Starting phenix.real_space_refine on Wed Feb 21 17:56:01 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pdt_20309/02_2024/6pdt_20309_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pdt_20309/02_2024/6pdt_20309.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pdt_20309/02_2024/6pdt_20309.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pdt_20309/02_2024/6pdt_20309.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pdt_20309/02_2024/6pdt_20309_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pdt_20309/02_2024/6pdt_20309_trim_updated.pdb" } resolution = 3.8 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= 0.000 sd= 0.003 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: 7 Type Number sf(0) Gaussians P 12 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 9888 2.51 5 N 2676 2.21 5 O 3064 1.98 5 H 15636 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 3": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 68": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 129": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 165": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 258": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 330": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 352": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 366": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 455": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 456": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 31364 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 7797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 7797 Classifications: {'peptide': 500} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 475} Chain: "B" Number of atoms: 7797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 7797 Classifications: {'peptide': 500} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 475} Chain: "C" Number of atoms: 7797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 7797 Classifications: {'peptide': 500} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 475} Chain: "D" Number of atoms: 7797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 7797 Classifications: {'peptide': 500} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'CIS': 2, 'PCIS': 1, 'PTRANS': 21, 'TRANS': 475} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {' MG': 1, 'ATP': 1, 'GLC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {' MG': 1, 'ATP': 1, 'GLC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {' MG': 1, 'ATP': 1, 'GLC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 44 Unusual residues: {' MG': 1, 'ATP': 1, 'GLC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 13.84, per 1000 atoms: 0.44 Number of scatterers: 31364 At special positions: 0 Unit cell: (95.55, 110.25, 171.15, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 84 16.00 P 12 15.00 Mg 4 11.99 O 3064 8.00 N 2676 7.00 C 9888 6.00 H 15636 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 248 " - pdb=" SG CYS A 448 " distance=2.21 Simple disulfide: pdb=" SG CYS B 248 " - pdb=" SG CYS B 448 " distance=2.21 Simple disulfide: pdb=" SG CYS C 248 " - pdb=" SG CYS C 448 " distance=2.21 Simple disulfide: pdb=" SG CYS D 248 " - pdb=" SG CYS D 448 " distance=2.21 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=0, symmetry=0 Time building additional restraints: 27.12 Conformation dependent library (CDL) restraints added in 3.2 seconds 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3696 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 92 helices and 12 sheets defined 47.8% alpha, 15.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.33 Creating SS restraints... Processing helix chain 'A' and resid 3 through 25 Processing helix chain 'A' and resid 29 through 47 Processing helix chain 'A' and resid 115 through 117 No H-bonds generated for 'chain 'A' and resid 115 through 117' Processing helix chain 'A' and resid 125 through 143 Processing helix chain 'A' and resid 145 through 150 Processing helix chain 'A' and resid 187 through 189 No H-bonds generated for 'chain 'A' and resid 187 through 189' Processing helix chain 'A' and resid 194 through 204 Processing helix chain 'A' and resid 218 through 228 Processing helix chain 'A' and resid 262 through 264 No H-bonds generated for 'chain 'A' and resid 262 through 264' Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.901A pdb=" N GLU A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 292 No H-bonds generated for 'chain 'A' and resid 290 through 292' Processing helix chain 'A' and resid 304 through 312 Processing helix chain 'A' and resid 323 through 326 No H-bonds generated for 'chain 'A' and resid 323 through 326' Processing helix chain 'A' and resid 328 through 344 Processing helix chain 'A' and resid 355 through 357 No H-bonds generated for 'chain 'A' and resid 355 through 357' Processing helix chain 'A' and resid 360 through 363 No H-bonds generated for 'chain 'A' and resid 360 through 363' Processing helix chain 'A' and resid 370 through 378 Processing helix chain 'A' and resid 381 through 395 removed outlier: 3.854A pdb=" N GLU A 388 " --> pdb=" O LEU A 384 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N LEU A 389 " --> pdb=" O ARG A 385 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU A 395 " --> pdb=" O LEU A 391 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 432 removed outlier: 3.525A pdb=" N ALA A 423 " --> pdb=" O ALA A 419 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL A 424 " --> pdb=" O TYR A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 451 through 455 Processing helix chain 'A' and resid 459 through 469 Processing helix chain 'A' and resid 473 through 479 removed outlier: 3.846A pdb=" N LYS A 479 " --> pdb=" O GLU A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 499 Processing helix chain 'B' and resid 3 through 25 Processing helix chain 'B' and resid 29 through 47 Processing helix chain 'B' and resid 115 through 117 No H-bonds generated for 'chain 'B' and resid 115 through 117' Processing helix chain 'B' and resid 125 through 143 Processing helix chain 'B' and resid 145 through 150 Processing helix chain 'B' and resid 187 through 189 No H-bonds generated for 'chain 'B' and resid 187 through 189' Processing helix chain 'B' and resid 194 through 204 Processing helix chain 'B' and resid 218 through 228 Processing helix chain 'B' and resid 262 through 264 No H-bonds generated for 'chain 'B' and resid 262 through 264' Processing helix chain 'B' and resid 270 through 279 removed outlier: 3.901A pdb=" N GLU B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 290 through 292 No H-bonds generated for 'chain 'B' and resid 290 through 292' Processing helix chain 'B' and resid 304 through 312 Processing helix chain 'B' and resid 323 through 326 No H-bonds generated for 'chain 'B' and resid 323 through 326' Processing helix chain 'B' and resid 328 through 344 Processing helix chain 'B' and resid 355 through 357 No H-bonds generated for 'chain 'B' and resid 355 through 357' Processing helix chain 'B' and resid 360 through 363 No H-bonds generated for 'chain 'B' and resid 360 through 363' Processing helix chain 'B' and resid 370 through 378 Processing helix chain 'B' and resid 381 through 395 removed outlier: 3.854A pdb=" N GLU B 388 " --> pdb=" O LEU B 384 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU B 389 " --> pdb=" O ARG B 385 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LEU B 395 " --> pdb=" O LEU B 391 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 432 removed outlier: 3.526A pdb=" N ALA B 423 " --> pdb=" O ALA B 419 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N VAL B 424 " --> pdb=" O TYR B 420 " (cutoff:3.500A) Proline residue: B 425 - end of helix Processing helix chain 'B' and resid 451 through 455 Processing helix chain 'B' and resid 459 through 469 Processing helix chain 'B' and resid 473 through 479 removed outlier: 3.846A pdb=" N LYS B 479 " --> pdb=" O GLU B 475 " (cutoff:3.500A) Processing helix chain 'B' and resid 488 through 499 Processing helix chain 'C' and resid 3 through 25 Processing helix chain 'C' and resid 29 through 47 Processing helix chain 'C' and resid 115 through 117 No H-bonds generated for 'chain 'C' and resid 115 through 117' Processing helix chain 'C' and resid 125 through 143 Processing helix chain 'C' and resid 145 through 150 Processing helix chain 'C' and resid 187 through 189 No H-bonds generated for 'chain 'C' and resid 187 through 189' Processing helix chain 'C' and resid 194 through 204 Processing helix chain 'C' and resid 218 through 228 Processing helix chain 'C' and resid 262 through 264 No H-bonds generated for 'chain 'C' and resid 262 through 264' Processing helix chain 'C' and resid 270 through 279 removed outlier: 3.900A pdb=" N GLU C 279 " --> pdb=" O LYS C 275 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 292 No H-bonds generated for 'chain 'C' and resid 290 through 292' Processing helix chain 'C' and resid 304 through 312 Processing helix chain 'C' and resid 323 through 326 No H-bonds generated for 'chain 'C' and resid 323 through 326' Processing helix chain 'C' and resid 328 through 344 Processing helix chain 'C' and resid 355 through 357 No H-bonds generated for 'chain 'C' and resid 355 through 357' Processing helix chain 'C' and resid 360 through 363 No H-bonds generated for 'chain 'C' and resid 360 through 363' Processing helix chain 'C' and resid 370 through 378 Processing helix chain 'C' and resid 381 through 395 removed outlier: 3.853A pdb=" N GLU C 388 " --> pdb=" O LEU C 384 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU C 389 " --> pdb=" O ARG C 385 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU C 395 " --> pdb=" O LEU C 391 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 432 removed outlier: 3.525A pdb=" N ALA C 423 " --> pdb=" O ALA C 419 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N VAL C 424 " --> pdb=" O TYR C 420 " (cutoff:3.500A) Proline residue: C 425 - end of helix Processing helix chain 'C' and resid 451 through 455 Processing helix chain 'C' and resid 459 through 469 Processing helix chain 'C' and resid 473 through 479 removed outlier: 3.846A pdb=" N LYS C 479 " --> pdb=" O GLU C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 488 through 499 Processing helix chain 'D' and resid 3 through 25 Processing helix chain 'D' and resid 29 through 47 Processing helix chain 'D' and resid 115 through 117 No H-bonds generated for 'chain 'D' and resid 115 through 117' Processing helix chain 'D' and resid 125 through 143 Processing helix chain 'D' and resid 145 through 150 Processing helix chain 'D' and resid 187 through 189 No H-bonds generated for 'chain 'D' and resid 187 through 189' Processing helix chain 'D' and resid 194 through 204 Processing helix chain 'D' and resid 218 through 228 Processing helix chain 'D' and resid 262 through 264 No H-bonds generated for 'chain 'D' and resid 262 through 264' Processing helix chain 'D' and resid 270 through 279 removed outlier: 3.901A pdb=" N GLU D 279 " --> pdb=" O LYS D 275 " (cutoff:3.500A) Processing helix chain 'D' and resid 290 through 292 No H-bonds generated for 'chain 'D' and resid 290 through 292' Processing helix chain 'D' and resid 304 through 312 Processing helix chain 'D' and resid 323 through 326 No H-bonds generated for 'chain 'D' and resid 323 through 326' Processing helix chain 'D' and resid 328 through 344 Processing helix chain 'D' and resid 355 through 357 No H-bonds generated for 'chain 'D' and resid 355 through 357' Processing helix chain 'D' and resid 360 through 363 No H-bonds generated for 'chain 'D' and resid 360 through 363' Processing helix chain 'D' and resid 370 through 378 Processing helix chain 'D' and resid 381 through 395 removed outlier: 3.853A pdb=" N GLU D 388 " --> pdb=" O LEU D 384 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N LEU D 389 " --> pdb=" O ARG D 385 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU D 395 " --> pdb=" O LEU D 391 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 432 removed outlier: 3.526A pdb=" N ALA D 423 " --> pdb=" O ALA D 419 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N VAL D 424 " --> pdb=" O TYR D 420 " (cutoff:3.500A) Proline residue: D 425 - end of helix Processing helix chain 'D' and resid 451 through 455 Processing helix chain 'D' and resid 459 through 469 Processing helix chain 'D' and resid 473 through 479 removed outlier: 3.846A pdb=" N LYS D 479 " --> pdb=" O GLU D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 488 through 499 Processing sheet with id= A, first strand: chain 'A' and resid 64 through 67 removed outlier: 3.917A pdb=" N ILE A 285 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY A 256 " --> pdb=" O VAL A 288 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL A 245 " --> pdb=" O MET A 259 " (cutoff:3.500A) removed outlier: 14.449A pdb=" N GLU A 261 " --> pdb=" O GLU A 243 " (cutoff:3.500A) removed outlier: 19.065A pdb=" N GLU A 243 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLY A 447 " --> pdb=" O VAL A 245 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLY A 247 " --> pdb=" O GLY A 447 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASP A 449 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE A 249 " --> pdb=" O ASP A 449 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 210 through 216 removed outlier: 6.039A pdb=" N MET A 157 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL A 213 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU A 159 " --> pdb=" O VAL A 213 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU A 215 " --> pdb=" O LEU A 159 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE A 161 " --> pdb=" O LEU A 215 " (cutoff:3.500A) removed outlier: 11.594A pdb=" N LYS A 158 " --> pdb=" O ARG A 78 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N VAL A 80 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N GLY A 160 " --> pdb=" O VAL A 80 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU A 82 " --> pdb=" O GLY A 160 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N THR A 162 " --> pdb=" O LEU A 82 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA A 84 " --> pdb=" O THR A 162 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 167 through 171 removed outlier: 6.830A pdb=" N SER A 174 " --> pdb=" O THR A 170 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 64 through 67 removed outlier: 3.917A pdb=" N ILE B 285 " --> pdb=" O ALA B 67 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY B 256 " --> pdb=" O VAL B 288 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL B 245 " --> pdb=" O MET B 259 " (cutoff:3.500A) removed outlier: 14.449A pdb=" N GLU B 261 " --> pdb=" O GLU B 243 " (cutoff:3.500A) removed outlier: 19.066A pdb=" N GLU B 243 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLY B 447 " --> pdb=" O VAL B 245 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLY B 247 " --> pdb=" O GLY B 447 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASP B 449 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE B 249 " --> pdb=" O ASP B 449 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 210 through 216 removed outlier: 6.040A pdb=" N MET B 157 " --> pdb=" O LYS B 211 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL B 213 " --> pdb=" O MET B 157 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU B 159 " --> pdb=" O VAL B 213 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU B 215 " --> pdb=" O LEU B 159 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE B 161 " --> pdb=" O LEU B 215 " (cutoff:3.500A) removed outlier: 11.593A pdb=" N LYS B 158 " --> pdb=" O ARG B 78 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL B 80 " --> pdb=" O LYS B 158 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N GLY B 160 " --> pdb=" O VAL B 80 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N LEU B 82 " --> pdb=" O GLY B 160 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N THR B 162 " --> pdb=" O LEU B 82 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N ALA B 84 " --> pdb=" O THR B 162 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 167 through 171 removed outlier: 6.830A pdb=" N SER B 174 " --> pdb=" O THR B 170 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 64 through 67 removed outlier: 3.916A pdb=" N ILE C 285 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY C 256 " --> pdb=" O VAL C 288 " (cutoff:3.500A) removed outlier: 7.767A pdb=" N VAL C 245 " --> pdb=" O MET C 259 " (cutoff:3.500A) removed outlier: 14.449A pdb=" N GLU C 261 " --> pdb=" O GLU C 243 " (cutoff:3.500A) removed outlier: 19.066A pdb=" N GLU C 243 " --> pdb=" O GLU C 261 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLY C 447 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N GLY C 247 " --> pdb=" O GLY C 447 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASP C 449 " --> pdb=" O GLY C 247 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE C 249 " --> pdb=" O ASP C 449 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 210 through 216 removed outlier: 6.040A pdb=" N MET C 157 " --> pdb=" O LYS C 211 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N VAL C 213 " --> pdb=" O MET C 157 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N LEU C 159 " --> pdb=" O VAL C 213 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU C 215 " --> pdb=" O LEU C 159 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE C 161 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 11.593A pdb=" N LYS C 158 " --> pdb=" O ARG C 78 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL C 80 " --> pdb=" O LYS C 158 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N GLY C 160 " --> pdb=" O VAL C 80 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU C 82 " --> pdb=" O GLY C 160 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N THR C 162 " --> pdb=" O LEU C 82 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA C 84 " --> pdb=" O THR C 162 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 167 through 171 removed outlier: 6.830A pdb=" N SER C 174 " --> pdb=" O THR C 170 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 64 through 67 removed outlier: 3.917A pdb=" N ILE D 285 " --> pdb=" O ALA D 67 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLY D 256 " --> pdb=" O VAL D 288 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N VAL D 245 " --> pdb=" O MET D 259 " (cutoff:3.500A) removed outlier: 14.449A pdb=" N GLU D 261 " --> pdb=" O GLU D 243 " (cutoff:3.500A) removed outlier: 19.066A pdb=" N GLU D 243 " --> pdb=" O GLU D 261 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N GLY D 447 " --> pdb=" O VAL D 245 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N GLY D 247 " --> pdb=" O GLY D 447 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N ASP D 449 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N ILE D 249 " --> pdb=" O ASP D 449 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 210 through 216 removed outlier: 6.040A pdb=" N MET D 157 " --> pdb=" O LYS D 211 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL D 213 " --> pdb=" O MET D 157 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N LEU D 159 " --> pdb=" O VAL D 213 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N LEU D 215 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE D 161 " --> pdb=" O LEU D 215 " (cutoff:3.500A) removed outlier: 11.594A pdb=" N LYS D 158 " --> pdb=" O ARG D 78 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N VAL D 80 " --> pdb=" O LYS D 158 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N GLY D 160 " --> pdb=" O VAL D 80 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU D 82 " --> pdb=" O GLY D 160 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N THR D 162 " --> pdb=" O LEU D 82 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N ALA D 84 " --> pdb=" O THR D 162 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 167 through 171 removed outlier: 6.830A pdb=" N SER D 174 " --> pdb=" O THR D 170 " (cutoff:3.500A) 720 hydrogen bonds defined for protein. 2160 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: 12.99 Time building geometry restraints manager: 28.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.15: 15616 1.15 - 1.35: 5350 1.35 - 1.54: 10087 1.54 - 1.74: 482 1.74 - 1.94: 121 Bond restraints: 31656 Sorted by residual: bond pdb=" NE ARG D 412 " pdb=" HE ARG D 412 " ideal model delta sigma weight residual 0.860 1.043 -0.183 2.00e-02 2.50e+03 8.41e+01 bond pdb=" NE2 GLN B 20 " pdb="HE22 GLN B 20 " ideal model delta sigma weight residual 0.860 1.043 -0.183 2.00e-02 2.50e+03 8.40e+01 bond pdb=" NE ARG A 412 " pdb=" HE ARG A 412 " ideal model delta sigma weight residual 0.860 1.043 -0.183 2.00e-02 2.50e+03 8.40e+01 bond pdb=" NE2 GLN C 20 " pdb="HE22 GLN C 20 " ideal model delta sigma weight residual 0.860 1.043 -0.183 2.00e-02 2.50e+03 8.39e+01 bond pdb=" NE ARG D 396 " pdb=" HE ARG D 396 " ideal model delta sigma weight residual 0.860 1.043 -0.183 2.00e-02 2.50e+03 8.37e+01 ... (remaining 31651 not shown) Histogram of bond angle deviations from ideal: 74.03 - 90.53: 32 90.53 - 107.04: 2532 107.04 - 123.55: 53790 123.55 - 140.06: 1010 140.06 - 156.57: 16 Bond angle restraints: 57380 Sorted by residual: angle pdb=" C VAL D 69 " pdb=" N THR D 70 " pdb=" CA THR D 70 " ideal model delta sigma weight residual 122.68 154.46 -31.78 1.47e+00 4.63e-01 4.67e+02 angle pdb=" C VAL B 69 " pdb=" N THR B 70 " pdb=" CA THR B 70 " ideal model delta sigma weight residual 122.68 154.45 -31.77 1.47e+00 4.63e-01 4.67e+02 angle pdb=" C VAL C 69 " pdb=" N THR C 70 " pdb=" CA THR C 70 " ideal model delta sigma weight residual 122.68 154.43 -31.75 1.47e+00 4.63e-01 4.67e+02 angle pdb=" C VAL A 69 " pdb=" N THR A 70 " pdb=" CA THR A 70 " ideal model delta sigma weight residual 122.68 154.42 -31.74 1.47e+00 4.63e-01 4.66e+02 angle pdb=" C ARG C 353 " pdb=" N SER C 354 " pdb=" CA SER C 354 " ideal model delta sigma weight residual 121.70 156.57 -34.87 1.80e+00 3.09e-01 3.75e+02 ... (remaining 57375 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 14152 17.64 - 35.28: 520 35.28 - 52.92: 204 52.92 - 70.56: 80 70.56 - 88.20: 20 Dihedral angle restraints: 14976 sinusoidal: 8416 harmonic: 6560 Sorted by residual: dihedral pdb=" CB CYS A 248 " pdb=" SG CYS A 248 " pdb=" SG CYS A 448 " pdb=" CB CYS A 448 " ideal model delta sinusoidal sigma weight residual -86.00 -34.82 -51.18 1 1.00e+01 1.00e-02 3.58e+01 dihedral pdb=" CB CYS C 248 " pdb=" SG CYS C 248 " pdb=" SG CYS C 448 " pdb=" CB CYS C 448 " ideal model delta sinusoidal sigma weight residual -86.00 -34.87 -51.13 1 1.00e+01 1.00e-02 3.58e+01 dihedral pdb=" CB CYS B 248 " pdb=" SG CYS B 248 " pdb=" SG CYS B 448 " pdb=" CB CYS B 448 " ideal model delta sinusoidal sigma weight residual -86.00 -34.87 -51.13 1 1.00e+01 1.00e-02 3.58e+01 ... (remaining 14973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1202 0.065 - 0.131: 813 0.131 - 0.196: 308 0.196 - 0.262: 127 0.262 - 0.327: 46 Chirality restraints: 2496 Sorted by residual: chirality pdb=" CA ASP A 379 " pdb=" N ASP A 379 " pdb=" C ASP A 379 " pdb=" CB ASP A 379 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.67e+00 chirality pdb=" CA ASP D 379 " pdb=" N ASP D 379 " pdb=" C ASP D 379 " pdb=" CB ASP D 379 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CA ASP B 379 " pdb=" N ASP B 379 " pdb=" C ASP B 379 " pdb=" CB ASP B 379 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.63e+00 ... (remaining 2493 not shown) Planarity restraints: 4680 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO D 401 " 0.084 2.00e-02 2.50e+03 1.55e-01 2.41e+02 pdb=" N THR D 402 " -0.267 2.00e-02 2.50e+03 pdb=" CA THR D 402 " 0.071 2.00e-02 2.50e+03 pdb=" H THR D 402 " 0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO A 401 " -0.084 2.00e-02 2.50e+03 1.55e-01 2.41e+02 pdb=" N THR A 402 " 0.267 2.00e-02 2.50e+03 pdb=" CA THR A 402 " -0.071 2.00e-02 2.50e+03 pdb=" H THR A 402 " -0.113 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 401 " 0.084 2.00e-02 2.50e+03 1.55e-01 2.40e+02 pdb=" N THR B 402 " -0.267 2.00e-02 2.50e+03 pdb=" CA THR B 402 " 0.071 2.00e-02 2.50e+03 pdb=" H THR B 402 " 0.113 2.00e-02 2.50e+03 ... (remaining 4677 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.87: 379 1.87 - 2.55: 29623 2.55 - 3.23: 101864 3.23 - 3.92: 132712 3.92 - 4.60: 206580 Nonbonded interactions: 471158 Sorted by model distance: nonbonded pdb=" H THR C 402 " pdb=" H GLU C 403 " model vdw 1.187 2.100 nonbonded pdb=" H THR D 402 " pdb=" H GLU D 403 " model vdw 1.188 2.100 nonbonded pdb=" H THR A 402 " pdb=" H GLU A 403 " model vdw 1.188 2.100 nonbonded pdb=" H THR B 402 " pdb=" H GLU B 403 " model vdw 1.188 2.100 nonbonded pdb=" H SER A 354 " pdb=" HA SER A 354 " model vdw 1.606 1.816 ... (remaining 471153 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.770 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: 0.490 Extract box with map and model: 8.440 Check model and map are aligned: 0.460 Set scattering table: 0.280 Process input model: 103.060 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.140 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 118.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 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 : 0.022 0.140 16020 Z= 1.450 Angle : 2.060 34.868 21700 Z= 1.383 Chirality : 0.105 0.327 2496 Planarity : 0.012 0.140 2772 Dihedral : 11.590 88.198 6168 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 0.92 Ramachandran Plot: Outliers : 0.40 % Allowed : 1.91 % Favored : 97.69 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.18), residues: 1992 helix: -0.20 (0.15), residues: 936 sheet: 0.55 (0.32), residues: 204 loop : 1.07 (0.23), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.006 TRP B 180 HIS 0.010 0.002 HIS B 361 PHE 0.051 0.008 PHE C 104 TYR 0.075 0.010 TYR C 165 ARG 0.006 0.001 ARG A 417 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 446 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 446 time to evaluate : 2.746 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: 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: 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: 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: 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 246 ILE cc_start: 0.8723 (mt) cc_final: 0.8482 (mp) REVERT: A 496 CYS cc_start: 0.7809 (m) cc_final: 0.7539 (m) REVERT: B 219 THR cc_start: 0.8863 (p) cc_final: 0.8625 (p) REVERT: B 333 GLU cc_start: 0.8314 (tp30) cc_final: 0.7912 (tp30) REVERT: C 192 LYS cc_start: 0.7644 (mttp) cc_final: 0.7360 (tppt) REVERT: C 210 ILE cc_start: 0.7685 (mt) cc_final: 0.7426 (tt) REVERT: C 265 ILE cc_start: 0.8873 (mt) cc_final: 0.8649 (mt) REVERT: C 288 VAL cc_start: 0.8939 (t) cc_final: 0.8619 (m) REVERT: C 333 GLU cc_start: 0.8169 (tp30) cc_final: 0.7749 (tp30) REVERT: D 36 THR cc_start: 0.8359 (m) cc_final: 0.8139 (m) REVERT: D 219 THR cc_start: 0.8701 (p) cc_final: 0.8447 (p) REVERT: D 246 ILE cc_start: 0.8611 (mt) cc_final: 0.8387 (mp) REVERT: D 496 CYS cc_start: 0.7529 (m) cc_final: 0.7287 (m) outliers start: 0 outliers final: 0 residues processed: 446 average time/residue: 0.7039 time to fit residues: 446.6606 Evaluate side-chains 251 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 251 time to evaluate : 2.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 0.8980 chunk 151 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 80 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 95 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 181 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 42 GLN ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 367 GLN C 169 GLN D 169 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 16020 Z= 0.279 Angle : 0.920 22.658 21700 Z= 0.507 Chirality : 0.043 0.170 2496 Planarity : 0.005 0.046 2772 Dihedral : 9.175 79.008 2364 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.15 % Allowed : 3.51 % Favored : 96.34 % Rotamer: Outliers : 1.80 % Allowed : 7.25 % Favored : 90.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.57 (0.18), residues: 1992 helix: 0.81 (0.15), residues: 924 sheet: 0.15 (0.30), residues: 256 loop : 0.13 (0.22), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP B 180 HIS 0.007 0.001 HIS C 343 PHE 0.015 0.002 PHE A 330 TYR 0.024 0.002 TYR C 165 ARG 0.004 0.001 ARG B 385 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 268 time to evaluate : 2.831 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 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 43 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8572 (mtp) REVERT: A 294 ASP cc_start: 0.6994 (t0) cc_final: 0.6749 (t0) REVERT: A 323 GLU cc_start: 0.8452 (tt0) cc_final: 0.8191 (tt0) REVERT: B 132 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8103 (mt) REVERT: B 157 MET cc_start: 0.7116 (mmm) cc_final: 0.6769 (mmt) REVERT: B 295 ASN cc_start: 0.8045 (m-40) cc_final: 0.7743 (m-40) REVERT: B 323 GLU cc_start: 0.8103 (tt0) cc_final: 0.7704 (tt0) REVERT: C 109 MET cc_start: 0.7833 (ttm) cc_final: 0.7483 (ttm) REVERT: C 219 THR cc_start: 0.8823 (p) cc_final: 0.8498 (p) REVERT: C 265 ILE cc_start: 0.8805 (mt) cc_final: 0.8587 (mt) outliers start: 31 outliers final: 17 residues processed: 285 average time/residue: 0.5616 time to fit residues: 246.3416 Evaluate side-chains 233 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 214 time to evaluate : 2.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 43 MET Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 218 ASP Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 132 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 326 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 326 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 124 THR Chi-restraints excluded: chain D residue 218 ASP Chi-restraints excluded: chain D residue 326 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 123 optimal weight: 0.9990 chunk 50 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 180 optimal weight: 1.9990 chunk 62 optimal weight: 0.5980 chunk 145 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16020 Z= 0.229 Angle : 0.822 21.433 21700 Z= 0.446 Chirality : 0.041 0.167 2496 Planarity : 0.004 0.044 2772 Dihedral : 8.724 81.802 2364 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 8.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.22 % Allowed : 9.40 % Favored : 89.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.18), residues: 1992 helix: 1.13 (0.16), residues: 936 sheet: -0.31 (0.31), residues: 244 loop : 0.02 (0.23), residues: 812 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 180 HIS 0.008 0.001 HIS C 343 PHE 0.018 0.002 PHE C 330 TYR 0.015 0.001 TYR A 165 ARG 0.009 0.000 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 223 time to evaluate : 2.595 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: 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 43 MET cc_start: 0.8834 (mtm) cc_final: 0.8567 (mtp) REVERT: B 157 MET cc_start: 0.7400 (mmm) cc_final: 0.7021 (mmt) REVERT: B 219 THR cc_start: 0.8676 (p) cc_final: 0.8443 (p) REVERT: B 295 ASN cc_start: 0.8133 (m-40) cc_final: 0.7903 (m-40) REVERT: B 323 GLU cc_start: 0.8157 (tt0) cc_final: 0.7937 (tt0) REVERT: C 1 MET cc_start: 0.7319 (tpp) cc_final: 0.7059 (tpp) REVERT: C 219 THR cc_start: 0.8680 (p) cc_final: 0.8385 (p) REVERT: D 43 MET cc_start: 0.8839 (mtm) cc_final: 0.8507 (mtp) REVERT: D 157 MET cc_start: 0.7130 (mmm) cc_final: 0.6260 (mmm) outliers start: 21 outliers final: 13 residues processed: 235 average time/residue: 0.5733 time to fit residues: 209.0743 Evaluate side-chains 206 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 193 time to evaluate : 2.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 338 ILE Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 300 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 179 optimal weight: 1.9990 chunk 136 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 182 optimal weight: 0.9980 chunk 193 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 173 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 169 GLN ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.4359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16020 Z= 0.268 Angle : 0.787 21.005 21700 Z= 0.427 Chirality : 0.041 0.237 2496 Planarity : 0.004 0.047 2772 Dihedral : 8.533 84.113 2364 Min Nonbonded Distance : 1.772 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.62 % Allowed : 9.34 % Favored : 89.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.18), residues: 1992 helix: 1.28 (0.16), residues: 932 sheet: -0.59 (0.30), residues: 244 loop : -0.19 (0.23), residues: 816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 290 HIS 0.008 0.001 HIS C 343 PHE 0.016 0.001 PHE B 330 TYR 0.012 0.001 TYR A 165 ARG 0.007 0.001 ARG A 385 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 201 time to evaluate : 2.487 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: 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: symmetry clash REVERT: B 157 MET cc_start: 0.7592 (mmm) cc_final: 0.7260 (mmt) REVERT: B 219 THR cc_start: 0.8781 (p) cc_final: 0.8537 (p) REVERT: B 295 ASN cc_start: 0.8332 (m-40) cc_final: 0.8070 (m-40) REVERT: C 1 MET cc_start: 0.7081 (tpp) cc_final: 0.6747 (tpp) REVERT: C 219 THR cc_start: 0.8929 (p) cc_final: 0.8683 (p) REVERT: D 157 MET cc_start: 0.7209 (mmm) cc_final: 0.6529 (mmm) outliers start: 28 outliers final: 15 residues processed: 219 average time/residue: 0.5917 time to fit residues: 205.4885 Evaluate side-chains 199 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 184 time to evaluate : 2.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 272 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 272 LEU Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 272 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 161 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 143 optimal weight: 3.9990 chunk 79 optimal weight: 1.9990 chunk 164 optimal weight: 0.8980 chunk 133 optimal weight: 0.8980 chunk 0 optimal weight: 4.9990 chunk 98 optimal weight: 2.9990 chunk 173 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 201 GLN ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7537 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 16020 Z= 0.255 Angle : 0.765 21.148 21700 Z= 0.415 Chirality : 0.040 0.158 2496 Planarity : 0.004 0.046 2772 Dihedral : 8.442 85.743 2364 Min Nonbonded Distance : 1.798 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.05 % Allowed : 4.82 % Favored : 95.13 % Rotamer: Outliers : 1.45 % Allowed : 10.38 % Favored : 88.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.19), residues: 1992 helix: 1.42 (0.16), residues: 928 sheet: -0.66 (0.27), residues: 284 loop : -0.30 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP D 290 HIS 0.008 0.001 HIS C 343 PHE 0.016 0.001 PHE B 330 TYR 0.010 0.001 TYR A 165 ARG 0.003 0.000 ARG B 360 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 193 time to evaluate : 2.596 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: 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 259 MET cc_start: 0.8805 (tpt) cc_final: 0.8361 (tpt) REVERT: B 157 MET cc_start: 0.7637 (mmm) cc_final: 0.7350 (mmt) REVERT: B 295 ASN cc_start: 0.8450 (m-40) cc_final: 0.8169 (m-40) REVERT: D 157 MET cc_start: 0.7217 (mmm) cc_final: 0.6617 (mmm) outliers start: 25 outliers final: 17 residues processed: 208 average time/residue: 0.6026 time to fit residues: 198.8337 Evaluate side-chains 197 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 180 time to evaluate : 2.