Starting phenix.real_space_refine on Mon Nov 20 21:53:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pdt_20309/11_2023/6pdt_20309_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pdt_20309/11_2023/6pdt_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_20309/11_2023/6pdt_20309.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pdt_20309/11_2023/6pdt_20309.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pdt_20309/11_2023/6pdt_20309_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pdt_20309/11_2023/6pdt_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: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 13.97, per 1000 atoms: 0.45 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: 28.69 Conformation dependent library (CDL) restraints added in 3.3 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: 31.03 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: 13.30 Time building geometry restraints manager: 29.22 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: 12124 17.64 - 35.28: 320 35.28 - 52.92: 60 52.92 - 70.56: 36 70.56 - 88.20: 16 Dihedral angle restraints: 12556 sinusoidal: 5996 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 12553 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.932: 2492 0.932 - 1.863: 0 1.863 - 2.795: 0 2.795 - 3.726: 0 3.726 - 4.658: 4 Chirality restraints: 2496 Sorted by residual: chirality pdb=" C1 GLC A 601 " pdb=" C2 GLC A 601 " pdb=" O1 GLC A 601 " pdb=" O5 GLC A 601 " both_signs ideal model delta sigma weight residual False 2.33 -2.33 4.66 2.00e-01 2.50e+01 5.42e+02 chirality pdb=" C1 GLC D 601 " pdb=" C2 GLC D 601 " pdb=" O1 GLC D 601 " pdb=" O5 GLC D 601 " both_signs ideal model delta sigma weight residual False 2.33 -2.32 4.66 2.00e-01 2.50e+01 5.42e+02 chirality pdb=" C1 GLC B 601 " pdb=" C2 GLC B 601 " pdb=" O1 GLC B 601 " pdb=" O5 GLC B 601 " both_signs ideal model delta sigma weight residual False 2.33 -2.32 4.65 2.00e-01 2.50e+01 5.42e+02 ... (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: 1.350 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: 8.290 Check model and map are aligned: 0.500 Set scattering table: 0.280 Process input model: 104.740 Find NCS groups from input model: 1.520 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: 0.010 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 120.130 ------------------------------------------------------------------------------- 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 : 2.062 34.868 21700 Z= 1.383 Chirality : 0.213 4.658 2496 Planarity : 0.012 0.140 2772 Dihedral : 11.045 88.198 5984 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 *********************** 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 : 2.763 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 outliers start: 0 outliers final: 0 residues processed: 446 average time/residue: 0.6847 time to fit residues: 434.6222 Evaluate side-chains 244 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 1.961 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 2.4255 ------------------------------------------------------------------------------- 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: 0.9990 chunk 151 optimal weight: 0.7980 chunk 84 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 102 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 156 optimal weight: 0.7980 chunk 60 optimal weight: 6.9990 chunk 95 optimal weight: 0.6980 chunk 116 optimal weight: 0.6980 chunk 181 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7357 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 16020 Z= 0.257 Angle : 0.933 22.654 21700 Z= 0.515 Chirality : 0.043 0.167 2496 Planarity : 0.005 0.045 2772 Dihedral : 7.052 65.044 2180 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.80 % Allowed : 7.37 % Favored : 90.84 % 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: 0.83 (0.16), residues: 924 sheet: 0.10 (0.31), residues: 236 loop : 0.17 (0.22), residues: 832 *********************** 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 293 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 262 time to evaluate : 3.306 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 outliers start: 31 outliers final: 18 residues processed: 279 average time/residue: 0.5831 time to fit residues: 251.1721 Evaluate side-chains 228 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 210 time to evaluate : 2.525 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.4042 time to fit residues: 16.4539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 100 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 151 optimal weight: 3.9990 chunk 123 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 181 optimal weight: 2.9990 chunk 196 optimal weight: 0.9980 chunk 162 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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: 0.7459 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 16020 Z= 0.280 Angle : 0.839 21.430 21700 Z= 0.457 Chirality : 0.041 0.157 2496 Planarity : 0.004 0.041 2772 Dihedral : 6.377 54.931 2180 Min Nonbonded Distance : 1.735 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 0.64 % Allowed : 9.34 % Favored : 90.02 % 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: 1.02 (0.15), residues: 936 sheet: -0.22 (0.31), residues: 236 loop : -0.04 (0.23), residues: 820 *********************** 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 233 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 222 time to evaluate : 2.267 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 outliers start: 11 outliers final: 4 residues processed: 229 average time/residue: 0.5846 time to fit residues: 208.0608 Evaluate side-chains 196 residues out of total 1724 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 192 time to evaluate : 2.671 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.4058 time to fit residues: 6.4985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8980 chunk 94 optimal weight: 3.9990 chunk 20 optimal weight: 4.9990 chunk 86 optimal weight: 0.0670 chunk 122 optimal weight: 2.9990 chunk 182 optimal weight: 0.9990 chunk 193 optimal weight: 3.9990 chunk 95 optimal weight: 0.8980 chunk 173 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 overall best weight: 0.9722 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: