 385 MET cc_start: 0.8420 (ttm) cc_final: 0.8126 (ttm) REVERT: G 395 GLU cc_start: 0.8749 (mp0) cc_final: 0.8384 (mp0) REVERT: G 404 ASP cc_start: 0.9066 (t0) cc_final: 0.8796 (t70) REVERT: G 409 LYS cc_start: 0.8799 (ttmp) cc_final: 0.8424 (ttmt) REVERT: G 510 GLU cc_start: 0.7857 (tp30) cc_final: 0.7382 (tp30) REVERT: H 51 LEU cc_start: 0.9279 (OUTLIER) cc_final: 0.9000 (pp) REVERT: H 56 THR cc_start: 0.9028 (OUTLIER) cc_final: 0.8764 (t) REVERT: H 84 LEU cc_start: 0.8513 (OUTLIER) cc_final: 0.8102 (mm) REVERT: H 105 ARG cc_start: 0.8944 (mtm110) cc_final: 0.8675 (mtm110) REVERT: H 256 ASP cc_start: 0.9276 (m-30) cc_final: 0.8994 (p0) REVERT: H 258 TYR cc_start: 0.9174 (t80) cc_final: 0.8958 (t80) REVERT: H 332 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8561 (pp) REVERT: H 335 GLU cc_start: 0.8632 (tm-30) cc_final: 0.7766 (tm-30) REVERT: H 385 MET cc_start: 0.8728 (ttm) cc_final: 0.8410 (ttm) REVERT: H 395 GLU cc_start: 0.8847 (mp0) cc_final: 0.8296 (mp0) REVERT: H 404 ASP cc_start: 0.8974 (t0) cc_final: 0.8730 (t70) outliers start: 155 outliers final: 112 residues processed: 1026 average time/residue: 0.3331 time to fit residues: 537.4678 Evaluate side-chains 1079 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 944 time to evaluate : 3.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 82 MET Chi-restraints excluded: chain A residue 84 LEU Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 296 ASN Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 388 SER Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 37 ILE Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 235 LEU Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 284 ILE Chi-restraints excluded: chain B residue 296 ASN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 351 SER Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 469 GLN Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 260 LEU Chi-restraints excluded: chain C residue 296 ASN Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 351 SER Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 84 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 296 ASN Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 351 SER Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 469 GLN Chi-restraints excluded: chain D residue 500 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 21 GLN Chi-restraints excluded: chain E residue 51 LEU Chi-restraints excluded: chain E residue 56 THR Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 250 ILE Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 296 ASN Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 370 VAL Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 417 LEU 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 51 LEU Chi-restraints excluded: chain F residue 84 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 269 ASP Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 296 ASN Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 388 SER Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 471 ILE 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 7 SER Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 56 THR Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 84 LEU Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 260 LEU Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 296 ASN Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain G residue 500 GLU Chi-restraints excluded: chain G residue 513 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 51 LEU Chi-restraints excluded: chain H residue 56 THR Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 84 LEU Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 500 GLU Chi-restraints excluded: chain H residue 513 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 259 optimal weight: 6.9990 chunk 273 optimal weight: 0.6980 chunk 249 optimal weight: 1.9990 chunk 265 optimal weight: 0.7980 chunk 160 optimal weight: 0.9980 chunk 115 optimal weight: 0.0870 chunk 208 optimal weight: 0.0050 chunk 81 optimal weight: 0.9990 chunk 240 optimal weight: 0.8980 chunk 251 optimal weight: 0.0050 chunk 264 optimal weight: 0.0470 overall best weight: 0.1684 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 ASN C 469 GLN D 469 GLN ** E 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 469 GLN F 100 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 312 ASN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 285 ASN ** H 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23480 Z= 0.178 Angle : 0.666 10.895 31792 Z= 0.328 Chirality : 0.045 0.192 3656 Planarity : 0.004 0.039 4000 Dihedral : 8.611 82.575 3765 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 4.82 % Allowed : 30.20 % Favored : 64.97 % 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: -1.80 (0.15), residues: 2960 helix: -1.15 (0.15), residues: 1016 sheet: -2.32 (0.26), residues: 336 loop : -0.85 (0.15), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS B 92 PHE 0.012 0.001 PHE B 401 TYR 0.020 0.001 TYR B 258 ARG 0.011 0.001 ARG B 105 *********************** 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 1129 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1014 time to evaluate : 2.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.8089 (tm-30) REVERT: A 51 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8858 (pp) REVERT: A 108 LYS cc_start: 0.9526 (OUTLIER) cc_final: 0.9292 (tppp) REVERT: A 109 LYS cc_start: 0.9556 (mmmt) cc_final: 0.9170 (tmtt) REVERT: A 335 GLU cc_start: 0.8461 (tm-30) cc_final: 0.7651 (tm-30) REVERT: A 352 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8732 (tm-30) REVERT: A 395 GLU cc_start: 0.8807 (mp0) cc_final: 0.8353 (mp0) REVERT: A 399 GLU cc_start: 0.8455 (mp0) cc_final: 0.8222 (mp0) REVERT: A 400 TYR cc_start: 0.7838 (m-10) cc_final: 0.6978 (m-10) REVERT: A 406 ILE cc_start: 0.9229 (mm) cc_final: 0.9005 (mm) REVERT: A 407 ARG cc_start: 0.9100 (ttt90) cc_final: 0.8618 (ttt-90) REVERT: A 409 LYS cc_start: 0.8750 (ttmp) cc_final: 0.8522 (ttmt) REVERT: A 510 GLU cc_start: 0.7706 (tp30) cc_final: 0.7341 (tp30) REVERT: A 512 ARG cc_start: 0.7863 (ttm-80) cc_final: 0.7443 (ttm-80) REVERT: B 21 GLN cc_start: 0.8786 (OUTLIER) cc_final: 0.8342 (tm-30) REVERT: B 105 ARG cc_start: 0.8782 (mtm110) cc_final: 0.8391 (mtm110) REVERT: B 256 ASP cc_start: 0.9262 (m-30) cc_final: 0.8836 (p0) REVERT: B 335 GLU cc_start: 0.8565 (tm-30) cc_final: 0.7752 (tm-30) REVERT: B 352 GLU cc_start: 0.9106 (tm-30) cc_final: 0.8762 (tm-30) REVERT: B 395 GLU cc_start: 0.8773 (mp0) cc_final: 0.8305 (mp0) REVERT: B 404 ASP cc_start: 0.8989 (t0) cc_final: 0.8749 (t70) REVERT: B 406 ILE cc_start: 0.9096 (mp) cc_final: 0.8881 (mp) REVERT: B 410 LYS cc_start: 0.8737 (ptmm) cc_final: 0.8523 (ptmt) REVERT: B 510 GLU cc_start: 0.8069 (tp30) cc_final: 0.7763 (tp30) REVERT: C 21 GLN cc_start: 0.8789 (pt0) cc_final: 0.8550 (tt0) REVERT: C 51 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8990 (pp) REVERT: C 105 ARG cc_start: 0.8909 (mtm110) cc_final: 0.8390 (mtm110) REVERT: C 109 LYS cc_start: 0.9297 (mttp) cc_final: 0.9020 (mttm) REVERT: C 276 SER cc_start: 0.7522 (p) cc_final: 0.7125 (p) REVERT: C 279 ASN cc_start: 0.8861 (t0) cc_final: 0.7954 (t0) REVERT: C 332 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8431 (pp) REVERT: C 335 GLU cc_start: 0.8475 (tm-30) cc_final: 0.7604 (tm-30) REVERT: C 352 GLU cc_start: 0.8988 (tm-30) cc_final: 0.8627 (tm-30) REVERT: C 385 MET cc_start: 0.8699 (ttm) cc_final: 0.8259 (ttm) REVERT: C 395 GLU cc_start: 0.8688 (mp0) cc_final: 0.8359 (mp0) REVERT: C 404 ASP cc_start: 0.8948 (t0) cc_final: 0.8742 (t70) REVERT: C 407 ARG cc_start: 0.8977 (ttt90) cc_final: 0.8538 (tpt-90) REVERT: C 409 LYS cc_start: 0.8749 (tttp) cc_final: 0.8520 (ttmt) REVERT: C 510 GLU cc_start: 0.7720 (tp30) cc_final: 0.7432 (tp30) REVERT: D 21 GLN cc_start: 0.8734 (pt0) cc_final: 0.8359 (tm-30) REVERT: D 51 LEU cc_start: 0.9153 (OUTLIER) cc_final: 0.8837 (pp) REVERT: D 105 ARG cc_start: 0.8939 (mtm110) cc_final: 0.8573 (mtm110) REVERT: D 256 ASP cc_start: 0.9264 (m-30) cc_final: 0.8802 (p0) REVERT: D 276 SER cc_start: 0.8143 (p) cc_final: 0.7851 (p) REVERT: D 332 ILE cc_start: 0.8892 (OUTLIER) cc_final: 0.8393 (pp) REVERT: D 335 GLU cc_start: 0.8533 (tm-30) cc_final: 0.7682 (tm-30) REVERT: D 352 GLU cc_start: 0.9125 (tm-30) cc_final: 0.8773 (tm-30) REVERT: D 395 GLU cc_start: 0.8855 (mp0) cc_final: 0.8461 (mp0) REVERT: D 399 GLU cc_start: 0.8680 (pm20) cc_final: 0.8463 (mp0) REVERT: D 400 TYR cc_start: 0.7847 (m-10) cc_final: 0.7609 (m-10) REVERT: D 404 ASP cc_start: 0.8953 (t0) cc_final: 0.8728 (t0) REVERT: D 407 ARG cc_start: 0.9050 (ttt90) cc_final: 0.8805 (ttt90) REVERT: D 409 LYS cc_start: 0.8732 (ttmp) cc_final: 0.8306 (tttt) REVERT: D 438 LYS cc_start: 0.8564 (mmtt) cc_final: 0.8236 (mmtm) REVERT: D 510 GLU cc_start: 0.7881 (tp30) cc_final: 0.7534 (tp30) REVERT: E 21 GLN cc_start: 0.8803 (OUTLIER) cc_final: 0.8464 (tm-30) REVERT: E 25 ASN cc_start: 0.8981 (m-40) cc_final: 0.8378 (p0) REVERT: E 75 GLU cc_start: 0.7909 (mm-30) cc_final: 0.7641 (mm-30) REVERT: E 276 SER cc_start: 0.8099 (p) cc_final: 0.7774 (p) REVERT: E 335 GLU cc_start: 0.8561 (tm-30) cc_final: 0.7781 (tm-30) REVERT: E 352 GLU cc_start: 0.9039 (tm-30) cc_final: 0.8740 (tm-30) REVERT: E 386 MET cc_start: 0.8892 (mtm) cc_final: 0.8411 (mtm) REVERT: E 395 GLU cc_start: 0.8690 (mp0) cc_final: 0.8374 (mp0) REVERT: E 404 ASP cc_start: 0.9004 (t0) cc_final: 0.8782 (t70) REVERT: E 510 GLU cc_start: 0.7874 (tp30) cc_final: 0.7650 (tp30) REVERT: E 512 ARG cc_start: 0.7903 (ttm-80) cc_final: 0.7511 (ttm-80) REVERT: F 21 GLN cc_start: 0.8754 (pt0) cc_final: 0.8349 (tm-30) REVERT: F 51 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8868 (pp) REVERT: F 105 ARG cc_start: 0.8994 (mtm110) cc_final: 0.8669 (mtm110) REVERT: F 108 LYS cc_start: 0.9471 (tppp) cc_final: 0.9238 (mmtp) REVERT: F 109 LYS cc_start: 0.9457 (mttt) cc_final: 0.9203 (mttt) REVERT: F 276 SER cc_start: 0.7595 (p) cc_final: 0.7222 (p) REVERT: F 279 ASN cc_start: 0.9003 (t0) cc_final: 0.7898 (t0) REVERT: F 335 GLU cc_start: 0.8565 (tm-30) cc_final: 0.7765 (tm-30) REVERT: F 352 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8692 (tm-30) REVERT: F 355 ARG cc_start: 0.9164 (ptm-80) cc_final: 0.8910 (ptm-80) REVERT: F 385 MET cc_start: 0.8686 (ttm) cc_final: 0.8305 (ttm) REVERT: F 393 THR cc_start: 0.8978 (OUTLIER) cc_final: 0.8493 (m) REVERT: F 395 GLU cc_start: 0.8693 (mp0) cc_final: 0.8137 (mp0) REVERT: F 399 GLU cc_start: 0.8683 (pm20) cc_final: 0.8428 (pm20) REVERT: F 404 ASP cc_start: 0.8928 (t0) cc_final: 0.8679 (t0) REVERT: F 409 LYS cc_start: 0.8611 (ttmp) cc_final: 0.7919 (ttmt) REVERT: G 51 LEU cc_start: 0.9173 (OUTLIER) cc_final: 0.8855 (pp) REVERT: G 276 SER cc_start: 0.8267 (p) cc_final: 0.7940 (p) REVERT: G 332 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8322 (pp) REVERT: G 335 GLU cc_start: 0.8516 (tm-30) cc_final: 0.7573 (tm-30) REVERT: G 351 SER cc_start: 0.9127 (t) cc_final: 0.8922 (t) REVERT: G 352 GLU cc_start: 0.9000 (tm-30) cc_final: 0.8639 (tm-30) REVERT: G 355 ARG cc_start: 0.9170 (ptm-80) cc_final: 0.8807 (ptm-80) REVERT: G 395 GLU cc_start: 0.8691 (mp0) cc_final: 0.8421 (mp0) REVERT: G 404 ASP cc_start: 0.9012 (t0) cc_final: 0.8755 (t70) REVERT: G 409 LYS cc_start: 0.8826 (ttmp) cc_final: 0.8593 (ttmt) REVERT: G 510 GLU cc_start: 0.7865 (tp30) cc_final: 0.7416 (tp30) REVERT: H 21 GLN cc_start: 0.8714 (pt0) cc_final: 0.8352 (tm-30) REVERT: H 108 LYS cc_start: 0.9467 (mttm) cc_final: 0.9064 (mmtp) REVERT: H 109 LYS cc_start: 0.9441 (mttt) cc_final: 0.9145 (mttt) REVERT: H 256 ASP cc_start: 0.9269 (m-30) cc_final: 0.8963 (p0) REVERT: H 286 MET cc_start: 0.9492 (tpp) cc_final: 0.8753 (tpp) REVERT: H 332 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8507 (pp) REVERT: H 335 GLU cc_start: 0.8586 (tm-30) cc_final: 0.7683 (tm-30) REVERT: H 337 LEU cc_start: 0.9139 (mp) cc_final: 0.8911 (mt) REVERT: H 385 MET cc_start: 0.8733 (ttm) cc_final: 0.8453 (ttm) REVERT: H 395 GLU cc_start: 0.8797 (mp0) cc_final: 0.8311 (mp0) REVERT: H 404 ASP cc_start: 0.8964 (t0) cc_final: 0.8712 (t70) outliers start: 115 outliers final: 76 residues processed: 1056 average time/residue: 0.3272 time to fit residues: 537.9780 Evaluate side-chains 1072 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 982 time to evaluate : 2.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 56 THR Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 108 LYS Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 269 ASP Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 388 SER Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain D residue 513 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 21 GLN Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 102 ASN Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 327 SER Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 417 LEU Chi-restraints excluded: chain E residue 467 SER Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 500 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 296 random chunks: chunk 174 optimal weight: 0.9990 chunk 281 optimal weight: 0.1980 chunk 171 optimal weight: 0.7980 chunk 133 optimal weight: 0.5980 chunk 195 optimal weight: 3.9990 chunk 294 optimal weight: 3.9990 chunk 271 optimal weight: 0.9980 chunk 234 optimal weight: 6.9990 chunk 24 optimal weight: 0.6980 chunk 181 optimal weight: 2.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 285 ASN A 498 GLN ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 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** ** E 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 469 GLN ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 GLN ** G 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 285 ASN ** H 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.4198 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= 0.222 Angle : 0.703 10.881 31792 Z= 0.342 Chirality : 0.046 0.211 3656 Planarity : 0.004 0.050 4000 Dihedral : 8.471 81.196 3755 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 17.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.15 % Allowed : 31.21 % Favored : 64.64 % 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: -1.68 (0.15), residues: 2960 helix: -1.01 (0.15), residues: 1016 sheet: -2.33 (0.26), residues: 336 loop : -0.79 (0.16), residues: 1608 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS H 92 PHE 0.012 0.001 PHE E 24 TYR 0.023 0.001 TYR A 258 ARG 0.016 0.001 ARG H 105 ********************** 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 1082 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 983 time to evaluate : 2.494 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 21 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.8483 (tm-30) REVERT: A 25 ASN cc_start: 0.9051 (m-40) cc_final: 0.8679 (m-40) REVERT: A 51 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.8993 (pp) REVERT: A 105 ARG cc_start: 0.8992 (ttp80) cc_final: 0.8770 (ttp-110) REVERT: A 109 LYS cc_start: 0.9565 (mmmt) cc_final: 0.9158 (tmtt) REVERT: A 335 GLU cc_start: 0.8450 (tm-30) cc_final: 0.7611 (tm-30) REVERT: A 352 GLU cc_start: 0.9097 (tm-30) cc_final: 0.8857 (tm-30) REVERT: A 395 GLU cc_start: 0.8922 (mp0) cc_final: 0.8466 (mp0) REVERT: A 400 TYR cc_start: 0.7863 (m-10) cc_final: 0.6889 (m-10) REVERT: A 406 ILE cc_start: 0.9235 (mm) cc_final: 0.8902 (mp) REVERT: A 407 ARG cc_start: 0.9114 (ttt90) cc_final: 0.8386 (ttt-90) REVERT: A 409 LYS cc_start: 0.8740 (tttp) cc_final: 0.8290 (tttt) REVERT: A 510 GLU cc_start: 0.7711 (tp30) cc_final: 0.7352 (tp30) REVERT: A 512 ARG cc_start: 0.7850 (ttm-80) cc_final: 0.7428 (ttm-80) REVERT: B 21 GLN cc_start: 0.8851 (OUTLIER) cc_final: 0.8510 (tm-30) REVERT: B 25 ASN cc_start: 0.9072 (m-40) cc_final: 0.8426 (p0) REVERT: B 105 ARG cc_start: 0.8811 (mtm110) cc_final: 0.8432 (mtm110) REVERT: B 256 ASP cc_start: 0.9218 (m-30) cc_final: 0.8772 (p0) REVERT: B 335 GLU cc_start: 0.8560 (tm-30) cc_final: 0.7758 (tm-30) REVERT: B 352 GLU cc_start: 0.9118 (tm-30) cc_final: 0.8779 (tm-30) REVERT: B 395 GLU cc_start: 0.8803 (mp0) cc_final: 0.8342 (mp0) REVERT: B 404 ASP cc_start: 0.8992 (t0) cc_final: 0.8766 (t70) REVERT: B 406 ILE cc_start: 0.9102 (mp) cc_final: 0.8895 (mp) REVERT: B 510 GLU cc_start: 0.8069 (tp30) cc_final: 0.7769 (tp30) REVERT: C 21 GLN cc_start: 0.8838 (pt0) cc_final: 0.8428 (tm-30) REVERT: C 51 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8839 (pp) REVERT: C 105 ARG cc_start: 0.8926 (mtm110) cc_final: 0.8405 (mtm110) REVERT: C 109 LYS cc_start: 0.9255 (mttp) cc_final: 0.8989 (mttm) REVERT: C 276 SER cc_start: 0.7714 (p) cc_final: 0.7336 (p) REVERT: C 279 ASN cc_start: 0.8887 (t0) cc_final: 0.7942 (t0) REVERT: C 332 ILE cc_start: 0.8830 (OUTLIER) cc_final: 0.8428 (pp) REVERT: C 335 GLU cc_start: 0.8478 (tm-30) cc_final: 0.7609 (tm-30) REVERT: C 352 GLU cc_start: 0.8999 (tm-30) cc_final: 0.8638 (tm-30) REVERT: C 355 ARG cc_start: 0.9177 (ptm-80) cc_final: 0.8926 (ptm-80) REVERT: C 385 MET cc_start: 0.8714 (ttm) cc_final: 0.8251 (ttm) REVERT: C 395 GLU cc_start: 0.8831 (mp0) cc_final: 0.8482 (mp0) REVERT: C 510 GLU cc_start: 0.7740 (tp30) cc_final: 0.7385 (tp30) REVERT: D 21 GLN cc_start: 0.8793 (pt0) cc_final: 0.8488 (tm-30) REVERT: D 51 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.9007 (pp) REVERT: D 105 ARG cc_start: 0.9024 (mtm110) cc_final: 0.8648 (mtm110) REVERT: D 256 ASP cc_start: 0.9235 (m-30) cc_final: 0.8788 (p0) REVERT: D 276 SER cc_start: 0.8284 (p) cc_final: 0.7997 (p) REVERT: D 332 ILE cc_start: 0.8928 (OUTLIER) cc_final: 0.8443 (pp) REVERT: D 335 GLU cc_start: 0.8536 (tm-30) cc_final: 0.7687 (tm-30) REVERT: D 352 GLU cc_start: 0.9135 (tm-30) cc_final: 0.8799 (tm-30) REVERT: D 395 GLU cc_start: 0.8932 (mp0) cc_final: 0.8597 (mp0) REVERT: D 399 GLU cc_start: 0.8686 (pm20) cc_final: 0.8463 (mp0) REVERT: D 400 TYR cc_start: 0.7837 (m-10) cc_final: 0.7603 (m-10) REVERT: D 407 ARG cc_start: 0.9096 (ttt90) cc_final: 0.8808 (ttt90) REVERT: D 409 LYS cc_start: 0.8749 (ttmp) cc_final: 0.8301 (tttt) REVERT: D 438 LYS cc_start: 0.8541 (mmtt) cc_final: 0.8209 (mmtm) REVERT: D 510 GLU cc_start: 0.7874 (tp30) cc_final: 0.7542 (tp30) REVERT: E 21 GLN cc_start: 0.8835 (OUTLIER) cc_final: 0.8513 (tm-30) REVERT: E 25 ASN cc_start: 0.8991 (m-40) cc_final: 0.8371 (p0) REVERT: E 75 GLU cc_start: 0.7922 (mm-30) cc_final: 0.7643 (mm-30) REVERT: E 105 ARG cc_start: 0.8838 (mtm110) cc_final: 0.8451 (mtm110) REVERT: E 276 SER cc_start: 0.8161 (p) cc_final: 0.7931 (p) REVERT: E 335 GLU cc_start: 0.8564 (tm-30) cc_final: 0.7764 (tm-30) REVERT: E 352 GLU cc_start: 0.9040 (tm-30) cc_final: 0.8733 (tm-30) REVERT: E 355 ARG cc_start: 0.9120 (ptm-80) cc_final: 0.8776 (ptm-80) REVERT: E 395 GLU cc_start: 0.8730 (mp0) cc_final: 0.8386 (mp0) REVERT: E 510 GLU cc_start: 0.7866 (tp30) cc_final: 0.7644 (tp30) REVERT: E 512 ARG cc_start: 0.7895 (ttm-80) cc_final: 0.7470 (ttm-80) REVERT: F 21 GLN cc_start: 0.8743 (pt0) cc_final: 0.8473 (tm-30) REVERT: F 105 ARG cc_start: 0.8998 (mtm110) cc_final: 0.8658 (mtm110) REVERT: F 108 LYS cc_start: 0.9536 (tppp) cc_final: 0.9313 (mmtp) REVERT: F 109 LYS cc_start: 0.9435 (mttt) cc_final: 0.9193 (mttt) REVERT: F 276 SER cc_start: 0.7740 (p) cc_final: 0.7418 (p) REVERT: F 279 ASN cc_start: 0.9037 (t0) cc_final: 0.7936 (t0) REVERT: F 335 GLU cc_start: 0.8582 (tm-30) cc_final: 0.7759 (tm-30) REVERT: F 352 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8716 (tm-30) REVERT: F 355 ARG cc_start: 0.9190 (ptm-80) cc_final: 0.8913 (ptm-80) REVERT: F 385 MET cc_start: 0.8670 (ttm) cc_final: 0.8311 (ttm) REVERT: F 393 THR cc_start: 0.9001 (OUTLIER) cc_final: 0.8520 (m) REVERT: F 395 GLU cc_start: 0.8822 (mp0) cc_final: 0.8263 (mp0) REVERT: F 399 GLU cc_start: 0.8744 (pm20) cc_final: 0.8505 (pm20) REVERT: F 409 LYS cc_start: 0.8823 (ttmp) cc_final: 0.8319 (ttmt) REVERT: F 512 ARG cc_start: 0.7893 (ttm-80) cc_final: 0.7525 (ttm-80) REVERT: G 51 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8974 (pp) REVERT: G 276 SER cc_start: 0.8295 (p) cc_final: 0.7886 (p) REVERT: G 277 GLN cc_start: 0.8684 (tp40) cc_final: 0.8327 (tp40) REVERT: G 332 ILE cc_start: 0.8855 (OUTLIER) cc_final: 0.8357 (pp) REVERT: G 335 GLU cc_start: 0.8513 (tm-30) cc_final: 0.7556 (tm-30) REVERT: G 352 GLU cc_start: 0.9012 (tm-30) cc_final: 0.8666 (tm-30) REVERT: G 355 ARG cc_start: 0.9183 (ptm-80) cc_final: 0.8794 (ptm-80) REVERT: G 395 GLU cc_start: 0.8723 (mp0) cc_final: 0.8500 (mp0) REVERT: G 404 ASP cc_start: 0.9041 (t0) cc_final: 0.8796 (t70) REVERT: G 409 LYS cc_start: 0.8785 (ttmp) cc_final: 0.8445 (ttmt) REVERT: G 510 GLU cc_start: 0.7869 (tp30) cc_final: 0.7399 (tp30) REVERT: H 21 GLN cc_start: 0.8818 (pt0) cc_final: 0.8444 (tm-30) REVERT: H 105 ARG cc_start: 0.8874 (mtm110) cc_final: 0.8632 (mtm110) REVERT: H 108 LYS cc_start: 0.9489 (mttm) cc_final: 0.9149 (mmtp) REVERT: H 256 ASP cc_start: 0.9240 (m-30) cc_final: 0.8932 (p0) REVERT: H 286 MET cc_start: 0.9497 (tpp) cc_final: 0.8733 (tpp) REVERT: H 332 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8515 (pp) REVERT: H 335 GLU cc_start: 0.8585 (tm-30) cc_final: 0.7686 (tm-30) REVERT: H 385 MET cc_start: 0.8751 (ttm) cc_final: 0.8463 (ttm) REVERT: H 395 GLU cc_start: 0.8855 (mp0) cc_final: 0.8377 (mp0) REVERT: H 404 ASP cc_start: 0.8934 (t0) cc_final: 0.8704 (t0) outliers start: 99 outliers final: 81 residues processed: 1021 average time/residue: 0.3238 time to fit residues: 519.2494 Evaluate side-chains 1059 residues out of total 2384 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 966 time to evaluate : 2.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 21 GLN Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 73 VAL Chi-restraints excluded: chain A residue 107 VAL Chi-restraints excluded: chain A residue 269 ASP Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 309 GLN Chi-restraints excluded: chain A residue 327 SER Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain A residue 485 SER Chi-restraints excluded: chain A residue 500 GLU Chi-restraints excluded: chain B residue 21 GLN Chi-restraints excluded: chain B residue 250 ILE Chi-restraints excluded: chain B residue 269 ASP Chi-restraints excluded: chain B residue 281 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 384 VAL Chi-restraints excluded: chain B residue 417 LEU Chi-restraints excluded: chain B residue 500 GLU Chi-restraints excluded: chain B residue 513 LEU Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 61 LEU Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain C residue 384 VAL Chi-restraints excluded: chain C residue 417 LEU Chi-restraints excluded: chain C residue 500 GLU Chi-restraints excluded: chain D residue 30 LEU Chi-restraints excluded: chain D residue 51 LEU Chi-restraints excluded: chain D residue 73 VAL Chi-restraints excluded: chain D residue 250 ILE Chi-restraints excluded: chain D residue 284 ILE Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain D residue 332 ILE Chi-restraints excluded: chain D residue 370 VAL Chi-restraints excluded: chain D residue 373 ILE Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 384 VAL Chi-restraints excluded: chain D residue 417 LEU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 21 GLN Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 78 MET Chi-restraints excluded: chain E residue 260 LEU Chi-restraints excluded: chain E residue 269 ASP Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain E residue 384 VAL Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 469 GLN Chi-restraints excluded: chain E residue 499 VAL Chi-restraints excluded: chain F residue 250 ILE Chi-restraints excluded: chain F residue 284 ILE Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 299 VAL Chi-restraints excluded: chain F residue 384 VAL Chi-restraints excluded: chain F residue 393 THR Chi-restraints excluded: chain F residue 417 LEU Chi-restraints excluded: chain F residue 485 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 43 ASP Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain G residue 61 LEU Chi-restraints excluded: chain G residue 78 MET Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain G residue 284 ILE Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 313 LEU Chi-restraints excluded: chain G residue 332 ILE Chi-restraints excluded: chain G residue 377 LEU Chi-restraints excluded: chain G residue 384 VAL Chi-restraints excluded: chain G residue 417 LEU Chi-restraints excluded: chain H residue 5 LEU Chi-restraints excluded: chain H residue 65 LEU Chi-restraints excluded: chain H residue 269 ASP Chi-restraints excluded: chain H residue 296 ASN Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 332 ILE Chi-restraints excluded: chain H residue 351 SER Chi-restraints excluded: chain H residue 377 LEU Chi-restraints excluded: chain H residue 384 VAL Chi-restraints excluded: chain H residue 417 LEU Chi-restraints excluded: chain H residue 471 ILE Chi-restraints excluded: chain H residue 500 GLU 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: 0.9980 chunk 71 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 241 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 0.0000 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 469 GLN ** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 372 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 309 GLN ** E 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 279 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 285 ASN ** 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 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 309 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN ** H 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.108007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.086213 restraints weight = 41215.016| |-----------------------------------------------------------------------------| r_work (start): 0.3000 rms_B_bonded: 4.06 r_work: 0.2833 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7779 moved from start: 0.4179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23480 Z= 0.294 Angle : 0.738 11.287 31792 Z= 0.363 Chirality : 0.047 0.204 3656 Planarity : 0.004 0.043 4000 Dihedral : 8.546 82.116 3750 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 18.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 4.91 % Allowed : 30.96 % Favored : 64.14 % 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: -1.71 (0.15), residues: 2960 helix: -0.99 (0.16), residues: 1016 sheet: -2.43 (0.25), residues: 352 loop : -0.79 (0.16), residues: 1592 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS E 466 PHE 0.011 0.001 PHE B 24 TYR 0.030 0.002 TYR H 258 ARG 0.017 0.001 ARG H 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8222.72 seconds wall clock time: 146 minutes 31.97 seconds (8791.97 seconds total)