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 272 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 65 optimal weight: 0.5980 chunk 174 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 47 optimal weight: 4.9990 chunk 193 optimal weight: 0.5980 chunk 160 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.4841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 16020 Z= 0.195 Angle : 0.776 21.104 21700 Z= 0.421 Chirality : 0.041 0.381 2496 Planarity : 0.004 0.046 2772 Dihedral : 8.318 86.047 2364 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.02 % Favored : 94.88 % Rotamer: Outliers : 1.51 % Allowed : 10.96 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.19), residues: 1992 helix: 1.54 (0.16), residues: 932 sheet: -0.78 (0.28), residues: 288 loop : -0.26 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 290 HIS 0.007 0.001 HIS C 343 PHE 0.018 0.001 PHE C 250 TYR 0.009 0.001 TYR A 165 ARG 0.003 0.000 ARG B 360 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 198 time to evaluate : 2.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7281 (mmm) cc_final: 0.6805 (mmm) REVERT: B 157 MET cc_start: 0.7626 (mmm) cc_final: 0.7361 (mmt) REVERT: B 295 ASN cc_start: 0.8435 (m-40) cc_final: 0.8137 (m-40) REVERT: D 157 MET cc_start: 0.7384 (mmm) cc_final: 0.6784 (mmm) outliers start: 26 outliers final: 17 residues processed: 217 average time/residue: 0.5651 time to fit residues: 193.3535 Evaluate side-chains 203 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 186 time to evaluate : 2.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain A residue 448 CYS Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 248 CYS Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 448 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 186 optimal weight: 0.7980 chunk 21 optimal weight: 3.9990 chunk 110 optimal weight: 4.9990 chunk 141 optimal weight: 1.9990 chunk 109 optimal weight: 0.7980 chunk 162 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 192 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 117 optimal weight: 1.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.5010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16020 Z= 0.211 Angle : 0.779 21.049 21700 Z= 0.422 Chirality : 0.041 0.375 2496 Planarity : 0.004 0.045 2772 Dihedral : 8.261 86.647 2364 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 9.50 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.37 % Favored : 94.53 % Rotamer: Outliers : 1.45 % Allowed : 11.37 % Favored : 87.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.19), residues: 1992 helix: 1.60 (0.16), residues: 932 sheet: -0.89 (0.28), residues: 288 loop : -0.31 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 180 HIS 0.007 0.001 HIS C 343 PHE 0.018 0.001 PHE B 250 TYR 0.008 0.001 TYR A 165 ARG 0.003 0.000 ARG B 360 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 193 time to evaluate : 2.595 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: 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 81 LEU cc_start: 0.8141 (mt) cc_final: 0.7911 (mp) REVERT: A 157 MET cc_start: 0.7348 (mmm) cc_final: 0.6844 (mmm) REVERT: B 157 MET cc_start: 0.7637 (mmm) cc_final: 0.7408 (mmt) REVERT: B 295 ASN cc_start: 0.8432 (m-40) cc_final: 0.8120 (m-40) REVERT: D 43 MET cc_start: 0.8880 (mtm) cc_final: 0.8658 (mtp) REVERT: D 157 MET cc_start: 0.7391 (mmm) cc_final: 0.6777 (mmm) REVERT: D 259 MET cc_start: 0.8768 (tpt) cc_final: 0.8399 (tpt) outliers start: 25 outliers final: 16 residues processed: 211 average time/residue: 0.5429 time to fit residues: 179.4699 Evaluate side-chains 202 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 186 time to evaluate : 2.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 338 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 119 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 115 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 122 optimal weight: 1.9990 chunk 131 optimal weight: 0.8980 chunk 95 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 151 optimal weight: 2.9990 chunk 175 optimal weight: 1.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 169 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.5227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 16020 Z= 0.245 Angle : 0.771 21.329 21700 Z= 0.418 Chirality : 0.040 0.207 2496 Planarity : 0.004 0.044 2772 Dihedral : 8.224 88.177 2364 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.67 % Favored : 94.23 % Rotamer: Outliers : 1.57 % Allowed : 11.19 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.19), residues: 1992 helix: 1.57 (0.16), residues: 932 sheet: -1.15 (0.28), residues: 288 loop : -0.35 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 290 HIS 0.007 0.001 HIS A 343 PHE 0.015 0.001 PHE C 139 TYR 0.009 0.001 TYR A 165 ARG 0.003 0.000 ARG B 360 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 190 time to evaluate : 2.847 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: 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 81 LEU cc_start: 0.8140 (mt) cc_final: 0.7911 (mp) REVERT: A 157 MET cc_start: 0.7297 (mmm) cc_final: 0.6875 (mmm) REVERT: A 259 MET cc_start: 0.8731 (tpt) cc_final: 0.8491 (tpt) REVERT: B 157 MET cc_start: 0.7751 (mmm) cc_final: 0.7520 (mmt) REVERT: B 295 ASN cc_start: 0.8474 (m-40) cc_final: 0.8154 (m-40) REVERT: D 43 MET cc_start: 0.8865 (mtm) cc_final: 0.8626 (mtp) REVERT: D 157 MET cc_start: 0.7363 (mmm) cc_final: 0.6814 (mmm) REVERT: D 259 MET cc_start: 0.8766 (tpt) cc_final: 0.8401 (tpt) outliers start: 27 outliers final: 18 residues processed: 210 average time/residue: 0.5518 time to fit residues: 181.1256 Evaluate side-chains 202 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 184 time to evaluate : 2.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 109 MET Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 338 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 184 optimal weight: 1.9990 chunk 168 optimal weight: 1.9990 chunk 179 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 141 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 169 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 chunk 189 optimal weight: 0.6980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 169 GLN ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.5418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 16020 Z= 0.262 Angle : 0.770 21.203 21700 Z= 0.418 Chirality : 0.040 0.226 2496 Planarity : 0.004 0.044 2772 Dihedral : 8.236 89.223 2364 Min Nonbonded Distance : 1.809 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.12 % Favored : 93.78 % Rotamer: Outliers : 1.33 % Allowed : 11.89 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.19), residues: 1992 helix: 1.55 (0.16), residues: 932 sheet: -1.22 (0.28), residues: 288 loop : -0.41 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP C 180 HIS 0.007 0.001 HIS C 343 PHE 0.015 0.001 PHE A 250 TYR 0.010 0.001 TYR A 143 ARG 0.003 0.000 ARG B 360 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 191 time to evaluate : 2.624 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: 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 81 LEU cc_start: 0.8163 (mt) cc_final: 0.7923 (mp) REVERT: A 157 MET cc_start: 0.7317 (mmm) cc_final: 0.6921 (mmm) REVERT: A 219 THR cc_start: 0.8811 (p) cc_final: 0.8508 (p) REVERT: A 259 MET cc_start: 0.8718 (tpt) cc_final: 0.8484 (tpt) REVERT: B 157 MET cc_start: 0.7812 (mmm) cc_final: 0.7565 (mmt) REVERT: B 295 ASN cc_start: 0.8494 (m-40) cc_final: 0.8190 (m-40) REVERT: D 43 MET cc_start: 0.8875 (mtm) cc_final: 0.8640 (mtp) REVERT: D 157 MET cc_start: 0.7375 (mmm) cc_final: 0.6843 (mmm) REVERT: D 259 MET cc_start: 0.8754 (tpt) cc_final: 0.8406 (tpt) outliers start: 23 outliers final: 21 residues processed: 206 average time/residue: 0.5942 time to fit residues: 192.8639 Evaluate side-chains 207 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 186 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 338 ILE Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain C residue 33 ASP Chi-restraints excluded: chain C residue 182 LYS Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 338 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 115 optimal weight: 0.8980 chunk 90 optimal weight: 0.9980 chunk 132 optimal weight: 0.9990 chunk 199 optimal weight: 3.9990 chunk 183 optimal weight: 0.9990 chunk 158 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 122 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 169 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.5541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16020 Z= 0.210 Angle : 0.747 21.158 21700 Z= 0.405 Chirality : 0.039 0.184 2496 Planarity : 0.004 0.042 2772 Dihedral : 8.161 87.067 2364 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.82 % Favored : 94.08 % Rotamer: Outliers : 1.28 % Allowed : 12.24 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.19), residues: 1992 helix: 1.67 (0.16), residues: 932 sheet: -1.21 (0.29), residues: 288 loop : -0.36 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 180 HIS 0.006 0.001 HIS C 343 PHE 0.012 0.001 PHE B 330 TYR 0.008 0.001 TYR A 165 ARG 0.002 0.000 ARG B 360 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3984 Ramachandran restraints generated. 1992 Oldfield, 0 Emsley, 1992 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 198 time to evaluate : 2.783 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: 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 81 LEU cc_start: 0.8141 (mt) cc_final: 0.7911 (mp) REVERT: A 157 MET cc_start: 0.7269 (mmm) cc_final: 0.6885 (mmm) REVERT: A 219 THR cc_start: 0.8822 (p) cc_final: 0.8512 (p) REVERT: A 259 MET cc_start: 0.8680 (tpt) cc_final: 0.8434 (tpt) REVERT: B 157 MET cc_start: 0.7783 (mmm) cc_final: 0.7546 (mmt) REVERT: B 295 ASN cc_start: 0.8481 (m-40) cc_final: 0.8169 (m-40) REVERT: D 43 MET cc_start: 0.8848 (mtm) cc_final: 0.8598 (mtp) REVERT: D 157 MET cc_start: 0.7385 (mmm) cc_final: 0.6871 (mmm) REVERT: D 219 THR cc_start: 0.8949 (p) cc_final: 0.8625 (p) REVERT: D 259 MET cc_start: 0.8733 (tpt) cc_final: 0.8386 (tpt) outliers start: 22 outliers final: 18 residues processed: 213 average time/residue: 0.5511 time to fit residues: 184.4442 Evaluate side-chains 210 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 192 time to evaluate : 2.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 372 VAL Chi-restraints excluded: chain B residue 36 THR Chi-restraints excluded: chain B residue 182 LYS Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 348 LEU Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 431 ILE Chi-restraints excluded: chain C residue 215 LEU Chi-restraints excluded: chain C residue 252 THR Chi-restraints excluded: chain C residue 372 VAL Chi-restraints excluded: chain C residue 431 ILE Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 86 LEU Chi-restraints excluded: chain D residue 272 LEU Chi-restraints excluded: chain D residue 295 ASN Chi-restraints excluded: chain D residue 338 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 48 optimal weight: 2.9990 chunk 146 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 158 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 163 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 139 optimal weight: 0.0980 chunk 9 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.136576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.116723 restraints weight = 71959.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.121705 restraints weight = 35573.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3593 r_free = 0.3593 target = 0.124927 restraints weight = 21842.288| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 16020 Z= 0.276 Angle : 0.763 21.164 21700 Z= 0.415 Chirality : 0.040 0.206 2496 Planarity : 0.004 0.043 2772 Dihedral : 8.216 87.655 2364 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.16 % Allowed : 12.59 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.42 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.19), residues: 1992 helix: 1.57 (0.16), residues: 932 sheet: -1.21 (0.29), residues: 288 loop : -0.47 (0.24), residues: 772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 290 HIS 0.007 0.001 HIS A 343 PHE 0.014 0.001 PHE C 139 TYR 0.009 0.001 TYR A 165 ARG 0.003 0.000 ARG B 360 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6220.95 seconds wall clock time: 112 minutes 10.03 seconds (6730.03 seconds total)